From 70185c04ba065aacfcf29b241f6ffbdfec49f7a9 Mon Sep 17 00:00:00 2001 From: SarthakJariwala Date: Tue, 28 Apr 2020 11:30:13 -0700 Subject: [PATCH 01/10] change app style to fusion, modify add to mem for plot without irf to include the pl rise time in exported graph --- PythonGUI_apps/DataBrowser.py | 4 ++- .../Lifetime_analysis/Lifetime_plot_fit.py | 26 ++++++++++++++----- 2 files changed, 22 insertions(+), 8 deletions(-) diff --git a/PythonGUI_apps/DataBrowser.py b/PythonGUI_apps/DataBrowser.py index 3dea4ec..0279473 100644 --- a/PythonGUI_apps/DataBrowser.py +++ b/PythonGUI_apps/DataBrowser.py @@ -85,8 +85,10 @@ def load_app(self): def run(): + app = QtGui.QApplication(sys.argv)#.instance() + app.setStyle("Fusion") win = MainWindow() - QtGui.QApplication.instance().exec_() + sys.exit(app.exec_()) return run() \ No newline at end of file diff --git a/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py b/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py index 9437f9f..afe106a 100644 --- a/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py +++ b/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py @@ -95,10 +95,12 @@ def __init__(self): self.file = None self.out = None # output file after fitting self.data_list = [] - self.fit_lifetime_called = False + self.fit_lifetime_called_w_irf = False + self.fit_lifetime_called_wo_irf = False self.x_mem = [] # containers for adding x data to memory self.y_mem = [] # containers for adding y data to memory self.best_fit_mem = [] # containers for adding best fit data to memory + self.best_fit_mem_x = [] # containers for adding best fit data to memory self.legend = [] # containers for adding legend to memory #variables accounting for data received from FLIM analysis @@ -258,7 +260,8 @@ def plot(self): x,y = self.acquire_settings() #get data self.ui.plot.plot(x, y, clear=self.ui.clear_plot_checkBox.isChecked(), pen=pg.mkPen(self.plot_color)) - self.fit_lifetime_called = False + self.fit_lifetime_called_w_irf = False + self.fit_lifetime_called_wo_irf = False try: self.ui.Result_textBrowser.setText("Integral Counts :\n" "{:.2E}".format( @@ -347,7 +350,8 @@ def fit_and_plot(self): #add fit params to data_list self.data_list.append("Data Channel: " + str(self.ui.Data_channel_spinBox.value()) + "\n" + self.ui.Result_textBrowser.toPlainText()) - self.fit_lifetime_called = True + self.fit_lifetime_called_wo_irf = True + self.fit_lifetime_called_w_irf = False self.ui.plot.setLabel('left', 'Intensity', units='a.u.') self.ui.plot.setLabel('bottom', 'Time (ns)') @@ -475,7 +479,8 @@ def fit_and_plot_with_irf(self): #add fit params to data_list self.data_list.append("Data Channel: " + str(self.ui.Data_channel_spinBox.value()) + "\n" + self.ui.Result_textBrowser.toPlainText()) - self.fit_lifetime_called = True + self.fit_lifetime_called_w_irf = True + self.fit_lifetime_called_wo_irf = False except Exception as e: self.ui.Result_textBrowser.append(format(e)) @@ -548,12 +553,19 @@ def clean_up_after_fig_export(self): self.y_mem = [] self.legend = [] self.best_fit_mem = [] + self.best_fit_mem_x = [] def add_trace_to_mem(self): try: - if self.fit_lifetime_called == True: + if self.fit_lifetime_called_w_irf == True: self.x_mem.append(self.out[:,0]) self.y_mem.append(self.out[:,1]) + self.best_fit_mem_x.append(self.out[:,0]) + self.best_fit_mem.append(self.out[:,2]) + elif self.fit_lifetime_called_wo_irf == True: + self.x_mem.append(self.acquire_settings()[0]) + self.y_mem.append(self.acquire_settings()[1]) + self.best_fit_mem_x.append(self.out[:,0]) self.best_fit_mem.append(self.out[:,2]) else: self.x_mem.append(self.acquire_settings()[0]) @@ -578,8 +590,8 @@ def pub_ready_plot_export(self): plt.tick_params(direction='out', length=8, width=3.5) for i in range(len(self.x_mem)): plt.plot(self.x_mem[i], self.y_mem[i], label=str(self.legend[i])) - if self.fit_lifetime_called == True: - plt.plot(self.x_mem[i], self.best_fit_mem[i],'k--') + if self.fit_lifetime_called_w_irf == True or self.fit_lifetime_called_wo_irf == True: + plt.plot(self.best_fit_mem_x[i], self.best_fit_mem[i],'k--') plt.yscale('log') plt.xlabel("Time (ns)", fontsize=20, fontweight='bold') From 57845ef915d6bf1381434b57eec3d036cd1b061c Mon Sep 17 00:00:00 2001 From: SarthakJariwala Date: Fri, 1 May 2020 16:57:50 -0700 Subject: [PATCH 02/10] fix residual func in fit_wo_irf, change export for fit_wo_irf to include raw PL with rise --- .../Lifetime_analysis/Fit_functions.py | 56 ++++++++++--------- .../Lifetime_analysis/Lifetime_plot_fit.py | 15 +++-- 2 files changed, 40 insertions(+), 31 deletions(-) diff --git a/PythonGUI_apps/Lifetime_analysis/Fit_functions.py b/PythonGUI_apps/Lifetime_analysis/Fit_functions.py index 2afed57..7ad5c3e 100644 --- a/PythonGUI_apps/Lifetime_analysis/Fit_functions.py +++ b/PythonGUI_apps/Lifetime_analysis/Fit_functions.py @@ -9,10 +9,10 @@ from scipy.optimize import differential_evolution from scipy.special import gamma -def stretch_exp_fit(TRPL, t, Tc = (0,1e5), Beta = (0,1), A = (0,1e6)): +def stretch_exp_fit(TRPL, t, Tc = (0,1e5), Beta = (0,1), A = (0,1e6), noise=(0,1e6)): - def exp_stretch(t, tc, beta, a): - return (a * np.exp(-((1.0 / tc) * t) ** beta)) + def exp_stretch(t, tc, beta, a, noise): + return ((a * np.exp(-((1.0 / tc) * t) ** beta)) + noise) def avg_tau_from_exp_stretch(tc, beta): return (tc / beta) * gamma(1.0 / beta) @@ -25,13 +25,14 @@ def residuals(params):#params are the parameters to be adjusted by differential tc = params[0] beta = params[1] a = params[2] + noise = params[3] - PL_sim = exp_stretch(t,tc,beta,a) + PL_sim = exp_stretch(t,tc,beta,a, noise) - Resid= np.sqrt(np.sum(((PL_sim-TRPL)**2)/(np.sqrt(PL_sim)**2))) + Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) return Resid #returns the difference between the PL data and simulated data - bounds = [Tc, Beta, A] + bounds = [Tc, Beta, A, noise] result = differential_evolution(residuals, bounds) return result.x @@ -41,20 +42,21 @@ def residuals(params):#params are the parameters to be adjusted by differential tc = p[0] beta = p[1] a = p[2] + noise = p[3] - PL_fit = exp_stretch(t,tc,beta,a) + PL_fit = exp_stretch(t,tc,beta,a, noise) avg_tau = avg_tau_from_exp_stretch(tc,beta) - return tc, beta, a, avg_tau, PL_fit + return tc, beta, a, avg_tau, PL_fit, noise -def double_exp_fit(TRPL, t, tau1_bounds=(0,100), a1_bounds=(0,1e5), tau2_bounds=(0,100), a2_bounds=(0,1e5)): +def double_exp_fit(TRPL, t, tau1_bounds=(0,1000), a1_bounds=(0,1e6), tau2_bounds=(0,10000), a2_bounds=(0,1e5), noise=(0,1e6)): def single_exp(t, tau, a): - return (a * np.exp(-((1.0 / tau)*t) )) + return (a * np.exp(-((1.0 / tau)*t))) - def double_exp(t, tau1, a1, tau2, a2): - return ((single_exp(t, tau1, a1)) + (single_exp(t, tau2, a2))) + def double_exp(t, tau1, a1, tau2, a2, noise): + return ((single_exp(t, tau1, a1)) + (single_exp(t, tau2, a2)) + noise) def avg_tau_from_double_exp(tau1, a1, tau2, a2): return (((tau1*a1) + (tau2*a2))/(a1+a2)) @@ -68,13 +70,14 @@ def residuals(params):#params are the parameters to be adjusted by differential a1 = params[1] tau2 = params[2] a2 = params[3] + noise = params[4] - PL_sim = double_exp(t,tau1, a1, tau2, a2) + PL_sim = double_exp(t,tau1, a1, tau2, a2, noise) - Resid= np.sqrt(np.sum(((PL_sim-TRPL)**2)/(np.sqrt(PL_sim)**2))) + Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) return Resid #returns the difference between the PL data and simulated data - bounds = [tau1_bounds, a1_bounds, tau2_bounds, a2_bounds] + bounds = [tau1_bounds, a1_bounds, tau2_bounds, a2_bounds, noise] result = differential_evolution(residuals, bounds) return result.x @@ -85,17 +88,18 @@ def residuals(params):#params are the parameters to be adjusted by differential a1 = p[1] tau2 = p[2] a2 = p[3] + noise = p[4] - PL_fit = double_exp(t, tau1, a1, tau2, a2) + PL_fit = double_exp(t, tau1, a1, tau2, a2, noise) avg_tau = avg_tau_from_double_exp(tau1, a1, tau2, a2) - return tau1, a1, tau2, a2, avg_tau, PL_fit + return tau1, a1, tau2, a2, avg_tau, PL_fit, noise -def single_exp_fit(TRPL, t, tau_bounds=(0,1000), a_bounds=(0,1e5)): +def single_exp_fit(TRPL, t, tau_bounds=(0,10000), a_bounds=(0,1e6), noise=(0,1e6)): - def single_exp(t, tau, a): - return (a * np.exp(-((1.0 / tau)*t) )) + def single_exp(t, tau, a, noise): + return (a * np.exp(-((1.0 / tau)*t) ) + noise) def Diff_Ev_Fit_singleExp(TRPL): TRPL = TRPL @@ -104,13 +108,14 @@ def residuals(params):#params are the parameters to be adjusted by differential #Variable Rates tau = params[0] a = params[1] + noise = params[2] - PL_sim = single_exp(t, tau, a) + PL_sim = single_exp(t, tau, a, noise) - Resid= np.sqrt(np.sum(((PL_sim-TRPL)**2)/(np.sqrt(PL_sim)**2))) + Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) return Resid #returns the difference between the PL data and simulated data - bounds = [tau_bounds, a_bounds] + bounds = [tau_bounds, a_bounds, noise] result = differential_evolution(residuals, bounds) return result.x @@ -119,8 +124,9 @@ def residuals(params):#params are the parameters to be adjusted by differential tau = p[0] a = p[1] + noise = p[2] - PL_fit = single_exp(t, tau, a) + PL_fit = single_exp(t, tau, a, noise) - return tau, a, PL_fit + return tau, a, PL_fit, noise \ No newline at end of file diff --git a/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py b/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py index afe106a..7967a1e 100644 --- a/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py +++ b/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py @@ -306,7 +306,7 @@ def fit_and_plot(self): self.ui.plot.plot(t, y, clear=self.ui.clear_plot_checkBox.isChecked(), pen=pg.mkPen(self.plot_color)) if fit_func == "Stretched Exponential": #stretch exponential tab - tc, beta, a, avg_tau, PL_fit = stretch_exp_fit(TRPL_interp, t) + tc, beta, a, avg_tau, PL_fit, noise = stretch_exp_fit(TRPL_interp, t) self.out = np.empty((len(t), 3)) self.out[:,0] = t #time self.out[:,1] = TRPL_interp #Raw PL @@ -316,11 +316,12 @@ def fit_and_plot(self): "\nFit Method: " + "diff_ev" + #TODO : change when diff_ev and fmin_tnc implemented for non-irf "\nAverage Lifetime = " + str(avg_tau)+ " ns" "\nCharacteristic Tau = " + str(tc)+" ns" - "\nBeta = "+str(beta)) + "\nBeta = "+str(beta)+ + "\nNoise = "+ str(noise)) self.ui.average_lifetime_spinBox.setValue(avg_tau) elif fit_func == "Double Exponential": #double exponential tab - tau1, a1, tau2, a2, avg_tau, PL_fit = double_exp_fit(TRPL_interp, t) + tau1, a1, tau2, a2, avg_tau, PL_fit, noise = double_exp_fit(TRPL_interp, t) self.out = np.empty((len(t), 3)) self.out[:,0] = t #time self.out[:,1] = TRPL_interp #Raw PL @@ -332,11 +333,12 @@ def fit_and_plot(self): "\nTau 1 = " + str(tau1)+" ns" "\nA 1 = " + str(a1)+ "\nTau 2 = " + str(tau2)+" ns" - "\nA 2 = " + str(a2)) + "\nA 2 = " + str(a2)+ + "\nNoise = "+ str(noise)) #TODO - once tau_avg implemented, set average lifetime spinbox to tau_avg value elif fit_func == "Single Exponential": #single exponential tab - tau, a, PL_fit = single_exp_fit(TRPL_interp, t) + tau, a, PL_fit, noise = single_exp_fit(TRPL_interp, t) self.out = np.empty((len(t), 3)) self.out[:,0] = t #time self.out[:,1] = TRPL_interp #Raw PL @@ -345,7 +347,8 @@ def fit_and_plot(self): self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Single Exponential" "\nFit Method: " + "diff_ev" + "\nLifetime = " + str(tau)+ " ns" - "\nA = " + str(a)) + "\nA = " + str(a)+ + "\nNoise = "+ str(noise)) self.ui.average_lifetime_spinBox.setValue(tau) #add fit params to data_list From 69931ef5c52dbd57f1ed02faff50ebcbfd41a3c1 Mon Sep 17 00:00:00 2001 From: Sarthak Jariwala Date: Wed, 1 Jul 2020 17:18:01 -0700 Subject: [PATCH 03/10] Starting port to fbs structure --- src/build/settings/base.json | 6 + src/build/settings/linux.json | 6 + src/build/settings/mac.json | 3 + src/main/icons/Icon.ico | Bin 0 -> 168229 bytes src/main/icons/README.md | 11 + src/main/icons/base/16.png | Bin 0 -> 544 bytes src/main/icons/base/24.png | Bin 0 -> 783 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This is because otherwise they look too +big (eg. in the Dock or in the app switcher). + +You can create Icon.ico from the .png files with +[an online tool](http://icoconvert.com/Multi_Image_to_one_icon/). \ No newline at end of file diff --git a/src/main/icons/base/16.png b/src/main/icons/base/16.png new file mode 100644 index 0000000000000000000000000000000000000000..f7d02dc268f79c183376b30dddf5ea0cf5827dfe GIT binary patch literal 544 zcmV+*0^j|KP)TmGsBvSN0G7{E%tE_-gl|fEv;0aRau+G)01lU7P2{XIYtU(DY*`z5wZh-t$ z17;xV-$KBe25cyY`gJ9TKA2b zQ`OPi4q_$n+Q`u1Rq4iCqev!2*O%K1W{B_hXa`+h=PJlsp!i@kPT6X zFgMtf4&AdjLi@^LEPz?gPFhert=$)fabl?(6T3=?Mx5-d`oLZ)@tUkX_s2+$#>F(4wKl3YIpWCbP|H9s!5%<RuTU6aQntuM7@! zJkGa2f3Hqhe%Cykf0SrKM}494z#-;LdXvexZ{ zdcbzc3-LACtO$GJb`m+Ec0Hhy4FPV@8I-klM7`(%Jex>U7OJ7wQzqfr0= N002ovPDHLkV1g}~Xzc(1 literal 0 HcmV?d00001 diff --git a/src/main/icons/base/32.png b/src/main/icons/base/32.png new file mode 100644 index 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+ + + + + 30 + 75 + true + + + + GLabViz + + + Qt::AlignCenter + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + 15 + + + + Analysis Tool : + + + + + + + + 15 + + + + + + + + + 15 + + + + Load + + + + + + + + + 0 + 0 + 435 + 21 + + + + + + + + diff --git a/src/main/python/Export_Windows/Export_window.py b/src/main/python/Export_Windows/Export_window.py new file mode 100644 index 0000000..0e5cc63 --- /dev/null +++ b/src/main/python/Export_Windows/Export_window.py @@ -0,0 +1,77 @@ +# -*- coding: utf-8 -*- +""" +Created on Sun Nov 3 20:43:12 2019 + +@author: sarth +""" +from pathlib import Path +import pyqtgraph as pg +from pyqtgraph.Qt import QtCore, QtGui + +"""Export Images GUI""" +base_path = Path(__file__).parent +ui_file_path = (base_path / "export_fig_gui.ui").resolve() +exportFig_WindowTemplate, exportFig_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) + +class ExportFigureWindow(exportFig_TemplateBaseClass): + + export_fig_signal = QtCore.pyqtSignal() + + def __init__(self): + exportFig_TemplateBaseClass.__init__(self) + + self.ui = exportFig_WindowTemplate() + self.ui.setupUi(self) + self.ui.cmap_comboBox.addItems(['viridis', 'plasma', 'inferno', 'magma', + 'cividis','Greys', 'Purples', 'Blues', + 'Greens', 'Oranges', 'Reds', 'YlOrBr', + 'YlOrRd', 'OrRd', 'PuRd', 'RdPu', 'BuPu', + 'GnBu', 'PuBu', 'YlGnBu', 'PuBuGn', 'BuGn', + 'YlGn', 'binary', 'gist_yarg', 'gist_gray', + 'gray', 'bone', 'pink', 'spring', 'summer', + 'autumn', 'winter', 'cool', 'Wistia', 'hot', + 'afmhot', 'gist_heat', 'copper', 'rainbow', 'jet']) + self.ui.cbar_checkBox.stateChanged.connect(self.cbar_title_state) + self.ui.exportFig_pushButton.clicked.connect(self.export) + self.show() + + def cbar_title_state(self): + if self.ui.cbar_checkBox.isChecked(): + self.ui.cbar_label.setEnabled(True) + else: + self.ui.cbar_label.setEnabled(False) + + def export(self): + self.export_fig_signal.emit() + self.close() + +"""Export plot GUI""" +ui_file_path = (base_path / "export_plot.ui").resolve() +export_WindowTemplate, export_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) + +class ExportPlotWindow(export_TemplateBaseClass): + + export_fig_signal = QtCore.pyqtSignal() + + def __init__(self): + export_TemplateBaseClass.__init__(self) + + self.ui = export_WindowTemplate() + self.ui.setupUi(self) + #self.ui.traceColor_comboBox.addItems(["C0","C1","C2","C3","C4","C5","C6","C7", "r", "g", "b", "y", "k"]) + #self.ui.fitColor_comboBox.addItems(["k", "r", "b", "y", "g","C0","C1","C2","C3","C4","C5","C6","C7"]) + self.ui.export_pushButton.clicked.connect(self.export) + #self.ui.legend_checkBox.stateChanged.connect(self.legend_title) + self.show() + + #def legend_title(self): + # if self.ui.legend_checkBox.isChecked(): + # self.ui.legend1_lineEdit.setEnabled(True) + # self.ui.legend2_lineEdit.setEnabled(True) + # else: + # self.ui.legend1_lineEdit.setEnabled(False) + # self.ui.legend2_lineEdit.setEnabled(False) + + def export(self): + self.export_fig_signal.emit() + self.close() \ No newline at end of file diff --git a/src/main/python/Export_Windows/Multi_Trace_Exporter.py b/src/main/python/Export_Windows/Multi_Trace_Exporter.py new file mode 100644 index 0000000..5d5555d --- /dev/null +++ b/src/main/python/Export_Windows/Multi_Trace_Exporter.py @@ -0,0 +1,147 @@ +import pyqtgraph as pg +from pathlib import Path +from pyqtgraph.Qt import QtCore, QtGui, QtWidgets +try: + from Lifetime_analysis.read_ph_phd import read_picoharp_phd, get_x_y +except Exception as e: + print(e) +import matplotlib.pyplot as plt + +"""Recylce params for plotting""" +plt.rc('xtick', labelsize = 20) +plt.rc('xtick.major', pad = 3) +plt.rc('ytick', labelsize = 20) +plt.rc('lines', lw = 2.5, markersize = 7.5) +plt.rc('legend', fontsize = 20) +plt.rc('axes', linewidth=3.5) + +pg.mkQApp() + +base_path = Path(__file__).parent +file_path = (base_path / "Multi_Trace_Exporter.ui").resolve() + +uiFile = file_path + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +class MainWindow(TemplateBaseClass): + + def __init__(self): + super(TemplateBaseClass, self).__init__() + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + + self.temp_layout = pg.GraphicsLayoutWidget() + + # file system tree + self.fs_model = QtWidgets.QFileSystemModel() + self.fs_model.setRootPath(QtCore.QDir.currentPath()) + self.ui.treeView.setModel(self.fs_model) + self.ui.treeView.setIconSize(QtCore.QSize(25,25)) + self.ui.treeView.setSortingEnabled(True) + + self.tree_selectionModel = self.ui.treeView.selectionModel() + self.tree_selectionModel.selectionChanged.connect(self.on_treeview_selection_change) + + self.ui.comboBox.currentIndexChanged.connect(self.add_trace_to_temp_plot) + self.ui.add_pushButton.clicked.connect(self.add_trace_to_mem) + self.ui.export_pushButton.clicked.connect(self.pub_ready_plot_export) + + self.x_i = [] + self.y_i = [] + self.x_mem = [] + self.y_mem = [] + self.legend = [] + + self.show() + + def on_treeview_selection_change(self): + try: + fname = self.fs_model.filePath(self.tree_selectionModel.currentIndex()) + _ , ext = fname.rsplit('.',1) + + self.ui.comboBox.clear() + self.ui.textBrowser.clear() + self.x_i = [] + self.y_i = [] + + if ext in ['phd']: + self.parser = read_picoharp_phd(fname) + curve_list = [] + + for i in range(self.parser.no_of_curves()): + curve_list.append("Curve "+str(i)) + x, y = get_x_y(i, self.parser, smooth_trace=self.ui.smooth_checkBox.isChecked(), boxwidth=self.ui.smooth_spinBox.value()) + self.x_i.append(x) + self.y_i.append(y) + + self.ui.comboBox.addItems(curve_list) + self.ui.textBrowser.setText(str(self.parser.info())) + + else: + self.ui.textBrowser.setText(str("Select a PicoHarp File")) + except Exception as e: + print(e) + + def add_trace_to_temp_plot(self): + try: + #self.temp_layout = pg.GraphicsLayoutWidget() + self.temp_layout.clear() + self.temp_plot = self.temp_layout.addPlot(title = "Current Selection") + self.temp_plot.plot(self.x_i[self.ui.comboBox.currentIndex()], self.y_i[self.ui.comboBox.currentIndex()], pen='r') + self.temp_plot.setLogMode(False, True) + self.temp_layout.show() + except Exception as e: + print(e) + + def add_trace_to_mem(self): + try: + self.x_mem.append(self.x_i[self.ui.comboBox.currentIndex()]) + self.y_mem.append(self.y_i[self.ui.comboBox.currentIndex()]) + self.legend.append(self.ui.lineEdit.text()) + except Exception as e: + print(e) + + def pub_ready_plot_export(self): + try: + filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") + + plt.figure(figsize=(8,6)) + plt.tick_params(direction='out', length=8, width=3.5) + for i in range(len(self.x_mem)): + if self.ui.Normalize_checkBox.isChecked(): + plt.plot(self.x_mem[i], self.y_mem[i]/max(self.y_mem[i]), label=str(self.legend[i])) + else: + plt.plot(self.x_mem[i], self.y_mem[i], label=str(self.legend[i])) + + plt.yscale('log') + plt.xlabel("Time (ns)", fontsize=20, fontweight='bold') + plt.ylabel("Intensity (norm.)", fontsize=20, fontweight='bold') + plt.legend() + plt.tight_layout() + + plt.savefig(filename[0],bbox_inches='tight', dpi=300) + plt.close() + + self.clear_memory() + + except Exception as e: + print(e) + pass + + def clear_memory(self): + self.x_mem = [] + self.y_mem = [] + self.legend = [] + + + + +def run(): + win = MainWindow() + QtGui.QApplication.instance().exec_() + return win + +#run() \ No newline at end of file diff --git a/src/main/python/Export_Windows/Multi_Trace_Exporter.ui b/src/main/python/Export_Windows/Multi_Trace_Exporter.ui new file mode 100644 index 0000000..7b59ef1 --- /dev/null +++ b/src/main/python/Export_Windows/Multi_Trace_Exporter.ui @@ -0,0 +1,85 @@ + + + MainWindow + + + + 0 + 0 + 1108 + 1063 + + + + MainWindow + + + + + + + + + + Smoothen Trace + + + + + + + Enter Trace Legend Here + + + + + + + Add + + + + + + + Normalize (for export) + + + + + + + 1 + + + + + + + Export + + + + + + + + + + + + + + + 0 + 0 + 1108 + 38 + + + + + + + + diff --git a/src/main/python/Export_Windows/__init__.py b/src/main/python/Export_Windows/__init__.py new file mode 100644 index 0000000..7c68785 --- /dev/null +++ b/src/main/python/Export_Windows/__init__.py @@ -0,0 +1 @@ +# -*- coding: utf-8 -*- \ No newline at end of file diff --git a/src/main/python/Export_Windows/export_fig_gui.ui b/src/main/python/Export_Windows/export_fig_gui.ui new file mode 100644 index 0000000..e80e065 --- /dev/null +++ b/src/main/python/Export_Windows/export_fig_gui.ui @@ -0,0 +1,171 @@ + + + ExportFigure + + + + 0 + 0 + 420 + 369 + + + + Form + + + + + + + 15 + + + + 1000000000 + + + + + + + + 15 + + + + Color Bar Label + + + + + + + + 15 + + + + Data Channel to Save + + + + + + + + 15 + + + + + + + + + 15 + + + + + + + + + 15 + + + + ColorMap + + + + + + + + 15 + + + + 1000000000 + + + + + + + + 15 + + + + ColorBar Min + + + + + + + + 15 + + + + ColorBar Max + + + + + + + false + + + + 15 + + + + + + + + + 15 + + + + Export Figure + + + + + + + + 15 + + + + Reversed + + + + + + + + 15 + + + + + + + + + + + + diff --git a/src/main/python/Export_Windows/export_plot.ui b/src/main/python/Export_Windows/export_plot.ui new file mode 100644 index 0000000..840264f --- /dev/null +++ b/src/main/python/Export_Windows/export_plot.ui @@ -0,0 +1,186 @@ + + + Form + + + + 0 + 0 + 930 + 435 + + + + Form + + + + + + + 10 + + + + 4 + + + -100.000000000000000 + + + 10000000000000000000000.000000000000000 + + + 1.500000000000000 + + + + + + + + 10 + + + + Lower + + + + + + + + 10 + + + + Lower + + + + + + + + 10 + + + + Upper + + + + + + + + 15 + + + + Export Graph + + + + + + + + 12 + + + + Y limits + + + + + + + + 10 + + + + Upper + + + + + + + + 12 + + + + X limits + + + + + + + + 10 + + + + 4 + + + -10000.000000000000000 + + + 1000000000000000000.000000000000000 + + + 0.010000000000000 + + + + + + + + 10 + + + + 4 + + + -10000000.000000000000000 + + + 100000000000.000000000000000 + + + + + + + + 10 + + + + 4 + + + -1000000000.000000000000000 + + + 10000000000000.000000000000000 + + + 10000.000000000000000 + + + + + + + + diff --git a/src/main/python/FLIM_analysis/FLIM_plot.py b/src/main/python/FLIM_analysis/FLIM_plot.py new file mode 100644 index 0000000..5f5744f --- /dev/null +++ b/src/main/python/FLIM_analysis/FLIM_plot.py @@ -0,0 +1,374 @@ +import sys +import h5py +from pathlib import Path +import os.path +import pyqtgraph as pg +from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog +import numpy as np +import matplotlib.pyplot as plt +import pickle +#import time +from lmfit.models import GaussianModel +import customplotting.mscope as cpm + +sys.path.append(os.path.abspath('../Lifetime_analysis')) +sys.path.append(os.path.abspath('../Spectrum_analysis')) +sys.path.append(os.path.abspath('../H5_Pkl')) +sys.path.append(os.path.abspath('../Export_Windows')) +from Lifetime_analysis import Lifetime_plot_fit +from Spectrum_analysis import Spectra_plot_fit +from H5_Pkl import h5_pkl_view +try: + from Export_window import ExportFigureWindow +except: + from Export_Windows.Export_window import ExportFigureWindow +# local modules + +pg.mkQApp() +pg.setConfigOption('background', 'w') + + +base_path = Path(__file__).parent +file_path = (base_path / "flim_plot_gui.ui").resolve() + +uiFile = file_path + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +def updateDelay(scale, time): + """ Hack fix for scalebar inaccuracy """ + QtCore.QTimer.singleShot(time, scale.updateBar) + +class MainWindow(TemplateBaseClass): + + hist_data_signal = QtCore.pyqtSignal() + + def __init__(self): + pg.setConfigOption('imageAxisOrder', 'row-major') + super(TemplateBaseClass, self).__init__() + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + + #set up ui signals + self.ui.load_scan_pushButton.clicked.connect(self.open_file) + self.ui.plot_intensity_sums_pushButton.clicked.connect(self.plot_intensity_sums) + self.ui.plot_raw_hist_data_pushButton.clicked.connect(self.plot_raw_scan) + self.ui.save_intensities_image_pushButton.clicked.connect(self.export_window) + self.ui.save_intensities_array_pushButton.clicked.connect(self.save_intensities_array) + self.ui.compare_checkBox.stateChanged.connect(self.switch_compare) + self.ui.intensity_sums_viewBox.roi.sigRegionChanged.connect(self.line_profile_update_plot) + self.ui.import_pkl_pushButton.clicked.connect(self.import_pkl_to_convert) + self.ui.pkl_to_h5_pushButton.clicked.connect(self.pkl_to_h5) + self.ui.analyze_lifetime_pushButton.clicked.connect(self.on_analyze_lifetime) + self.ui.analyze_psf_pushButton.clicked.connect(self.on_analyze_psf) + + self.show() + + def open_file(self): + """ Open FLIM scan file """ + try: + self.filename = QtWidgets.QFileDialog.getOpenFileName(self, filter="Scan files (*.pkl *.h5 *.txt)") + if ".pkl" in self.filename[0]: + self.flim_scan_file = pickle.load(open(self.filename[0], 'rb')) + self.scan_file_type = "pkl" + self.launch_h5_pkl_viewer() + self.get_data_params() + elif ".h5" in self.filename[0]: + self.flim_scan_file = h5py.File(self.filename[0], 'r') + self.scan_file_type = "h5" + self.launch_h5_pkl_viewer() + self.get_data_params() + elif ".txt" in self.filename[0]: + self.intensity_sums = np.loadtxt(self.filename[0]).T + self.stepsize_window = StepSizeWindow() + self.stepsize_window.stepsize_signal.connect(self.get_stepsize) + self.scan_file_type = "txt" + # self.pkl_file = pickle.load(open(self.filename[0], 'rb')) + except Exception as err: + print(format(err)) + + def launch_h5_pkl_viewer(self): + """ Launches H5/PKL viewer to give an insight into the data and its structure""" + viewer_window = h5_pkl_view.H5PklView(sys.argv) + viewer_window.settings['data_filename'] = self.filename[0] + + def import_pkl_to_convert(self): + """ Open pkl file to convert to h5 """ + try: + self.pkl_to_convert = QtWidgets.QFileDialog.getOpenFileName(self) + self.ui.result_textBrowser.append("Done Loading - .pkl to convert") + except: + pass + + def get_stepsize(self): + """ Get step size from user input -- specfically written for loading + txt files from legacy labview code, but can also be run on txt file + saved using the new FLIM acquistion code """ + self.stepsize = self.stepsize_window.ui.stepsize_doubleSpinBox.value() + self.x_step_size = self.stepsize + self.y_step_size = self.stepsize + + def get_data_params(self): + + data = self.flim_scan_file + if self.scan_file_type == "pkl": + self.x_scan_size = data['Scan Parameters']['X scan size (um)'] + self.y_scan_size = data['Scan Parameters']['Y scan size (um)'] + self.x_step_size = data['Scan Parameters']['X step size (um)'] + self.y_step_size = data['Scan Parameters']['Y step size (um)'] + self.hist_data = data['Histogram data'] + self.time_data = data['Time data'] + else: #run this if scan file is h5 + self.x_scan_size = data['Scan Parameters'].attrs['X scan size (um)'] + self.y_scan_size = data['Scan Parameters'].attrs['Y scan size (um)'] + self.x_step_size = data['Scan Parameters'].attrs['X step size (um)'] + self.y_step_size = data['Scan Parameters'].attrs['Y step size (um)'] + self.hist_data = data['Histogram data'][()] #get dataset values + self.time_data = data['Time data'][()] + + self.numb_x_pixels = int(self.x_scan_size/self.x_step_size) + self.numb_y_pixels = int(self.y_scan_size/self.y_step_size) + + + def plot_intensity_sums(self): + try: + if self.scan_file_type is "pkl" or self.scan_file_type is "h5": + pg.setConfigOption('imageAxisOrder', 'row-major') + self.hist_data = np.reshape(self.hist_data, newshape=(self.hist_data.shape[0], self.numb_x_pixels*self.numb_y_pixels)) + self.intensity_sums = np.sum(self.hist_data, axis=0) #sum intensities for each pixel + self.intensity_sums = np.reshape(self.intensity_sums, newshape=(self.numb_x_pixels, self.numb_y_pixels)) + else: + pg.setConfigOption('imageAxisOrder', 'col-major') + self.ui.intensity_sums_viewBox.view.invertY(False) # stop y axis invert + self.ui.intensity_sums_viewBox.setImage(self.intensity_sums, scale= + (self.x_step_size, + self.y_step_size)) + if self.scan_file_type is "pkl" or self.scan_file_type is "h5": + self.ui.intensity_sums_viewBox.roi.setSize([self.x_scan_size, self.y_step_size]) #line roi + scale = pg.ScaleBar(size=1,suffix='um') + scale.setParentItem(self.ui.intensity_sums_viewBox.view) + scale.anchor((1, 1), (1, 1), offset=(-30, -30)) + self.ui.intensity_sums_viewBox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) + except Exception as err: + print(format(err)) + + def line_profile_update_plot(self): + """ Handle line profile for intensity sum viewbox """ + if hasattr(self, "intensity_sums"): + roiPlot = self.ui.intensity_sums_viewBox.getRoiPlot() + roiPlot.clear() + roi = self.ui.intensity_sums_viewBox.roi + + image = self.ui.intensity_sums_viewBox.getProcessedImage() + + # Extract image data from ROI + axes = (self.ui.intensity_sums_viewBox.axes['x'], self.ui.intensity_sums_viewBox.axes['y']) + data, coords = roi.getArrayRegion(image.view(np.ndarray), self.ui.intensity_sums_viewBox.imageItem, axes, returnMappedCoords=True) + + #calculate sums along columns in region + sums_to_plot = np.mean(data, axis=0) + + #get scan x-coordinates in region + x_values = coords[1][0] + + try: + roiPlot.plot(x_values, sums_to_plot) + except: + pass + + def on_analyze_psf(self): + self.spectrum_window = Spectra_plot_fit.MainWindow() + self.spectrum_window.show() + self.spectrum_window.opened_from_flim = True + sum_data = self.ui.intensity_sums_viewBox.getRoiPlot().getPlotItem().curves[0].getData() + self.spectrum_window.sum_data_from_flim = np.asarray(sum_data) + self.spectrum_window.ui.plot_without_bck_radioButton.setChecked(True) + self.spectrum_window.ui.result_textBrowser.setText("Data successfully loaded from FLIM analysis.") + + def plot_raw_scan(self): + try: + self.hist_image = np.reshape(self.hist_data, newshape=(self.hist_data.shape[0],self.numb_x_pixels,self.numb_y_pixels)) + self.times = self.time_data[:, 0, 0]*1e-3 + self.ui.raw_hist_data_viewBox.view.invertY(False) # stops y-axis invert + self.ui.raw_hist_data_viewBox.setImage(self.hist_image, scale= + (self.x_step_size, + self.y_step_size), xvals=self.times) + self.ui.raw_hist_data_viewBox.roi.setSize([self.x_scan_size, self.y_scan_size]) + # if self.ui.compare_checkBox.isChecked(): + # self.ui.imv2.setImage(self.hist_image, scale= (data['Scan Parameters']['X step size (um)'], + # data['Scan Parameters']['Y step size (um)']), xvals=self.times) + self.switch_compare() + self.ui.raw_hist_data_viewBox.ui.roiBtn.clicked.connect(self.switch_compare) + scale = pg.ScaleBar(size=1,suffix='um') + scale.setParentItem(self.ui.raw_hist_data_viewBox.view) + scale.anchor((1, 1), (1, 1), offset=(-30, -30)) + self.ui.raw_hist_data_viewBox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) + + except Exception as err: + print(format(err)) + + def switch_compare(self): + """ + Handles compare checkbox. If checked, show second ROI on raw histogram data that user can use for comparison to first ROI. + """ + if self.ui.compare_checkBox.isChecked() and hasattr(self, "hist_image"): + if not hasattr(self, "roi2"): #create roi if doesn't exist yet + self.roi2 = pg.ROI(pos=[0,0], size=[int(self.x_scan_size/2), int(self.y_scan_size/2)], movable=True, pen='r') + self.roi2.addScaleHandle([1, 1], [0, 0]) + self.roi2.addRotateHandle([0, 0], [1, 1]) + self.roi2.sigRegionChanged.connect(self.update_roi2_plot) + self.ui.raw_hist_data_viewBox.addItem(self.roi2) + self.update_roi2_plot() + self.roi2.hide() + self.roi2_plot.hide() + if self.ui.raw_hist_data_viewBox.ui.roiBtn.isChecked(): + self.roi2.show() + self.roi2_plot.show() + else: + self.roi2.hide() + self.roi2_plot.hide() + else: #if not checked, hide roi + if hasattr(self, "roi2"): + self.roi2.hide() + self.roi2_plot.hide() + + def update_roi2_plot(self): + """ Update plot corresponding to second roi """ + #Adapted from pyqtgraph imageview sourcecode + + image = self.ui.raw_hist_data_viewBox.getProcessedImage() + + # Extract image data from ROI + axes = (self.ui.raw_hist_data_viewBox.axes['x'], self.ui.raw_hist_data_viewBox.axes['y']) + data, coords = self.roi2.getArrayRegion(image.view(np.ndarray), self.ui.raw_hist_data_viewBox.imageItem, axes, returnMappedCoords=True) + if data is None: + return + + # Average data within entire ROI for each frame + data = data.mean(axis=max(axes)).mean(axis=min(axes)) + xvals = self.ui.raw_hist_data_viewBox.tVals + if hasattr(self, "roi2_plot"): #make sure second plot is properly cleared everytime + self.roi2_plot.clear() + c = self.ui.raw_hist_data_viewBox.getRoiPlot().getPlotItem().curves.pop() + c.scene().removeItem(c) + self.roi2_plot = self.ui.raw_hist_data_viewBox.getRoiPlot().plot(xvals, data, pen='r') + + def get_raw_hist_curve(self, curve_index): + #curve_index = 0 for original roi + #curve_index = 1 for second comparison roi + curves = self.ui.raw_hist_data_viewBox.getRoiPlot().getPlotItem().curves + return curves[curve_index].getData() + + def on_analyze_lifetime(self): + self.lifetime_window = Lifetime_plot_fit.MainWindow() + self.lifetime_window.show() + self.lifetime_window.opened_from_flim = True + self.lifetime_window.hist_data_from_flim = np.asarray(self.get_raw_hist_curve(0)) + self.lifetime_window.ui.Result_textBrowser.setText("Data successfully loaded from FLIM analysis.") + + def export_window(self): + self.export_window = ExportFigureWindow() + self.export_window.ui.vmin_spinBox.setValue(np.min(self.intensity_sums)) + self.export_window.ui.vmax_spinBox.setValue(np.max(self.intensity_sums)) + self.export_window.export_fig_signal.connect(self.save_intensities_image) + + def save_intensities_image(self): + try: + folder = os.path.dirname(self.filename[0]) + filename_ext = os.path.basename(self.filename[0]) + filename = os.path.splitext(filename_ext)[0] #get filename without extension + save_to = folder + "\\" + filename + "_intensity_sums.png" + if self.export_window.ui.reverse_checkBox.isChecked(): + colormap = str(self.export_window.ui.cmap_comboBox.currentText())+"_r" + else: + colormap = str(self.export_window.ui.cmap_comboBox.currentText()) + if self.export_window.ui.cbar_checkBox.isChecked(): + label = str(self.export_window.ui.cbar_label.text()) + else: + label = "PL Intensity (a.u.)" + cpm.plot_confocal(self.intensity_sums, FLIM_adjust=False, + stepsize=np.abs(self.x_step_size),cmap=colormap, + cbar_label=label, vmin=self.export_window.ui.vmin_spinBox.value(), + vmax=self.export_window.ui.vmax_spinBox.value()) + plt.savefig(save_to, bbox_inches='tight', dpi=300) + except Exception as e: + print(format(e)) + + def save_intensities_array(self): + try: + folder = os.path.dirname(self.filename[0]) + filename_ext = os.path.basename(self.filename[0]) + filename = os.path.splitext(filename_ext)[0] #get filename without extension + save_to = folder + "\\" + filename + "_intensity_sums.txt" + np.savetxt(save_to, self.intensity_sums.T, fmt='%f') #save transposed intensity sums, as original array handles x in cols and y in rows + except: + pass + + def pkl_to_h5(self): + #Convert scan .pkl file into h5 + try: + folder = os.path.dirname(self.pkl_to_convert[0]) + filename_ext = os.path.basename(self.pkl_to_convert[0]) + filename = os.path.splitext(filename_ext)[0] #get filename without extension + pkl_file = pickle.load(open(self.pkl_to_convert[0], 'rb')) + + h5_filename = folder + "/" + filename + ".h5" + h5_file = h5py.File(h5_filename, "w") + self.traverse_dict_into_h5(pkl_file, h5_file) + except Exception as err: + print(format(err)) + + def traverse_dict_into_h5(self, dictionary, h5_output): + #Create an h5 file using .pkl with scan data and params + for key in dictionary: + if type(dictionary[key]) == dict: #if subdictionary, create a group + group = h5_output.create_group(key) + previous_dict = dictionary[key] + self.traverse_dict_into_h5(dictionary[key], group) #traverse subdictionary + else: + if key == "Histogram data" or key == "Time data": + h5_output.create_dataset(key, data=dictionary[key]) + else: + h5_output.attrs[key] = dictionary[key] #if not dataset, create attribute + + def close_application(self): + choice = QtGui.QMessageBox.question(self, 'EXIT!', + "Do you want to exit the app?", + QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) + if choice == QtGui.QMessageBox.Yes: + sys.exit() + else: + pass + +"""Skip rows GUI""" +ui_file_path = (base_path / "step_size_labview_files.ui").resolve() +stepsize_WindowTemplate, stepsize_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) + +class StepSizeWindow(stepsize_TemplateBaseClass): + + stepsize_signal = QtCore.pyqtSignal() #signal to help with pass info back to MainWindow + + def __init__(self): + stepsize_TemplateBaseClass.__init__(self) + + # Create the param window + self.ui = stepsize_WindowTemplate() + self.ui.setupUi(self) + self.ui.done_pushButton.clicked.connect(self.done) + self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False) + self.show() + + def done(self): + self.stepsize_signal.emit() + self.close() + +"""Run the Main Window""" +def run(): + win = MainWindow() + QtGui.QApplication.instance().exec_() + return win + +#Uncomment below if you want to run this as standalone +#run() \ No newline at end of file diff --git a/src/main/python/FLIM_analysis/flim_plot_gui.ui b/src/main/python/FLIM_analysis/flim_plot_gui.ui new file mode 100644 index 0000000..bbfef2a --- /dev/null +++ b/src/main/python/FLIM_analysis/flim_plot_gui.ui @@ -0,0 +1,185 @@ + + + Form + + + + 0 + 0 + 738 + 876 + + + + FLIM Analysis + + + + + + 0 + + + + Analysis + + + + + + + + Load Scan + + + + + + + + + Plot + + + + + + + Save intensities array + + + + + + + Save intensities image + + + + + + + Analyze PSF + + + + + + + + + + 500 + 300 + + + + + + + + + 12 + + + + Histogram Intensity Sums + + + + + + + + 12 + + + + Raw Histogram Data + + + + + + + + 500 + 300 + + + + + + + + + + Plot + + + + + + + Analyze lifetime + + + + + + + Compare ROIs + + + + + + + + + + + + .pkl to .h5 + + + + + 20 + 20 + 171 + 34 + + + + Import .pkl file + + + + + + 20 + 80 + 171 + 34 + + + + .pkl to .h5 + + + + + + + + + + ImageView + QGraphicsView +

pyqtgraph
+ + + + + diff --git a/src/main/python/FLIM_analysis/step_size_labview_files.ui b/src/main/python/FLIM_analysis/step_size_labview_files.ui new file mode 100644 index 0000000..2078fb7 --- /dev/null +++ b/src/main/python/FLIM_analysis/step_size_labview_files.ui @@ -0,0 +1,61 @@ + + + Form + + + + 0 + 0 + 255 + 75 + + + + Form + + + + + + + 12 + + + + Step Size (um) + + + + + + + Done! + + + + + + + + 12 + + + + 4 + + + 100.000000000000000 + + + 0.100000000000000 + + + 0.100000000000000 + + + + + + + + diff --git a/src/main/python/H5_Pkl/h5_pkl_view.py b/src/main/python/H5_Pkl/h5_pkl_view.py new file mode 100644 index 0000000..7be99a5 --- /dev/null +++ b/src/main/python/H5_Pkl/h5_pkl_view.py @@ -0,0 +1,124 @@ +from __future__ import division, print_function, absolute_import +from ScopeFoundry import BaseApp +from ScopeFoundry.helper_funcs import load_qt_ui_file, sibling_path +from collections import OrderedDict +import os +from qtpy import QtCore, QtWidgets, QtGui +import pyqtgraph as pg +import pyqtgraph.dockarea as dockarea +import numpy as np +from ScopeFoundry.logged_quantity import LQCollection +from scipy.stats import spearmanr +import argparse +from .h5_tree import H5TreeSearchView +from .pkl_tree import PklTreeSearchView + +pg.setConfigOption('imageAxisOrder', 'row-major') + +class H5PklView(BaseApp): + + name = "h5_pkl_view" + + def __init__(self, argv): + BaseApp.__init__(self, argv) + self.setup() + parser = argparse.ArgumentParser() + for lq in self.settings.as_list(): + parser.add_argument("--" + lq.name) + args = parser.parse_args() + for lq in self.settings.as_list(): + if lq.name in args: + val = getattr(args,lq.name) + if val is not None: + lq.update_value(val) + + def setup(self): + self.ui_filename = sibling_path(__file__, "h5_pkl_view_gui.ui") + self.ui = load_qt_ui_file(self.ui_filename) + self.ui.show() + self.ui.raise_() + + self.views = OrderedDict() + + self.settings.New('data_filename', dtype='file') + self.settings.New('auto_select_view',dtype=bool, initial=True) + self.settings.New('view_name', dtype=str, initial='0', choices=('0',)) + + self.settings.data_filename.add_listener(self.on_change_data_filename) + + # UI Connections/ + self.settings.data_filename.connect_to_browse_widgets(self.ui.data_filename_lineEdit, + self.ui.data_filename_browse_pushButton) + + # set views + self.h5treeview = H5TreeSearchView(self) + self.load_view(self.h5treeview) + self.pkltreeview = PklTreeSearchView(self) + self.load_view(self.pkltreeview) + + self.settings.view_name.add_listener(self.on_change_view_name) + + self.current_view = None + + self.ui.show() + + def load_view(self, new_view): + # add to views dict + self.views[new_view.name] = new_view + + self.ui.dataview_page.layout().addWidget(new_view.ui) + new_view.ui.hide() + + # update choices for view_name + self.settings.view_name.change_choice_list(list(self.views.keys())) + return new_view + + def on_change_data_filename(self): + #Handle file change + try: + fname = self.settings.data_filename.val + if not self.settings['auto_select_view']: + self.current_view.on_change_data_filename(fname) + else: + view_name = self.auto_select_view(fname) + if self.current_view is None or view_name != self.current_view.name: + # update view (automatically calls on_change_data_filename) + self.settings['view_name'] = view_name + else: + # force update + if os.path.isfile(fname): + self.current_view.on_change_data_filename(fname) + except: + pass + + def on_change_view_name(self): + #Handle view change - happens when filetype changes + self.ui.dataview_placeholder.hide() + previous_view = self.current_view + + self.current_view = self.views[self.settings['view_name']] + # hide current view + # (handle the initial case where previous_view is None ) + if previous_view: + previous_view.ui.hide() + + # show new view + self.current_view.ui.show() + + # set datafile for new (current) view + fname = self.settings['data_filename'] + if os.path.isfile(fname): + self.current_view.on_change_data_filename(self.settings['data_filename']) + + def auto_select_view(self, fname): + #return the name of the last supported view for the given fname + for view_name, view in list(self.views.items())[::-1]: + if view.is_file_supported(fname): + return view_name + # return default file_info view if no others work + return "h5_tree_search" + +# if __name__ == '__main__': +# import sys +# app = H5PklView(sys.argv) +# sys.exit(app.exec_()) diff --git a/src/main/python/H5_Pkl/h5_pkl_view_gui.ui b/src/main/python/H5_Pkl/h5_pkl_view_gui.ui new file mode 100644 index 0000000..d147ddc --- /dev/null +++ b/src/main/python/H5_Pkl/h5_pkl_view_gui.ui @@ -0,0 +1,89 @@ + + + MainWindow + + + + 0 + 0 + 856 + 925 + + + + H5/pkl View + + + + + + + Qt::Horizontal + + + + File + + + + + + + + + File: + + + + + + + Browse... + + + + + + + true + + + 0 + + + + Data View + + + + + + Once a file is loaded, data will show up here. + + + + + + + + + + + + + + + + + 0 + 0 + 856 + 21 + + + + + + + + diff --git a/src/main/python/H5_Pkl/h5_tree.py b/src/main/python/H5_Pkl/h5_tree.py new file mode 100644 index 0000000..6d82566 --- /dev/null +++ b/src/main/python/H5_Pkl/h5_tree.py @@ -0,0 +1,100 @@ +from ScopeFoundry.data_browser import DataBrowserView +from qtpy import QtWidgets +import h5py + +class H5TreeSearchView(DataBrowserView): + + name = 'h5_tree_search' + + def is_file_supported(self, fname): + return ('.h5' in fname) + + def setup(self): + #self.settings.New('search_text', dtype=str, initial="") + + self.ui = QtWidgets.QWidget() + self.ui.setLayout(QtWidgets.QVBoxLayout()) + self.search_lineEdit = QtWidgets.QLineEdit() + self.search_lineEdit.setPlaceholderText("Search") + self.tree_textEdit = QtWidgets.QTextEdit("") + + self.ui.layout().addWidget(self.search_lineEdit) + self.ui.layout().addWidget(self.tree_textEdit) + + #self.settings.search_text.connect_to_widget(self.search_lineEdit) + #self.settings.search_text.add_listener(self.on_new_search_text) + self.search_text = "" + + self.search_lineEdit.textChanged.connect(self.on_new_search_text) + + def on_change_data_filename(self, fname=None): + """ Handle file change """ + self.tree_textEdit.setText("loading {}".format(fname)) + try: + #if using h5_plot_and_view + if hasattr(self.databrowser.ui, "dataset_listWidget"): + self.dataset_dict = {} + self.databrowser.ui.dataset_listWidget.clear() + + self.fname = fname + self.f = h5py.File(fname, 'r') + self.on_new_search_text() + self.databrowser.ui.statusbar.showMessage("") + return self.f + + except Exception as err: + msg = "Failed to load %s:\n%s" %(fname, err) + self.databrowser.ui.statusbar.showMessage(msg) + self.tree_textEdit.setText(msg) + raise(err) + + def on_new_search_text(self, x=None): + if x is not None: + self.search_text = x.lower() + old_scroll_pos = self.tree_textEdit.verticalScrollBar().value() + self.tree_str = "" + self.f.visititems(self._visitfunc) + + self.tree_text_html = \ + """{}
+
+ {} +
+ """.format(self.fname, self.tree_str) + + self.tree_textEdit.setText(self.tree_text_html) + self.tree_textEdit.verticalScrollBar().setValue(old_scroll_pos) + + def _visitfunc(self, name, node): + level = len(name.split('/')) + indent = ' '*4*(level-1) + + #indent = ''.format(level*4) + localname = name.split('/')[-1] + + #search_text = self.settings['search_text'].lower() + search_text = self.search_text + if search_text and (search_text in localname.lower()): #highlight terms that contain search text + localname = """{}""".format(localname) + + if isinstance(node, h5py.Group): + self.tree_str += indent +"|> {}/
".format(localname) + elif isinstance(node, h5py.Dataset): + self.tree_str += indent +"|D {}: {} {}
".format(localname, node.shape, node.dtype) + + #if using h5_plot_and_view + if hasattr(self.databrowser.ui, "dataset_listWidget"): + item_name = "{}: {} {}".format(localname, node.shape, node.dtype) + self.databrowser.ui.dataset_listWidget.addItem(item_name) + if not hasattr(self, "dataset_dict"): + self.dataset_dict = {} + self.dataset_dict[item_name] = node + + + for key, val in node.attrs.items(): #highlight terms that contain search text + if search_text: + if search_text in str(key).lower(): + key = """{}""".format(key) + if search_text in str(val).lower(): + val = """{}""".format(val) + self.tree_str += indent+"     |- {} = {}
".format(key, val) \ No newline at end of file diff --git a/src/main/python/H5_Pkl/h5_view_and_plot.py b/src/main/python/H5_Pkl/h5_view_and_plot.py new file mode 100644 index 0000000..18f3635 --- /dev/null +++ b/src/main/python/H5_Pkl/h5_view_and_plot.py @@ -0,0 +1,141 @@ +from __future__ import division, print_function, absolute_import +from ScopeFoundry import BaseApp +from ScopeFoundry.helper_funcs import load_qt_ui_file, sibling_path +from collections import OrderedDict +import os +from qtpy import QtCore, QtWidgets, QtGui +import pyqtgraph as pg +import pyqtgraph.dockarea as dockarea +import numpy as np +from ScopeFoundry.logged_quantity import LQCollection +from scipy.stats import spearmanr +import argparse +from .h5_tree import H5TreeSearchView +from .pkl_tree import PklTreeSearchView + + + +class H5ViewPlot(BaseApp): + + name = "h5_view_plot" + + def __init__(self, argv): + pg.setConfigOption('imageAxisOrder', 'row-major') + BaseApp.__init__(self, argv) + self.setup() + parser = argparse.ArgumentParser() + for lq in self.settings.as_list(): + parser.add_argument("--" + lq.name) + args = parser.parse_args() + for lq in self.settings.as_list(): + if lq.name in args: + val = getattr(args,lq.name) + if val is not None: + lq.update_value(val) + + def setup(self): + self.ui_filename = sibling_path(__file__, "h5_view_and_plot_gui.ui") + self.ui = load_qt_ui_file(self.ui_filename) + self.ui.show() + self.ui.raise_() + + self.settings.New('data_filename', dtype='file') + + self.settings.data_filename.add_listener(self.on_change_data_filename) + + self.settings.New('view_name', dtype=str, initial='0', choices=('0',)) + + # UI Connections + self.settings.data_filename.connect_to_browse_widgets(self.ui.data_filename_lineEdit, + self.ui.data_filename_browse_pushButton) + self.ui.plot_pushButton.clicked.connect(self.plot_dataset) + self.ui.dataset_listWidget.currentItemChanged.connect(self.on_data_selection) + self.ui.plot_radioButton.toggled.connect(self.update_data_widget) + self.ui.image_radioButton.toggled.connect(self.update_data_widget) + + #set up image item for 2d array + self.data_img_layout = pg.GraphicsLayoutWidget() + self.ui.imageItem_page.layout().addWidget(self.data_img_layout) + self.data_img_layout = self.data_img_layout.addViewBox() + self.data_img = pg.ImageItem() + self.data_img_layout.addItem(self.data_img) + + #set up image view for 3d array + self.ui.data_imageView.getView().invertY(False) + + self.h5treeview = H5TreeSearchView(self) + self.ui.dataview_page.layout().addWidget(self.h5treeview.ui) + self.h5treeview.ui.hide() + self.ui.show() + + def on_change_data_filename(self): + """ Handle file change """ + try: + fname = self.settings.data_filename.val + if os.path.isfile(fname): + self.f = self.h5treeview.on_change_data_filename(fname) + self.ui.dataview_placeholder.hide() + self.h5treeview.ui.show() + except: + pass + + def plot_dataset(self): + """ Plot data set depending on dataset shape and plot type option. """ + self.plot = self.ui.data_plotWidget.getPlotItem() + self.plot.clear() + + data = self.dataset[()] + if self.dataset_shape == 1: + x_start = self.ui.plotWidget_x_start_spinBox.value() + x_end = self.ui.plotWidget_x_end_spinBox.value() + num_points = self.dataset.shape[0] + x_values = np.linspace(x_start, x_end, num_points) + self.plot.plot(x_values, data) + elif self.dataset_shape == 2 and self.ui.plot_radioButton.isChecked(): + self.plot.plot(data[0], data[1]) # TODO check and test this + elif self.dataset_shape == 2 and self.ui.image_radioButton.isChecked(): + self.data_img.setImage(data) + elif self.dataset_shape == 3: + if self.f['Cube/Info/Cube'].attrs['AcqMode'] == b'Hyperspectral Acquisition': # This works for our PhotonEtc. Hyperspectral Camera output + x_start = int(self.f['Cube/Info/Cube'].attrs['LowerWavelength']) + x_end = int(self.f['Cube/Info/Cube'].attrs['UpperWavelength']) + else: + x_start = self.ui.imageView_x_start_spinBox.value() + x_end = self.ui.imageView_x_end_spinBox.value() + num_points = self.dataset.shape[0] + x_values = np.linspace(x_start, x_end, num_points) #scale x axis + self.ui.data_imageView.setImage(data, xvals=x_values) + + def on_data_selection(self): + """ Handle dataset selection """ + try: + dataset_name = self.ui.dataset_listWidget.currentItem().text() + self.dataset = self.h5treeview.dataset_dict[dataset_name] + self.dataset_shape = len(self.dataset[()].shape) + self.update_data_widget() + if self.dataset_shape == 1: + self.ui.plot_type_groupBox.setEnabled(False) + self.ui.plot_radioButton.setChecked(True) + elif self.dataset_shape == 2: + self.ui.plot_type_groupBox.setEnabled(True) + elif self.dataset_shape == 3: + self.ui.plot_type_groupBox.setEnabled(False) + self.ui.image_radioButton.setChecked(True) + except: + pass + + def update_data_widget(self): + """ Decide which widget to display based on dataset shape and plot type option. """ + if self.dataset_shape == 1: + self.ui.data_stackedWidget.setCurrentIndex(0) + elif self.dataset_shape == 2 and self.ui.plot_radioButton.isChecked(): + self.ui.data_stackedWidget.setCurrentIndex(0) + elif self.dataset_shape == 2 and self.ui.image_radioButton.isChecked(): + self.ui.data_stackedWidget.setCurrentIndex(1) + elif self.dataset_shape == 3: + self.ui.data_stackedWidget.setCurrentIndex(2) + +# if __name__ == '__main__': +# import sys +# app = H5ViewPlot(sys.argv) +# sys.exit(app.exec_()) \ No newline at end of file diff --git a/src/main/python/H5_Pkl/h5_view_and_plot_gui.ui b/src/main/python/H5_Pkl/h5_view_and_plot_gui.ui new file mode 100644 index 0000000..a7bcc01 --- /dev/null +++ b/src/main/python/H5_Pkl/h5_view_and_plot_gui.ui @@ -0,0 +1,280 @@ + + + MainWindow + + + + 0 + 0 + 856 + 925 + + + + H5 View and Plot + + + + + + + Qt::Horizontal + + + + File + + + + + + + + + File: + + + + + + + Browse... + + + + + + + true + + + 0 + + + + Data View + + + + + + Once a file is loaded, data will show up here. + + + + + + + + true + + + Plot + + + + + + Datasets + + + + + + + + + + + + Plot data + + + + + + 0 + + + + + + + + + + + + + 203 + 16777215 + + + + 9999999.000000000000000 + + + 0.000000000000000 + + + + + + + X start + + + + + + + 9999999.000000000000000 + + + + + + + X end + + + + + + + + + + + + + + + + + + + + + 9999999.000000000000000 + + + + + + + + 203 + 16777215 + + + + 9999999.000000000000000 + + + 0.000000000000000 + + + + + + + X start + + + + + + + X end + + + + + + + + + + + + + Plot + + + + + + + true + + + Type + + + + + + true + + + Plot + + + true + + + + + + + true + + + Image + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 856 + 21 + + + + + + + + PlotWidget + QGraphicsView +
pyqtgraph
+ + + ImageView + QGraphicsView +
pyqtgraph
+ + + + + diff --git a/src/main/python/H5_Pkl/pkl_tree.py b/src/main/python/H5_Pkl/pkl_tree.py new file mode 100644 index 0000000..e60a85e --- /dev/null +++ b/src/main/python/H5_Pkl/pkl_tree.py @@ -0,0 +1,103 @@ +from ScopeFoundry.data_browser import DataBrowserView +from qtpy import QtWidgets +import h5py +import pickle +import numpy as np +import lmfit + +class PklTreeSearchView(DataBrowserView): + + name = 'pkl_tree_search' + + def is_file_supported(self, fname): + return ('.pkl' in fname) + + def setup(self): + #self.settings.New('search_text', dtype=str, initial="") + + self.ui = QtWidgets.QWidget() + self.ui.setLayout(QtWidgets.QVBoxLayout()) + self.search_lineEdit = QtWidgets.QLineEdit() + self.search_lineEdit.setPlaceholderText("Search") + self.tree_textEdit = QtWidgets.QTextEdit("") + + self.ui.layout().addWidget(self.search_lineEdit) + self.ui.layout().addWidget(self.tree_textEdit) + + #self.settings.search_text.connect_to_widget(self.search_lineEdit) + #self.settings.search_text.add_listener(self.on_new_search_text) + self.search_text = "" + + self.search_lineEdit.textChanged.connect(self.on_new_search_text) + + def on_change_data_filename(self, fname=None): + """ Handle file change """ + self.tree_textEdit.setText("loading {}".format(fname)) + try: + self.fname = fname + #self.f = h5py.File(fname, 'r') + self.dictionary = pickle.load(open(self.fname, 'rb')) + self.on_new_search_text() + self.databrowser.ui.statusbar.showMessage("") + + except Exception as err: + msg = "Failed to load %s:\n%s" %(fname, err) + self.databrowser.ui.statusbar.showMessage(msg) + self.tree_textEdit.setText(msg) + raise(err) + + def on_new_search_text(self, x=None): + if x is not None: + self.search_text = x.lower() + old_scroll_pos = self.tree_textEdit.verticalScrollBar().value() + self.tree_str = "" + #self.f.visititems(self._visitfunc) + self.traverse_dict(self.dictionary, self.dictionary, 0) + + + self.tree_text_html = \ + """{}
+
+ {} +
+ """.format(self.fname, self.tree_str) + + self.tree_textEdit.setText(self.tree_text_html) + self.tree_textEdit.verticalScrollBar().setValue(old_scroll_pos) + + def traverse_dict(self, dictionary, previous_dict, level): + """ + Visit all values in the dictionary and its subdictionaries. + + dictionary -- dictionary to traverse + previous_dict -- dictionary one level up + level -- track how far to indent + """ + for key in dictionary: + if key not in previous_dict: + level -=1 + indent = " "*4*(level) + + if type(dictionary[key]) == dict: + print_string = key + if self.search_text and self.search_text in print_string: + self.tree_str += indent + """{}""".format(print_string) + else: + self.tree_str += indent + "|> {}/
".format(print_string) + level += 1 + previous_dict = dictionary[key] + self.traverse_dict(dictionary[key], previous_dict, level) + else: + value = dictionary[key] + if type(value) == np.ndarray or type(value)==np.memmap: + value = str(value.shape) + " " + str(value.dtype) + elif type(value) == lmfit.model.ModelResult: + value = "lmfit.model.ModelResult" + # if type(value) == list and len(value) > 5: ##account for data stored in lists + # value = str(np.asarray(value).shape) + " " + str(type(value[0])) + + print_string = key + " = " + str(value) + if self.search_text and self.search_text in print_string: + self.tree_str += indent + """{}""".format(print_string) + else: + self.tree_str += indent + "|- {}
".format(print_string) \ No newline at end of file diff --git a/src/main/python/Image_analysis/Image_analysis.py b/src/main/python/Image_analysis/Image_analysis.py new file mode 100644 index 0000000..50b2d1c --- /dev/null +++ b/src/main/python/Image_analysis/Image_analysis.py @@ -0,0 +1,222 @@ +import sys +from pathlib import Path +import os.path +import pyqtgraph as pg +from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog +import numpy as np +import matplotlib.pyplot as plt +from PIL import Image + +# local modules + +pg.mkQApp() + + +base_path = Path(__file__).parent +file_path = (base_path / "image_analysis_gui.ui").resolve() + +uiFile = file_path + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +def updateDelay(scale, time): + """ Hack fix for scalebar inaccuracy""" + QtCore.QTimer.singleShot(time, scale.updateBar) + +class MainWindow(TemplateBaseClass): + + def __init__(self): + pg.setConfigOption('imageAxisOrder', 'col-major') + super(TemplateBaseClass, self).__init__() + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + + #setup image plot + self.image_plot_layout=pg.GraphicsLayoutWidget() + self.ui.image_groupBox.layout().addWidget(self.image_plot_layout) + self.image_plot = self.image_plot_layout.addPlot() + self.img_item = pg.ImageItem() + self.image_plot.addItem(self.img_item) + self.image_plot_view = self.image_plot.getViewBox() + + #setup lookup table + self.hist_lut = pg.HistogramLUTItem() + self.image_plot_layout.addItem(self.hist_lut) + + #region of interest - allows user to select scan area + self.roi = pg.ROI([0,0],[10, 10], movable=True) + self.roi.addScaleHandle([1, 1], [0, 0]) + self.roi.addRotateHandle([0, 0], [1, 1]) + self.roi.translateSnap = True + self.roi.scaleSnap = True + self.roi.sigRegionChanged.connect(self.line_profile_update_plot) + self.image_plot.addItem(self.roi) + + #setup rgb plot + self.rgb_plot_layout=pg.GraphicsLayoutWidget() + self.ui.rgb_plot_groupBox.layout().addWidget(self.rgb_plot_layout) + self.rgb_plot = self.rgb_plot_layout.addPlot() + + #set up ui signals + self.ui.load_image_pushButton.clicked.connect(self.load_image) + self.ui.custom_pixel_size_checkBox.stateChanged.connect(self.switch_custom_pixel_size) + self.ui.update_settings_pushButton.clicked.connect(self.reload_image) + self.ui.spot_radioButton.toggled.connect(self.update_camera) + + self.update_camera() #initialize camera pixel size + self.update_scaling_factor() #initialize scaling_factor + self.show() + + #row major. invert y false, rotate false + def load_image(self): + """ + Prompts the user to select a text file containing image data. + """ + try: + file = QtWidgets.QFileDialog.getOpenFileName(self, 'Open file', os.getcwd()) + self.original_image = Image.open(file[0]) + self.original_image = self.original_image.rotate(-90, expand=True) #correct image orientation + self.resize_to_scaling_factor(self.original_image) + except Exception as err: + print(format(err)) + + def resize_to_scaling_factor(self, image): + """ + Handles loading of image according to scaling_factor + """ + self.update_scaling_factor() + + if self.ui.spot_radioButton.isChecked() and self.ui.resize_image_checkBox.isChecked(): + image = self.original_image.resize((round(image.size[0]*self.scaling_factor), round(image.size[1]*self.scaling_factor))) + self.image_plot.getAxis("bottom").setScale(scale = 1) + self.image_plot.getAxis("left").setScale(scale = 1) + else: + image = self.original_image + self.image_plot.getAxis("bottom").setScale(scale = self.scaling_factor) + self.image_plot.getAxis("left").setScale(scale = self.scaling_factor) + + if self.ui.greyscale_checkBox.isChecked(): + image = image.convert("L") #convert to greyscale + + self.image_array = np.array(image) + width = self.image_array.shape[0] + height = self.image_array.shape[1] + + try: + #set image bounds with qrect + self.img_item_rect = QtCore.QRectF(0, 0, width, height) + self.img_item.setImage(image=self.image_array) + self.img_item.setRect(self.img_item_rect) + + # if self.ui.greyscale_checkBox.isChecked(): + # self.hist_lut.setImageItem(self.img_item) + + if self.ui.vertical_radioButton.isChecked(): + roi_height = self.scaling_factor * height + self.roi.setSize([width, roi_height]) + elif self.ui.horizontal_radioButton.isChecked(): + roi_height = self.scaling_factor * width + self.roi.setSize([roi_height, height]) + self.roi.setAngle(0) + self.roi.setPos(0, 0) + self.line_profile_update_plot() + except: + pass + + def line_profile_update_plot(self): + """ Handle line profile for intensity sum viewbox """ + self.rgb_plot.clear() + + # Extract image data from ROI + data, coords = self.roi.getArrayRegion(self.image_array, self.img_item, returnMappedCoords=True) + if data is None: + return + + if self.ui.vertical_radioButton.isChecked(): + x_values = coords[0,:,0] + elif self.ui.horizontal_radioButton.isChecked(): + x_values = coords[1,0,:] + + if self.ui.pixera_radioButton.isChecked() or (self.ui.spot_radioButton.isChecked() and not self.ui.resize_image_checkBox.isChecked()): + x_values = x_values * self.scaling_factor + + #calculate average along columns in region + if len(data.shape) <= 2: #if grayscale, average intensities + if self.ui.vertical_radioButton.isChecked(): + avg_to_plot = np.mean(data, axis=-1) + elif self.ui.horizontal_radioButton.isChecked(): + avg_to_plot = np.mean(data, axis=0) + try: + self.rgb_plot.plot(x_values, avg_to_plot) + except: + pass + elif len(data.shape) > 2: #if rgb arrays, plot individual components + r_values = data[:,:,0] + g_values = data[:,:,1] + b_values = data[:,:,2] + if self.ui.vertical_radioButton.isChecked(): + r_avg = np.mean(r_values, axis=-1) #average red values across columns + g_avg = np.mean(g_values, axis=-1) #average green values + b_avg = np.mean(b_values, axis=-1) #average blue values + elif self.ui.horizontal_radioButton.isChecked(): + r_avg = np.mean(r_values, axis=0) + g_avg = np.mean(g_values, axis=0) + b_avg = np.mean(b_values, axis=0) + try: + self.rgb_plot.plot(x_values, r_avg, pen='r') + self.rgb_plot.plot(x_values, g_avg, pen='g') + self.rgb_plot.plot(x_values, b_avg, pen='b') + except Exception as e: + pass + + def update_scaling_factor(self): + """ + Calculate scaling factor + """ + if self.ui.custom_pixel_size_checkBox.isChecked(): + self.camera_pixel_size = self.ui.custom_pixel_size_spinBox.value() + self.scaling_factor = self.camera_pixel_size + else: + self.scaling_factor = self.camera_pixel_size/int(self.ui.magnification_comboBox.currentText()) + self.roi.snapSize = self.scaling_factor #roi snaps to multiples of scaling_factor + + def reload_image(self): + if hasattr(self, "original_image"): + self.resize_to_scaling_factor(self.original_image) #resize image, sets up roi + + def switch_custom_pixel_size(self): + checked = self.ui.custom_pixel_size_checkBox.isChecked() + self.ui.custom_pixel_size_spinBox.setEnabled(checked) + self.ui.magnification_comboBox.setEnabled(not checked) + + def update_camera(self): + if self.ui.spot_radioButton.isChecked(): + self.camera_pixel_size = 7.4 + self.ui.greyscale_checkBox.setChecked(False) + self.ui.resize_image_checkBox.setEnabled(True) + self.update_scaling_factor() + elif self.ui.pixera_radioButton.isChecked(): + self.camera_pixel_size = 3 + self.ui.greyscale_checkBox.setChecked(True) + self.ui.resize_image_checkBox.setEnabled(False) + self.update_scaling_factor() + + def close_application(self): + choice = QtGui.QMessageBox.question(self, 'EXIT!', + "Do you want to exit the app?", + QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) + if choice == QtGui.QMessageBox.Yes: + sys.exit() + else: + pass + +"""Run the Main Window""" +def run(): + win = MainWindow() + QtGui.QApplication.instance().exec_() + return win + +#Uncomment below if you want to run this as standalone +#run() \ No newline at end of file diff --git a/src/main/python/Image_analysis/image_analysis_gui.ui b/src/main/python/Image_analysis/image_analysis_gui.ui new file mode 100644 index 0000000..9fcffd9 --- /dev/null +++ b/src/main/python/Image_analysis/image_analysis_gui.ui @@ -0,0 +1,208 @@ + + + MainWindow + + + + 0 + 0 + 1029 + 743 + + + + Image Analysis + + + QTabWidget::Triangular + + + + + + + Settings + + + + + + + + + + + + + Greyscale image + + + + + + + Load image + + + + + + + + 50 + + + + + 75 + + + + + 100 + + + + + 150 + + + + + + + + Magnification + + + + + + + Update settings + + + + + + + false + + + + + + + Custom pixel size (um) + + + + + + + Camera + + + + + + SPOT + + + true + + + + + + + Pixera + + + + + + + Resize image + + + + + + + + + + Direction to average pixels + + + + + + Vertical + + + true + + + + + + + Horizontal + + + + + + + + + + + + + + + + 0 + 0 + + + + + 600 + 0 + + + + Image + + + + + + + + RGB Plot + + + + + + + + + + 0 + 0 + 1029 + 31 + + + + + + + + diff --git a/src/main/python/Lifetime_analysis/Fit_functions.py b/src/main/python/Lifetime_analysis/Fit_functions.py new file mode 100644 index 0000000..7ad5c3e --- /dev/null +++ b/src/main/python/Lifetime_analysis/Fit_functions.py @@ -0,0 +1,132 @@ +# -*- coding: utf-8 -*- +""" +Created on Fri Mar 29 11:21:59 2019 + +@author: Sarthak +""" + +import numpy as np +from scipy.optimize import differential_evolution +from scipy.special import gamma + +def stretch_exp_fit(TRPL, t, Tc = (0,1e5), Beta = (0,1), A = (0,1e6), noise=(0,1e6)): + + def exp_stretch(t, tc, beta, a, noise): + return ((a * np.exp(-((1.0 / tc) * t) ** beta)) + noise) + + def avg_tau_from_exp_stretch(tc, beta): + return (tc / beta) * gamma(1.0 / beta) + + def Diff_Ev_Fit_SE(TRPL): + TRPL = TRPL + + def residuals(params):#params are the parameters to be adjusted by differential evolution or leastsq, interp is the data to compare to the model. + #Variable Rates + tc = params[0] + beta = params[1] + a = params[2] + noise = params[3] + + PL_sim = exp_stretch(t,tc,beta,a, noise) + + Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) + return Resid #returns the difference between the PL data and simulated data + + bounds = [Tc, Beta, A, noise] + + result = differential_evolution(residuals, bounds) + return result.x + + p = Diff_Ev_Fit_SE(TRPL) + + tc = p[0] + beta = p[1] + a = p[2] + noise = p[3] + + PL_fit = exp_stretch(t,tc,beta,a, noise) + + avg_tau = avg_tau_from_exp_stretch(tc,beta) + + return tc, beta, a, avg_tau, PL_fit, noise + +def double_exp_fit(TRPL, t, tau1_bounds=(0,1000), a1_bounds=(0,1e6), tau2_bounds=(0,10000), a2_bounds=(0,1e5), noise=(0,1e6)): + + def single_exp(t, tau, a): + return (a * np.exp(-((1.0 / tau)*t))) + + def double_exp(t, tau1, a1, tau2, a2, noise): + return ((single_exp(t, tau1, a1)) + (single_exp(t, tau2, a2)) + noise) + + def avg_tau_from_double_exp(tau1, a1, tau2, a2): + return (((tau1*a1) + (tau2*a2))/(a1+a2)) + + def Diff_Ev_Fit_DE(TRPL): + TRPL = TRPL + + def residuals(params):#params are the parameters to be adjusted by differential evolution or leastsq, interp is the data to compare to the model. + #Variable Rates + tau1 = params[0] + a1 = params[1] + tau2 = params[2] + a2 = params[3] + noise = params[4] + + PL_sim = double_exp(t,tau1, a1, tau2, a2, noise) + + Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) + return Resid #returns the difference between the PL data and simulated data + + bounds = [tau1_bounds, a1_bounds, tau2_bounds, a2_bounds, noise] + + result = differential_evolution(residuals, bounds) + return result.x + + p = Diff_Ev_Fit_DE(TRPL) + + tau1 = p[0] + a1 = p[1] + tau2 = p[2] + a2 = p[3] + noise = p[4] + + PL_fit = double_exp(t, tau1, a1, tau2, a2, noise) + + avg_tau = avg_tau_from_double_exp(tau1, a1, tau2, a2) + + return tau1, a1, tau2, a2, avg_tau, PL_fit, noise + +def single_exp_fit(TRPL, t, tau_bounds=(0,10000), a_bounds=(0,1e6), noise=(0,1e6)): + + def single_exp(t, tau, a, noise): + return (a * np.exp(-((1.0 / tau)*t) ) + noise) + + def Diff_Ev_Fit_singleExp(TRPL): + TRPL = TRPL + + def residuals(params):#params are the parameters to be adjusted by differential evolution or leastsq, interp is the data to compare to the model. + #Variable Rates + tau = params[0] + a = params[1] + noise = params[2] + + PL_sim = single_exp(t, tau, a, noise) + + Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) + return Resid #returns the difference between the PL data and simulated data + + bounds = [tau_bounds, a_bounds, noise] + + result = differential_evolution(residuals, bounds) + return result.x + + p = Diff_Ev_Fit_singleExp(TRPL) + + tau = p[0] + a = p[1] + noise = p[2] + + PL_fit = single_exp(t, tau, a, noise) + + return tau, a, PL_fit, noise + \ No newline at end of file diff --git a/src/main/python/Lifetime_analysis/Fit_functions_with_irf.py b/src/main/python/Lifetime_analysis/Fit_functions_with_irf.py new file mode 100644 index 0000000..5b454af --- /dev/null +++ b/src/main/python/Lifetime_analysis/Fit_functions_with_irf.py @@ -0,0 +1,329 @@ +import numpy as np +import matplotlib.pyplot as plt +from scipy.optimize import fmin_tnc, differential_evolution +from scipy.special import gamma +from scipy.signal import fftconvolve +from scipy.integrate import odeint + + +"""Fit TCSPC data to a model by reconvolution with the IRF +Convolution is done in time domain with np.convolve() +Convolution can be done in the frequency domain of np.convolve() is replaced by scipy.signal.fftconvolve() + +For a good tutorial on numerical convolution, see section 13.1 of Numerical Recipes: + +Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P., +Numerical Recipes 3rd Edition: The Art of Scientific Computing. 3 ed.; +Cambridge University Press: New York, 2007 + +***Note that algorithm given in Numerical Recipes does convolution in the frequency +domain using the FFT. However the discussion of convolution in 13.1 applies to the time +domain and can be used to understand this Python code.*** + +-MZ, 2/2017 +""" + +def convolve_sig_resp(signal_array, response_array, t_array, tstep): + + def normalize_response(response_array, t_array): + area = np.trapz(response_array, x = t_array) + return response_array / area + + def array_zeropad_neg(array, pad_length): + + return np.pad(array, (pad_length, 0), 'constant', constant_values = (0,0)) + + def array_zeropad_pos(array, pad_length): + return np.pad(array, (0, pad_length), 'constant', constant_values = (0,0)) + +# def array_symmetricpad_neg(array, pad_length): +# +# return np.pad(array, (pad_length, 0), 'symmetric') + + def signal_and_resp_forconv(signal_array, response_array): + resp_pad_negtime = array_zeropad_neg(normalize_response(response_array, t_array), len(response_array) - 1) + sig_pad_negtime = array_zeropad_neg(signal_array, len(signal_array) - 1) + sig_pad_postime = array_zeropad_pos(sig_pad_negtime, len(response_array)) + return [resp_pad_negtime, sig_pad_postime] + + resp, sig = signal_and_resp_forconv(signal_array, response_array) + convolution = tstep * fftconvolve(sig, resp, mode = 'same')#np.convolve(resp, sig, mode = 'same') + + return convolution[len(signal_array) - 1 : (2*len(signal_array)) - 1] + +def convolution_plusnoise(signal_array, response_array, t_array, tstep, noiselevel): + return convolve_sig_resp(signal_array, response_array, t_array, tstep) + noiselevel + +def herz_ode(t, n0, params): + a = params[0] + k1 = params[1] + k2 = params[2] + k3 = params[3] + def odefun(n, t, k1, k2, k3): + dndt = -(k1 * n) - (k2 * (n ** 2.0)) - (k3 * (n ** 3.0)) + return dndt + ode_sol = odeint(odefun, n0, t, args = (k1, k2, k3))[:,0] + pl = k2 * (ode_sol ** 2.0) + return a*pl + +def fit_herz_ode_global_3traces_fmin_tnc(t1, t2, t3, tstep, d1, d2, d3, irf, init_params, bounds, n0array): + time_array1 = t1 + time_array2 = t2 + time_array3 = t3 + data_array1 = d1 + data_array2 = d2 + data_array3 = d3 + n0 = n0array[0] + n1 = n0array[1] + n2 = n0array[2] + def min_fit_decay(params): + #Minimize chi-squre for data set with Poisson distribution () + + a0 = params[0] + a1 = params[1] + a2 = params[2] + k1 = params[3] + k2 = params[4] + k3 = params[5] + noise1 = params[6] + noise2 = params[7] + noise3 = params[8] + decaymodel1 = herz_ode(time_array1, n0, np.array([a0,k1,k2,k3])) + decaymodel2 = herz_ode(time_array2, n1, np.array([a1,k1,k2,k3])) + decaymodel3 = herz_ode(time_array3, n2, np.array([a2,k1,k2,k3])) + model1 = convolution_plusnoise(decaymodel1, irf, time_array1, tstep, noise1) + model2 = convolution_plusnoise(decaymodel2, irf, time_array2, tstep, noise2) + + model3 = convolution_plusnoise(decaymodel3, irf, time_array3, tstep, noise3) + + data_fit_idx1 = np.nonzero(data_array1) + data_fit_idx2 = np.nonzero(data_array2) + data_fit_idx3 = np.nonzero(data_array3) + data_array_fit1 = data_array1[data_fit_idx1] + data_array_fit2 = data_array2[data_fit_idx2] + data_array_fit3 = data_array3[data_fit_idx3] + + model_fit1 = model1[data_fit_idx1] + model_fit2 = model2[data_fit_idx2] + model_fit3 = model3[data_fit_idx3] + + min1 = np.sum(((data_array_fit1 - model_fit1)** 2.0) / (np.sqrt(data_array_fit1) ** 2.0)) + min2 = np.sum(((data_array_fit2 - model_fit2)** 2.0) / (np.sqrt(data_array_fit2) ** 2.0)) + min3 = np.sum(((data_array_fit3 - model_fit3)** 2.0) / (np.sqrt(data_array_fit3) ** 2.0)) + return np.sqrt((min1 ** 2.0) + (min2 ** 2.0) + (min3 ** 2.0)) + bestfit_params = fmin_tnc(min_fit_decay, init_params, approx_grad = True, bounds = bounds)[0] + def bestfit_decay(params): + a0 = params[0] + a1 = params[1] + a2 = params[2] + k1 = params[3] + k2 = params[4] + k3 = params[5] + noise1 = params[6] + # noise2 = params[7] + # noise3 = params[8] + decaymodel1 = herz_ode(time_array, n0, np.array([a0,k1,k2,k3])) + decaymodel2 = herz_ode(time_array, n1, np.array([a1,k1,k2,k3])) + decaymodel3 = herz_ode(time_array, n2, np.array([a2,k1,k2,k3])) + + model1 = convolution_plusnoise(decaymodel1, irf, time_array, tstep, noise1) + model2 = convolution_plusnoise(decaymodel2, irf, time_array, tstep, noise2) + model3 = convolution_plusnoise(decaymodel3, irf, time_array, tstep, noise3) + return [model1, model2, model3] + + bestfit_model = bestfit_decay(bestfit_params) + # plt.figure() + # plt.ylabel('PL Counts') + # plt.xlabel('Time (ns)') + # plt.semilogy(time_array1, data_array1,'b', label = 'Data') + # plt.semilogy(time_array1, bestfit_model[0], 'r', label = 'Fit') + # plt.semilogy(time_array2, data_array2,'b', label = 'Data') + # plt.semilogy(time_array2, bestfit_model[1], 'r', label = 'Fit') + # plt.semilogy(time_array3, data_array3,'b', label = 'Data') + # plt.semilogy(time_array3, bestfit_model[2], 'r', label = 'Fit') + # plt.legend(loc = 'best') + return bestfit_params, bestfit_model, data_array, time_array, irf + +def multi_exp(t, params, num_exp): + exp_array = np.empty((len(t), num_exp)) + + i = 0 + while (i + + MainWindow + + + + 0 + 0 + 2620 + 1676 + + + + Lifetime Analysis + + + + + + + + + true + + + + 10 + + + + Fitting Controls + + + false + + + + + + + + + 10 + + + + Fit with IRF + + + true + + + false + + + + + + + + 10 + + + + Fitting Function + + + + + + + + 10 + + + + + + + + true + + + + 10 + + + + Fitting method + + + + + + + + 10 + + + + + + + + + + + + + + + + + 0 + + + + + + + true + + + + 10 + + + + Bounds + + + + + + 4 + + + 9999999.000000000000000 + + + 1.100000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 0.900000000000000 + + + + + + + 4 + + + 1.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 10000.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + tc (ns) + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + beta + + + + + + + noise + + + + + + + 4 + + + 1.000000000000000 + + + 1.000000000000000 + + + + + + + a + + + + + + + 4 + + + 9999999.000000000000000 + + + 10000.000000000000000 + + + + + + + min + + + + + + + max + + + + + + + + + + false + + + + 10 + + + + Initial Guess + + + + + + a + + + + + + + noise + + + + + + + beta + + + + + + + tc (ns) + + + + + + + 4 + + + 9999999.000000000000000 + + + 5.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 1.000000000000000 + + + + + + + 4 + + + 1.000000000000000 + + + 0.500000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 0.100000000000000 + + + + + + + + + + + + + + Bounds + + + + + + min + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + max + + + + + + + a1 + + + + + + + + + + + + + + noise + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 300.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 10000.000000000000000 + + + + + + + tau2 (ns) + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 10000.000000000000000 + + + + + + + a2 + + + + + + + 4 + + + 9999999.000000000000000 + + + 10000.000000000000000 + + + + + + + tau1 (ns) + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 10.000000000000000 + + + + + + + + + + Initial Guess + + + + + + 4 + + + 9999999.000000000000000 + + + 1.000000000000000 + + + + + + + a1 + + + + + + + 4 + + + 9999999.000000000000000 + + + 1.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + 20.000000000000000 + + + + + + + a2 + + + + + + + 4 + + + 9999999.000000000000000 + + + 0.100000000000000 + + + + + + + tau2 (ns) + + + + + + + noise + + + + + + + tau1 (ns) + + + + + + + 4 + + + 9999999.000000000000000 + + + 1.000000000000000 + + + + + + + + + + + + + + Bounds + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + max + + + + + + + 4 + + + 9999999.000000000000000 + + + 10.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + + + + + + + + noise + + + + + + + a + + + + + + + 4 + + + 9999999.000000000000000 + + + 10000.000000000000000 + + + + + + + tau (ns) + + + + + + + 4 + + + 9999999.000000000000000 + + + 10000.000000000000000 + + + + + + + min + + + + + + + + + + Initial Guess + + + + + + 4 + + + 9999999.000000000000000 + + + 1.000000000000000 + + + + + + + a + + + + + + + tau (ns) + + + + + + + 4 + + + 9999999.000000000000000 + + + 1.000000000000000 + + + + + + + noise + + + + + + + 4 + + + 9999999.000000000000000 + + + 0.100000000000000 + + + + + + + + + + + + + + + + + + 10 + + + + Get Lifetime! + + + + + + + true + + + + 10 + + + + Calculate SRV + + + true + + + false + + + + + + Bulk Lifetime (ns) + + + + + + + Thickness (nm) + + + + + + + 100000.000000000000000 + + + 250.000000000000000 + + + + + + + 1000000.000000000000000 + + + 3.000000000000000 + + + + + + + 4 + + + 9999999.000000000000000 + + + + + + + 0 + + + + + + + 0 + + + + + + + SRV (cm/s) + + + + + + + 100000.000000000000000 + + + 8000.000000000000000 + + + + + + + Diffusion Coefficient (cm2/s) + + + + + + + Surface Lifetime (ns) + + + + + + + Average Lifetime (ns) + + + + + + + Calculate + + + + + + + SRV (cm/s) + + + + + + + 0 + + + + + + + + 75 + true + + + + SRV1 = SRV2 + + + + + + + + 75 + true + + + + SRV1 = 0 + + + + + + + + + + + + + 2 + 0 + + + + + + + + + 15 + + + + Settings + + + + + + + 12 + + + + Export Settings + + + + + + For Figure: + + + + + + + Export Fit Data + + + + + + + Clear Export Memory + + + + + + + + 12 + 50 + false + + + + Export figure + + + + + + + For Data: + + + + + + + Enter Legend Here... + + + + + + + Add trace to memory + + + + + + + + + + + 12 + + + + Plot Controls + + + + + + + 12 + 50 + false + + + + Plot + + + + + + + Y Axis Log + + + + + + + Plot color + + + + + + + + 12 + false + + + + Clear Plot + + + + + + + + + + + + Normalize + + + + + + + Clear plot everytime + + + + + + + + + + + 12 + + + + + + + + + 12 + + + + Resolution (ns) + + + + + + + false + + + + 12 + + + + true + + + + + + + + 12 + + + + 512 + + + 1 + + + + + + + + 12 + + + + IRF Channel No + + + + + + + + 12 + + + + Data Channel No + + + + + + + + 12 + + + + + + + + + 12 + + + + Load separate IRF file + + + + + + + + 12 + + + + Smooth Data + + + + + + + false + + + + 12 + + + + 1 + + + 1000 + + + + + + + + + + + + 0 + 0 + 2620 + 38 + + + + + File + + + + + + + + + + + + Open + + + + + Exit + + + + + Save + + + + + false + + + Open IRF File + + + + + + PlotWidget + QGraphicsView +
pyqtgraph
+ + + + + diff --git a/src/main/python/Lifetime_analysis/Lifetime_plot_fit.py b/src/main/python/Lifetime_analysis/Lifetime_plot_fit.py new file mode 100644 index 0000000..7967a1e --- /dev/null +++ b/src/main/python/Lifetime_analysis/Lifetime_plot_fit.py @@ -0,0 +1,653 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Mar 27 16:50:26 2019 + +@author: Sarthak +""" + +# system imports +import sys +import os +from pathlib import Path + +# module imports +import pyqtgraph as pg +from pyqtgraph.Qt import QtCore, QtGui, QtWidgets +import numpy as np +import matplotlib.pyplot as plt + +sys.path.append(os.path.abspath('../Export_Windows')) +try: + from Export_window import ExportPlotWindow +except: + from Export_Windows.Export_window import ExportPlotWindow + +# local module imports +try: + from Lifetime_analysis.Fit_functions import stretch_exp_fit, double_exp_fit, single_exp_fit + from Lifetime_analysis.picoharp_phd import read_picoharp_phd + from Lifetime_analysis.Fit_functions_with_irf import fit_exp_stretch_diffev, fit_exp_stretch_fmin_tnc, fit_multi_exp_diffev, fit_multi_exp_fmin_tnc +except: + from Fit_functions import stretch_exp_fit, double_exp_fit, single_exp_fit + from Fit_functions_with_irf import fit_exp_stretch_diffev, fit_exp_stretch_fmin_tnc, fit_multi_exp_diffev, fit_multi_exp_fmin_tnc + from picoharp_phd import read_picoharp_phd + +"""Recylce params for plotting""" +plt.rc('xtick', labelsize = 20) +plt.rc('xtick.major', pad = 3) +plt.rc('ytick', labelsize = 20) +plt.rc('lines', lw = 2.5, markersize = 7.5) +plt.rc('legend', fontsize = 20) +plt.rc('axes', linewidth=3.5) + +pg.mkQApp() +pg.setConfigOption('background', 'w') +##pg.setConfigOption('crashWarning', True) + +base_path = Path(__file__).parent +file_path = (base_path / "Lifetime_analysis_gui_layout.ui").resolve() + +uiFile = file_path + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +class MainWindow(TemplateBaseClass): + + def __init__(self): + TemplateBaseClass.__init__(self) + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + self.ui.Res_comboBox.addItems(["0.004","0.008","0.016","0.032","0.064","0.128","0.256","0.512"]) + self.ui.FittingFunc_comboBox.addItems(["Stretched Exponential","Double Exponential", "Single Exponential"]) + self.ui.FittingMethod_comboBox.addItems(["diff_ev", "fmin_tnc"]) + + #set up file menu + self.ui.actionOpen.triggered.connect(self.open_file) + self.ui.actionOpen_IRF_File.triggered.connect(self.open_irf_file) + self.ui.actionSave.triggered.connect(self.save_file) + self.ui.actionExit.triggered.connect(self.close_application) + + #set up ui signals + self.ui.plot_pushButton.clicked.connect(self.plot) + self.ui.fit_pushButton.clicked.connect(self.call_fit_and_plot) + self.ui.clear_pushButton.clicked.connect(self.clear_plot) + self.ui.export_plot_pushButton.clicked.connect(self.export_window)#pub_ready_plot_export + self.ui.calculate_srv_pushButton.clicked.connect(self.calculate_srv) + + self.ui.log_checkBox.stateChanged.connect(self.make_semilog) + self.ui.fit_with_irf_checkBox.stateChanged.connect(self.switch_fit_settings) + self.ui.FittingFunc_comboBox.currentTextChanged.connect(self.switch_function_tab) + self.ui.FittingMethod_comboBox.currentTextChanged.connect(self.switch_init_params_groupBox) + self.ui.separate_irf_checkBox.stateChanged.connect(self.switch_open_irf) + self.ui.add_to_mem_pushButton.clicked.connect(self.add_trace_to_mem) + self.ui.export_data_pushButton.clicked.connect(self.export_data) + self.ui.clear_export_data_pushButton.clicked.connect(self.clear_export_data) + self.ui.smoothData_checkBox.stateChanged.connect(self.smooth_trace_enabled) + + #set up plot color button + self.plot_color_button = pg.ColorButton(color=(255,0,0)) + self.ui.plot_color_button_container.layout().addWidget(self.plot_color_button) + self.plot_color = self.plot_color_button.color() + self.plot_color_button.sigColorChanged.connect(self.plot_color_changed) + + self.file = None + self.out = None # output file after fitting + self.data_list = [] + self.fit_lifetime_called_w_irf = False + self.fit_lifetime_called_wo_irf = False + self.x_mem = [] # containers for adding x data to memory + self.y_mem = [] # containers for adding y data to memory + self.best_fit_mem = [] # containers for adding best fit data to memory + self.best_fit_mem_x = [] # containers for adding best fit data to memory + self.legend = [] # containers for adding legend to memory + + #variables accounting for data received from FLIM analysis + self.opened_from_flim = False #switched to True in FLIM_plot when "analyze lifetime" clicked + self.hist_data_from_flim = [] #container for flim roi data + + self.show() + + def open_file(self): + """ Open data file """ +# try: + self.filename = QtWidgets.QFileDialog.getOpenFileName(self) + try: + if ".csv" in self.filename[0] or ".txt" in self.filename[0]: #if txt or csv, prompt user to enter # of rows to skip + self.skip_rows_window = SkipRowsWindow() + self.skip_rows_window.skip_rows_signal.connect(self.open_with_skip_rows_window) + self.ui.Res_comboBox.setEnabled(True) + else: + self.file = read_picoharp_phd(self.filename[0]) + self.opened_from_flim = False + except: + pass + + def open_with_skip_rows_window(self): + """ Prompts user to enter how many rows to skip """ + skip_rows = self.skip_rows_window.ui.skip_rows_spinBox.value() + if ".txt" in self.filename[0]: + self.file = np.loadtxt(self.filename[0], skiprows=skip_rows) + elif ".csv" in self.filename[0]: + self.file = np.genfromtxt(self.filename[0], skip_header=skip_rows, delimiter=",") + + def open_irf_file(self): + """ Open file with irf - enabled if 'load separate irf' is checled """ + self.irf_filename = QtWidgets.QFileDialog.getOpenFileName(self) + try: + if ".txt" in self.irf_filename[0] or ".csv" in self.irf_filename[0]: + self.irf_skip_rows_window = SkipRowsWindow() + self.irf_skip_rows_window.skip_rows_signal.connect(self.open_irf_with_skip_rows_window) + self.ui.Res_comboBox.setEnabled(True) + else: + self.irf_file = read_picoharp_phd(self.irf_filename[0]) + except: + pass + + def open_irf_with_skip_rows_window(self): + irf_skip_rows = self.irf_skip_rows_window.ui.skip_rows_spinBox.value() + if ".txt" in self.irf_filename[0]: + self.irf_file = np.loadtxt(self.irf_filename[0], skiprows=irf_skip_rows) + elif ".csv" in self.irf_filename[0]: + self.irf_file = np.genfrontxt(self.irf_filename[0], skip_header=irf_skip_rows, delimiter=",") + + def save_file(self): + try: + filename = QtWidgets.QFileDialog.getSaveFileName(self) + np.savetxt(filename[0], self.out, fmt = '%.5f', header = 'Time, Raw_PL, Sim_PL', delimiter = ' ') + except: + pass + + def switch_open_irf(self): + """ Handle 'load separate irf' checkbox """ + self.ui.actionOpen_IRF_File.setEnabled(self.ui.separate_irf_checkBox.isChecked()) + + def switch_fit_settings(self): + """ Enable bounds/initial guess groupboxes only when 'Fit with IRF' is checked """ + checked = self.ui.fit_with_irf_checkBox.isChecked() + for func in "str de se".split(" "): + boundsGb = eval("self.ui."+func+"_bounds_groupBox") + #initGb = eval("self.ui."+func+"_init_groupBox") + boundsGb.setEnabled(checked) + #initGb.setEnabled(checked) + if checked == True: + self.switch_init_params_groupBox() + else: + initGb = eval("self.ui."+func+"_init_groupBox") + initGb.setEnabled(checked) + self.ui.FittingMethod_comboBox.setEnabled(checked) + + def switch_function_tab(self): + """ Switch bounds groupbox contents depending on selected fit function """ + fitting_func = self.ui.FittingFunc_comboBox.currentText() + if fitting_func == "Stretched Exponential": + self.ui.fitting_params_stackedWidget.setCurrentIndex(0) + elif fitting_func == "Double Exponential": + self.ui.fitting_params_stackedWidget.setCurrentIndex(1) + elif fitting_func == "Single Exponential": + self.ui.fitting_params_stackedWidget.setCurrentIndex(2) + + def switch_init_params_groupBox(self): + """ Enable initial guess groupbox only when fmin_tnc fit method selected """ + if self.ui.FittingMethod_comboBox.currentText() == "diff_ev": + for func in "str de se".split(" "): + initGb = eval("self.ui."+func+"_init_groupBox") + initGb.setEnabled(False) + #initGb.setEnabled(checked) + elif self.ui.FittingMethod_comboBox.currentText() == "fmin_tnc": + for func in "str de se".split(" "): + initGb = eval("self.ui."+func+"_init_groupBox") + initGb.setEnabled(True) + + def plot_color_changed(self): + """ Grab new plot_color when color button value is changed """ + self.plot_color = self.plot_color_button.color() + + def smooth_trace_enabled(self): + """Enable smooth spin box when smooth data is checked""" + if self.ui.smoothData_checkBox.isChecked(): + self.ui.smoothData_spinBox.setEnabled(True) + else: + self.ui.smoothData_spinBox.setEnabled(False) + + def acquire_settings(self, mode="data"): + """ + Acquire data or irf from channel specified in spinbox. + + mode -- string specifying whether to use data or irf channel (default "data") + """ + if mode == "data": + channel = int(self.ui.Data_channel_spinBox.value()) + elif mode == "irf": + channel = int(self.ui.irf_channel_spinBox.value()) + try: + try: # + if self.ui.separate_irf_checkBox.isChecked() and mode=="irf": #if separate irf, get from irf file + try: + y = self.irf_file[:,channel] + except: + y = self.irf_file.get_curve(channel)[1] + else: #otherwise, get data/irf from data file + y = self.file[:,channel] + + self.resolution = float(self.ui.Res_comboBox.currentText()) + except: + res, y = self.file.get_curve(channel) + time_window = int(np.floor(self.file.get_time_window_in_ns(channel))) + y = y[0:time_window] + self.resolution = res + + length = np.shape(y)[0] + x = np.arange(0, length*self.resolution, self.resolution, np.float) + + if self.ui.smoothData_checkBox.isChecked() and mode=="data": + y = np.convolve(y, np.ones(self.ui.smoothData_spinBox.value())/self.ui.smoothData_spinBox.value(), mode="same") + + if self.ui.normalize_checkBox.isChecked(): + y = y / np.amax(y) + + return x,y + + except Exception as e: + self.ui.Result_textBrowser.setText(str(e)) + + def plot(self): + try: + if self.opened_from_flim: + x, y = self.hist_data_from_flim + else: + x,y = self.acquire_settings() #get data + + self.ui.plot.plot(x, y, clear=self.ui.clear_plot_checkBox.isChecked(), pen=pg.mkPen(self.plot_color)) + self.fit_lifetime_called_w_irf = False + self.fit_lifetime_called_wo_irf = False + + try: + self.ui.Result_textBrowser.setText("Integral Counts :\n" "{:.2E}".format( + self.file.get_integral_counts(int(self.ui.Channel_spinBox.value())))) + except: + self.ui.Result_textBrowser.setText("Integral Counts :\n" "{:.2E}".format(np.sum(y))) + except: + pass + self.ui.plot.setLabel('left', 'Intensity', units='a.u.') + self.ui.plot.setLabel('bottom', 'Time (ns)') + + def make_semilog(self): + """ Switch y-log on/off """ + self.ui.plot.setLogMode(False,self.ui.log_checkBox.isChecked()) + + def clear_plot(self): + self.ui.plot.clear() + self.ui.Result_textBrowser.clear() + + def fit_and_plot(self): + """ Fit and plot without IRF """ + try: + if not hasattr(self, "file"): + self.ui.Result_textBrowser.setText("You need to load a data file.") + else: + if self.opened_from_flim: + x, y = self.hist_data_from_flim + else: + x,y = self.acquire_settings() #get data + y_norm = y/np.max(y) #normalized y + + # find the max intensity in the array and start things from there + find_max_int = np.nonzero(y_norm == 1) + y = y[np.asscalar(find_max_int[0]):] + x = x[np.asscalar(find_max_int[0]):] + + t = x + time_fit = t + TRPL_interp = np.interp(time_fit, t, y) + + fit_func = self.ui.FittingFunc_comboBox.currentText() + self.ui.plot.plot(t, y, clear=self.ui.clear_plot_checkBox.isChecked(), pen=pg.mkPen(self.plot_color)) + + if fit_func == "Stretched Exponential": #stretch exponential tab + tc, beta, a, avg_tau, PL_fit, noise = stretch_exp_fit(TRPL_interp, t) + self.out = np.empty((len(t), 3)) + self.out[:,0] = t #time + self.out[:,1] = TRPL_interp #Raw PL + self.out[:,2] = PL_fit # PL fit + self.ui.plot.plot(t, PL_fit, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') + self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Stretched Exponential" + "\nFit Method: " + "diff_ev" + #TODO : change when diff_ev and fmin_tnc implemented for non-irf + "\nAverage Lifetime = " + str(avg_tau)+ " ns" + "\nCharacteristic Tau = " + str(tc)+" ns" + "\nBeta = "+str(beta)+ + "\nNoise = "+ str(noise)) + self.ui.average_lifetime_spinBox.setValue(avg_tau) + + elif fit_func == "Double Exponential": #double exponential tab + tau1, a1, tau2, a2, avg_tau, PL_fit, noise = double_exp_fit(TRPL_interp, t) + self.out = np.empty((len(t), 3)) + self.out[:,0] = t #time + self.out[:,1] = TRPL_interp #Raw PL + self.out[:,2] = PL_fit # PL fit + self.ui.plot.plot(t, PL_fit, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') + self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Double Exponential" + "\nFit Method: " + "diff_ev" + + "\nAverage Lifetime = " + str(avg_tau)+ " ns" + "\nTau 1 = " + str(tau1)+" ns" + "\nA 1 = " + str(a1)+ + "\nTau 2 = " + str(tau2)+" ns" + "\nA 2 = " + str(a2)+ + "\nNoise = "+ str(noise)) + #TODO - once tau_avg implemented, set average lifetime spinbox to tau_avg value + + elif fit_func == "Single Exponential": #single exponential tab + tau, a, PL_fit, noise = single_exp_fit(TRPL_interp, t) + self.out = np.empty((len(t), 3)) + self.out[:,0] = t #time + self.out[:,1] = TRPL_interp #Raw PL + self.out[:,2] = PL_fit # PL fit + self.ui.plot.plot(t, PL_fit, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') + self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Single Exponential" + "\nFit Method: " + "diff_ev" + + "\nLifetime = " + str(tau)+ " ns" + "\nA = " + str(a)+ + "\nNoise = "+ str(noise)) + self.ui.average_lifetime_spinBox.setValue(tau) + + #add fit params to data_list + self.data_list.append("Data Channel: " + str(self.ui.Data_channel_spinBox.value()) + "\n" + self.ui.Result_textBrowser.toPlainText()) + self.fit_lifetime_called_wo_irf = True + self.fit_lifetime_called_w_irf = False + + self.ui.plot.setLabel('left', 'Intensity', units='a.u.') + self.ui.plot.setLabel('bottom', 'Time (ns)') + return self.out + + except Exception as e: + self.ui.Result_textBrowser.append(format(e)) + + def fit_and_plot_with_irf(self): + """ Fit and plot with IRF """ + try: + self.ui.Result_textBrowser.clear() + if not hasattr(self, "file"): + self.ui.Result_textBrowser.append("You need to load a data file.") + if not hasattr(self, "irf_file") and self.ui.separate_irf_checkBox.isChecked(): + self.ui.Result_textBrowser.append("You need to load an IRF file.") + else: + if self.opened_from_flim: + x,y = self.hist_data_from_flim + else: + x,y = self.acquire_settings() #get data + _, irf_counts = self.acquire_settings(mode="irf") #get irf counts + + #make sure Irf and data have the same length + if len(y) != len(irf_counts): + y = y[0:min(len(y), len(irf_counts))] + irf_counts = irf_counts[0:min(len(y), len(irf_counts))] + x = x[0:min(len(y), len(irf_counts))] + + y_norm = y/np.max(y) #normalized y + irf_norm = irf_counts/np.amax(irf_counts) #normalized irf + + t = x + time_fit = t + y = y_norm + irf_counts = irf_norm + + TRPL_interp = np.interp(time_fit, t, y) + + fit_func = self.ui.FittingFunc_comboBox.currentText() + self.ui.plot.plot(t, y, clear=self.ui.clear_plot_checkBox.isChecked(), pen=pg.mkPen(self.plot_color)) + if fit_func == "Stretched Exponential": #stretched exponential tab + tc_bounds = (self.ui.str_tc_min_spinBox.value(), self.ui.str_tc_max_spinBox.value()) #(0, 10000) + a_bounds = (self.ui.str_a_min_spinBox.value(), self.ui.str_a_max_spinBox.value())#(0.9, 1.1) + beta_bounds = (self.ui.str_beta_min_spinBox.value(), self.ui.str_beta_max_spinBox.value())#(0,1) + noise_bounds = (self.ui.str_noise_min_spinBox.value(), self.ui.str_noise_max_spinBox.value())#(0, 1e4) + stretch_exp_bounds = [tc_bounds, beta_bounds, a_bounds, noise_bounds] + stretch_exp_init_params = [self.ui.str_tc_init_spinBox.value(), self.ui.str_a_init_spinBox.value(), self.ui.str_beta_init_spinBox.value(), self.ui.str_noise_init_spinBox.value()] + + #tc, beta, a, avg_tau, PL_fit = stretch_exp_fit(TRPL_interp, t) + # resolution = float(self.ui.Res_comboBox.currentText()) + if self.ui.FittingMethod_comboBox.currentText() == "diff_ev": + bestfit_params, t_avg, bestfit_model, data_array, time_array, irf = fit_exp_stretch_diffev(t, self.resolution, TRPL_interp, irf_counts, stretch_exp_bounds) + else: #if fmin_tnc fitting method selected + bestfit_params, t_avg, bestfit_model, data_array, time_array, irf = fit_exp_stretch_fmin_tnc(t, self.resolution, TRPL_interp, irf_counts, stretch_exp_init_params, stretch_exp_bounds) + self.out = np.empty((len(t), 3)) + self.out[:,0] = t #time + self.out[:,1] = TRPL_interp #Raw PL + self.out[:,2] = bestfit_model # PL fit + self.ui.plot.plot(t, bestfit_model, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') + self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Stretched Exponential with IRF" + "\nFit Method: "+ self.ui.FittingMethod_comboBox.currentText() + + "\ntau_avg = %.5f ns" + "\nbeta = %.5f" + "\ntau_c = %.5f ns" + "\na = %.5f \nnoise = %.5f counts" %(t_avg, bestfit_params[1], bestfit_params[0], bestfit_params[2], bestfit_params[3])) + #self.effective_lifetime = t_avg + self.ui.average_lifetime_spinBox.setValue(t_avg) + + elif fit_func == "Double Exponential": #double exponential tab + a1_bounds = (self.ui.de_a1_min_spinBox.value(), self.ui.de_a1_max_spinBox.value()) + tau1_bounds = (self.ui.de_tau1_min_spinBox.value(), self.ui.de_tau1_max_spinBox.value()) + a2_bounds = (self.ui.de_a2_min_spinBox.value(), self.ui.de_a2_max_spinBox.value()) + tau2_bounds = (self.ui.de_tau2_min_spinBox.value(), self.ui.de_tau2_max_spinBox.value()) + noise_bounds = (self.ui.de_noise_min_spinBox.value(), self.ui.de_noise_max_spinBox.value()) + double_exp_bounds = [a1_bounds, tau1_bounds, a2_bounds, tau2_bounds, noise_bounds] + double_exp_init_params = [self.ui.de_a1_init_spinBox.value(), self.ui.de_tau1_init_spinBox.value(), self.ui.de_a2_init_spinBox.value(), + self.ui.de_tau2_init_spinBox.value(), self.ui.de_noise_init_spinBox.value()] + + if self.ui.FittingMethod_comboBox.currentText() == "diff_ev": + bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_diffev(t, self.resolution, TRPL_interp, irf_counts, double_exp_bounds, 2) + #bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_diffev(t, resolution, TRPL_interp, irf_counts, double_exp_init_bounds, 2) + else: + bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_fmin_tnc(t, self.resolution, TRPL_interp, irf_counts, double_exp_init_params, double_exp_bounds, 2) + self.out = np.empty((len(t), 3)) + self.out[:,0] = t #time + self.out[:,1] = TRPL_interp #Raw PL + self.out[:,2] = bestfit_model # PL fit + self.ui.plot.plot(t, bestfit_model, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') + self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Double Exponential with IRF" + "\nFit Method: "+ self.ui.FittingMethod_comboBox.currentText() + + "\na1 = %.5f" + "\ntau1 = %.5f ns" + "\na2 = %.5f" + "\ntau2 = %.5f ns" + "\nnoise = %.5f counts" %(bestfit_params[0], bestfit_params[1], bestfit_params[2], bestfit_params[3], bestfit_params[4])) + #TODO - once tau_avg implemented, set average lifetime spinbox to tau_avg value + if bestfit_params[3] > bestfit_params[1]: + self.ui.average_lifetime_spinBox.setValue(bestfit_params[3]) + elif bestfit_params[1] > bestfit_params[3]: + self.ui.average_lifetime_spinBox.setValue(bestfit_params[1]) + + elif fit_func == "Single Exponential": #single exponential tab + a_bounds = (self.ui.se_a_min_spinBox.value(), self.ui.se_a_max_spinBox.value()) + tau_bounds = (self.ui.se_tau_min_spinBox.value(), self.ui.se_tau_max_spinBox.value()) + noise_bounds = (self.ui.se_noise_min_spinBox.value(), self.ui.se_noise_max_spinBox.value()) + single_exp_bounds = [a_bounds, tau_bounds, noise_bounds] + single_exp_init_params = [self.ui.se_a_init_spinBox.value(), self.ui.se_tau_init_spinBox.value(), self.ui.se_noise_init_spinBox.value()] + + if self.ui.FittingMethod_comboBox.currentText() == "diff_ev": + bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_diffev(t, self.resolution, TRPL_interp, irf_counts, single_exp_bounds, 1) + else: + bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_fmin_tnc(t, self.resolution, TRPL_interp, irf_counts, single_exp_init_params, single_exp_bounds, 1) + self.out = np.empty((len(t), 3)) + self.out[:,0] = t #time + self.out[:,1] = TRPL_interp #Raw PL + self.out[:,2] = bestfit_model # PL fit + self.ui.plot.plot(t, bestfit_model, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') + self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Single Exponential with IRF" + "\nFit Method: "+ self.ui.FittingMethod_comboBox.currentText() + + "\na = %.5f" + "\ntau = %.5f ns" + "\nnoise = %.5f counts" %(bestfit_params[0], bestfit_params[1], bestfit_params[2])) + self.ui.average_lifetime_spinBox.setValue(bestfit_params[1]) #set spinbox to tau value + + #add fit params to data_list + self.data_list.append("Data Channel: " + str(self.ui.Data_channel_spinBox.value()) + "\n" + self.ui.Result_textBrowser.toPlainText()) + self.fit_lifetime_called_w_irf = True + self.fit_lifetime_called_wo_irf = False + except Exception as e: + self.ui.Result_textBrowser.append(format(e)) + + def call_fit_and_plot(self): + if self.ui.fit_with_irf_checkBox.isChecked(): + self.fit_and_plot_with_irf() + else: + self.fit_and_plot() + if self.ui.calculate_srv_groupBox.isChecked(): + self.calculate_srv() #calculate srv on plot + self.data_list.append(self.get_srv_string()) #add srv params to data_list + + def calculate_surface_lifetime(self): + effective_lifetime = self.ui.average_lifetime_spinBox.value() + self.bulk_lifetime = self.ui.bulk_lifetime_spinBox.value() # in ns + self.surface_lifetime = (effective_lifetime * self.bulk_lifetime)/(self.bulk_lifetime - effective_lifetime) + self.ui.surface_lifetime_label.setText(str(self.surface_lifetime)) + + def calculate_srv (self): + self.calculate_surface_lifetime() + self.thickness = self.ui.thickness_spinBox.value()*1e-7 # convert to cm + self.diffusion_coeffecient = self.ui.diffusion_coefficient_spinBox.value() # in cm2/s + + self.srv1_srv2_equal = self.thickness / (2*((1e-9*self.surface_lifetime) - ((1/self.diffusion_coeffecient)*((self.thickness/np.pi)**2)) )) + self.srv1_zero = self.thickness / ((1e-9*self.surface_lifetime) - ((4/self.diffusion_coeffecient)*((self.thickness/np.pi)**2)) ) + + self.ui.srv1_srv2_equal_label.setText(str(self.srv1_srv2_equal)) + self.ui.srv1_zero_label.setText(str(self.srv1_zero)) + + def get_srv_string(self): + """ Get info from SRV Calculation groupbox as string """ + srv_string = "SRV Calculation:"\ + + "\nAverage Lifetime (ns): " + str(self.ui.average_lifetime_spinBox.value()) \ + + "\nBulk Lifetime (ns): " + str(self.ui.bulk_lifetime_spinBox.value()) \ + + "\nThickness (nm): " + str(self.ui.thickness_spinBox.value()) \ + + "\nDiffusion Coefficient (cm2/s): " + str(self.ui.diffusion_coefficient_spinBox.value()) + srv_string += "\nSurface Lifetime (ns): " + self.ui.surface_lifetime_label.text() + + srv_string += "\nSRV1 = SRV2"\ + + "\nSRV (cm/s): " + self.ui.srv1_srv2_equal_label.text() + + srv_string += "\nSRV1 = 0"\ + + "\nSRV (cm/s): " + self.ui.srv1_zero_label.text() + return srv_string + + def export_data(self): + """ Save fit params and srv calculations stored in data_list as .txt """ + folder = os.path.dirname(self.filename[0]) + filename_ext = os.path.basename(self.filename[0]) + filename = os.path.splitext(filename_ext)[0] #get filename without extension + + path = folder + "/" + filename + "_fit_results.txt" + if not os.path.exists(path): + file = open(path, "w+") + else: + file = open(path, "a+") + + for i in range(len(self.data_list)): + file.write(self.data_list[i] + "\n\n") + + self.data_list = [] + file.close() + + def clear_export_data(self): + self.data_list = [] + self.clean_up_after_fig_export() + + def clean_up_after_fig_export(self): + self.x_mem = [] + self.y_mem = [] + self.legend = [] + self.best_fit_mem = [] + self.best_fit_mem_x = [] + + def add_trace_to_mem(self): + try: + if self.fit_lifetime_called_w_irf == True: + self.x_mem.append(self.out[:,0]) + self.y_mem.append(self.out[:,1]) + self.best_fit_mem_x.append(self.out[:,0]) + self.best_fit_mem.append(self.out[:,2]) + elif self.fit_lifetime_called_wo_irf == True: + self.x_mem.append(self.acquire_settings()[0]) + self.y_mem.append(self.acquire_settings()[1]) + self.best_fit_mem_x.append(self.out[:,0]) + self.best_fit_mem.append(self.out[:,2]) + else: + self.x_mem.append(self.acquire_settings()[0]) + self.y_mem.append(self.acquire_settings()[1]) + self.legend.append(self.ui.lineEdit.text()) + except Exception as e: + print(e) + + def export_window(self): + self.exportplotwindow = ExportPlotWindow() + self.exportplotwindow.export_fig_signal.connect(self.pub_ready_plot_export) + + def pub_ready_plot_export(self): + try: + if self.x_mem == []: + self.ui.result_textBrowser.setText("Add traces to memory first!") + + else: + filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") + + plt.figure(figsize=(8,6)) + plt.tick_params(direction='out', length=8, width=3.5) + for i in range(len(self.x_mem)): + plt.plot(self.x_mem[i], self.y_mem[i], label=str(self.legend[i])) + if self.fit_lifetime_called_w_irf == True or self.fit_lifetime_called_wo_irf == True: + plt.plot(self.best_fit_mem_x[i], self.best_fit_mem[i],'k--') + + plt.yscale('log') + plt.xlabel("Time (ns)", fontsize=20, fontweight='bold') + plt.ylabel("Intensity (norm.)", fontsize=20, fontweight='bold') + plt.legend() + plt.tight_layout() + plt.xlim([self.exportplotwindow.ui.lowerX_spinBox.value(),self.exportplotwindow.ui.upperX_spinBox.value()]) + plt.ylim([self.exportplotwindow.ui.lowerY_spinBox.value(),self.exportplotwindow.ui.upperY_doubleSpinBox.value()]) + + plt.savefig(filename[0],bbox_inches='tight', dpi=300) + plt.close() + self.clean_up_after_fig_export() + + except Exception as e: + self.ui.Result_textBrowser.append(format(e)) + pass + + def close_application(self): + choice = QtGui.QMessageBox.question(self, 'EXIT!', + "Do you want to exit the app?", + QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) + if choice == QtGui.QMessageBox.Yes: + sys.exit() + else: + pass + +"""Skip rows GUI""" +ui_file_path = (base_path / "skip_rows.ui").resolve() +skiprows_WindowTemplate, skiprows_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) + +class SkipRowsWindow(skiprows_TemplateBaseClass): + + skip_rows_signal = QtCore.pyqtSignal() #signal to help with pass info back to MainWindow + + def __init__(self): + skiprows_TemplateBaseClass.__init__(self) + + # Create the param window + self.ui = skiprows_WindowTemplate() + self.ui.setupUi(self) + self.ui.done_pushButton.clicked.connect(self.done) + self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False) + self.show() + + def done(self): + self.skip_rows_signal.emit() + self.close() + + +def run(): + win = MainWindow() + QtGui.QApplication.instance().exec_() + return win + +#Uncomment below if you want to run this as standalone +#run() \ No newline at end of file diff --git a/src/main/python/Lifetime_analysis/__init__.py b/src/main/python/Lifetime_analysis/__init__.py new file mode 100644 index 0000000..b4011af --- /dev/null +++ b/src/main/python/Lifetime_analysis/__init__.py @@ -0,0 +1 @@ +from __future__ import absolute_import, division, print_function \ No newline at end of file diff --git a/src/main/python/Lifetime_analysis/picoharp_phd.py b/src/main/python/Lifetime_analysis/picoharp_phd.py new file mode 100644 index 0000000..455e1bc --- /dev/null +++ b/src/main/python/Lifetime_analysis/picoharp_phd.py @@ -0,0 +1,408 @@ +# -*- coding: utf-8 -*- +""" +Majority of this PicoHarp Parser was written by skyjur. +Check out the original code here --- +https://github.com/skyjur/picoharp300-curvefit-ui + +Modified by Sarthak --- +Created on Fri Apr 5 15:50:36 2019 + +@author: Sarthak +""" + +""" +PicoHarp 300 file parser +""" +import datetime +import numpy as np +from ctypes import c_uint, c_ulong, c_char, c_int, c_int64, c_float, \ + Structure, sizeof, memmove, addressof + +DISPCURVES = 8 +MAXCURVES = 512 +MAXCHANNELS = 65536 + + +class tParamStruct(Structure): + _pack_ = 4 + _fields_ = [ + ('Start', c_float), + ('Step', c_float), + ('End', c_float), + ] + + +class tCurveMapping(Structure): + _pack_ = 4 + _fields_ = [ + ('MapTo', c_int), + ('Show', c_int), + ] + + +class TxtHdr(Structure): + _pack_ = 4 + _fields_ = [ + ('Ident', c_char * 16), + ('FormatVersion', c_char * 6), + ('CreatorName', c_char * 18), + ('CreatorVersion', c_char * 12), + ('FileTime', c_char * 18), + ('CRLF', c_char * 2), + ('CommentField', c_char * 256), + ] + + +class BinHdr(Structure): + _pack_ = 4 + _fields_ = [ + ('Curves', c_int), + ('BitsPerHistoBin', c_int), + ('RoutingChannels', c_int), + ('NumberOfBoards', c_int), + ('ActiveCurve', c_int), + ('MeasMode', c_int), + ('SubMode', c_int), + ('RangeNo', c_int), + ('Offset', c_int), + ('Tacq', c_int), # in m + ('StopAt', c_int), + ('StopOnOvfl', c_int), + ('Restart', c_int), + ('DispLinLog', c_int), + ('DispTimeFrom', c_int), + ('DispTimeTo', c_int), + ('DispCountsFrom', c_int), + ('DispCountsTo', c_int), + ('DispCurves', tCurveMapping * DISPCURVES), + ('Params', tParamStruct * 3), + ('RepeatMode', c_int), + ('RepeatsPerCurve', c_int), + ('RepeatTime', c_int), + ('RepeatWaitTime', c_int), + ('ScriptName', c_char * 20), + ] + + +class BoardHdr(Structure): + _pack_ = 4 + _fields_ = [ + ('HardwareIdent', c_char * 16), + ('HardwareVersion', c_char * 8), + ('HardwareSerial', c_int), + ('SyncDivider', c_int), + ('CFDZeroCross0', c_int), + ('CFDLevel0', c_int), + ('CFDZeroCross1', c_int), + ('CFDLevel1', c_int), + ('Resolution', c_float), + ('RouterModelCode', c_int), + ('RouterEnabled', c_int), + ('RtChan1_InputType;', c_int), + ('RtChan1_InputLevel', c_int), + ('RtChan1_InputEdge', c_int), + ('RtChan1_CFDPresent', c_int), + ('RtChan1_CFDLevel', c_int), + ('RtChan1_CFDZeroCross', c_int), + ('RtChan2_InputType;', c_int), + ('RtChan2_InputLevel', c_int), + ('RtChan2_InputEdge', c_int), + ('RtChan2_CFDPresent', c_int), + ('RtChan2_CFDLevel', c_int), + ('RtChan2_CFDZeroCross', c_int), + ('RtChan3_InputType;', c_int), + ('RtChan3_InputLevel', c_int), + ('RtChan3_InputEdge', c_int), + ('RtChan3_CFDPresent', c_int), + ('RtChan3_CFDLevel', c_int), + ('RtChan3_CFDZeroCross', c_int), + ('RtChan4_InputType;', c_int), + ('RtChan4_InputLevel', c_int), + ('RtChan4_InputEdge', c_int), + ('RtChan4_CFDPresent', c_int), + ('RtChan4_CFDLevel', c_int), + ('RtChan4_CFDZeroCross', c_int), + ] + + +class CurveHdr(Structure): + _pack_ = 4 + _fields_ = [ + ('CurveIndex', c_int), + ('TimeOfRecording', c_ulong), + ('HardwareIdent', c_char * 16), + ('HardwareVersion', c_char * 8), + ('HardwareSerial', c_int), + ('SyncDivider', c_int), + ('CFDZeroCross0', c_int), + ('CFDLevel0', c_int), + ('CFDZeroCross1', c_int), + ('CFDLevel1', c_int), + ('Offset', c_int), + ('RoutingChannel', c_int), + ('ExtDevices', c_int), + ('MeasMode', c_int), + ('SubMode', c_int), + ('P1', c_float), + ('P2', c_float), + ('P3', c_float), + ('RangeNo', c_int), + ('Resolution', c_float), + ('Channels', c_int), + ('Tacq', c_int), + ('StopAfter', c_int), + ('StopReason', c_int), + ('InpRate0', c_int), + ('InpRate1', c_int), + ('HistCountRate', c_int), + ('IntegralCount', c_int64), + ('reserved', c_int), + ('DataOffset', c_int), + ('RouterModelCode', c_int), + ('RouterEnabled', c_int), + ('RtChan_InputType;', c_int), + ('RtChan_InputLevel', c_int), + ('RtChan_InputEdge', c_int), + ('RtChan_CFDPresent', c_int), + ('RtChan_CFDLevel', c_int), + ('RtChan_CFDZeroCross', c_int), + ] + + +class ParseError(Exception): pass + + +def _read(f, CType): + data = f.read(sizeof(CType)) + obj = CType() + memmove(addressof(obj), data, len(data)) + return obj + + +def _validate_header(header): + if not header.Ident == 'PicoHarp 300' or not header.FormatVersion == '2.0': + raise ParseError('Does not look like a PicoHarp 300 file.') + + +class Curve(object): + res = None + data = None + + def __repr__(self): + return 'Curve' % ( + self.res, + len(self.data) + ) + + +def timefmt(t): + d = datetime.datetime.fromtimestamp(t) + return d.strftime('%a %b %d %H:%M:%S %Y') + + +class PicoharpParser(object): + _ready = False + + def __init__(self, filename): + if isinstance(filename, (str)):#, unicode)): + filename = open(filename, mode='rb') + self.f = filename + self._prepare() + + def _prepare(self): + self.f.seek(0) + + header = self._header = _read(self.f, TxtHdr) + """SJ commented this --- it was giving ParseError""" +# _validate_header(header) + + bin_header = self._bin_header = _read(self.f, BinHdr) + + self._boards = [] + for i in range(bin_header.NumberOfBoards): + self._boards.append(_read(self.f, BoardHdr)) + + self._curves = [] + for i in range(bin_header.Curves): + self._curves.append(_read(self.f, CurveHdr)) + + def header(self): + return [(k, getattr(self._header, k)) for k, t in self._header._fields_] + + def no_of_curves(self): + return self._bin_header.Curves + + def get_curve(self, n): + header = self._curves[n] + res = header.Resolution + + self.f.seek(header.DataOffset) + array = np.fromfile(self.f, c_uint, header.Channels) + + return res, array + + def get_time_window_in_ns(self, curve_no): + curve = self._curves[curve_no] + rep_rate = curve.InpRate0 + res, _ = self.get_curve(curve_no) + time_window_s = (1/rep_rate)/res # in seconds + + return time_window_s * 1e9 # in nannoseconds + + def get_integral_counts(self, curve_no): + curve = self._curves[curve_no] + integral_counts = curve.IntegralCount + + return integral_counts + + def info(self): + txthdr = self._header + binhdr = self._bin_header + boards = self._boards + curves = self._curves + r = [] + w = r.append + yesno = lambda x: 'true' if x else 'false' + + w("Ident : %s" % txthdr.Ident) + w("Format Version : %s" % txthdr.FormatVersion) + w("Creator Name : %s" % txthdr.CreatorName) + w("Creator Version : %s" % txthdr.CreatorVersion) + w("Time of Creation : %s" % txthdr.FileTime) + w("File Comment : %s" % txthdr.CommentField) + + w("No of Curves : %s" % binhdr.Curves) + w("Bits per HistoBin: %s" % binhdr.BitsPerHistoBin) + w("RoutingChannels : %s" % binhdr.RoutingChannels) + w("No of Boards : %s" % binhdr.NumberOfBoards) + w("Active Curve : %s" % binhdr.ActiveCurve) + w("Measurement Mode : %s" % binhdr.MeasMode) + w("Sub-Mode : %s" % binhdr.SubMode) + w("Range No : %s" % binhdr.RangeNo) + w("Offset : %s" % binhdr.Offset) + w("AcquisitionTime : %s" % binhdr.Tacq) + w("Stop at : %s" % binhdr.StopAt) + w("Stop on Ovfl. : %s" % binhdr.StopOnOvfl) + w("Restart : %s" % binhdr.Restart) + w("DispLinLog : %s" % binhdr.DispLinLog) + w("DispTimeAxisFrom : %s" % binhdr.DispTimeFrom) + w("DispTimeAxisTo : %s" % binhdr.DispTimeTo) + w("DispCountAxisFrom: %s" % binhdr.DispCountsFrom) + w("DispCountAxisTo : %s" % binhdr.DispCountsTo) + + for i in range(DISPCURVES): + w("---------------------") + w("Curve No %s" % i) + w(" MapTo : %s" % binhdr.DispCurves[i].MapTo) + w(" Show : %s" % yesno(binhdr.DispCurves[i].Show)) + w("---------------------") + + for i in range(3): + w("---------------------") + w("Parameter No %s" % i) + w(" Start : %f" % binhdr.Params[i].Start) + w(" Step : %f" % binhdr.Params[i].Step) + w(" End : %f" % binhdr.Params[i].End) + w("---------------------") + + w("Repeat Mode : %d" % binhdr.RepeatMode) + w("Repeats per Curve: %d" % binhdr.RepeatsPerCurve) + w("Repeat Time : %d" % binhdr.RepeatTime) + w("Repeat wait Time : %d" % binhdr.RepeatWaitTime) + w("Script Name : %s" % binhdr.ScriptName) + + for i, board in enumerate(boards): + w("---------------------") + w("Board No %d" % i) + w(" HardwareIdent : %s" % board.HardwareIdent) + w(" HardwareVersion : %s" % board.HardwareVersion) + w(" HardwareSerial : %d" % board.HardwareSerial) + w(" SyncDivider : %d" % board.SyncDivider) + w(" CFDZeroCross0 : %d" % board.CFDZeroCross0) + w(" CFDLevel0 : %d" % board.CFDLevel0) + w(" CFDZeroCross1 : %d" % board.CFDZeroCross1) + w(" CFDLevel1 : %d" % board.CFDLevel1) + w(" Resolution : %.6f" % board.Resolution) + + if board.RouterModelCode: + w(" RouterModelCode : %d" % board.RouterModelCode) + w(" RouterEnabled : %d" % board.RouterEnabled) + + w(" RtChan1_InputType : %d" % board.RtChan1_InputType) + w(" RtChan1_InputLevel : %d" % board.RtChan1_InputLevel) + w(" RtChan1_InputEdge : %d" % board.RtChan1_InputEdge) + w(" RtChan1_CFDPresent : %d" % board.RtChan1_CFDPresent) + w(" RtChan1_CFDLevel : %d" % board.RtChan1_CFDLevel) + w(" RtChan1_CFDZeroCross : %d" % board.RtChan1_CFDZeroCross) + + w(" RtChan2_InputType : %d" % board.RtChan2_InputType) + w(" RtChan2_InputLevel : %d" % board.RtChan2_InputLevel) + w(" RtChan2_InputEdge : %d" % board.RtChan2_InputEdge) + w(" RtChan2_CFDPresent : %d" % board.RtChan2_CFDPresent) + w(" RtChan2_CFDLevel : %d" % board.RtChan2_CFDLevel) + w(" RtChan2_CFDZeroCross : %d" % board.RtChan2_CFDZeroCross) + + w(" RtChan3_InputType : %d" % board.RtChan3_InputType) + w(" RtChan3_InputLevel : %d" % board.RtChan3_InputLevel) + w(" RtChan3_InputEdge : %d" % board.RtChan3_InputEdge) + w(" RtChan3_CFDPresent : %d" % board.RtChan3_CFDPresent) + w(" RtChan3_CFDLevel : %d" % board.RtChan3_CFDLevel) + w(" RtChan3_CFDZeroCross : %d" % board.RtChan3_CFDZeroCross) + + w(" RtChan4_InputType : %d" % board.RtChan4_InputType) + w(" RtChan4_InputLevel : %d" % board.RtChan4_InputLevel) + w(" RtChan4_InputEdge : %d" % board.RtChan4_InputEdge) + w(" RtChan4_CFDPresent : %d" % board.RtChan4_CFDPresent) + w(" RtChan4_CFDLevel : %d" % board.RtChan4_CFDLevel) + w(" RtChan4_CFDZeroCross : %d" % board.RtChan4_CFDZeroCross) + + w("---------------------") + + for i, curve in enumerate(curves): + w("---------------------") + w("Curve Index : %d" % curve.CurveIndex) + w("Time of Recording : %s" % timefmt(curve.TimeOfRecording)) + w("HardwareIdent : %s" % curve.HardwareIdent) + w("HardwareVersion : %s" % curve.HardwareVersion) + w("HardwareSerial : %d" % curve.HardwareSerial) + w("SyncDivider : %d" % curve.SyncDivider) + w("CFDZeroCross0 : %d" % curve.CFDZeroCross0) + w("CFDLevel0 : %d" % curve.CFDLevel0 ) + w("CFDZeroCross1 : %d" % curve.CFDZeroCross1) + w("CFDLevel1 : %d" % curve.CFDLevel1) + w("Offset : %d" % curve.Offset) + w("RoutingChannel : %d" % curve.RoutingChannel) + w("ExtDevices : %d" % curve.ExtDevices) + w("Meas. Mode : %d" % curve.MeasMode) + w("Sub-Mode : %d" % curve.SubMode) + w("Par. 1 : %f" % curve.P1) + w("Par. 2 : %.6f" % curve.P2) + w("Par. 3 : %.6f" % curve.P3) + w("Range No : %d" % curve.RangeNo) + w("Resolution : %f" % curve.Resolution) + w("Channels : %d" % curve.Channels) + w("Acq. Time : %d" % curve.Tacq) + w("Stop after : %d" % curve.StopAfter) + w("Stop Reason : %d" % curve.StopReason) + w("InpRate0 : %d" % curve.InpRate0) + w("InpRate1 : %d" % curve.InpRate1) + w("HistCountRate : %d" % curve.HistCountRate) + w("IntegralCount : %d" % curve.IntegralCount) + w("reserved : %d" % curve.reserved) + w("dataoffset : %d" % curve.DataOffset) + + if curve.RouterModelCode: + w("RouterModelCode : %d" % curve.RouterModelCode) + w("RouterEnabled : %d" % curve.RouterEnabled) + w("RtChan_InputType : %d" % curve.RtChan_InputType) + w("RtChan_InputLevel : %d" % curve.RtChan_InputLevel) + w("RtChan_InputEdge : %d" % curve.RtChan_InputEdge) + w("RtChan_CFDPresent : %d" % curve.RtChan_CFDPresent) + w("RtChan_CFDLevel : %d" % curve.RtChan_CFDLevel) + w("RtChan_CFDZeroCross : %d" % curve.RtChan_CFDZeroCross) + + return '\n'.join(r) + +def read_picoharp_phd(datafile): + parser = PicoharpParser(datafile) + return parser \ No newline at end of file diff --git a/src/main/python/Lifetime_analysis/read_ph_phd.py b/src/main/python/Lifetime_analysis/read_ph_phd.py new file mode 100644 index 0000000..1d35203 --- /dev/null +++ b/src/main/python/Lifetime_analysis/read_ph_phd.py @@ -0,0 +1,54 @@ +# -*- coding: utf-8 -*- +""" +Created on Fri Apr 5 15:52:05 2019 + +@author: Sarthak +""" + +try: + from Lifetime_analysis import picoharp_phd +except: + import picoharp_phd +import numpy as np +import matplotlib.pyplot as plt +#import sys + +#datafile = "E:/Python code/APTES_APTMS.phd" + + +def read_picoharp_phd(datafile): + parser = picoharp_phd.PicoharpParser(datafile) + return parser + +#def phd_to_csv(datafile, return_df = False): +# parser = read_picoharp_phd(datafile) +# name, ext = datafile.rsplit('.', 1) +# +# total_curves = parser.no_of_curves() +# y = [] +# for i in range(total_curves): +# res, curve = parser.get_curve(i) +# time_window = int(np.floor(parser.get_time_window_in_ns(curve_no))) +# curve = curve[0:time_window] +# y.append(curve) +# +# df = pd.DataFrame(y) +# df.T.to_csv(name+".csv", index=False, header=False) +# if return_df == True: +# return df.T + +def smooth(curve, boxwidth): + sm_curve = np.convolve(curve, np.ones(boxwidth)/boxwidth, mode="same") + return sm_curve + +def get_x_y(curve_no, parser, smooth_trace = False, boxwidth = 3): + + assert type(parser) == picoharp_phd.PicoharpParser, 'must be picoharp parser' + res, curve = parser.get_curve(curve_no) + time_window = int(np.floor(parser.get_time_window_in_ns(curve_no))) + curve = curve[0:time_window] + size = len(curve) + x = np.arange(0, size*res, res, np.float) + if smooth_trace == True: + curve = smooth(curve, boxwidth=boxwidth) + return x,curve diff --git a/src/main/python/Lifetime_analysis/skip_rows.ui b/src/main/python/Lifetime_analysis/skip_rows.ui new file mode 100644 index 0000000..35a4e6b --- /dev/null +++ b/src/main/python/Lifetime_analysis/skip_rows.ui @@ -0,0 +1,42 @@ + + + Form + + + + 0 + 0 + 413 + 94 + + + + Enter rows to skip + + + + + + Rows to skip + + + + + + + 10 + + + + + + + Done + + + + + + + + diff --git a/src/main/python/OceanOptics_acquire/OO_PZstageScan_acquire_gui.ui b/src/main/python/OceanOptics_acquire/OO_PZstageScan_acquire_gui.ui new file mode 100644 index 0000000..77dacb8 --- /dev/null +++ b/src/main/python/OceanOptics_acquire/OO_PZstageScan_acquire_gui.ui @@ -0,0 +1,750 @@ + + + MainWindow + + + + 0 + 0 + 1219 + 901 + + + + MainWindow + + + + + + + + + + 15 + + + + Settings + + + + + + Stage Settings for Scan + + + + + + + 12 + + + + X Scan Size (um) + + + + + + + + 12 + + + + 5.000000000000000 + + + + + + + + 12 + + + + Initialize Piezo Stage + + + + + + + + 12 + + + + 0.100000000000000 + + + + + + + + 12 + + + + 5.000000000000000 + + + + + + + + 12 + + + + X Step (um) + + + + + + + + 12 + + + + 100.000000000000000 + + + 50.000000000000000 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + 12 + + + + Y Scan Size (um) + + + + + + + + 12 + + + + X Start (um) + + + + + + + + 12 + + + + 1.000000000000000 + + + 0.100000000000000 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + 12 + + + + Y Start (um) + + + + + + + + 12 + + + + Y Step (um) + + + + + + + + 12 + + + + Start X-Y Scan + + + + + + + + 12 + + + + Estimate Scan Time + + + + + + + + 12 + + + + 100.000000000000000 + + + 50.000000000000000 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + 15 + + + + OceanOptics Save Settings + + + + + + + 12 + + + + Save Every Spectrum + + + + + + + + 12 + + + + Save Single Spectrum + + + + + + + + + + Spectrometer Settings + + + + + + + 12 + + + + 1 + + + + + + + + 12 + + + + 3 + + + 3000 + + + 100 + + + + + + + + 12 + + + + Scans to Average + + + + + + + + 12 + + + + Intg. Time (ms) + + + + + + + + 12 + + + + Correct Dark Counts + + + true + + + + + + + + 12 + + + + Connect to Spectrometer + + + + + + + + 12 + + + + Live + + + + + + + + + + Scan Save Settings + + + + + + + 12 + + + + + + + + + 12 + + + + Sample Name: + + + + + + + + 12 + + + + Path to Folder + + + + + + + + + + + + + + + + + + 15 + + + + Independent Stage Movements + + + + + + + 12 + + + + Where is the stage? + + + + + + + + 12 + + + + Show Current Position + + + + + + + + 12 + + + + Center the Piezo Stage: + + + + + + + + 12 + + + + Center Stage + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + 12 + + + + Absolute Movements + + + + + + + + 12 + + + + X (um) + + + + + + + + 12 + + + + + + + + + 12 + + + + Y (um) + + + + + + + + 12 + + + + + + + + + 12 + + + + OK + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + 12 + + + + Relative Movements + + + + + + + + 12 + + + + X (um) + + + + + + + + 12 + + + + + + + + + 12 + + + + Y (um) + + + + + + + + 12 + + + + + + + + + 12 + + + + Ok + + + + + + + + + + + + + + 12 + + + + + + + + + 15 + + + + Information: + + + + + + + + 15 + + + + Scan Progress: + + + + + + + + 12 + + + + 0 + + + + + + + + + + + 0 + 0 + 1219 + 21 + + + + + + + + PlotWidget + QGraphicsView +
pyqtgraph
+ + + + + diff --git a/src/main/python/OceanOptics_acquire/OO_acquire_gui.ui b/src/main/python/OceanOptics_acquire/OO_acquire_gui.ui new file mode 100644 index 0000000..33c8b19 --- /dev/null +++ b/src/main/python/OceanOptics_acquire/OO_acquire_gui.ui @@ -0,0 +1,240 @@ + + + MainWindow + + + + 0 + 0 + 1206 + 668 + + + + MainWindow + + + + + + + + + + 15 + + + + Acquire Settings + + + + + + + 15 + + + + Save Settings + + + + + + + 12 + + + + Configure Folder to Save + + + + + + + + 12 + + + + Save Every Spectrum + + + + + + + + 12 + + + + Save Single Spectrum + + + + + + + + + + + 12 + + + + Correct Dark Counts + + + true + + + + + + + + 15 + + + + Close Connection + + + + + + + + 12 + + + + + + + + + 15 + + + + ALWAYS CLOSE CONNECTION!!! +BEFORE EXITING APP + + + + + + + + 12 + + + + Intg. Time (ms) + + + + + + + + 12 + + + + Scans to Average + + + + + + + + 10 + + + + 3 + + + 3000 + + + + + + + + 10 + + + + 1 + + + + + + + + 15 + + + + Live + + + + + + + + 12 + + + + Connect to Spectrometer + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 1206 + 21 + + + + + + + + PlotWidget + QGraphicsView +
pyqtgraph
+ + + + + diff --git a/src/main/python/OceanOptics_acquire/OceanOptics_acquire_plot.py b/src/main/python/OceanOptics_acquire/OceanOptics_acquire_plot.py new file mode 100644 index 0000000..8de85c0 --- /dev/null +++ b/src/main/python/OceanOptics_acquire/OceanOptics_acquire_plot.py @@ -0,0 +1,297 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Mar 27 16:50:26 2019 + +@author: Sarthak +""" + +import pyqtgraph as pg +from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog +import numpy as np +import pickle +import sys +import seabreeze.spectrometers as sb +from pipython import GCSDevice +import time + +pg.mkQApp() +pg.setConfigOption('background', 'w') + +#uiFile = "OO_acquire_gui.ui" "OO_PZstageScan_acquire_gui" +uiFile = "OO_PZstageScan_acquire_gui.ui" + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +class MainWindow(TemplateBaseClass): + + def __init__(self): + TemplateBaseClass.__init__(self) + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + + self.ui.connect_checkBox.stateChanged.connect(self._handle_spectrometer_connection) + self.ui.live_pushButton.clicked.connect(self.live) + + self.ui.path_to_folder_pushButton.clicked.connect(self.save_file_location) + self.ui.save_single_spec_pushButton.clicked.connect(self.save_single_spec) + + self.ui.init_stage_pushButton.clicked.connect(self.init_piezo_stage) + self.ui.show_curr_pos_pushButton.clicked.connect(self.current_piezo_stage_pos) + self.ui.center_stage_pushButton.clicked.connect(self.center_piezo) + self.ui.abs_mov_pushButton.clicked.connect(self.abs_mov) + self.ui.rel_mov_pushButton.clicked.connect(self.rel_mov) + self.ui.estimate_scan_time_pushButton.clicked.connect(self.estimate_scan_time) + self.ui.start_x_y_sacan_pushButton.clicked.connect(self.x_y_scan) + +# self.ui.clear_pushButton.clicked.connect(self.clear_plot) + self.pi_device = None + self.spec = None + + self.ui.status_textBrowser.setText("Welcome!\nGUI Initiated!") + + self.show() + + def _handle_spectrometer_connection(self): + if self.ui.connect_checkBox.isChecked(): + self.connect_spectrometer() + else: + self.close_connection() + + def connect_spectrometer(self): + if self.spec is None: + devices = sb.list_devices() + self.spec = sb.Spectrometer(devices[0]) + self.ui.status_textBrowser.append("Ocean Optics Device Connected!\n\n Device:\n\n"+str(sb.list_devices()[0])) + else: + self.ui.status_textBrowser.append("Already Connected") + + def init_piezo_stage(self): + if self.pi_device is None: + self.pi_device = GCSDevice("E-710") # Creates a Controller instant + self.pi_device.ConnectNIgpib(board=0,device=4) # Connect to GPIB board + self.ui.status_textBrowser.append('Connected: {}'.format(self.pi_device.qIDN().strip())) + # print('connected: {}'.format(self.pi_device.qIDN().strip())) + + self.axes = self.pi_device.axes[0:2] # selecting x and y axis of the stage + + self.pi_device.INI() + self.pi_device.REF(axes=self.axes) + + self.pi_device.SVO(axes=self.axes, values=[True,True]) # Turn on servo control for both axes + self.ui.status_textBrowser.append("Current Stage Position:\n{}".format(self.pi_device.qPOS(axes=self.axes))) + # print(self.pi_device.qPOS(axes=self.axes)) + else: + self.ui.status_textBrowser.append("Piezo Stage Is Already Initialized!") + + def center_piezo(self): + if self.pi_device is None: + self.init_piezo_stage() + self.pi_device.MOV(axes=self.axes, values=[50,50]) + self.ui.status_textBrowser.append("Piezo Stage Centered: [50x,50y]") + + def current_piezo_stage_pos(self): + if self.pi_device is None: + self.init_piezo_stage() + self.ui.status_textBrowser.append("Current Stage Position:\n{}".format(self.pi_device.qPOS(axes=self.axes))) + + def abs_mov(self): + if self.pi_device is None: + self.init_piezo_stage() + x_abs_pos = self.ui.x_abs_doubleSpinBox.value() + y_abs_pos = self.ui.y_abs_doubleSpinBox.value() + self.pi_device.MOV(axes=self.axes, values=[x_abs_pos,y_abs_pos]) + + def rel_mov(self): + if self.pi_device is None: + self.init_piezo_stage() + x_rel_pos = self.ui.x_rel_doubleSpinBox.value() + y_rel_pos = self.ui.y_rel_doubleSpinBox.value() + self.pi_device.MVR(axes=self.axes, values=[x_rel_pos,y_rel_pos]) + + def estimate_scan_time(self): + x_scan_size = self.ui.x_size_doubleSpinBox.value() + y_scan_size = self.ui.y_size_doubleSpinBox.value() + + x_step = self.ui.x_step_doubleSpinBox.value() + y_step = self.ui.y_step_doubleSpinBox.value() + + if y_scan_size == 0: + y_scan_size = 1 + + if x_scan_size == 0: + x_scan_size = 1 + + if y_step == 0: + y_step = 1 + + if x_step == 0: + x_step = 1 + + y_range = int(np.ceil(y_scan_size/y_step)) + x_range = int(np.ceil(x_scan_size/x_step)) + + total_points = x_range*y_range + + intg_time_ms = self.ui.intg_time_spinBox.value() + scans_to_avg = self.ui.scan_to_avg_spinBox.value() + + total_time = total_points*(intg_time_ms*1e-3)*(scans_to_avg) # in seconds + + self.ui.status_textBrowser.append("Estimated scan time: "+str(np.float16(total_time/60))+" mins") + + def x_y_scan(self): + if self.pi_device is None: + self.init_piezo_stage() + + if self.spec is None: + self.ui.status_textBrowser.append("Spectrometer not connected!\nForce connecting the spectrometer...") + self.connect_spectrometer() + + start_time = time.time() + x_start = self.ui.x_start_doubleSpinBox.value() + y_start = self.ui.y_start_doubleSpinBox.value() + + x_scan_size = self.ui.x_size_doubleSpinBox.value() + y_scan_size = self.ui.y_size_doubleSpinBox.value() + + x_step = self.ui.x_step_doubleSpinBox.value() + y_step = self.ui.y_step_doubleSpinBox.value() + + if y_scan_size == 0: + y_scan_size = 1 + + if x_scan_size == 0: + x_scan_size = 1 + + if y_step == 0: + y_step = 1 + + if x_step == 0: + x_step = 1 + + y_range = int(np.ceil(y_scan_size/y_step)) + x_range = int(np.ceil(x_scan_size/x_step)) + + # Define empty array for saving intensities + data_array = np.zeros(shape=(x_range*y_range,2048)) + + self.ui.status_textBrowser.append("Starting Scan...") + # Move to the starting position + self.pi_device.MOV(axes=self.axes, values=[x_start,y_start]) + + self.ui.status_textBrowser.append("Scan in Progress...") + + k = 0 + for i in range(y_range): + for j in range(x_range): +# print(self.pi_device.qPOS(axes=self.axes)) + + self._read_spectrometer() + data_array[k,:] = self.y + self.ui.plot.plot(self.spec.wavelengths(), self.y, pen='r', clear=True) + pg.QtGui.QApplication.processEvents() + + self.pi_device.MVR(axes=self.axes[0], values=[x_step]) + + self.ui.progressBar.setValue(100*((k+1)/(x_range*y_range))) + k+=1 + # TODO + # if statement needs to be modified to keep the stage at the finish y-pos for line scans in x, and same for y + if i == y_range-1: # this if statement is there to keep the stage at the finish position (in x) and not bring it back like we were doing during the scan + self.pi_device.MVR(axes=self.axes[1], values=[y_step]) + else: + self.pi_device.MVR(axes=self.axes, values=[-x_scan_size, y_step]) + + self.ui.status_textBrowser.append("Scan Complete!\nSaving Data...") + + save_dict = {"Wavelengths": self.spec.wavelengths(), "Intensities": data_array, + "Scan Parameters":{"X scan start (um)": x_start, "Y scan start (um)": y_start, + "X scan size (um)": x_scan_size, "Y scan size (um)": y_scan_size, + "X step size (um)": x_step, "Y step size (um)": y_step}, + "OceanOptics Parameters":{"Integration Time (ms)": self.ui.intg_time_spinBox.value(), + "Scans Averages": self.ui.scan_to_avg_spinBox.value(), + "Correct Dark Counts": self.ui.correct_dark_counts_checkBox.isChecked()} + } + + pickle.dump(save_dict, open(self.save_folder+"/"+self.ui.lineEdit.text()+"_raw_PL_spectra_data.pkl", "wb")) + + self.ui.status_textBrowser.append("Data saved!\nTotal time taken:"+str(np.float16((time.time()-start_time)/60))+" mins") + + def save_file_location(self): + self.save_folder = QtWidgets.QFileDialog.getExistingDirectory(self, caption="Select Folder") + + def save_single_spec(self): + save_array = np.zeros(shape=(2048,2)) + self._read_spectrometer() + save_array[:,1] = self.y + save_array[:,0] = self.spec.wavelengths() + + np.savetxt(self.save_folder+"/"+self.ui.lineEdit.text()+".txt", save_array, fmt = '%.5f', + header = 'Wavelength (nm), Intensity (counts)', delimiter = ' ') + + def live(self): + save_array = np.zeros(shape=(2048,2)) + + self.ui.plot.setLabel('left', 'Intensity', units='a.u.') + self.ui.plot.setLabel('bottom', 'Wavelength', units='nm') + j = 0 + while self.spec is not None:#self.ui.connect_checkBox.isChecked(): # this while loop works! + self._read_spectrometer() + save_array[:,1] = self.y + + self.ui.plot.plot(self.spec.wavelengths(), self.y, pen='r', clear=True) + + if self.ui.save_every_spec_checkBox.isChecked(): + save_array[:,0] = self.spec.wavelengths() + np.savetxt(self.save_folder+"/"+self.ui.lineEdit.text()+str(j)+".txt", save_array, fmt = '%.5f', + header = 'Wavelength (nm), Intensity (counts)', delimiter = ' ') + + pg.QtGui.QApplication.processEvents() + j += 1 + + def _read_spectrometer(self): + if self.spec is not None: + + intg_time_ms = self.ui.intg_time_spinBox.value() + self.spec.integration_time_micros(intg_time_ms*1e3) + + scans_to_avg = self.ui.scan_to_avg_spinBox.value() + Int_array = np.zeros(shape=(2048,scans_to_avg)) + + for i in range(scans_to_avg): #software average + data = self.spec.spectrum(correct_dark_counts=self.ui.correct_dark_counts_checkBox.isChecked()) + Int_array[:,i] = data[1] + self.y = np.mean(Int_array, axis=-1) + + else: + self.ui.status_textBrowser.append("Connect to Spectrometer!") + raise Exception("Must connect to spectrometer first!") + + + def close_connection(self): + if self.spec is not None: + self.spec.close() + self.ui.status_textBrowser.append("Ocean Optics Device Disconnected") + del self.spec + self.spec = None + + def close_application(self): + choice = QtGui.QMessageBox.question(self, 'EXIT!', + "Do you want to exit the app?", + QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) + if choice == QtGui.QMessageBox.Yes: + sys.exit() + else: + pass + + +win = MainWindow() + + +## Start Qt event loop unless running in interactive mode or using pyside. +if __name__ == '__main__': + import sys + if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'): + QtGui.QApplication.instance().exec_() diff --git a/src/main/python/PLQE_analysis/column_selection_gui.ui b/src/main/python/PLQE_analysis/column_selection_gui.ui new file mode 100644 index 0000000..c20125c --- /dev/null +++ b/src/main/python/PLQE_analysis/column_selection_gui.ui @@ -0,0 +1,107 @@ + + + MainWindow + + + + 0 + 0 + 800 + 600 + + + + Select number of columns + + + + + + + Data preview + + + + + + + + Select data columns + + + + + + + + Ref + + + + + + + Inpath + + + + + + + Outpath + + + + + + + 2 + + + + + + + 3 + + + + + + + 4 + + + + + + + Done + + + + + + + + + + + + + + + + + 0 + 0 + 800 + 31 + + + + + + + + diff --git a/src/main/python/PLQE_analysis/plqe_analysis.py b/src/main/python/PLQE_analysis/plqe_analysis.py new file mode 100644 index 0000000..3e42a4f --- /dev/null +++ b/src/main/python/PLQE_analysis/plqe_analysis.py @@ -0,0 +1,212 @@ +# system imports +from pathlib import Path +import os.path +import pyqtgraph as pg +from pyqtgraph import exporters +from pyqtgraph.Qt import QtCore, QtGui, QtWidgets +import matplotlib.pyplot as plt +import numpy as np + +# local modules + +pg.mkQApp() +pg.setConfigOption('background', 'w') + +base_path = Path(__file__).parent +file_path = (base_path / "plqe_analysis_gui.ui").resolve() + +uiFile = file_path + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +"""params for plotting""" +plt.rc('xtick', labelsize = 20) +plt.rc('xtick.major', pad = 3) +plt.rc('ytick', labelsize = 20) +plt.rc('lines', lw = 1.5, markersize = 7.5) +plt.rc('legend', fontsize = 20) +plt.rc('axes', linewidth = 3.5) + +class MainWindow(TemplateBaseClass): + + def __init__(self): + super(TemplateBaseClass, self).__init__() + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + + #setup uv vis plot + self.plot = self.ui.plotWidget.getPlotItem() + self.plot.setTitle(title="Wavelength vs. Intensity") + self.plot.setLabel('bottom', 'Wavelength', unit='nm') + self.plot.setLabel('left', 'Intensity', unit='a.u.') + self.plot.setLogMode(x=None, y=1) + + #setup line rois for laser and emission + self.laser_region = pg.LinearRegionItem(brush=QtGui.QBrush(QtGui.QColor(255, 0, 0, 50))) + self.laser_region.sigRegionChanged.connect(self.update_laser_spinBoxes) + self.emission_region = pg.LinearRegionItem() + self.emission_region.sigRegionChanged.connect(self.update_emission_spinBoxes) + self.laser_region.setRegion((200, 400)) + self.emission_region.setRegion((700, 800)) + + #setup ui signals + self.ui.load_data_pushButton.clicked.connect(self.open_data_file) + self.ui.plot_pushButton.clicked.connect(self.plot_intensity) + self.ui.clear_pushButton.clicked.connect(self.clear) + self.ui.calculate_plqe_pushButton.clicked.connect(self.calculate_plqe) + self.ui.laser_start_spinBox.valueChanged.connect(self.update_laser_region) + self.ui.laser_stop_spinBox.valueChanged.connect(self.update_laser_region) + self.ui.emission_start_spinBox.valueChanged.connect(self.update_emission_region) + self.ui.emission_stop_spinBox.valueChanged.connect(self.update_emission_region) + + self.show() + + def open_data_file(self): + """ Open data file """ + try: + self.filename = QtWidgets.QFileDialog.getOpenFileName(self) + #self.data = np.loadtxt(self.filename[0], delimiter = '\t', skiprows = 1) + if ".txt" in self.filename[0]: + self.data = np.loadtxt(self.filename[0], delimiter = '\t', skiprows = 1) + elif ".csv" in self.filename[0]: + self.data = np.loadtxt(self.filename[0], delimiter = ',', skiprows = 1) + elif ".qua" in self.filename[0]:#TODO: Include a Pop-up window for input for skipping header + self.data = np.genfromtxt(self.filename[0], delimiter = '\t', skip_header = 28) + self.cs_window = ColSelectionWindow(self.data) + self.cs_window.col_selection_signal.connect(self.open_with_col_selection) + self.nm = np.copy(self.data[:,0]) + #self.ref_data = np.copy(self.data[:,1]) + #self.inpath_data = np.copy(self.data[:,2]) + #self.outpath_data = np.copy(self.data[:,3]) + except Exception as err: + print(format(err)) + + def open_with_col_selection(self): + ref_data_col = self.cs_window.ui.ref_spinBox.value() - 1 #subtract since spinboxes refer to column num and not index + inpath_data_col = self.cs_window.ui.inpath_spinBox.value() - 1 + outpath_data_col = self.cs_window.ui.outpath_spinBox.value() - 1 + self.ref_data = np.copy(self.data[:,ref_data_col]) + self.inpath_data = np.copy(self.data[:,inpath_data_col]) + self.outpath_data = np.copy(self.data[:,outpath_data_col]) + + def update_laser_spinBoxes(self): + """ Update laser spinboxes based on line rois """ + self.laser_start, self.laser_stop = self.laser_region.getRegion() + self.ui.laser_start_spinBox.setValue(self.laser_start) + self.ui.laser_stop_spinBox.setValue(self.laser_stop) + + + def update_emission_spinBoxes(self): + """ Update emission spinboxes based on line rois """ + self.emission_start, self.emission_stop = self.emission_region.getRegion() + self.ui.emission_start_spinBox.setValue(self.emission_start) + self.ui.emission_stop_spinBox.setValue(self.emission_stop) + + def update_laser_region(self): + """ Update laser line rois based on spinboxes """ + laser_start = self.ui.laser_start_spinBox.value() + laser_stop = self.ui.laser_stop_spinBox.value() + self.laser_region.setRegion((laser_start, laser_stop)) + + def update_emission_region(self): + """ Update emission line rois based on spinboxes """ + emission_start = self.ui.emission_start_spinBox.value() + emission_stop = self.ui.emission_stop_spinBox.value() + self.emission_region.setRegion((emission_start, emission_stop)) + + def plot_intensity(self): + try: + self.plot.plot(self.nm, self.inpath_data, pen='r') + self.plot.addItem(self.laser_region, ignoreBounds=True) + self.plot.addItem(self.emission_region, ignoreBounds=True) + except Exception as err: + print(format(err)) + + def find_nearest(self,array,value): + idx = (np.abs(array-value)).argmin() + return idx + + def calculate_plqe(self): + + nm_interp_step = 1 + nm_interp_start = np.ceil(self.nm[0] / nm_interp_step) * nm_interp_step + nm_interp_stop = np.floor(self.nm[len(self.nm) - 1] / nm_interp_step) * nm_interp_step + nm_interp = np.arange(nm_interp_start, nm_interp_stop + nm_interp_step, nm_interp_step) + + ref_interp = np.interp(nm_interp, self.nm, self.ref_data) + + + inpath_interp = np.interp(nm_interp, self.nm, self.inpath_data) + outpath_interp = np.interp(nm_interp, self.nm, self.outpath_data) + + + """L_x is area under laser profile for experiment x""" + """P_x_ is area under emission profile for experiment x""" + + + #plt.semilogy(nm, a1_outpath_data[:,1]) + + emission_start_idx = self.find_nearest(nm_interp, self.emission_start) + emission_stop_idx = self.find_nearest(nm_interp, self.emission_stop) + + laser_start_idx = self.find_nearest(nm_interp, self.laser_start) + laser_stop_idx = self.find_nearest(nm_interp, self.laser_stop) + + la = np.trapz(ref_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx]) + lb = np.trapz(outpath_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx]) + lc = np.trapz(inpath_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx]) + + pa = np.trapz(ref_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx]) + pb = np.trapz(outpath_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx]) + pc = np.trapz(inpath_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx]) + + absorb = 1.0 - (lc / lb) + + plqe = 100 * (pc - ((1.0 - absorb) * pb)) / (la * absorb) + #print('PLQE Percent = %.3f' %(plqe)) + #return plqe + self.ui.plqe_label.setText("%.3f" %(plqe)) + + def clear(self): + self.plot.clear() + +"""Table view GUI""" +ui_file_path = (base_path / "column_selection_gui.ui").resolve() +col_selection_WindowTemplate, col_selection_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) + +class ColSelectionWindow(col_selection_TemplateBaseClass): + + col_selection_signal = QtCore.pyqtSignal() #signal to help with pass info back to MainWindow + + def __init__(self, data): + col_selection_TemplateBaseClass.__init__(self) + # Create the param window + self.ui = col_selection_WindowTemplate() + self.ui.setupUi(self) + self.ui.done_pushButton.clicked.connect(self.done) + + self.table_widget = pg.TableWidget() + self.ui.data_preview_groupBox.layout().addWidget(self.table_widget) + + self.table_widget.setData(data) + + #self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False) + self.show() + + def done(self): + self.col_selection_signal.emit() + self.ui.textBrowser.setText("Data successfully loaded.") + #self.close() + + def closeEvent(self, event): + self.col_selection_signal.emit() + +"""Run the Main Window""" +def run(): + win = MainWindow() + QtGui.QApplication.instance().exec_() + return win + +#run() diff --git a/src/main/python/PLQE_analysis/plqe_analysis_gui.ui b/src/main/python/PLQE_analysis/plqe_analysis_gui.ui new file mode 100644 index 0000000..7720b49 --- /dev/null +++ b/src/main/python/PLQE_analysis/plqe_analysis_gui.ui @@ -0,0 +1,150 @@ + + + Form + + + + 0 + 0 + 575 + 524 + + + + PLQE Analysis + + + + + + PLQE + + + + + + Laser start + + + + + + + 9999.000000000000000 + + + 200.000000000000000 + + + + + + + Laser stop + + + + + + + 9999.000000000000000 + + + 400.000000000000000 + + + + + + + Emission start + + + + + + + 9999.000000000000000 + + + 700.000000000000000 + + + + + + + Emission stop + + + + + + + 9999.000000000000000 + + + 800.000000000000000 + + + + + + + PLQE Percent + + + + + + + 0 + + + + + + + Calculate PLQE + + + + + + + + + + Clear + + + + + + + Plot + + + + + + + Load data + + + + + + + + + + + PlotWidget + QGraphicsView +
pyqtgraph
+ + + + + diff --git a/src/main/python/Spectrum_analysis/Spectra_fit_funcs.py b/src/main/python/Spectrum_analysis/Spectra_fit_funcs.py new file mode 100644 index 0000000..a96f782 --- /dev/null +++ b/src/main/python/Spectrum_analysis/Spectra_fit_funcs.py @@ -0,0 +1,241 @@ +# -*- coding: utf-8 -*- +""" +Created on Sun Mar 31 15:46:54 2019 + +@author: Sarthak +""" + +# -*- coding: utf-8 -*- +""" +Created on Thu Jan 31 20:48:03 2019 + +@author: Sarthak +""" +import numpy as np +from lmfit.models import GaussianModel, LorentzianModel + +class Spectra_Fit(object): + """ + Fit a spectrum. + + Attributes: + data: spectrum data (x-axis and y-axis) + ref: reference spectrum (both x and y-axis) for background correction + """ + + def __init__(self, data, ref, wlref = None, fit_in_eV = True): + self.data = data + self.ref = ref + self.wlref = wlref + self.fit_in_eV = fit_in_eV + + def background_correction(self): + """Return the background corrected spectrum""" + x = self.data[:, 0] # wavelengths + y = self.data[:, 1] # intensity + yref = self.ref[:, 1] + y = y - yref # background correction + if self.wlref is not None: + wlref = self.wlref[:,1] + y = y/wlref + + if self.fit_in_eV is True: + x = np.sort(1240/self.data[:, 0]) # converting to eV and sorting in ascending order + y = [y[i] for i in np.argsort(1240/x)] # sorting argument of y acc to x sorting index + # need to do this because data is collected in wavelength + + return [x,y] + +class Single_Gaussian(Spectra_Fit): + """Fit a single gaussian to the spectrum + + Attributes: + data: spectrum data (x-axis and y-axis) + ref: reference spectrum (both x and y-axis) for background correction + """ + + def gaussian_model(self): + x,y = self.background_correction() + gmodel = GaussianModel(prefix = 'g1_') # calling gaussian model + pars = gmodel.guess(y, x=x) # parameters - center, width, height + result = gmodel.fit(y, pars, x=x, nan_policy='propagate') + return result + + # def gaussian_model_w_lims(self, center_initial_guess=None, sigma_initial_guess=None, center_min=None, center_max=None): + # x,y = self.background_correction() + # gmodel = GaussianModel(prefix = 'g1_') # calling gaussian model + # pars = gmodel.guess(y, x=x) # parameters - center, width, height + # pars['g1_center'].set(center_initial_guess, min=center_min, max=center_max) + # pars['g1_sigma'].set(sigma_initial_guess) + # result = gmodel.fit(y, pars, x=x, nan_policy='propagate') + # return result #770 760 780 sigma 15 + def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range): + x,y = self.background_correction() + if self.fit_in_eV is True: + peak_pos = 1240/peak_pos + sigma = 1240/sigma + min_max_range = np.sort(1240/np.asarray(min_max_range)) + gmodel = GaussianModel(prefix = 'g1_') # calling gaussian model + pars = gmodel.guess(y, x=x) # parameters - center, width, height + pars['g1_center'].set(peak_pos, min=min_max_range[0], max=min_max_range[1]) + pars['g1_sigma'].set(sigma) + result = gmodel.fit(y, pars, x=x, nan_policy='propagate') + return result + +class Single_Lorentzian(Spectra_Fit): + """Fit a single Lorentzian to the spectrum + + Attributes: + data: spectrum data (x-axis and y-axis) + ref: reference spectrum (both x and y-axis) for background correction + """ + + def lorentzian_model(self): + x,y = self.background_correction() + lmodel = LorentzianModel(prefix = 'l1_') # calling lorentzian model + pars = lmodel.guess(y, x=x) # parameters - center, width, height + result = lmodel.fit(y, pars, x=x, nan_policy='propagate') + return result + + def lorentzian_model_w_lims(self, peak_pos, sigma, min_max_range): + x,y = self.background_correction() + if self.fit_in_eV is True: + peak_pos = 1240/peak_pos + sigma = 1240/sigma + min_max_range = np.sort(1240/np.asarray(min_max_range)) + lmodel = LorentzianModel(prefix = 'l1_') # calling lorentzian model + pars = lmodel.guess(y, x=x) # parameters - center, width, height + pars['l1_center'].set(peak_pos, min = min_max_range[0], max = min_max_range[1]) + pars['l1_sigma'].set(sigma) + result = lmodel.fit(y, pars, x=x, nan_policy='propagate') + return result + +class Double_Gaussian(Spectra_Fit): + """Fit two gaussians to the spectrum + + Attributes: + data: spectrum data (x-axis and y-axis) + ref: reference spectrum (both x and y-axis) for background correction + """ + + def gaussian_model(self): + + x,y = self.background_correction() + gmodel_1 = GaussianModel(prefix='g1_') # calling gaussian model + pars = gmodel_1.guess(y, x=x) # parameters - center, width, height + + gmodel_2 = GaussianModel(prefix='g2_') + pars.update(gmodel_2.make_params()) # update parameters - center, width, height + + gmodel = gmodel_1 + gmodel_2 + result = gmodel.fit(y, pars, x=x, nan_policy='propagate') + return result + + def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range): + #center_initial_guesses - list containing initial guesses for peak centers. [center_guess1, center_guess2] + #sigma_initial_guesses - list containing initial guesses for sigma. [sigma1, sigma2] + #min_max_range - list containing lists of min and max for peak center. [ [min1, max1], [min2, max2] ] + + x,y = self.background_correction() + if self.fit_in_eV is True: + peak_pos = 1240/np.asarray(peak_pos) + sigma = 1240/np.asarray(sigma) + min_max_range = np.sort(1240/np.asarray(min_max_range)) + gmodel_1 = GaussianModel(prefix='g1_') # calling gaussian model + pars = gmodel_1.guess(y, x=x) # parameters - center, width, height + pars['g1_center'].set(peak_pos[0], min = min_max_range[0][0], max = min_max_range[0][1]) + pars['g1_sigma'].set(sigma[0]) + pars['g1_amplitude'].set(min=0) + + gmodel_2 = GaussianModel(prefix='g2_') + pars.update(gmodel_2.make_params()) # update parameters - center, width, height + pars['g2_center'].set(peak_pos[1], min = min_max_range[1][0], max = min_max_range[1][1]) + pars['g2_sigma'].set(sigma[1], min = pars['g1_sigma'].value) + pars['g2_amplitude'].set(min = 0) + + gmodel = gmodel_1 + gmodel_2 + result = gmodel.fit(y, pars, x=x, nan_policy='propagate') + return result + +class Multi_Gaussian(Spectra_Fit): + + # def __init__(self, data, ref, num_of_gaussians, peak_pos, sigma, min_max_range): + # Spectra_Fit.__init__(self, data, ref) + # self.num_of_gaussians = num_of_gaussians + # self.peak_pos = peak_pos + # self.min_max_range = min_max_range + def __init__(self, data, ref, num_of_gaussians, wlref=None, fit_in_eV = True): + Spectra_Fit.__init__(self, data, ref, wlref, fit_in_eV=True) + self.num_of_gaussians = num_of_gaussians + + def gaussian_model(self): + composite_model = None + composite_pars = None + + x,y = self.background_correction() + + for i in range(self.num_of_gaussians): + + model = GaussianModel(prefix='g'+str(i+1)+'_') + + if composite_pars is None: + composite_pars = model.guess(y, x=x) +# composite_pars = model.make_params() + + else: + composite_pars.update(model.make_params()) + + if composite_model is None: + composite_model = model + else: + composite_model += model + + result = composite_model.fit(y, composite_pars, x=x, nan_policy='propagate') + return result + + def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range): + self.peak_pos = peak_pos + self.sigma = sigma + self.min_max_range = min_max_range + + composite_model = None + composite_pars = None + + x,y = self.background_correction() + + assert self.num_of_gaussians == len(self.peak_pos), ("Number of gaussians must be equal to the number of peak positions") + assert len(self.min_max_range) == len(self.peak_pos), ("Number of bounds on the range must be equal to the number of peak positions") + + if self.fit_in_eV is True: + peak_pos = 1240/np.asarray(peak_pos) + sigma = 1240/np.asarray(sigma) + min_max_range = np.sort(1240/np.asarray(min_max_range)) + + + for i in range(self.num_of_gaussians): + + model = GaussianModel(prefix='g'+str(i+1)+'_') + + if composite_pars is None: + composite_pars = model.guess(y, x=x) +# composite_pars = model.make_params() + composite_pars['g'+str(i+1)+'_center'].set(self.peak_pos[i], + min = self.min_max_range[0][0], max = self.min_max_range[0][1]) + composite_pars['g'+str(i+1)+'_sigma'].set(self.sigma[i]) + composite_pars['g'+str(i+1)+'_amplitude'].set(min = 0) + + else: + composite_pars.update(model.make_params()) + composite_pars['g'+str(i+1)+'_center'].set(self.peak_pos[i], + min = self.min_max_range[i][0], max = self.min_max_range[i][1]) + composite_pars['g'+str(i+1)+'_sigma'].set(self.sigma[i], min = composite_pars['g1_sigma'].value) + composite_pars['g'+str(i+1)+'_amplitude'].set(min = 0) + + + if composite_model is None: + composite_model = model + else: + composite_model += model + + result = composite_model.fit(y, composite_pars, x=x, nan_policy='propagate') + return result \ No newline at end of file diff --git a/src/main/python/Spectrum_analysis/Spectra_plot_fit.py b/src/main/python/Spectrum_analysis/Spectra_plot_fit.py new file mode 100644 index 0000000..69f182b --- /dev/null +++ b/src/main/python/Spectrum_analysis/Spectra_plot_fit.py @@ -0,0 +1,1020 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Mar 27 16:50:26 2019 + +@author: Sarthak +""" + +# system imports +import sys +import h5py +from pathlib import Path +import os.path +import pyqtgraph as pg +from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog +import numpy as np +import matplotlib.pyplot as plt +import matplotlib +import pickle +import lmfit +from lmfit.models import GaussianModel, LinearModel +from scipy import interpolate +import customplotting.mscope as cpm + +sys.path.append(os.path.abspath('../H5_Pkl')) +from H5_Pkl import h5_pkl_view +sys.path.append(os.path.abspath('../Export_Windows')) +try: + from Export_window import ExportFigureWindow, ExportPlotWindow +except: + from Export_Windows.Export_window import ExportFigureWindow, ExportPlotWindow +# local modules +try: + from Spectra_fit_funcs import Spectra_Fit, Single_Gaussian, Single_Lorentzian, Double_Gaussian, Multi_Gaussian + from pyqtgraph_MATPLOTLIBWIDGET import MatplotlibWidget +except: + from Spectrum_analysis.Spectra_fit_funcs import Spectra_Fit, Single_Gaussian, Single_Lorentzian, Double_Gaussian, Multi_Gaussian + from Spectrum_analysis.pyqtgraph_MATPLOTLIBWIDGET import MatplotlibWidget + +matplotlib.use('Qt5Agg') + +"""Recylce params for plotting""" +plt.rc('xtick', labelsize = 10) +plt.rc('xtick.major', pad = 1) +plt.rc('ytick', labelsize = 10) +plt.rc('lines', lw = 1.5, markersize = 3.5) +plt.rc('legend', fontsize = 10) +plt.rc('axes', linewidth=1.5) + +pg.mkQApp() +pg.setConfigOption('background', 'w') + + +base_path = Path(__file__).parent +file_path = (base_path / "Spectra_plot_fit_gui.ui").resolve() + +uiFile = file_path + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +def updateDelay(scale, time): + """ Hack fix for scalebar inaccuracy""" + QtCore.QTimer.singleShot(time, scale.updateBar) + +class MainWindow(TemplateBaseClass): + + def __init__(self): + pg.setConfigOption('imageAxisOrder', 'row-major') + super(TemplateBaseClass, self).__init__() + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + + # self.ui.fitFunc_comboBox.addItems(["Single Gaussian","Single Lorentzian", "Double Gaussian", "Multiple Gaussians"]) +# self.ui.actionExit.triggered.connect(self.close_application) + + ##setup ui signals + self.ui.importSpec_pushButton.clicked.connect(self.open_file) + self.ui.importBck_pushButton.clicked.connect(self.open_bck_file) + self.ui.importWLRef_pushButton.clicked.connect(self.open_wlref_file) + + self.ui.load_spectra_scan_pushButton.clicked.connect(self.open_spectra_scan_file) + self.ui.load_bck_file_pushButton.clicked.connect(self.open_spectra_bck_file) + self.ui.load_fitted_scan_pushButton.clicked.connect(self.open_fit_scan_file) + + self.ui.plot_pushButton.clicked.connect(self.plot) + self.ui.plot_fit_scan_pushButton.clicked.connect(self.plot_fit_scan) + self.ui.plot_raw_scan_pushButton.clicked.connect(self.plot_raw_scan) + self.ui.plot_intensity_sums_pushButton.clicked.connect(self.plot_intensity_sums) + + self.ui.fit_pushButton.clicked.connect(self.fit_and_plot) + self.ui.fit_scan_pushButton.clicked.connect(self.fit_and_plot_scan) + # self.ui.config_fit_params_pushButton.clicked.connect(self.configure_fit_params) + self.ui.clear_pushButton.clicked.connect(self.clear_plot) + self.ui.add_to_mem_pushButton.clicked.connect(self.add_trace_to_mem) + self.ui.export_single_figure_pushButton.clicked.connect(self.export_plot_window) + self.ui.export_scan_figure_pushButton.clicked.connect(self.export_window) + self.ui.analyze_spectra_fits_pushButton.clicked.connect(self.analyze_spectra_fits) + + self.ui.import_pkl_pushButton.clicked.connect(self.open_pkl_file) + self.ui.data_txt_pushButton.clicked.connect(self.pkl_data_to_txt) + self.ui.scan_params_txt_pushButton.clicked.connect(self.pkl_params_to_txt) + + self.ui.pkl_to_h5_pushButton.clicked.connect(self.pkl_to_h5) + + self.ui.tabWidget.currentChanged.connect(self.switch_overall_tab) + self.ui.fitFunc_comboBox.currentTextChanged.connect(self.switch_bounds_and_guess_tab) + self.ui.adjust_param_checkBox.stateChanged.connect(self.switch_adjust_param) + + self.ui.export_data_pushButton.clicked.connect(self.export_data) + self.ui.clear_export_data_pushButton.clicked.connect(self.clear_export_data) + + # for i in reversed(range(self.ui.bounds_groupBox.layout().count())): + # self.ui.bounds_groupBox.layout().itemAt(i).widget().deleteLater() + #self.ui.single_bounds_page.layout().addWidget(QtWidgets.QPushButton("test")) + + self.ui.plot = pg.PlotWidget() + self.ui.plot.setTitle(title="Spectrum Plot") + #self.ui.plot.show() + + self.file = None + self.bck_file = None + self.wlref_file = None + self.x = None + self.y = None + self.out = None # output file after fitting + + # Peak parameters if adjust params is selected + self.center_min = None + self.center_max = None + + #variables accounting for data received from FLIM analysis + self.opened_from_flim = False #switched to True in FLIM_plot when "analyze lifetime" clicked + self.sum_data_from_flim = [] + + # fit scan file variable set to None for analyze_spectra_fits + self.fit_scan_file = None + + #container for data to append to txt file + self.data_list = [] + + #for adding traces to memory for plotting/exporting all at once + self.x_mem = [] + self.y_mem = [] + self.best_fit_mem = [] + self.legend = [] + self.single_spec_fit_called = False + + self.show() + + """ Open Single Spectrum files """ + def open_file(self): + try: + self.single_spec_filename = QtWidgets.QFileDialog.getOpenFileName(self) + try: + try: + self.file = np.loadtxt(self.single_spec_filename[0], skiprows = 1, delimiter=" ") + except: + self.file = np.loadtxt(self.single_spec_filename[0], skiprows = 16, delimiter='\t') + except: + self.file = np.genfromtxt(self.single_spec_filename[0], skip_header=1, skip_footer=3, delimiter='\t') + self.opened_from_flim = False + except: + pass + + def open_bck_file(self): + try: + filename = QtWidgets.QFileDialog.getOpenFileName(self) + try: + try: + self.bck_file = np.loadtxt(filename[0], skiprows=1, delimiter=" ") + except: + self.bck_file = np.loadtxt(filename[0], skiprows = 16, delimiter='\t') + except: + self.bck_file = np.genfromtxt(filename[0], skip_header=1, skip_footer=3, delimiter='\t') + except Exception as e: + self.ui.result_textBrowser.append(str(e)) + pass + + def open_wlref_file(self): + try: + filename = QtWidgets.QFileDialog.getOpenFileName(self) + try: + try: + self.wlref_file = np.loadtxt(filename[0], skiprows=1, delimiter= " ") + except: + self.wlref_file = np.loadtxt(filename[0], skiprows = 16, delimiter='\t') + except: + self.wlref_file = np.genfromtxt(filename[0], skip_header=1, skip_footer=3, delimiter='\t') + except: + pass + + """Open Scan Files""" + def open_spectra_scan_file(self): + try: + filename = QtWidgets.QFileDialog.getOpenFileName(self, filter="Scan files (*.pkl *.h5)") + self.filename_for_viewer_launch = filename[0] + if ".pkl" in filename[0]: + self.spec_scan_file = pickle.load(open(filename[0], 'rb')) + if self.ui.launch_data_viewer_checkBox.isChecked(): + self.launch_h5_pkl_viewer() + self.scan_file_type = "pkl" + elif ".h5" in filename[0]: + self.spec_scan_file = h5py.File(filename[0], 'r') + if self.ui.launch_data_viewer_checkBox.isChecked(): + self.launch_h5_pkl_viewer() + self.scan_file_type = "h5" + self.get_data_params() + self.ui.result_textBrowser2.append("Done Loading - Spectra Scan File") + except Exception as e: + self.ui.result_textBrowser2.append(str(e)) + pass + + def open_spectra_bck_file(self): + try: + filename = QtWidgets.QFileDialog.getOpenFileName(self) + self.bck_file = np.loadtxt(filename[0])#, skiprows=1, delimiter=None) + self.ui.result_textBrowser2.append("Done Loading - Background File") + except Exception as e: + self.ui.result_textBrowser2.append(str(e)) + pass + + def open_fit_scan_file(self): + try: + filename = QtWidgets.QFileDialog.getOpenFileName(self) + with pg.BusyCursor(): + self.filename_for_viewer_launch = filename[0] + self.fit_scan_file = pickle.load(open(filename[0], 'rb')) + if self.ui.launch_data_viewer_checkBox.isChecked(): + self.launch_h5_pkl_viewer() # TODO Needs to implement reading the fit result datatype in PKL Viewer + self.ui.result_textBrowser2.append("Done Loading - Scan Fit File") + except Exception as e: + self.ui.result_textBrowser2.append(str(e)) + pass + + def open_pkl_file(self): + """ Open pkl file to convert to txt """ + try: + self.pkl_to_convert = QtWidgets.QFileDialog.getOpenFileNames(self) + files = self.pkl_to_convert[0] + for i in range(len(files)): + self.filename_for_viewer_launch = files[i] + if self.ui.launch_data_viewer_checkBox_2.isChecked(): + self.launch_h5_pkl_viewer() + except: + pass + + def launch_h5_pkl_viewer(self): + """ Launches H5/PKL viewer to give an insight into the data and its structure""" + viewer_window = h5_pkl_view.H5PklView(sys.argv) + viewer_window.settings['data_filename'] = self.filename_for_viewer_launch + + def analyze_spectra_fits(self): + """Analyze fits to the individual spectrum within a spectra scan fit file""" + if self.fit_scan_file is None: + self.open_fit_scan_file() + + #result_no = int(self.ui.result_spinBox.value()) + #self.matplotlibwidget = MatplotlibWidget(size=(12,8), dpi=300) + #self.fit_scan_file['result_'+str(0)].plot(fig=self.matplotlibwidget.getFigure().add_subplot(111)) + #self.matplotlibwidget.draw() + #self.matplotlibwidget.show() + analyze_window = Analyze(scan_fit_file=self.fit_scan_file) + analyze_window.run() + + def switch_overall_tab(self): + """ Enable/disable fit settings on right depending on current tab """ + if self.ui.tabWidget.currentIndex() == 0: + self.ui.fitting_settings_groupBox.setEnabled(True) + self.ui.fit_pushButton.setEnabled(True) + self.ui.fit_scan_pushButton.setEnabled(False) + self.ui.save_all_checkBox.setEnabled(False) + self.ui.scan_fit_settings_groupBox.setEnabled(False) + elif self.ui.tabWidget.currentIndex() == 1: + self.ui.fitting_settings_groupBox.setEnabled(False) + self.ui.fit_pushButton.setEnabled(False) + self.ui.fit_scan_pushButton.setEnabled(True) + self.ui.save_all_checkBox.setEnabled(True) + self.ui.scan_fit_settings_groupBox.setEnabled(True) + elif self.ui.tabWidget.currentIndex() == 2: + self.ui.fitting_settings_groupBox.setEnabled(False) + self.ui.fit_pushButton.setEnabled(False) + self.ui.fit_scan_pushButton.setEnabled(False) + self.ui.save_all_checkBox.setEnabled(False) + self.ui.scan_fit_settings_groupBox.setEnabled(False) + + """ Single spectrum functions """ + def switch_bounds_and_guess_tab(self): + """ Show the appropriate bounds and initial guess params based on fit function """ + fit_func = self.ui.fitFunc_comboBox.currentText() + if fit_func == "Single Gaussian" or fit_func == "Single Lorentzian": + self.ui.n_label.setEnabled(False) + self.ui.n_spinBox.setEnabled(False) + self.ui.bounds_stackedWidget.setCurrentIndex(0) + self.ui.guess_stackedWidget.setCurrentIndex(0) + self.ui.plot_components_checkBox.setEnabled(False) + self.ui.n_spinBox.setValue(1) + elif fit_func == "Double Gaussian": + self.ui.n_label.setEnabled(False) + self.ui.n_spinBox.setEnabled(False) + self.ui.bounds_stackedWidget.setCurrentIndex(1) + self.ui.guess_stackedWidget.setCurrentIndex(1) + self.ui.plot_components_checkBox.setEnabled(True) + self.ui.n_spinBox.setValue(2) + elif fit_func == "Triple Gaussian": + self.ui.n_label.setEnabled(False) + self.ui.n_spinBox.setEnabled(False) + self.ui.bounds_stackedWidget.setCurrentIndex(2) + self.ui.guess_stackedWidget.setCurrentIndex(2) + self.ui.plot_components_checkBox.setEnabled(True) + self.ui.n_spinBox.setValue(3) + + def switch_adjust_param(self): + """ Enable bounds and initial guess only when adjust parameters is checked """ + checked = self.ui.adjust_param_checkBox.isChecked() + self.ui.bounds_groupBox.setEnabled(checked) + self.ui.guess_groupBox.setEnabled(checked) + + def check_loaded_files(self): + """ + Check if 'subtract background' or 'white light correction' is checked + and if required files have been loaded. + """ + if self.ui.subtract_bck_radioButton.isChecked() and self.bck_file is None: + self.ui.result_textBrowser.setText("You need to load a background file.") + elif self.wlref_file is not None and self.ui.WLRef_checkBox.isChecked() == False: + self.ui.result_textBrowser.setText("You need to check the White Light Correction option!") + elif self.wlref_file is None and self.ui.WLRef_checkBox.isChecked(): + self.ui.result_textBrowser.setText("You need to load a White Light Ref file.") + else: + return True + + def plot(self): + try: + if self.opened_from_flim: + flim_data = self.sum_data_from_flim.T + interp = interpolate.interp1d(flim_data[:,0], flim_data[:,1]) + x_range = [flim_data[:,0][0], flim_data[:,0][-1]] + xnew = np.linspace(x_range[0], x_range[1], 100 ) + ynew = interp(xnew) + self.file = np.zeros((xnew.shape[0], 2)) + self.file[:,0] = xnew + self.file[:,1] = ynew + self.x = xnew + self.y = ynew + + elif self.file is None: #elif + self.ui.result_textBrowser.setText("You need to load a data file.") + else: + self.x = self.file[:,0] + self.y = self.file[:,1] + + self.check_loaded_files() + + if self.check_loaded_files() == True: #check the following conditions if all required files have been provided + if self.ui.subtract_bck_radioButton.isChecked() == True and self.ui.WLRef_checkBox.isChecked() == False: + bck_y = self.bck_file[:,1] + self.y = self.y - bck_y + elif self.ui.subtract_bck_radioButton.isChecked() == False and self.ui.WLRef_checkBox.isChecked() == True: + wlref_y = self.wlref_file[:,1] + self.y = (self.y)/wlref_y + + elif self.ui.subtract_bck_radioButton.isChecked() == True and self.ui.WLRef_checkBox.isChecked() == True: + bck_y = self.bck_file[:,1] + wlref_y = self.wlref_file[:,1] + self.y = (self.y-bck_y)/wlref_y + + + if self.ui.norm_checkBox.isChecked(): + self.normalize() + + self.check_eV_state() + self.ui.plot.show() + self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') + + except Exception as e: + self.ui.result_textBrowser.append(str(e)) + pass + self.ui.plot.setLabel('left', 'Intensity', units='a.u.') + if self.ui.fit_in_eV.isChecked(): + self.ui.plot.setLabel('bottom', 'Energy (eV)') + else: + self.ui.plot.setLabel('bottom', 'Wavelength (nm)') + + self.single_spec_fit_called = False + + def normalize(self): + self.y = (self.y) / np.amax(self.y) + + def check_eV_state(self): + if self.ui.fit_in_eV.isChecked(): + self.x = np.sort(1240/self.file[:,0]) + self.y = [self.y[i] for i in np.argsort(1240/self.file[:,0])] + else: + self.x = self.file[:,0] + self.y = self.file[:,1] + + def clear_plot(self): + self.ui.plot.clear() + self.ui.result_textBrowser.clear() + + def clear_check(self): + if self.ui.clear_checkBox.isChecked() == True: + return True + elif self.ui.clear_checkBox.isChecked() == False: + return False + + def fit_and_plot(self): + fit_func = self.ui.fitFunc_comboBox.currentText() + + try: + self.plot() + if self.opened_from_flim: + self.file = np.zeros((self.x.shape[0], 2)) + self.file[:,0] = self.x + self.file[:,1] = self.y + bck = lmfit.models.LinearModel(prefix='line_') + gmodel = GaussianModel(prefix='g1_') + pars = bck.make_params(intercept=self.y.min(), slope=0) + pars += gmodel.guess(self.y, x=self.x) + comp_model = gmodel + bck + self.result = comp_model.fit(self.y, pars, x=self.x, nan_policy='propagate') + self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') + self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') + self.ui.result_textBrowser.setText(self.result.fit_report()) + + + if self.ui.plot_without_bck_radioButton.isChecked(): #if plot w/o bck, create dummy bck_file + self.bck_file = np.zeros(shape=(self.file.shape[0], 2)) + self.bck_file[:,0] = self.file[:,0] + + # if self.ui.subtract_bck_radioButton.isChecked() == False: + # self.ui.result_textBrowser.setText("You need to check the subtract background option!") + if self.check_loaded_files is None: + pass + elif self.opened_from_flim: + pass + else: + self.check_eV_state() + if fit_func == "Single Gaussian": + single_gauss = Single_Gaussian(self.file, self.bck_file, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked()) + if self.ui.adjust_param_checkBox.isChecked(): + center1_min = self.ui.single_peakcenter1_min_spinBox.value() + center1_max = self.ui.single_peakcenter1_max_spinBox.value() + center1_guess = self.ui.single_peakcenter1_guess_spinBox.value() + sigma1_guess = self.ui.single_sigma1_guess_spinBox.value() + self.result = single_gauss.gaussian_model_w_lims(center1_guess, sigma1_guess, + [center1_min, center1_max]) + else: + self.result = single_gauss.gaussian_model() + #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') + self.plot() + self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') + self.ui.result_textBrowser.setText(self.result.fit_report()) + + elif fit_func == "Single Lorentzian": #and self.ui.subtract_bck_radioButton.isChecked() == True: + single_lorentzian = Single_Lorentzian(self.file, self.bck_file, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked()) + + if self.ui.adjust_param_checkBox.isChecked(): + center1_min = self.ui.single_peakcenter1_min_spinBox.value() + center1_max = self.ui.single_peakcenter1_max_spinBox.value() + center1_guess = self.ui.single_peakcenter1_guess_spinBox.value() + sigma1_guess = self.ui.single_sigma1_guess_spinBox.value() + self.result = single_lorentzian.lorentzian_model_w_lims(center1_guess, sigma1_guess, + [center1_min, center1_max]) + else: + self.result = single_lorentzian.lorentzian_model() + #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') + self.plot() + self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') + self.ui.result_textBrowser.setText(self.result.fit_report()) + + elif fit_func == "Double Gaussian": #and self.ui.subtract_bck_radioButton.isChecked() == True: + double_gauss = Double_Gaussian(self.file, self.bck_file, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked()) + if self.ui.adjust_param_checkBox.isChecked(): + center1_min = self.ui.double_peakcenter1_min_spinBox.value() + center1_max = self.ui.double_peakcenter1_max_spinBox.value() + center2_min = self.ui.double_peakcenter2_min_spinBox.value() + center2_max = self.ui.double_peakcenter2_max_spinBox.value() + center1_guess = self.ui.double_peakcenter1_guess_spinBox.value() + sigma1_guess = self.ui.double_sigma1_guess_spinBox.value() + center2_guess = self.ui.double_peakcenter2_guess_spinBox.value() + sigma2_guess = self.ui.double_sigma2_guess_spinBox.value() + + peak_pos = [center1_guess, center2_guess] + sigma = [sigma1_guess, sigma2_guess] + min_max_range = [ [center1_min, center1_max], [center2_min, center2_max] ] + self.result = double_gauss.gaussian_model_w_lims(peak_pos, sigma, min_max_range) + + else: + self.result = double_gauss.gaussian_model() + + #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') + self.plot() + self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') + if self.ui.plot_components_checkBox.isChecked(): + comps = self.result.eval_components(x=self.x) + self.ui.plot.plot(self.x, comps['g1_'], pen='b', clear=False) + self.ui.plot.plot(self.x, comps['g2_'], pen='g', clear=False) + + self.ui.result_textBrowser.setText(self.result.fit_report()) + + elif fit_func == "Triple Gaussian": #and self.ui.subtract_bck_radioButton.isChecked() == True: + #currently only works for triple gaussian (n=3) + multiple_gauss = Multi_Gaussian(self.file, self.bck_file, 3, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked()) + if self.ui.adjust_param_checkBox.isChecked(): + center1_min = self.ui.multi_peakcenter1_min_spinBox.value() + center1_max = self.ui.multi_peakcenter1_max_spinBox.value() + center2_min = self.ui.multi_peakcenter2_min_spinBox.value() + center2_max = self.ui.multi_peakcenter2_max_spinBox.value() + center3_min = self.ui.multi_peakcenter3_min_spinBox.value() + center3_max = self.ui.multi_peakcenter3_max_spinBox.value() + center1_guess = self.ui.multi_peakcenter1_guess_spinBox.value() + sigma1_guess = self.ui.multi_sigma1_guess_spinBox.value() + center2_guess = self.ui.multi_peakcenter2_guess_spinBox.value() + sigma2_guess = self.ui.multi_sigma2_guess_spinBox.value() + center3_guess = self.ui.multi_peakcenter3_guess_spinBox.value() + sigma3_guess = self.ui.multi_sigma3_guess_spinBox.value() +# num_gaussians = 3 + peak_pos = [center1_guess, center2_guess, center3_guess] + sigma = [sigma1_guess, sigma2_guess, sigma3_guess] + min_max_range = [ [center1_min, center1_max], [center2_min, center2_max], [center3_min, center3_max] ] + + self.result = multiple_gauss.gaussian_model_w_lims(peak_pos, sigma, min_max_range) + else: + self.result = multiple_gauss.gaussian_model() + + #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') + self.plot() + self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') + if self.ui.plot_components_checkBox.isChecked(): + comps = self.result.eval_components(x=self.x) + self.ui.plot.plot(self.x, comps['g1_'], pen='b', clear=False) + self.ui.plot.plot(self.x, comps['g2_'], pen='g', clear=False) + self.ui.plot.plot(self.x, comps['g3_'], pen='c', clear=False) + self.ui.result_textBrowser.setText(self.result.fit_report()) + + self.data_list.append(self.ui.result_textBrowser.toPlainText()) + self.single_spec_fit_called = True + + except Exception as e: + self.ui.result_textBrowser.append(str(e)) + + def export_window(self): + self.export_window = ExportImages() + self.export_window.export_fig_signal.connect(self.pub_ready_plot_export) + + def export_plot_window(self): + self.exportplotwindow = ExportPlotWindow() + self.exportplotwindow.export_fig_signal.connect(self.pub_ready_plot_export) + + def pub_ready_plot_export(self): + filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") + """Recylce params for plotting""" + plt.rc('xtick', labelsize = 20) + plt.rc('xtick.major', pad = 3) + plt.rc('ytick', labelsize = 20) + plt.rc('lines', lw = 1.5, markersize = 7.5) + plt.rc('legend', fontsize = 20) + plt.rc('axes', linewidth=3.5) + try: + try: + try: + data = self.spec_scan_file + except: + data = self.fit_scan_file + if self.export_window.ui.reverse_checkBox.isChecked(): + colormap = str(self.export_window.ui.cmap_comboBox.currentText())+"_r" + else: + colormap = str(self.export_window.ui.cmap_comboBox.currentText()) + if str(self.export_window.ui.dataChannel_comboBox.currentText()) == "Fitted": + param_selection = str(self.ui.comboBox.currentText()) + if param_selection == 'pk_pos': label = 'PL Peak Position (n.m.)' + elif param_selection == 'fwhm': label = 'PL FWHM (n.m.)' + cpm.plot_confocal(self.img, FLIM_adjust = False, stepsize = data['Scan Parameters']['X step size (um)'], cmap=colormap, cbar_label=label, + vmin=self.export_window.ui.vmin_spinBox.value(), vmax=self.export_window.ui.vmax_spinBox.value()) + elif str(self.export_window.ui.dataChannel_comboBox.currentText()) == "Raw": + cpm.plot_confocal(self.sums, FLIM_adjust = False, figsize=(10,10), stepsize = data['Scan Parameters']['X step size (um)'], cmap=colormap, + vmin=self.export_window.ui.vmin_spinBox.value(), vmax=self.export_window.ui.vmax_spinBox.value()) + plt.tick_params(direction='out', length=8, width=3.5) + plt.tight_layout() + plt.savefig(filename[0],bbox_inches='tight', dpi=300) + plt.close() + except: + if self.x_mem == []: + self.ui.result_textBrowser.setText("Add traces to memory first!") + else: + plt.figure(figsize=(8,6)) + plt.tick_params(direction='out', length=8, width=3.5) + for i in range(len(self.x_mem)): + plt.plot(self.x_mem[i], self.y_mem[i], label=str(self.legend[i])) + if self.single_spec_fit_called == True: + plt.plot(self.x_mem[i], self.best_fit_mem[i],'k') + + if self.ui.fit_in_eV.isChecked(): + plt.xlabel("Energy (eV)", fontsize=20, fontweight='bold') + else: + plt.xlabel("Wavelength (nm)", fontsize=20, fontweight='bold') + plt.ylabel("Intensity (a.u.)", fontsize=20, fontweight='bold') + plt.xlim([self.exportplotwindow.ui.lowerX_spinBox.value(),self.exportplotwindow.ui.upperX_spinBox.value()]) + plt.ylim([self.exportplotwindow.ui.lowerY_spinBox.value(),self.exportplotwindow.ui.upperY_doubleSpinBox.value()]) + plt.legend() + plt.tight_layout() + + plt.savefig(filename[0],bbox_inches='tight', dpi=300) + plt.close() + + except AttributeError: + self.ui.result_textBrowser.setText("Need to fit the data first!") + + def export_data(self): + """ Save fit params and srv calculations stored in data_list as .txt """ + folder = os.path.dirname(self.single_spec_filename[0]) + filename_ext = os.path.basename(self.single_spec_filename[0]) + filename = os.path.splitext(filename_ext)[0] #get filename without extension + + path = folder + "/" + filename + "_fit_results.txt" + if not os.path.exists(path): + file = open(path, "w+") + else: + file = open(path, "a+") + + for i in range(len(self.data_list)): + file.write(self.data_list[i] + "\n\n") + + self.data_list = [] + file.close() + + def clear_export_data(self): + self.data_list = [] + self.x_mem = [] + self.y_mem = [] + self.legend = [] + self.best_fit_mem = [] + + def add_trace_to_mem(self): + try: + self.x_mem.append(self.x) + self.y_mem.append(self.y) + if self.single_spec_fit_called == True: + self.best_fit_mem.append(self.result.best_fit) + self.legend.append(self.ui.lineEdit.text()) + except Exception as e: + print(e) + + + """ Scan spectra functions """ + def get_data_params(self): + data = self.spec_scan_file + if self.scan_file_type == "pkl": + self.intensities = data['Intensities'] + self.wavelengths = data['Wavelengths'] + # try: + self.x_scan_size = data['Scan Parameters']['X scan size (um)'] + self.y_scan_size = data['Scan Parameters']['Y scan size (um)'] + self.x_step_size = data['Scan Parameters']['X step size (um)'] + self.y_step_size = data['Scan Parameters']['Y step size (um)'] + # except: # TODO test and debug loading pkl file w/o scan parameters + # self.configure_scan_params() + # while not hasattr(self, "scan_params_entered"): + # pass + # self.x_scan_size = self.param_window.ui.x_scan_size_spinBox.value() + # self.y_scan_size = self.param_window.ui.y_scan_size_spinBox.value() + # self.x_step_size = self.param_window.ui.x_step_size_spinBox.value() + # self.y_step_size = self.param_window.ui.y_step_size_spinBox.value() + + else: #run this if scan file is h5 + self.x_scan_size = data['Scan Parameters'].attrs['X scan size (um)'] + self.y_scan_size = data['Scan Parameters'].attrs['Y scan size (um)'] + self.x_step_size = data['Scan Parameters'].attrs['X step size (um)'] + self.y_step_size = data['Scan Parameters'].attrs['Y step size (um)'] + self.intensities = data['Intensities'][()] #get dataset values + self.wavelengths = data['Wavelengths'][()] + + self.numb_x_pixels = int(np.ceil(self.x_scan_size/self.x_step_size)) + self.numb_y_pixels = int(np.ceil(self.y_scan_size/self.y_step_size)) + + """Open param window and get peak center range values and assign it to variables to use later""" + # def configure_scan_params(self): + # self.param_window = ParamWindow() + # self.param_window.peak_range.connect(self.peak_range) + + # def peak_range(self, peaks): + # self.center_min = peaks[0] + # self.center_max = peaks[1] + + def plot_fit_scan(self): + try: + if self.ui.use_raw_scan_settings.isChecked(): + num_x = self.numb_x_pixels + num_y =self.numb_y_pixels + else: + num_x = self.ui.num_x_spinBox.value() + num_y = self.ui.num_y_spinBox.value() + + numb_of_points = num_x * num_y #75*75 + + fwhm = np.zeros(shape=(numb_of_points,1)) + pk_pos = np.zeros(shape=(numb_of_points,1)) +# sigma = np.zeros(shape=(numb_of_points,1)) +# height = np.zeros(shape=(numb_of_points,1)) + + if type(self.fit_scan_file['result_0']) == dict: + for i in range(numb_of_points): + fwhm[i, 0] = 2.3548200*self.fit_scan_file['result_'+str(i)]['g1_sigma'] + pk_pos[i, 0] = self.fit_scan_file['result_'+str(i)]['g1_center'] +# sigma[i, 0] = self.fit_scan_file['result_'+str(i)]['g1_sigma'] +# height[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_height'] + + elif type(self.fit_scan_file['result_0']) == lmfit.model.ModelResult: + for i in range(numb_of_points): + fwhm[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_fwhm'] + pk_pos[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_center'] +# sigma[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_sigma'] +# height[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_height'] + + newshape = (num_x, num_y) + + param_selection = str(self.ui.comboBox.currentText()) + self.img = np.reshape(eval(param_selection), newshape) + + if num_y == 1: + x = np.linspace(0, self.x_scan_size, num_x) + self.graph_layout=pg.GraphicsLayoutWidget() + self.plot = self.graph_layout.addPlot(title="Line Scan") + self.plot.plot(x, self.img[:,0], pen="r") + self.graph_layout.show() + elif num_x == 1: + y = np.linspace(0, self.y_scan_size, num_y) + self.graph_layout=pg.GraphicsLayoutWidget() + self.plot = self.graph_layout.addPlot(title="Line Scan") + self.plot.plot(y, self.img[0,:], pen="r") + self.graph_layout.show() + + else: + self.fit_scan_viewbox = pg.ImageView() + if self.ui.use_raw_scan_settings.isChecked(): + self.fit_scan_viewbox.setImage(self.img, scale= + (self.x_step_size, + self.y_step_size)) + scale = pg.ScaleBar(size=2,suffix='um') + scale.setParentItem(self.fit_scan_viewbox.view) + scale.anchor((1, 1), (1, 1), offset=(-30, -30)) + self.fit_scan_viewbox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) + else: + self.fit_scan_viewbox.setImage(self.img) + + self.fit_scan_viewbox.view.invertY(False) + self.fit_scan_viewbox.show() + + except Exception as e: + self.ui.result_textBrowser2.append(str(e)) + pass + + def plot_raw_scan(self): + try: + # TODO test line scan plots + + intensities = self.intensities.T #this is only there because of how we are saving the data in the app + intensities = np.reshape(intensities, newshape=(2048,self.numb_x_pixels, self.numb_y_pixels)) + self.raw_scan_viewbox = pg.ImageView() + self.raw_scan_viewbox.setImage(intensities, scale= + (self.x_step_size, + self.y_step_size), xvals=self.wavelengths) + + #roi_plot = self.ui.raw_scan_viewBox.getRoiPlot() + #roi_plot.plot(data['Wavelengths'], intensities) + self.raw_scan_viewbox.view.invertY(False) + scale = pg.ScaleBar(size=2,suffix='um') + scale.setParentItem(self.raw_scan_viewbox.view) + scale.anchor((1, 1), (1, 1), offset=(-30, -30)) + self.raw_scan_viewbox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) + self.raw_scan_viewbox.show() + + except Exception as e: + self.ui.result_textBrowser2.append(str(e)) + + def plot_intensity_sums(self): + try: + # TODO test line scan plots + + #intensities = np.reshape(intensities, newshape=(2048, numb_pixels_X*numb_pixels_Y)) + + sums = np.sum(self.intensities, axis=-1) + self.sums = np.reshape(sums, newshape=(self.numb_x_pixels, self.numb_y_pixels)) + self.intensity_sums_viewBox = pg.ImageView() + + self.intensity_sums_viewBox.setImage(self.sums, scale= + (self.x_step_size, + self.y_step_size)) + self.intensity_sums_viewBox.view.invertY(False) + + scale = pg.ScaleBar(size=2,suffix='um') + scale.setParentItem(self.intensity_sums_viewBox.view) + scale.anchor((1, 1), (1, 1), offset=(-30, -30)) + self.intensity_sums_viewBox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) + self.intensity_sums_viewBox.show() + + except Exception as e: + self.ui.result_textBrowser2.append(str(e)) + + + def fit_and_plot_scan(self): +# self.ui.result_textBrowser.append("Starting Scan Fitting") + print("Starting Scan Fitting") + print("Using Single Gaussian to Fit\nThis is the only fitting functions implemented") + + with pg.BusyCursor(): + try: + """Define starting and stopping wavelength values here""" + start_nm = int(self.ui.start_nm_spinBox.value()) + stop_nm = int(self.ui.stop_nm_spinBox.value()) + + if self.bck_file is None: + print("Load Background file!") + ref = self.bck_file + index = (ref[:,0]>start_nm) & (ref[:,0]start_nm) & (x + + MainWindow + + + + 0 + 0 + 2115 + 1483 + + + + + 0 + 0 + + + + Spectral Analysis + + + + + + + + + + 12 + + + + Fit Settings + + + + + + false + + + + 10 + + + + n: + + + + + + + false + + + + 10 + + + + 1 + + + 1 + + + + + + + false + + + + 10 + + + + Plot components (>1 Gaussian) + + + true + + + + + + + false + + + + 10 + + + + Bounds + + + + + + 0 + + + + + + + + + + + + + + max + + + + + + + min + + + + + + + 9999.000000000000000 + + + 780.000000000000000 + + + + + + + 9999.000000000000000 + + + 760.000000000000000 + + + + + + + Peak Center 1 (nm) + + + + + + + + + + + + + + + + + + min + + + + + + + 9999.000000000000000 + + + 760.000000000000000 + + + + + + + 9999.000000000000000 + + + 820.000000000000000 + + + + + + + 9999.000000000000000 + + + 795.000000000000000 + + + + + + + Peak Center 2 (nm) + + + + + + + 9999.000000000000000 + + + 775.000000000000000 + + + + + + + max + + + + + + + Peak Center 1 (nm) + + + + + + + + + + + 9999.000000000000000 + + + 760.000000000000000 + + + + + + + 9999.000000000000000 + + + 820.000000000000000 + + + + + + + 9999.000000000000000 + + + 775.000000000000000 + + + + + + + 9999.000000000000000 + + + 755.000000000000000 + + + + + + + 9999.000000000000000 + + + 740.000000000000000 + + + + + + + Peak Center 1 (nm) + + + + + + + max + + + + + + + Peak Center 2 (nm) + + + + + + + Peak Center 3 (nm) + + + + + + + 9999.000000000000000 + + + 795.000000000000000 + + + + + + + min + + + + + + + + + + + + + + + + + + + + + + 10 + + + + Adjust Parameters + + + + + + + + 10 + + + + + Single Gaussian + + + + + Single Lorentzian + + + + + Double Gaussian + + + + + Triple Gaussian + + + + + + + + false + + + + 10 + + + + Initial Guess + + + + + + 0 + + + + + + + Sigma 1 (nm) + + + + + + + Peak Center 1 (nm) + + + + + + + 9999.000000000000000 + + + 770.000000000000000 + + + + + + + 15.000000000000000 + + + + + + + + + + + 9999.000000000000000 + + + 767.000000000000000 + + + + + + + 15.000000000000000 + + + + + + + Peak Center 1 (nm) + + + + + + + 9999.000000000000000 + + + 800.000000000000000 + + + + + + + Sigma 1 (nm) + + + + + + + Peak Center 2 (nm) + + + + + + + Sigma 2 (nm) + + + + + + + 15.000000000000000 + + + + + + + + + + + Peak Center 2 (nm) + + + + + + + Sigma 2 (nm) + + + + + + + Peak Center 3 (nm) + + + + + + + Sigma 3 (nm) + + + + + + + Peak Center 1 (nm) + + + + + + + Sigma 1 (nm) + + + + + + + 9999.000000000000000 + + + 800.000000000000000 + + + + + + + 15.000000000000000 + + + + + + + 9999.000000000000000 + + + 767.000000000000000 + + + + + + + 15.000000000000000 + + + + + + + 9999.000000000000000 + + + 750.000000000000000 + + + + + + + 15.000000000000000 + + + + + + + + + + + + + + + + + + 10 + + + + Fit/Plot in eV + + + true + + + + + + + + 10 + + + + Fit Single Spectrum + + + + + + + false + + + Save Entire Fit Model (File will be large and will take longer) + + + + + + + false + + + + 10 + + + + Fit Entire Scan + + + + + + + false + + + + 12 + + + + Scan Fit Settings + + + + + + + 10 + + + + Stop at (nm): + + + + + + + + 10 + + + + 300 + + + 1100 + + + 600 + + + + + + + + 10 + + + + Start at (nm): + + + + + + + + 10 + + + + Qt::ImhDigitsOnly + + + 300 + + + 1100 + + + 900 + + + + + + + + + + + + + 15 + + + + 0 + + + false + + + + Single Spectrum + + + + + + + 0 + 0 + + + + + 350 + 16777215 + + + + + 12 + + + + Load Settings + + + + + + + 10 + + + + Spectrum File + + + + + + + + 10 + + + + Export Figure + + + + + + + + 10 + + + + Clear Export Memory + + + + + + + + 10 + + + + Correct for White Light + + + + + + + + 10 + + + + White Light Ref File + + + + + + + + 10 + + + + Enter Legend Here... + + + + + + + + 10 + + + + For Single Spectrum + + + + + + + + 10 + + + + Subtract Background + + + true + + + + + + + + 10 + + + + Export Fit Data + + + + + + + + 10 + + + + Add Trace to Memory + + + + + + + + 10 + + + + Plot without Background + + + + + + + + 10 + 50 + false + + + + Plot + + + + + + + + 10 + + + + Background File + + + + + + + + 10 + + + + Clear Plots Everytime + + + true + + + + + + + + 10 + + + + Normalize + + + + + + + + 10 + false + + + + Clear Plot + + + + + + + Export Settings + + + + + + + For Data + + + + + + + For Figure + + + + + + + Plot Control + + + + + + + + + + + 10 + + + + + + + + + Scan Spectra Data + + + + + + + + + 210 + 16777215 + + + + + 12 + + + + Load Settings + + + + + + + 12 + + + + Spectra Scan +File + + + + + + + + 12 + + + + Background +File + + + + + + + + 12 + + + + Load Only + Fit File + + + + + + + + 12 + + + + For Scan Data + + + + + + + + + + + 12 + + + + + + + + + 12 + + + + Export Fitted +Scan + + + + + + + + 12 + + + + Launch Data Viewer + + + + + + + + 12 + + + + After Fitting Scan Data + + + + + + + + 12 + + + + Intensity Sums + + + + + + + + 12 + + + + For Raw Scan Data + + + + + + + + 12 + + + + Plot + + + + + + + + 12 + + + + Plot + + + + + + + + 12 + + + + + pk_pos + + + + + fwhm + + + + + + + + + 12 + + + + Plot + + + + + + + + 12 + + + + Export Settings + + + + + + + + 12 + + + + Analyze Spectra Fits + + + + + + + + 12 + + + + For Fit Scale + + + + + + + + 12 + + + + Use Raw Scan Settings + + + true + + + + + + + + 12 + + + + # X points + + + + + + + + 12 + + + + # Y points + + + + + + + 2000 + + + 100 + + + + + + + 2000 + + + 100 + + + + + + + + + + .pkl conversion + + + + + 10 + 70 + 351 + 251 + + + + txt + + + + + + + 12 + + + + Data to .txt + + + + + + + + 12 + + + + Scan params to .txt + + + + + + + + + 390 + 70 + 321 + 251 + + + + h5 + + + + + 50 + 80 + 221 + 41 + + + + + 12 + + + + .pkl to .h5 + + + + + + + 20 + 20 + 323 + 40 + + + + + 12 + + + + Import .pkl file + + + + + + 390 + 20 + 327 + 43 + + + + + 12 + + + + Launch Data Viewer + + + + + + + + + + + 0 + 0 + 2115 + 38 + + + + + + + + diff --git a/src/main/python/Spectrum_analysis/__init__.py b/src/main/python/Spectrum_analysis/__init__.py new file mode 100644 index 0000000..b4011af --- /dev/null +++ b/src/main/python/Spectrum_analysis/__init__.py @@ -0,0 +1 @@ +from __future__ import absolute_import, division, print_function \ No newline at end of file diff --git a/src/main/python/Spectrum_analysis/analyze_fit_results.ui b/src/main/python/Spectrum_analysis/analyze_fit_results.ui new file mode 100644 index 0000000..7669c5a --- /dev/null +++ b/src/main/python/Spectrum_analysis/analyze_fit_results.ui @@ -0,0 +1,91 @@ + + + Form + + + + 0 + 0 + 664 + 136 + + + + Analze Fit Results + + + + + + + + QFrame::StyledPanel + + + QFrame::Raised + + + + + + + 12 + + + + Check! + + + + + + + + 12 + + + + 1000000000 + + + + + + + + 12 + + + + Result number: + + + Qt::AlignCenter + + + + + + + + 15 + + + + Analyze Fit Results + + + Qt::AlignCenter + + + + + + + + + + + + + diff --git a/src/main/python/Spectrum_analysis/pyqtgraph_MATPLOTLIBWIDGET.py b/src/main/python/Spectrum_analysis/pyqtgraph_MATPLOTLIBWIDGET.py new file mode 100644 index 0000000..ba2f59c --- /dev/null +++ b/src/main/python/Spectrum_analysis/pyqtgraph_MATPLOTLIBWIDGET.py @@ -0,0 +1,56 @@ +# -*- coding: utf-8 -*- +""" +Created on Mon Sep 2 13:02:50 2019 + +@author: Sarthak +""" + +from pyqtgraph.Qt import QtGui, QtCore, USE_PYSIDE, USE_PYQT5 +import matplotlib + +#if not USE_PYQT5: +# if USE_PYSIDE: +# matplotlib.rcParams['backend.qt4']='PySide' +# +# from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas +# from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar +#else: +from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas +from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar + +from matplotlib.figure import Figure + +if matplotlib.get_backend() is not 'Qt5Agg': + matplotlib.use('Qt5Agg') + +class MatplotlibWidget(QtGui.QWidget): + """ + Implements a Matplotlib figure inside a QWidget. + Use getFigure() and redraw() to interact with matplotlib. + + Example:: + + mw = MatplotlibWidget() + subplot = mw.getFigure().add_subplot(111) + subplot.plot(x,y) + mw.draw() + """ + + def __init__(self, size=(5.0, 4.0), dpi=100): + QtGui.QWidget.__init__(self) + self.fig = Figure(size, dpi=dpi) + self.canvas = FigureCanvas(self.fig) + self.canvas.setParent(self) + self.toolbar = NavigationToolbar(self.canvas, self) + + self.vbox = QtGui.QVBoxLayout() + self.vbox.addWidget(self.toolbar) + self.vbox.addWidget(self.canvas) + + self.setLayout(self.vbox) + + def getFigure(self): + return self.fig + + def draw(self): + self.canvas.draw() \ No newline at end of file diff --git a/src/main/python/Spectrum_analysis/scan_params_input.ui b/src/main/python/Spectrum_analysis/scan_params_input.ui new file mode 100644 index 0000000..4df8d40 --- /dev/null +++ b/src/main/python/Spectrum_analysis/scan_params_input.ui @@ -0,0 +1,68 @@ + + + Form + + + + 0 + 0 + 542 + 211 + + + + Form + + + + + + X scan size + + + + + + + + + + Y scan size + + + + + + + + + + X step size + + + + + + + + + + Y step size + + + + + + + + + + Done + + + + + + + + diff --git a/src/main/python/Table/Table_widget.py b/src/main/python/Table/Table_widget.py new file mode 100644 index 0000000..4c7b447 --- /dev/null +++ b/src/main/python/Table/Table_widget.py @@ -0,0 +1,145 @@ +# -*- coding: utf-8 -*- +""" +Created on Mon Sep 2 17:04:49 2019 + +@author: Sarthak +""" + +from pathlib import Path +import pyqtgraph as pg +from pyqtgraph.python2_3 import asUnicode +from pyqtgraph.Qt import QtCore, QtGui + + +pg.mkQApp() +pg.setConfigOption('background', 'w') + + +base_path = Path(__file__).parent +file_path = (base_path / "Table_widget_gui.ui").resolve() + +uiFile = file_path + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +class MainWindow(TemplateBaseClass): + + def __init__(self): + super(TemplateBaseClass, self).__init__() + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + + self.clear() + + self.ui.clear_pushButton.clicked.connect(self.clear) + self.ui.add_row_pushButton.clicked.connect(self.add_row) + self.ui.add_column_pushButton.clicked.connect(self.add_column) + + """Saving and Copying --- implemented from pyqtgraph TableWidget""" + self.contextMenu = QtGui.QMenu() + self.contextMenu.addAction('Copy Selection').triggered.connect(self.copySel) + self.contextMenu.addAction('Copy All').triggered.connect(self.copyAll) + self.contextMenu.addAction('Save Selection').triggered.connect(self.saveSel) + self.contextMenu.addAction('Save All').triggered.connect(self.saveAll) + + self.show() + + def clear(self): + self.ui.tableWidget.clear() + self.verticalHeadersSet = False + self.horizontalHeadersSet = False + + def add_row(self): + row_position = self.ui.tableWidget.rowCount() + self.ui.tableWidget.insertRow(row_position) + + def add_column(self): + column_position = self.ui.tableWidget.columnCount() + self.ui.tableWidget.insertColumn(column_position) + + def save_table(self):# Needs to be implemented + print(self.ui.tableWidget.currentItem().text()) + + def serialize(self, useSelection=False): + """Convert entire table (or just selected area) into tab-separated text values""" + if useSelection: + selection = self.ui.tableWidget.selectedRanges()[0] + rows = list(range(selection.topRow(), + selection.bottomRow() + 1)) + columns = list(range(selection.leftColumn(), + selection.rightColumn() + 1)) + else: + rows = list(range(self.ui.tableWidget.rowCount())) + columns = list(range(self.ui.tableWidget.columnCount())) + + data = [] + if self.horizontalHeadersSet: + row = [] + if self.verticalHeadersSet: + row.append(asUnicode('')) + + for c in columns: + row.append(asUnicode(self.ui.tableWidget.horizontalHeaderItem(c).text())) + data.append(row) + + for r in rows: + row = [] + if self.verticalHeadersSet: + row.append(asUnicode(self.ui.tableWidget.verticalHeaderItem(r).text())) + for c in columns: + item = self.ui.tableWidget.item(r, c) + if item is not None: + row.append(asUnicode(item.text())) + else: + row.append(asUnicode('')) + data.append(row) + + s = '' + for row in data: + s += ('\t'.join(row) + '\n') + return s + + + def copySel(self): + """Copy selected data to clipboard.""" + QtGui.QApplication.clipboard().setText(self.serialize(useSelection=True)) + + def copyAll(self): + """Copy all data to clipboard.""" + QtGui.QApplication.clipboard().setText(self.serialize(useSelection=False)) + + + def saveSel(self): + """Save selected data to file.""" + self.save(self.serialize(useSelection=True)) + + + def saveAll(self): + """Save all data to file.""" + self.save(self.serialize(useSelection=False)) + + + def save(self, data): + fileName = QtGui.QFileDialog.getSaveFileName(self, "Save As..", "", "Tab-separated values (*.tsv)") + if fileName == '': + return + open(fileName[0], 'w').write(data) + + def contextMenuEvent(self, ev): + self.contextMenu.popup(ev.globalPos()) + + def keyPressEvent(self, ev): + if ev.key() == QtCore.Qt.Key_C and ev.modifiers() == QtCore.Qt.ControlModifier: + ev.accept() + self.copySel() +# else: +# QtGui.QTableWidget.keyPressEvent(self, ev) +"""Run the Main Window""" +def run(): + win = MainWindow() + QtGui.QApplication.instance().exec_() + return win + +#run() \ No newline at end of file diff --git a/src/main/python/Table/Table_widget_gui.ui b/src/main/python/Table/Table_widget_gui.ui new file mode 100644 index 0000000..d5fae7e --- /dev/null +++ b/src/main/python/Table/Table_widget_gui.ui @@ -0,0 +1,70 @@ + + + Form + + + + 0 + 0 + 658 + 438 + + + + TableWidget + + + + + + Add Row + + + + + + + Add Column + + + + + + + Clear + + + + + + + 12 + + + 6 + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/main/python/Table/__init__.py b/src/main/python/Table/__init__.py new file mode 100644 index 0000000..1a21e72 --- /dev/null +++ b/src/main/python/Table/__init__.py @@ -0,0 +1,7 @@ +# -*- coding: utf-8 -*- +""" +Created on Mon Sep 2 17:52:35 2019 + +@author: Sarthak +""" + diff --git a/src/main/python/UV_Vis_analysis/uv_vis_analysis.py b/src/main/python/UV_Vis_analysis/uv_vis_analysis.py new file mode 100644 index 0000000..6302a40 --- /dev/null +++ b/src/main/python/UV_Vis_analysis/uv_vis_analysis.py @@ -0,0 +1,188 @@ +# system imports +from pathlib import Path +import os.path +import pyqtgraph as pg +from pyqtgraph import exporters +from pyqtgraph.Qt import QtCore, QtGui, QtWidgets +import matplotlib.pyplot as plt + +import numpy as np +import time + +# local modules + +pg.mkQApp() +pg.setConfigOption('background', 'w') + +base_path = Path(__file__).parent +file_path = (base_path / "uv_vis_analysis_gui.ui").resolve() + +uiFile = file_path + +WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +"""params for plotting""" +plt.rc('xtick', labelsize = 20) +plt.rc('xtick.major', pad = 3) +plt.rc('ytick', labelsize = 20) +plt.rc('lines', lw = 1.5, markersize = 7.5) +plt.rc('legend', fontsize = 20) +plt.rc('axes', linewidth = 3.5) + +class MainWindow(TemplateBaseClass): + + def __init__(self): + super(TemplateBaseClass, self).__init__() + + # Create the main window + self.ui = WindowTemplate() + self.ui.setupUi(self) + + #setup uv vis plot + self.absorbance_plot_layout = pg.GraphicsLayoutWidget() + self.ui.absorbance_plot_container.layout().addWidget(self.absorbance_plot_layout) + self.absorbance_plot = self.absorbance_plot_layout.addPlot(title="Wavelengths vs. Absorbance") + self.absorbance_plot.setLabel('bottom', 'Wavelength', unit='nm') + self.absorbance_plot.setLabel('left', 'Absorbance', unit='a.u.') + + #setup correction region for uv vis + self.correction_region = pg.LinearRegionItem() + self.correction_region_min = 600 + self.correction_region_max = 900 + self.correction_region.setRegion((self.correction_region_min, self.correction_region_max)) + + #setup uv vis ui signals + self.ui.correct_for_scattering_checkBox.stateChanged.connect(self.scattering_checkBox_state) + self.scatter_corrected = False + self.ui.actionLoad_data.triggered.connect(self.open_data_file) + self.ui.plot_absorbance_pushButton.clicked.connect(self.plot_absorbance) + self.ui.clear_uvvis_pushButton.clicked.connect(self.clear_uvvis) + self.ui.export_uv_vis_pushButton.clicked.connect(self.export_uv_vis) + self.correction_region.sigRegionChanged.connect(self.update_correction_region) + + #setup tauc plot + self.tauc_plot_layout = pg.GraphicsLayoutWidget() + self.ui.tauc_plot_container.layout().addWidget(self.tauc_plot_layout) + self.tauc_plot = self.tauc_plot_layout.addPlot(title="Tauc plot fit") + self.tauc_plot.setLabel('bottom', 'hv', unit='ev') + y_label = '(ahv)' + chr(0x00B2) #char is superscripted 2 + self.tauc_plot.setLabel('left', y_label) + + #setup tauc ui signals + self.ui.plot_tauc_pushButton.clicked.connect(self.plot_tauc) + self.ui.clear_tauc_pushButton.clicked.connect(self.clear_tauc) + self.ui.export_tauc_pushButton.clicked.connect(self.export_tauc) + + self.show() + + def open_data_file(self): + try: + self.filename = QtWidgets.QFileDialog.getOpenFileName(self) + self.data = np.loadtxt(self.filename[0], delimiter = ',', skiprows = 2) + self.Wavelength = self.data[:,0] # in nm + self.Absorbance = self.data[:,1] + except Exception as err: + print(format(err)) + + def update_correction_region(self): + """ Update correction region variables from region """ + self.correction_region_min, self.correction_region_max = self.correction_region.getRegion() + + def scattering_checkBox_state(self): + if self.ui.correct_for_scattering_checkBox.isChecked(): + self.scatter_corrected = True + self.ui.mean_radioButton.setEnabled(True) + self.ui.fourth_orderpoly_radioButton.setEnabled(True) + else: + self.scatter_corrected = False + self.ui.mean_radioButton.setEnabled(False) + self.ui.fourth_orderpoly_radioButton.setEnabled(False) + + def plot_absorbance(self): + try: + self.plotted_absorbance = self.Absorbance #by default set to original absorbance data + if self.scatter_corrected == True: + if self.ui.fourth_orderpoly_radioButton.isChecked(): + p = (np.polyfit(self.Wavelength[(self.Wavelength>self.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelength self.hv_min) & (self.hv < self.hv_max) + model = np.polyfit(self.hv[self.index], self.Alpha_hv[self.index], 1) + self.Alpha_hv_fit = self.hv * model[0] + model[1] #This is the linear fit + self.tauc_plot.plot(self.hv, self.Alpha_hv, pen='r') + self.tauc_plot.plot(self.hv, self.Alpha_hv_fit, pen='k') + self.tauc_plot.setXRange(1,2) + self.tauc_plot.setYRange(0, np.max(self.Alpha_hv[self.index]) + 1) + + self.Eg = - model[1]/model[0] + self.ui.bandgap_label.setText(str(self.Eg)) + except: + pass + + def clear_tauc(self): + self.tauc_plot.clear() + + def export_uv_vis(self): + """ Export publication ready uv vis figure """ + try: + filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") + plt.figure(figsize=(8,6)) + plt.tick_params(direction='out', length=8, width=3.5) + plt.plot(self.Wavelength, self.plotted_absorbance, linewidth = 3, color = 'r') + if self.scatter_corrected: + plt.xlim(self.correction_region_min, self.correction_region_max) + plt.ylim(0, np.max(self.plotted_absorbance[(self.Wavelength>self.correction_region_min)]) +0.5) + else: + plt.xlim(self.correction_region_min, self.correction_region_max) + plt.ylim(0, np.max(self.plotted_absorbance[(self.Wavelength>self.correction_region_min)] +0.5)) + plt.xlabel('Wavelength (nm)', fontsize = 20) + plt.ylabel('Absorbance (a.u.)', fontsize = 20) + plt.savefig(filename[0],bbox_inches='tight', dpi=300) + plt.close() + except: + pass + + def export_tauc(self): + """ Export publication ready tauc figure""" + try: + filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") + plt.figure(figsize=(8,6)) + plt.tick_params(direction='out', length=8, width=3.5) + plt.plot(self.hv, self.Alpha_hv, linewidth = 3, color = 'r') + plt.plot(self.hv, self.Alpha_hv_fit, linewidth = 2, color = 'black') + plt.xlim(1,2) + plt.ylim(0, np.max(self.Alpha_hv[self.index]) + 1) + plt.xlabel('h$\\nu$ (eV)', fontsize = 20) + plt.ylabel('($\\alpha$h$\\nu$)$^2$', fontsize = 20) + #plt.title(Plot_title, fontsize = 20) + + plt.text(1.2, 1.2, r'E$_{g}$ = %.2f eV'%self.Eg, fontsize = 15) + plt.tight_layout() + plt.savefig(filename[0],bbox_inches='tight', dpi=300) + plt.close() + except: + pass + +"""Run the Main Window""" +def run(): + win = MainWindow() + QtGui.QApplication.instance().exec_() + return win \ No newline at end of file diff --git a/src/main/python/UV_Vis_analysis/uv_vis_analysis_gui.ui b/src/main/python/UV_Vis_analysis/uv_vis_analysis_gui.ui new file mode 100644 index 0000000..85bd935 --- /dev/null +++ b/src/main/python/UV_Vis_analysis/uv_vis_analysis_gui.ui @@ -0,0 +1,268 @@ + + + MainWindow + + + + 0 + 0 + 742 + 924 + + + + UV-Vis Analysis + + + + + + + UV-Vis plot + + + + + + + + Scattering Correction + + + + + + + Plot + + + + + + + false + + + 4th Order Polynomial + + + true + + + + + + + Clear + + + + + + + Correct for scattering + + + + + + + false + + + Simple Mean + + + + + + + + + + 0 + 0 + + + + + + + + + Export UV-Vis plot + + + + + + + + + + Tauc plot + + + true + + + false + + + + + + + + hv min (ev) + + + + + + + + 180 + 0 + + + + -9999999.000000000000000 + + + 9999999.000000000000000 + + + 0.010000000000000 + + + 1.500000000000000 + + + + + + + + 180 + 0 + + + + -9999999.000000000000000 + + + 9999999.000000000000000 + + + 0.010000000000000 + + + 1.800000000000000 + + + + + + + hv max (ev) + + + + + + + Plot + + + + + + + Clear + + + + + + + + + + 0 + 0 + + + + + + + + + + + Bandgap (ev): + + + + + + + 0 + + + + + + + + 16777215 + 16777215 + + + + Export tauc plot + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 742 + 21 + + + + + File + + + + + + + + + Load data + + + + + + diff --git a/src/main/python/__init__.py b/src/main/python/__init__.py new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/src/main/python/__init__.py @@ -0,0 +1 @@ + diff --git a/src/main/python/main.py b/src/main/python/main.py new file mode 100644 index 0000000..63b241d --- /dev/null +++ b/src/main/python/main.py @@ -0,0 +1,111 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Apr 10 14:41:08 2019 + +@author: Sarthak +""" + +# system imports +import sys +from pathlib import Path + +import pyqtgraph as pg +from pyqtgraph.Qt import QtGui, QtCore + +from fbs_runtime.application_context.PyQt5 import ApplicationContext, cached_property +from PyQt5.QtWidgets import QMainWindow +from PyQt5 import uic + +from Lifetime_analysis import Lifetime_plot_fit +from Spectrum_analysis import Spectra_plot_fit +from FLIM_analysis import FLIM_plot +from UV_Vis_analysis import uv_vis_analysis +from PLQE_analysis import plqe_analysis +from H5_Pkl import h5_pkl_view, h5_view_and_plot +from Image_analysis import Image_analysis +from Table import Table_widget +from Export_Windows import Multi_Trace_Exporter + +class AppContext(ApplicationContext): + def run(self): + self.main_window.show() + return self.app.exec_() + + def get_main_ui(self): + qtCreatorFile = self.get_resource("DataBrowser_GUI.ui") + return qtCreatorFile + + @cached_property + def main_window(self): + return MainWindow(self.get_main_ui()) + +# pg.mkQApp() +# #pg.setConfigOption('background', 'w') + +# base_path = Path(__file__).parent +# file_path = (base_path / "DataBrowser_GUI.ui").resolve() + +# uiFile = file_path + +# WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) + +class MainWindow(QMainWindow): + + def __init__(self, uiFile): + super(MainWindow, self).__init__() + + # Create the main window + self.ui = uic.loadUi(uiFile, self) + # self.ui.setupUi(self) + self.ui.select_comboBox.addItems(["Lifetime Analysis", "Spectrum Analysis", "FLIM Analysis", + "UV-Vis Analysis", "PLQE Analysis", "H5 View/Plot", "H5/PKL Viewer", "Image Analysis", "Table View", + "Mulit-Trace Exporter"]) + self.ui.load_pushButton.clicked.connect(self.load_app) + + self.show() + + + def load_app(self): + + analysis_software = self.ui.select_comboBox.currentText() + + if analysis_software == "Lifetime Analysis": + self.lifetime_window = Lifetime_plot_fit.MainWindow() + self.lifetime_window.show() + elif analysis_software == "Spectrum Analysis": + self.spectrum_window = Spectra_plot_fit.MainWindow() + self.spectrum_window.show() + elif analysis_software == "FLIM Analysis": + self.flim_window = FLIM_plot.MainWindow() + self.flim_window.show() + elif analysis_software == "UV-Vis Analysis": + self.uv_vis_window = uv_vis_analysis.MainWindow() + self.uv_vis_window.show() + elif analysis_software == "PLQE Analysis": + self.plqe_window = plqe_analysis.MainWindow() + self.plqe_window.show() + elif analysis_software == "H5 View/Plot": + app = h5_view_and_plot.H5ViewPlot(sys.argv) + #sys.exit(app.exec_()) + elif analysis_software == "H5/PKL Viewer": + app = h5_pkl_view.H5PklView(sys.argv) + #sys.exit(app.exec_()) + elif analysis_software == "Image Analysis": + self.image_window = Image_analysis.MainWindow() + self.image_window.show() + elif analysis_software == "Table View": + self.table_widget = Table_widget.MainWindow() + self.table_widget.show() + elif analysis_software == "Mulit-Trace Exporter": + self.trace_exporter = Multi_Trace_Exporter.MainWindow() + self.trace_exporter.show() + + +def run(): + appctxt = AppContext() # 1. Instantiate ApplicationContext + appctxt.app.setStyle("Fusion") + exit_code = appctxt.run() + sys.exit(exit_code) # 2. Invoke appctxt.app.exec_() + +if __name__ == '__main__': + run() \ No newline at end of file diff --git a/src/main/python/main_0.py b/src/main/python/main_0.py new file mode 100644 index 0000000..4038d57 --- /dev/null +++ b/src/main/python/main_0.py @@ -0,0 +1,15 @@ +from fbs_runtime.application_context.PyQt5 import ApplicationContext +from PyQt5.QtWidgets import QMainWindow + +import sys + +class AppContext(ApplicationContext): + pass + +if __name__ == '__main__': + appctxt = AppContext() # 1. Instantiate ApplicationContext + window = QMainWindow() + window.resize(250, 150) + window.show() + exit_code = appctxt.app.exec_() # 2. Invoke appctxt.app.exec_() + sys.exit(exit_code) \ No newline at end of file diff --git a/src/main/resources/base/DataBrowser_GUI.ui b/src/main/resources/base/DataBrowser_GUI.ui new file mode 100644 index 0000000..054b4ef --- /dev/null +++ b/src/main/resources/base/DataBrowser_GUI.ui @@ -0,0 +1,97 @@ + + + MainWindow + + + + 0 + 0 + 435 + 221 + + + + GLabViz - DataBrowser + + + + + + + + 30 + 75 + true + + + + GLabViz + + + Qt::AlignCenter + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + 15 + + + + Analysis Tool : + + + + + + + + 15 + + + + + + + + + 15 + + + + Load + + + + + + + + + 0 + 0 + 435 + 21 + + + + + + + + From 44098293afb429e355f473f6ff7172deaab9a5ec Mon Sep 17 00:00:00 2001 From: Sarthak Jariwala Date: Thu, 19 Nov 2020 16:42:29 -0800 Subject: [PATCH 04/10] Picoharp parser now works properly on mac --- .../Lifetime_analysis/picoharp_phd.py | 294 +++++++++--------- 1 file changed, 150 insertions(+), 144 deletions(-) diff --git a/PythonGUI_apps/Lifetime_analysis/picoharp_phd.py b/PythonGUI_apps/Lifetime_analysis/picoharp_phd.py index 455e1bc..072dfa3 100644 --- a/PythonGUI_apps/Lifetime_analysis/picoharp_phd.py +++ b/PythonGUI_apps/Lifetime_analysis/picoharp_phd.py @@ -1,22 +1,27 @@ -# -*- coding: utf-8 -*- """ Majority of this PicoHarp Parser was written by skyjur. Check out the original code here --- https://github.com/skyjur/picoharp300-curvefit-ui -Modified by Sarthak --- -Created on Fri Apr 5 15:50:36 2019 - -@author: Sarthak +Modified by Sarthak Jariwala +Fixed CurveHdr (Sarthak) """ -""" -PicoHarp 300 file parser -""" import datetime import numpy as np -from ctypes import c_uint, c_ulong, c_char, c_int, c_int64, c_float, \ - Structure, sizeof, memmove, addressof +from ctypes import ( + Structure, + addressof, + c_char, + c_float, + c_int, + c_int32, + c_int64, + c_uint, + c_ulong, + memmove, + sizeof +) DISPCURVES = 8 MAXCURVES = 512 @@ -26,150 +31,151 @@ class tParamStruct(Structure): _pack_ = 4 _fields_ = [ - ('Start', c_float), - ('Step', c_float), - ('End', c_float), + ("Start", c_float), + ("Step", c_float), + ("End", c_float), ] class tCurveMapping(Structure): _pack_ = 4 _fields_ = [ - ('MapTo', c_int), - ('Show', c_int), + ("MapTo", c_int), + ("Show", c_int), ] class TxtHdr(Structure): _pack_ = 4 _fields_ = [ - ('Ident', c_char * 16), - ('FormatVersion', c_char * 6), - ('CreatorName', c_char * 18), - ('CreatorVersion', c_char * 12), - ('FileTime', c_char * 18), - ('CRLF', c_char * 2), - ('CommentField', c_char * 256), + ("Ident", c_char * 16), + ("FormatVersion", c_char * 6), + ("CreatorName", c_char * 18), + ("CreatorVersion", c_char * 12), + ("FileTime", c_char * 18), + ("CRLF", c_char * 2), + ("CommentField", c_char * 256), ] class BinHdr(Structure): _pack_ = 4 _fields_ = [ - ('Curves', c_int), - ('BitsPerHistoBin', c_int), - ('RoutingChannels', c_int), - ('NumberOfBoards', c_int), - ('ActiveCurve', c_int), - ('MeasMode', c_int), - ('SubMode', c_int), - ('RangeNo', c_int), - ('Offset', c_int), - ('Tacq', c_int), # in m - ('StopAt', c_int), - ('StopOnOvfl', c_int), - ('Restart', c_int), - ('DispLinLog', c_int), - ('DispTimeFrom', c_int), - ('DispTimeTo', c_int), - ('DispCountsFrom', c_int), - ('DispCountsTo', c_int), - ('DispCurves', tCurveMapping * DISPCURVES), - ('Params', tParamStruct * 3), - ('RepeatMode', c_int), - ('RepeatsPerCurve', c_int), - ('RepeatTime', c_int), - ('RepeatWaitTime', c_int), - ('ScriptName', c_char * 20), + ("Curves", c_int), + ("BitsPerHistoBin", c_int), + ("RoutingChannels", c_int), + ("NumberOfBoards", c_int), + ("ActiveCurve", c_int), + ("MeasMode", c_int), + ("SubMode", c_int), + ("RangeNo", c_int), + ("Offset", c_int), + ("Tacq", c_int), # in m + ("StopAt", c_int), + ("StopOnOvfl", c_int), + ("Restart", c_int), + ("DispLinLog", c_int), + ("DispTimeFrom", c_int), + ("DispTimeTo", c_int), + ("DispCountsFrom", c_int), + ("DispCountsTo", c_int), + ("DispCurves", tCurveMapping * DISPCURVES), + ("Params", tParamStruct * 3), + ("RepeatMode", c_int), + ("RepeatsPerCurve", c_int), + ("RepeatTime", c_int), + ("RepeatWaitTime", c_int), + ("ScriptName", c_char * 20), ] class BoardHdr(Structure): _pack_ = 4 _fields_ = [ - ('HardwareIdent', c_char * 16), - ('HardwareVersion', c_char * 8), - ('HardwareSerial', c_int), - ('SyncDivider', c_int), - ('CFDZeroCross0', c_int), - ('CFDLevel0', c_int), - ('CFDZeroCross1', c_int), - ('CFDLevel1', c_int), - ('Resolution', c_float), - ('RouterModelCode', c_int), - ('RouterEnabled', c_int), - ('RtChan1_InputType;', c_int), - ('RtChan1_InputLevel', c_int), - ('RtChan1_InputEdge', c_int), - ('RtChan1_CFDPresent', c_int), - ('RtChan1_CFDLevel', c_int), - ('RtChan1_CFDZeroCross', c_int), - ('RtChan2_InputType;', c_int), - ('RtChan2_InputLevel', c_int), - ('RtChan2_InputEdge', c_int), - ('RtChan2_CFDPresent', c_int), - ('RtChan2_CFDLevel', c_int), - ('RtChan2_CFDZeroCross', c_int), - ('RtChan3_InputType;', c_int), - ('RtChan3_InputLevel', c_int), - ('RtChan3_InputEdge', c_int), - ('RtChan3_CFDPresent', c_int), - ('RtChan3_CFDLevel', c_int), - ('RtChan3_CFDZeroCross', c_int), - ('RtChan4_InputType;', c_int), - ('RtChan4_InputLevel', c_int), - ('RtChan4_InputEdge', c_int), - ('RtChan4_CFDPresent', c_int), - ('RtChan4_CFDLevel', c_int), - ('RtChan4_CFDZeroCross', c_int), + ("HardwareIdent", c_char * 16), + ("HardwareVersion", c_char * 8), + ("HardwareSerial", c_int), + ("SyncDivider", c_int), + ("CFDZeroCross0", c_int), + ("CFDLevel0", c_int), + ("CFDZeroCross1", c_int), + ("CFDLevel1", c_int), + ("Resolution", c_float), + ("RouterModelCode", c_int), + ("RouterEnabled", c_int), + ("RtChan1_InputType;", c_int), + ("RtChan1_InputLevel", c_int), + ("RtChan1_InputEdge", c_int), + ("RtChan1_CFDPresent", c_int), + ("RtChan1_CFDLevel", c_int), + ("RtChan1_CFDZeroCross", c_int), + ("RtChan2_InputType;", c_int), + ("RtChan2_InputLevel", c_int), + ("RtChan2_InputEdge", c_int), + ("RtChan2_CFDPresent", c_int), + ("RtChan2_CFDLevel", c_int), + ("RtChan2_CFDZeroCross", c_int), + ("RtChan3_InputType;", c_int), + ("RtChan3_InputLevel", c_int), + ("RtChan3_InputEdge", c_int), + ("RtChan3_CFDPresent", c_int), + ("RtChan3_CFDLevel", c_int), + ("RtChan3_CFDZeroCross", c_int), + ("RtChan4_InputType;", c_int), + ("RtChan4_InputLevel", c_int), + ("RtChan4_InputEdge", c_int), + ("RtChan4_CFDPresent", c_int), + ("RtChan4_CFDLevel", c_int), + ("RtChan4_CFDZeroCross", c_int), ] class CurveHdr(Structure): _pack_ = 4 _fields_ = [ - ('CurveIndex', c_int), - ('TimeOfRecording', c_ulong), - ('HardwareIdent', c_char * 16), - ('HardwareVersion', c_char * 8), - ('HardwareSerial', c_int), - ('SyncDivider', c_int), - ('CFDZeroCross0', c_int), - ('CFDLevel0', c_int), - ('CFDZeroCross1', c_int), - ('CFDLevel1', c_int), - ('Offset', c_int), - ('RoutingChannel', c_int), - ('ExtDevices', c_int), - ('MeasMode', c_int), - ('SubMode', c_int), - ('P1', c_float), - ('P2', c_float), - ('P3', c_float), - ('RangeNo', c_int), - ('Resolution', c_float), - ('Channels', c_int), - ('Tacq', c_int), - ('StopAfter', c_int), - ('StopReason', c_int), - ('InpRate0', c_int), - ('InpRate1', c_int), - ('HistCountRate', c_int), - ('IntegralCount', c_int64), - ('reserved', c_int), - ('DataOffset', c_int), - ('RouterModelCode', c_int), - ('RouterEnabled', c_int), - ('RtChan_InputType;', c_int), - ('RtChan_InputLevel', c_int), - ('RtChan_InputEdge', c_int), - ('RtChan_CFDPresent', c_int), - ('RtChan_CFDLevel', c_int), - ('RtChan_CFDZeroCross', c_int), + ("CurveIndex", c_int32), + ("TimeOfRecording", c_uint), + ("HardwareIdent", c_char * 16), + ("HardwareVersion", c_char * 8), + ("HardwareSerial", c_int32), + ("SyncDivider", c_int32), + ("CFDZeroCross0", c_int32), + ("CFDLevel0", c_int32), + ("CFDZeroCross1", c_int32), + ("CFDLevel1", c_int32), + ("Offset", c_int32), + ("RoutingChannel", c_int32), + ("ExtDevices", c_int32), + ("MeasMode", c_int32), + ("SubMode", c_int32), + ("P1", c_float), + ("P2", c_float), + ("P3", c_float), + ("RangeNo", c_int32), + ("Resolution", c_float), + ("Channels", c_int32), + ("Tacq", c_int32), + ("StopAfter", c_int32), + ("StopReason", c_int32), + ("InpRate0", c_int32), + ("InpRate1", c_int32), + ("HistCountRate", c_int32), + ("IntegralCount", c_int64), + ("reserved", c_int32), + ("DataOffset", c_int32), + ("RouterModelCode", c_int32), + ("RouterEnabled", c_int32), + ("RtChan_InputType;", c_int32), + ("RtChan_InputLevel", c_int32), + ("RtChan_InputEdge", c_int32), + ("RtChan_CFDPresent", c_int32), + ("RtChan_CFDLevel", c_int32), + ("RtChan_CFDZeroCross", c_int32), ] -class ParseError(Exception): pass +class ParseError(Exception): + pass def _read(f, CType): @@ -180,8 +186,8 @@ def _read(f, CType): def _validate_header(header): - if not header.Ident == 'PicoHarp 300' or not header.FormatVersion == '2.0': - raise ParseError('Does not look like a PicoHarp 300 file.') + if not header.Ident == "PicoHarp 300" or not header.FormatVersion == "2.0": + raise ParseError("Does not look like a PicoHarp 300 file.") class Curve(object): @@ -189,23 +195,20 @@ class Curve(object): data = None def __repr__(self): - return 'Curve' % ( - self.res, - len(self.data) - ) + return "Curve" % (self.res, len(self.data)) def timefmt(t): d = datetime.datetime.fromtimestamp(t) - return d.strftime('%a %b %d %H:%M:%S %Y') + return d.strftime("%a %b %d %H:%M:%S %Y") class PicoharpParser(object): _ready = False def __init__(self, filename): - if isinstance(filename, (str)):#, unicode)): - filename = open(filename, mode='rb') + if isinstance(filename, (str)): # , unicode)): + filename = open(filename, mode="rb") self.f = filename self._prepare() @@ -214,7 +217,7 @@ def _prepare(self): header = self._header = _read(self.f, TxtHdr) """SJ commented this --- it was giving ParseError""" -# _validate_header(header) + # _validate_header(header) bin_header = self._bin_header = _read(self.f, BinHdr) @@ -240,19 +243,26 @@ def get_curve(self, n): array = np.fromfile(self.f, c_uint, header.Channels) return res, array - + + def get_all_curves(self): + all_curves = [] + for i in range(len(self._curves)): + all_curves.append(self.get_curve(i)) + + return all_curves + def get_time_window_in_ns(self, curve_no): curve = self._curves[curve_no] rep_rate = curve.InpRate0 res, _ = self.get_curve(curve_no) - time_window_s = (1/rep_rate)/res # in seconds - - return time_window_s * 1e9 # in nannoseconds - + time_window_s = (1 / rep_rate) / res # in seconds + + return time_window_s * 1e9 # in nannoseconds + def get_integral_counts(self, curve_no): curve = self._curves[curve_no] integral_counts = curve.IntegralCount - + return integral_counts def info(self): @@ -262,7 +272,7 @@ def info(self): curves = self._curves r = [] w = r.append - yesno = lambda x: 'true' if x else 'false' + yesno = lambda x: "true" if x else "false" w("Ident : %s" % txthdr.Ident) w("Format Version : %s" % txthdr.FormatVersion) @@ -367,7 +377,7 @@ def info(self): w("HardwareSerial : %d" % curve.HardwareSerial) w("SyncDivider : %d" % curve.SyncDivider) w("CFDZeroCross0 : %d" % curve.CFDZeroCross0) - w("CFDLevel0 : %d" % curve.CFDLevel0 ) + w("CFDLevel0 : %d" % curve.CFDLevel0) w("CFDZeroCross1 : %d" % curve.CFDZeroCross1) w("CFDLevel1 : %d" % curve.CFDLevel1) w("Offset : %d" % curve.Offset) @@ -401,8 +411,4 @@ def info(self): w("RtChan_CFDLevel : %d" % curve.RtChan_CFDLevel) w("RtChan_CFDZeroCross : %d" % curve.RtChan_CFDZeroCross) - return '\n'.join(r) - -def read_picoharp_phd(datafile): - parser = PicoharpParser(datafile) - return parser \ No newline at end of file + return "\n".join(r) From 25297c538dd13a57c5f6a1464d3b6185658cb32a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 2 Feb 2021 22:47:48 +0000 Subject: [PATCH 05/10] Bump bleach from 3.1.4 to 3.3.0 Bumps [bleach](https://github.com/mozilla/bleach) from 3.1.4 to 3.3.0. - [Release notes](https://github.com/mozilla/bleach/releases) - [Changelog](https://github.com/mozilla/bleach/blob/master/CHANGES) - [Commits](https://github.com/mozilla/bleach/compare/v3.1.4...v3.3.0) Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4d5abd3..f74b5d1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ altgraph==0.16.1 asteval==0.9.14 attrs==19.1.0 backcall==0.1.0 -bleach==3.1.4 +bleach==3.3.0 bokeh==1.3.2 certifi==2019.6.16 Click==7.0 From 440dd45ec230eda0d6bbfb853a3eff88a54ea966 Mon Sep 17 00:00:00 2001 From: Sarthak Jariwala Date: Tue, 16 Feb 2021 16:04:43 -0800 Subject: [PATCH 06/10] FIX: reading error for files with single trace --- PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py b/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py index 7967a1e..c7eb5a6 100644 --- a/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py +++ b/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py @@ -129,6 +129,10 @@ def open_with_skip_rows_window(self): skip_rows = self.skip_rows_window.ui.skip_rows_spinBox.value() if ".txt" in self.filename[0]: self.file = np.loadtxt(self.filename[0], skiprows=skip_rows) + + if self.file.ndim == 1: # if there is only one trace, reshape to 2D + self.file = self.file.reshape(self.file.shape[0], 1) + elif ".csv" in self.filename[0]: self.file = np.genfromtxt(self.filename[0], skip_header=skip_rows, delimiter=",") @@ -149,6 +153,10 @@ def open_irf_with_skip_rows_window(self): irf_skip_rows = self.irf_skip_rows_window.ui.skip_rows_spinBox.value() if ".txt" in self.irf_filename[0]: self.irf_file = np.loadtxt(self.irf_filename[0], skiprows=irf_skip_rows) + + if self.irf_file.ndim == 1: # if there is only one trace, reshape to 2d array + self.irf_file = self.irf_file.reshape(self.irf_file.shape[0], 1) + elif ".csv" in self.irf_filename[0]: self.irf_file = np.genfrontxt(self.irf_filename[0], skip_header=irf_skip_rows, delimiter=",") From e3efda4df67ff2045f5897593dea09c4aa6d8e7b Mon Sep 17 00:00:00 2001 From: SarthakJariwala Date: Wed, 3 Mar 2021 13:32:29 -0800 Subject: [PATCH 07/10] fix import error --- PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py b/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py index c7eb5a6..89a32b9 100644 --- a/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py +++ b/PythonGUI_apps/Lifetime_analysis/Lifetime_plot_fit.py @@ -25,12 +25,12 @@ # local module imports try: from Lifetime_analysis.Fit_functions import stretch_exp_fit, double_exp_fit, single_exp_fit - from Lifetime_analysis.picoharp_phd import read_picoharp_phd + from Lifetime_analysis.read_ph_phd import read_picoharp_phd from Lifetime_analysis.Fit_functions_with_irf import fit_exp_stretch_diffev, fit_exp_stretch_fmin_tnc, fit_multi_exp_diffev, fit_multi_exp_fmin_tnc except: from Fit_functions import stretch_exp_fit, double_exp_fit, single_exp_fit from Fit_functions_with_irf import fit_exp_stretch_diffev, fit_exp_stretch_fmin_tnc, fit_multi_exp_diffev, fit_multi_exp_fmin_tnc - from picoharp_phd import read_picoharp_phd + from read_ph_phd import read_picoharp_phd """Recylce params for plotting""" plt.rc('xtick', labelsize = 20) From ba958651c0167351fdae954181b9ebc46677f121 Mon Sep 17 00:00:00 2001 From: SarthakJariwala Date: Wed, 3 Mar 2021 13:50:57 -0800 Subject: [PATCH 08/10] dont port to fbs structure --- src/build/settings/base.json | 6 - src/build/settings/linux.json | 6 - src/build/settings/mac.json | 3 - src/main/icons/Icon.ico | Bin 168229 -> 0 bytes src/main/icons/README.md | 11 - src/main/icons/base/16.png | Bin 544 -> 0 bytes src/main/icons/base/24.png | Bin 783 -> 0 bytes src/main/icons/base/32.png | Bin 912 -> 0 bytes src/main/icons/base/48.png | Bin 1497 -> 0 bytes src/main/icons/base/64.png | Bin 1657 -> 0 bytes src/main/icons/linux/1024.png | Bin 26841 -> 0 bytes src/main/icons/linux/128.png | Bin 3177 -> 0 bytes src/main/icons/linux/256.png | Bin 5641 -> 0 bytes src/main/icons/linux/512.png | Bin 11653 -> 0 bytes src/main/icons/mac/1024.png | Bin 47311 -> 0 bytes src/main/icons/mac/128.png | Bin 4978 -> 0 bytes src/main/icons/mac/256.png | Bin 10278 -> 0 bytes src/main/icons/mac/512.png | Bin 21699 -> 0 bytes src/main/python/DataBrowser_GUI.ui | 97 -- .../python/Export_Windows/Export_window.py | 77 - .../Export_Windows/Multi_Trace_Exporter.py | 147 -- .../Export_Windows/Multi_Trace_Exporter.ui | 85 - src/main/python/Export_Windows/__init__.py | 1 - .../python/Export_Windows/export_fig_gui.ui | 171 -- src/main/python/Export_Windows/export_plot.ui | 186 --- src/main/python/FLIM_analysis/FLIM_plot.py | 374 ----- .../python/FLIM_analysis/flim_plot_gui.ui | 185 --- .../FLIM_analysis/step_size_labview_files.ui | 61 - src/main/python/H5_Pkl/h5_pkl_view.py | 124 -- src/main/python/H5_Pkl/h5_pkl_view_gui.ui | 89 - src/main/python/H5_Pkl/h5_tree.py | 100 -- src/main/python/H5_Pkl/h5_view_and_plot.py | 141 -- .../python/H5_Pkl/h5_view_and_plot_gui.ui | 280 ---- src/main/python/H5_Pkl/pkl_tree.py | 103 -- .../python/Image_analysis/Image_analysis.py | 222 --- .../Image_analysis/image_analysis_gui.ui | 208 --- .../python/Lifetime_analysis/Fit_functions.py | 132 -- .../Fit_functions_with_irf.py | 329 ---- .../Lifetime_analysis_gui_layout.ui | 1392 ---------------- .../Lifetime_analysis/Lifetime_plot_fit.py | 653 -------- src/main/python/Lifetime_analysis/__init__.py | 1 - .../python/Lifetime_analysis/picoharp_phd.py | 408 ----- .../python/Lifetime_analysis/read_ph_phd.py | 54 - .../python/Lifetime_analysis/skip_rows.ui | 42 - .../OO_PZstageScan_acquire_gui.ui | 750 --------- .../OceanOptics_acquire/OO_acquire_gui.ui | 240 --- .../OceanOptics_acquire_plot.py | 297 ---- .../PLQE_analysis/column_selection_gui.ui | 107 -- .../python/PLQE_analysis/plqe_analysis.py | 212 --- .../python/PLQE_analysis/plqe_analysis_gui.ui | 150 -- .../Spectrum_analysis/Spectra_fit_funcs.py | 241 --- .../Spectrum_analysis/Spectra_plot_fit.py | 1020 ------------ .../Spectrum_analysis/Spectra_plot_fit_gui.ui | 1464 ----------------- src/main/python/Spectrum_analysis/__init__.py | 1 - 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displayed for your app. Feel free to -change them. - -The difference between the icons on Mac and the other platforms is that on Mac, -they contain a ~5% transparent margin. This is because otherwise they look too -big (eg. in the Dock or in the app switcher). - -You can create Icon.ico from the .png files with -[an online tool](http://icoconvert.com/Multi_Image_to_one_icon/). \ No newline at end of file diff --git a/src/main/icons/base/16.png b/src/main/icons/base/16.png deleted file mode 100644 index f7d02dc268f79c183376b30dddf5ea0cf5827dfe..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 544 zcmV+*0^j|KP)TmGsBvSN0G7{E%tE_-gl|fEv;0aRau+G)01lU7P2{XIYtU(DY*`z5wZh-t$ z17;xV-$KBe25cyY`gJ9TKA2b zQ`OPi4q_$n+Q`u1Rq4iCqev!2*O%K1W{B_hXa`+h=PJlsp!i@kPT6X zFgMtf4&AdjLi@^LEPz?gPFhert=$)fabl?(6T3=?Mx5-d`oLZ)@tUkX_s2+$#>F(4wKl3YIpWCbP|H9s!5%<RuTU6aQntuM7@! zJkGa2f3Hqhe%Cykf0SrKM}494z#-;LdXvexZ{ zdcbzc3-LACtO$GJb`m+Ec0Hhy4FPV@8I-klM7`(%Jex>U7OJ7wQzqfr0= N002ovPDHLkV1g}~Xzc(1 diff --git a/src/main/icons/base/32.png b/src/main/icons/base/32.png deleted file mode 100644 index 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- - - - - 30 - 75 - true - - - - GLabViz - - - Qt::AlignCenter - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 15 - - - - Analysis Tool : - - - - - - - - 15 - - - - - - - - - 15 - - - - Load - - - - - - - - - 0 - 0 - 435 - 21 - - - - - - - - diff --git a/src/main/python/Export_Windows/Export_window.py b/src/main/python/Export_Windows/Export_window.py deleted file mode 100644 index 0e5cc63..0000000 --- a/src/main/python/Export_Windows/Export_window.py +++ /dev/null @@ -1,77 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Sun Nov 3 20:43:12 2019 - -@author: sarth -""" -from pathlib import Path -import pyqtgraph as pg -from pyqtgraph.Qt import QtCore, QtGui - -"""Export Images GUI""" -base_path = Path(__file__).parent -ui_file_path = (base_path / "export_fig_gui.ui").resolve() -exportFig_WindowTemplate, exportFig_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) - -class ExportFigureWindow(exportFig_TemplateBaseClass): - - export_fig_signal = QtCore.pyqtSignal() - - def __init__(self): - exportFig_TemplateBaseClass.__init__(self) - - self.ui = exportFig_WindowTemplate() - self.ui.setupUi(self) - self.ui.cmap_comboBox.addItems(['viridis', 'plasma', 'inferno', 'magma', - 'cividis','Greys', 'Purples', 'Blues', - 'Greens', 'Oranges', 'Reds', 'YlOrBr', - 'YlOrRd', 'OrRd', 'PuRd', 'RdPu', 'BuPu', - 'GnBu', 'PuBu', 'YlGnBu', 'PuBuGn', 'BuGn', - 'YlGn', 'binary', 'gist_yarg', 'gist_gray', - 'gray', 'bone', 'pink', 'spring', 'summer', - 'autumn', 'winter', 'cool', 'Wistia', 'hot', - 'afmhot', 'gist_heat', 'copper', 'rainbow', 'jet']) - self.ui.cbar_checkBox.stateChanged.connect(self.cbar_title_state) - self.ui.exportFig_pushButton.clicked.connect(self.export) - self.show() - - def cbar_title_state(self): - if self.ui.cbar_checkBox.isChecked(): - self.ui.cbar_label.setEnabled(True) - else: - self.ui.cbar_label.setEnabled(False) - - def export(self): - self.export_fig_signal.emit() - self.close() - -"""Export plot GUI""" -ui_file_path = (base_path / "export_plot.ui").resolve() -export_WindowTemplate, export_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) - -class ExportPlotWindow(export_TemplateBaseClass): - - export_fig_signal = QtCore.pyqtSignal() - - def __init__(self): - export_TemplateBaseClass.__init__(self) - - self.ui = export_WindowTemplate() - self.ui.setupUi(self) - #self.ui.traceColor_comboBox.addItems(["C0","C1","C2","C3","C4","C5","C6","C7", "r", "g", "b", "y", "k"]) - #self.ui.fitColor_comboBox.addItems(["k", "r", "b", "y", "g","C0","C1","C2","C3","C4","C5","C6","C7"]) - self.ui.export_pushButton.clicked.connect(self.export) - #self.ui.legend_checkBox.stateChanged.connect(self.legend_title) - self.show() - - #def legend_title(self): - # if self.ui.legend_checkBox.isChecked(): - # self.ui.legend1_lineEdit.setEnabled(True) - # self.ui.legend2_lineEdit.setEnabled(True) - # else: - # self.ui.legend1_lineEdit.setEnabled(False) - # self.ui.legend2_lineEdit.setEnabled(False) - - def export(self): - self.export_fig_signal.emit() - self.close() \ No newline at end of file diff --git a/src/main/python/Export_Windows/Multi_Trace_Exporter.py b/src/main/python/Export_Windows/Multi_Trace_Exporter.py deleted file mode 100644 index 5d5555d..0000000 --- a/src/main/python/Export_Windows/Multi_Trace_Exporter.py +++ /dev/null @@ -1,147 +0,0 @@ -import pyqtgraph as pg -from pathlib import Path -from pyqtgraph.Qt import QtCore, QtGui, QtWidgets -try: - from Lifetime_analysis.read_ph_phd import read_picoharp_phd, get_x_y -except Exception as e: - print(e) -import matplotlib.pyplot as plt - -"""Recylce params for plotting""" -plt.rc('xtick', labelsize = 20) -plt.rc('xtick.major', pad = 3) -plt.rc('ytick', labelsize = 20) -plt.rc('lines', lw = 2.5, markersize = 7.5) -plt.rc('legend', fontsize = 20) -plt.rc('axes', linewidth=3.5) - -pg.mkQApp() - -base_path = Path(__file__).parent -file_path = (base_path / "Multi_Trace_Exporter.ui").resolve() - -uiFile = file_path - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -class MainWindow(TemplateBaseClass): - - def __init__(self): - super(TemplateBaseClass, self).__init__() - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - - self.temp_layout = pg.GraphicsLayoutWidget() - - # file system tree - self.fs_model = QtWidgets.QFileSystemModel() - self.fs_model.setRootPath(QtCore.QDir.currentPath()) - self.ui.treeView.setModel(self.fs_model) - self.ui.treeView.setIconSize(QtCore.QSize(25,25)) - self.ui.treeView.setSortingEnabled(True) - - self.tree_selectionModel = self.ui.treeView.selectionModel() - self.tree_selectionModel.selectionChanged.connect(self.on_treeview_selection_change) - - self.ui.comboBox.currentIndexChanged.connect(self.add_trace_to_temp_plot) - self.ui.add_pushButton.clicked.connect(self.add_trace_to_mem) - self.ui.export_pushButton.clicked.connect(self.pub_ready_plot_export) - - self.x_i = [] - self.y_i = [] - self.x_mem = [] - self.y_mem = [] - self.legend = [] - - self.show() - - def on_treeview_selection_change(self): - try: - fname = self.fs_model.filePath(self.tree_selectionModel.currentIndex()) - _ , ext = fname.rsplit('.',1) - - self.ui.comboBox.clear() - self.ui.textBrowser.clear() - self.x_i = [] - self.y_i = [] - - if ext in ['phd']: - self.parser = read_picoharp_phd(fname) - curve_list = [] - - for i in range(self.parser.no_of_curves()): - curve_list.append("Curve "+str(i)) - x, y = get_x_y(i, self.parser, smooth_trace=self.ui.smooth_checkBox.isChecked(), boxwidth=self.ui.smooth_spinBox.value()) - self.x_i.append(x) - self.y_i.append(y) - - self.ui.comboBox.addItems(curve_list) - self.ui.textBrowser.setText(str(self.parser.info())) - - else: - self.ui.textBrowser.setText(str("Select a PicoHarp File")) - except Exception as e: - print(e) - - def add_trace_to_temp_plot(self): - try: - #self.temp_layout = pg.GraphicsLayoutWidget() - self.temp_layout.clear() - self.temp_plot = self.temp_layout.addPlot(title = "Current Selection") - self.temp_plot.plot(self.x_i[self.ui.comboBox.currentIndex()], self.y_i[self.ui.comboBox.currentIndex()], pen='r') - self.temp_plot.setLogMode(False, True) - self.temp_layout.show() - except Exception as e: - print(e) - - def add_trace_to_mem(self): - try: - self.x_mem.append(self.x_i[self.ui.comboBox.currentIndex()]) - self.y_mem.append(self.y_i[self.ui.comboBox.currentIndex()]) - self.legend.append(self.ui.lineEdit.text()) - except Exception as e: - print(e) - - def pub_ready_plot_export(self): - try: - filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") - - plt.figure(figsize=(8,6)) - plt.tick_params(direction='out', length=8, width=3.5) - for i in range(len(self.x_mem)): - if self.ui.Normalize_checkBox.isChecked(): - plt.plot(self.x_mem[i], self.y_mem[i]/max(self.y_mem[i]), label=str(self.legend[i])) - else: - plt.plot(self.x_mem[i], self.y_mem[i], label=str(self.legend[i])) - - plt.yscale('log') - plt.xlabel("Time (ns)", fontsize=20, fontweight='bold') - plt.ylabel("Intensity (norm.)", fontsize=20, fontweight='bold') - plt.legend() - plt.tight_layout() - - plt.savefig(filename[0],bbox_inches='tight', dpi=300) - plt.close() - - self.clear_memory() - - except Exception as e: - print(e) - pass - - def clear_memory(self): - self.x_mem = [] - self.y_mem = [] - self.legend = [] - - - - -def run(): - win = MainWindow() - QtGui.QApplication.instance().exec_() - return win - -#run() \ No newline at end of file diff --git a/src/main/python/Export_Windows/Multi_Trace_Exporter.ui b/src/main/python/Export_Windows/Multi_Trace_Exporter.ui deleted file mode 100644 index 7b59ef1..0000000 --- a/src/main/python/Export_Windows/Multi_Trace_Exporter.ui +++ /dev/null @@ -1,85 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 1108 - 1063 - - - - MainWindow - - - - - - - - - - Smoothen Trace - - - - - - - Enter Trace Legend Here - - - - - - - Add - - - - - - - Normalize (for export) - - - - - - - 1 - - - - - - - Export - - - - - - - - - - - - - - - 0 - 0 - 1108 - 38 - - - - - - - - diff --git a/src/main/python/Export_Windows/__init__.py b/src/main/python/Export_Windows/__init__.py deleted file mode 100644 index 7c68785..0000000 --- a/src/main/python/Export_Windows/__init__.py +++ /dev/null @@ -1 +0,0 @@ -# -*- coding: utf-8 -*- \ No newline at end of file diff --git a/src/main/python/Export_Windows/export_fig_gui.ui b/src/main/python/Export_Windows/export_fig_gui.ui deleted file mode 100644 index e80e065..0000000 --- a/src/main/python/Export_Windows/export_fig_gui.ui +++ /dev/null @@ -1,171 +0,0 @@ - - - ExportFigure - - - - 0 - 0 - 420 - 369 - - - - Form - - - - - - - 15 - - - - 1000000000 - - - - - - - - 15 - - - - Color Bar Label - - - - - - - - 15 - - - - Data Channel to Save - - - - - - - - 15 - - - - - - - - - 15 - - - - - - - - - 15 - - - - ColorMap - - - - - - - - 15 - - - - 1000000000 - - - - - - - - 15 - - - - ColorBar Min - - - - - - - - 15 - - - - ColorBar Max - - - - - - - false - - - - 15 - - - - - - - - - 15 - - - - Export Figure - - - - - - - - 15 - - - - Reversed - - - - - - - - 15 - - - - - - - - - - - - diff --git a/src/main/python/Export_Windows/export_plot.ui b/src/main/python/Export_Windows/export_plot.ui deleted file mode 100644 index 840264f..0000000 --- a/src/main/python/Export_Windows/export_plot.ui +++ /dev/null @@ -1,186 +0,0 @@ - - - Form - - - - 0 - 0 - 930 - 435 - - - - Form - - - - - - - 10 - - - - 4 - - - -100.000000000000000 - - - 10000000000000000000000.000000000000000 - - - 1.500000000000000 - - - - - - - - 10 - - - - Lower - - - - - - - - 10 - - - - Lower - - - - - - - - 10 - - - - Upper - - - - - - - - 15 - - - - Export Graph - - - - - - - - 12 - - - - Y limits - - - - - - - - 10 - - - - Upper - - - - - - - - 12 - - - - X limits - - - - - - - - 10 - - - - 4 - - - -10000.000000000000000 - - - 1000000000000000000.000000000000000 - - - 0.010000000000000 - - - - - - - - 10 - - - - 4 - - - -10000000.000000000000000 - - - 100000000000.000000000000000 - - - - - - - - 10 - - - - 4 - - - -1000000000.000000000000000 - - - 10000000000000.000000000000000 - - - 10000.000000000000000 - - - - - - - - diff --git a/src/main/python/FLIM_analysis/FLIM_plot.py b/src/main/python/FLIM_analysis/FLIM_plot.py deleted file mode 100644 index 5f5744f..0000000 --- a/src/main/python/FLIM_analysis/FLIM_plot.py +++ /dev/null @@ -1,374 +0,0 @@ -import sys -import h5py -from pathlib import Path -import os.path -import pyqtgraph as pg -from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog -import numpy as np -import matplotlib.pyplot as plt -import pickle -#import time -from lmfit.models import GaussianModel -import customplotting.mscope as cpm - -sys.path.append(os.path.abspath('../Lifetime_analysis')) -sys.path.append(os.path.abspath('../Spectrum_analysis')) -sys.path.append(os.path.abspath('../H5_Pkl')) -sys.path.append(os.path.abspath('../Export_Windows')) -from Lifetime_analysis import Lifetime_plot_fit -from Spectrum_analysis import Spectra_plot_fit -from H5_Pkl import h5_pkl_view -try: - from Export_window import ExportFigureWindow -except: - from Export_Windows.Export_window import ExportFigureWindow -# local modules - -pg.mkQApp() -pg.setConfigOption('background', 'w') - - -base_path = Path(__file__).parent -file_path = (base_path / "flim_plot_gui.ui").resolve() - -uiFile = file_path - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -def updateDelay(scale, time): - """ Hack fix for scalebar inaccuracy """ - QtCore.QTimer.singleShot(time, scale.updateBar) - -class MainWindow(TemplateBaseClass): - - hist_data_signal = QtCore.pyqtSignal() - - def __init__(self): - pg.setConfigOption('imageAxisOrder', 'row-major') - super(TemplateBaseClass, self).__init__() - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - - #set up ui signals - self.ui.load_scan_pushButton.clicked.connect(self.open_file) - self.ui.plot_intensity_sums_pushButton.clicked.connect(self.plot_intensity_sums) - self.ui.plot_raw_hist_data_pushButton.clicked.connect(self.plot_raw_scan) - self.ui.save_intensities_image_pushButton.clicked.connect(self.export_window) - self.ui.save_intensities_array_pushButton.clicked.connect(self.save_intensities_array) - self.ui.compare_checkBox.stateChanged.connect(self.switch_compare) - self.ui.intensity_sums_viewBox.roi.sigRegionChanged.connect(self.line_profile_update_plot) - self.ui.import_pkl_pushButton.clicked.connect(self.import_pkl_to_convert) - self.ui.pkl_to_h5_pushButton.clicked.connect(self.pkl_to_h5) - self.ui.analyze_lifetime_pushButton.clicked.connect(self.on_analyze_lifetime) - self.ui.analyze_psf_pushButton.clicked.connect(self.on_analyze_psf) - - self.show() - - def open_file(self): - """ Open FLIM scan file """ - try: - self.filename = QtWidgets.QFileDialog.getOpenFileName(self, filter="Scan files (*.pkl *.h5 *.txt)") - if ".pkl" in self.filename[0]: - self.flim_scan_file = pickle.load(open(self.filename[0], 'rb')) - self.scan_file_type = "pkl" - self.launch_h5_pkl_viewer() - self.get_data_params() - elif ".h5" in self.filename[0]: - self.flim_scan_file = h5py.File(self.filename[0], 'r') - self.scan_file_type = "h5" - self.launch_h5_pkl_viewer() - self.get_data_params() - elif ".txt" in self.filename[0]: - self.intensity_sums = np.loadtxt(self.filename[0]).T - self.stepsize_window = StepSizeWindow() - self.stepsize_window.stepsize_signal.connect(self.get_stepsize) - self.scan_file_type = "txt" - # self.pkl_file = pickle.load(open(self.filename[0], 'rb')) - except Exception as err: - print(format(err)) - - def launch_h5_pkl_viewer(self): - """ Launches H5/PKL viewer to give an insight into the data and its structure""" - viewer_window = h5_pkl_view.H5PklView(sys.argv) - viewer_window.settings['data_filename'] = self.filename[0] - - def import_pkl_to_convert(self): - """ Open pkl file to convert to h5 """ - try: - self.pkl_to_convert = QtWidgets.QFileDialog.getOpenFileName(self) - self.ui.result_textBrowser.append("Done Loading - .pkl to convert") - except: - pass - - def get_stepsize(self): - """ Get step size from user input -- specfically written for loading - txt files from legacy labview code, but can also be run on txt file - saved using the new FLIM acquistion code """ - self.stepsize = self.stepsize_window.ui.stepsize_doubleSpinBox.value() - self.x_step_size = self.stepsize - self.y_step_size = self.stepsize - - def get_data_params(self): - - data = self.flim_scan_file - if self.scan_file_type == "pkl": - self.x_scan_size = data['Scan Parameters']['X scan size (um)'] - self.y_scan_size = data['Scan Parameters']['Y scan size (um)'] - self.x_step_size = data['Scan Parameters']['X step size (um)'] - self.y_step_size = data['Scan Parameters']['Y step size (um)'] - self.hist_data = data['Histogram data'] - self.time_data = data['Time data'] - else: #run this if scan file is h5 - self.x_scan_size = data['Scan Parameters'].attrs['X scan size (um)'] - self.y_scan_size = data['Scan Parameters'].attrs['Y scan size (um)'] - self.x_step_size = data['Scan Parameters'].attrs['X step size (um)'] - self.y_step_size = data['Scan Parameters'].attrs['Y step size (um)'] - self.hist_data = data['Histogram data'][()] #get dataset values - self.time_data = data['Time data'][()] - - self.numb_x_pixels = int(self.x_scan_size/self.x_step_size) - self.numb_y_pixels = int(self.y_scan_size/self.y_step_size) - - - def plot_intensity_sums(self): - try: - if self.scan_file_type is "pkl" or self.scan_file_type is "h5": - pg.setConfigOption('imageAxisOrder', 'row-major') - self.hist_data = np.reshape(self.hist_data, newshape=(self.hist_data.shape[0], self.numb_x_pixels*self.numb_y_pixels)) - self.intensity_sums = np.sum(self.hist_data, axis=0) #sum intensities for each pixel - self.intensity_sums = np.reshape(self.intensity_sums, newshape=(self.numb_x_pixels, self.numb_y_pixels)) - else: - pg.setConfigOption('imageAxisOrder', 'col-major') - self.ui.intensity_sums_viewBox.view.invertY(False) # stop y axis invert - self.ui.intensity_sums_viewBox.setImage(self.intensity_sums, scale= - (self.x_step_size, - self.y_step_size)) - if self.scan_file_type is "pkl" or self.scan_file_type is "h5": - self.ui.intensity_sums_viewBox.roi.setSize([self.x_scan_size, self.y_step_size]) #line roi - scale = pg.ScaleBar(size=1,suffix='um') - scale.setParentItem(self.ui.intensity_sums_viewBox.view) - scale.anchor((1, 1), (1, 1), offset=(-30, -30)) - self.ui.intensity_sums_viewBox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) - except Exception as err: - print(format(err)) - - def line_profile_update_plot(self): - """ Handle line profile for intensity sum viewbox """ - if hasattr(self, "intensity_sums"): - roiPlot = self.ui.intensity_sums_viewBox.getRoiPlot() - roiPlot.clear() - roi = self.ui.intensity_sums_viewBox.roi - - image = self.ui.intensity_sums_viewBox.getProcessedImage() - - # Extract image data from ROI - axes = (self.ui.intensity_sums_viewBox.axes['x'], self.ui.intensity_sums_viewBox.axes['y']) - data, coords = roi.getArrayRegion(image.view(np.ndarray), self.ui.intensity_sums_viewBox.imageItem, axes, returnMappedCoords=True) - - #calculate sums along columns in region - sums_to_plot = np.mean(data, axis=0) - - #get scan x-coordinates in region - x_values = coords[1][0] - - try: - roiPlot.plot(x_values, sums_to_plot) - except: - pass - - def on_analyze_psf(self): - self.spectrum_window = Spectra_plot_fit.MainWindow() - self.spectrum_window.show() - self.spectrum_window.opened_from_flim = True - sum_data = self.ui.intensity_sums_viewBox.getRoiPlot().getPlotItem().curves[0].getData() - self.spectrum_window.sum_data_from_flim = np.asarray(sum_data) - self.spectrum_window.ui.plot_without_bck_radioButton.setChecked(True) - self.spectrum_window.ui.result_textBrowser.setText("Data successfully loaded from FLIM analysis.") - - def plot_raw_scan(self): - try: - self.hist_image = np.reshape(self.hist_data, newshape=(self.hist_data.shape[0],self.numb_x_pixels,self.numb_y_pixels)) - self.times = self.time_data[:, 0, 0]*1e-3 - self.ui.raw_hist_data_viewBox.view.invertY(False) # stops y-axis invert - self.ui.raw_hist_data_viewBox.setImage(self.hist_image, scale= - (self.x_step_size, - self.y_step_size), xvals=self.times) - self.ui.raw_hist_data_viewBox.roi.setSize([self.x_scan_size, self.y_scan_size]) - # if self.ui.compare_checkBox.isChecked(): - # self.ui.imv2.setImage(self.hist_image, scale= (data['Scan Parameters']['X step size (um)'], - # data['Scan Parameters']['Y step size (um)']), xvals=self.times) - self.switch_compare() - self.ui.raw_hist_data_viewBox.ui.roiBtn.clicked.connect(self.switch_compare) - scale = pg.ScaleBar(size=1,suffix='um') - scale.setParentItem(self.ui.raw_hist_data_viewBox.view) - scale.anchor((1, 1), (1, 1), offset=(-30, -30)) - self.ui.raw_hist_data_viewBox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) - - except Exception as err: - print(format(err)) - - def switch_compare(self): - """ - Handles compare checkbox. If checked, show second ROI on raw histogram data that user can use for comparison to first ROI. - """ - if self.ui.compare_checkBox.isChecked() and hasattr(self, "hist_image"): - if not hasattr(self, "roi2"): #create roi if doesn't exist yet - self.roi2 = pg.ROI(pos=[0,0], size=[int(self.x_scan_size/2), int(self.y_scan_size/2)], movable=True, pen='r') - self.roi2.addScaleHandle([1, 1], [0, 0]) - self.roi2.addRotateHandle([0, 0], [1, 1]) - self.roi2.sigRegionChanged.connect(self.update_roi2_plot) - self.ui.raw_hist_data_viewBox.addItem(self.roi2) - self.update_roi2_plot() - self.roi2.hide() - self.roi2_plot.hide() - if self.ui.raw_hist_data_viewBox.ui.roiBtn.isChecked(): - self.roi2.show() - self.roi2_plot.show() - else: - self.roi2.hide() - self.roi2_plot.hide() - else: #if not checked, hide roi - if hasattr(self, "roi2"): - self.roi2.hide() - self.roi2_plot.hide() - - def update_roi2_plot(self): - """ Update plot corresponding to second roi """ - #Adapted from pyqtgraph imageview sourcecode - - image = self.ui.raw_hist_data_viewBox.getProcessedImage() - - # Extract image data from ROI - axes = (self.ui.raw_hist_data_viewBox.axes['x'], self.ui.raw_hist_data_viewBox.axes['y']) - data, coords = self.roi2.getArrayRegion(image.view(np.ndarray), self.ui.raw_hist_data_viewBox.imageItem, axes, returnMappedCoords=True) - if data is None: - return - - # Average data within entire ROI for each frame - data = data.mean(axis=max(axes)).mean(axis=min(axes)) - xvals = self.ui.raw_hist_data_viewBox.tVals - if hasattr(self, "roi2_plot"): #make sure second plot is properly cleared everytime - self.roi2_plot.clear() - c = self.ui.raw_hist_data_viewBox.getRoiPlot().getPlotItem().curves.pop() - c.scene().removeItem(c) - self.roi2_plot = self.ui.raw_hist_data_viewBox.getRoiPlot().plot(xvals, data, pen='r') - - def get_raw_hist_curve(self, curve_index): - #curve_index = 0 for original roi - #curve_index = 1 for second comparison roi - curves = self.ui.raw_hist_data_viewBox.getRoiPlot().getPlotItem().curves - return curves[curve_index].getData() - - def on_analyze_lifetime(self): - self.lifetime_window = Lifetime_plot_fit.MainWindow() - self.lifetime_window.show() - self.lifetime_window.opened_from_flim = True - self.lifetime_window.hist_data_from_flim = np.asarray(self.get_raw_hist_curve(0)) - self.lifetime_window.ui.Result_textBrowser.setText("Data successfully loaded from FLIM analysis.") - - def export_window(self): - self.export_window = ExportFigureWindow() - self.export_window.ui.vmin_spinBox.setValue(np.min(self.intensity_sums)) - self.export_window.ui.vmax_spinBox.setValue(np.max(self.intensity_sums)) - self.export_window.export_fig_signal.connect(self.save_intensities_image) - - def save_intensities_image(self): - try: - folder = os.path.dirname(self.filename[0]) - filename_ext = os.path.basename(self.filename[0]) - filename = os.path.splitext(filename_ext)[0] #get filename without extension - save_to = folder + "\\" + filename + "_intensity_sums.png" - if self.export_window.ui.reverse_checkBox.isChecked(): - colormap = str(self.export_window.ui.cmap_comboBox.currentText())+"_r" - else: - colormap = str(self.export_window.ui.cmap_comboBox.currentText()) - if self.export_window.ui.cbar_checkBox.isChecked(): - label = str(self.export_window.ui.cbar_label.text()) - else: - label = "PL Intensity (a.u.)" - cpm.plot_confocal(self.intensity_sums, FLIM_adjust=False, - stepsize=np.abs(self.x_step_size),cmap=colormap, - cbar_label=label, vmin=self.export_window.ui.vmin_spinBox.value(), - vmax=self.export_window.ui.vmax_spinBox.value()) - plt.savefig(save_to, bbox_inches='tight', dpi=300) - except Exception as e: - print(format(e)) - - def save_intensities_array(self): - try: - folder = os.path.dirname(self.filename[0]) - filename_ext = os.path.basename(self.filename[0]) - filename = os.path.splitext(filename_ext)[0] #get filename without extension - save_to = folder + "\\" + filename + "_intensity_sums.txt" - np.savetxt(save_to, self.intensity_sums.T, fmt='%f') #save transposed intensity sums, as original array handles x in cols and y in rows - except: - pass - - def pkl_to_h5(self): - #Convert scan .pkl file into h5 - try: - folder = os.path.dirname(self.pkl_to_convert[0]) - filename_ext = os.path.basename(self.pkl_to_convert[0]) - filename = os.path.splitext(filename_ext)[0] #get filename without extension - pkl_file = pickle.load(open(self.pkl_to_convert[0], 'rb')) - - h5_filename = folder + "/" + filename + ".h5" - h5_file = h5py.File(h5_filename, "w") - self.traverse_dict_into_h5(pkl_file, h5_file) - except Exception as err: - print(format(err)) - - def traverse_dict_into_h5(self, dictionary, h5_output): - #Create an h5 file using .pkl with scan data and params - for key in dictionary: - if type(dictionary[key]) == dict: #if subdictionary, create a group - group = h5_output.create_group(key) - previous_dict = dictionary[key] - self.traverse_dict_into_h5(dictionary[key], group) #traverse subdictionary - else: - if key == "Histogram data" or key == "Time data": - h5_output.create_dataset(key, data=dictionary[key]) - else: - h5_output.attrs[key] = dictionary[key] #if not dataset, create attribute - - def close_application(self): - choice = QtGui.QMessageBox.question(self, 'EXIT!', - "Do you want to exit the app?", - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if choice == QtGui.QMessageBox.Yes: - sys.exit() - else: - pass - -"""Skip rows GUI""" -ui_file_path = (base_path / "step_size_labview_files.ui").resolve() -stepsize_WindowTemplate, stepsize_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) - -class StepSizeWindow(stepsize_TemplateBaseClass): - - stepsize_signal = QtCore.pyqtSignal() #signal to help with pass info back to MainWindow - - def __init__(self): - stepsize_TemplateBaseClass.__init__(self) - - # Create the param window - self.ui = stepsize_WindowTemplate() - self.ui.setupUi(self) - self.ui.done_pushButton.clicked.connect(self.done) - self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False) - self.show() - - def done(self): - self.stepsize_signal.emit() - self.close() - -"""Run the Main Window""" -def run(): - win = MainWindow() - QtGui.QApplication.instance().exec_() - return win - -#Uncomment below if you want to run this as standalone -#run() \ No newline at end of file diff --git a/src/main/python/FLIM_analysis/flim_plot_gui.ui b/src/main/python/FLIM_analysis/flim_plot_gui.ui deleted file mode 100644 index bbfef2a..0000000 --- a/src/main/python/FLIM_analysis/flim_plot_gui.ui +++ /dev/null @@ -1,185 +0,0 @@ - - - Form - - - - 0 - 0 - 738 - 876 - - - - FLIM Analysis - - - - - - 0 - - - - Analysis - - - - - - - - Load Scan - - - - - - - - - Plot - - - - - - - Save intensities array - - - - - - - Save intensities image - - - - - - - Analyze PSF - - - - - - - - - - 500 - 300 - - - - - - - - - 12 - - - - Histogram Intensity Sums - - - - - - - - 12 - - - - Raw Histogram Data - - - - - - - - 500 - 300 - - - - - - - - - - Plot - - - - - - - Analyze lifetime - - - - - - - Compare ROIs - - - - - - - - - - - - .pkl to .h5 - - - - - 20 - 20 - 171 - 34 - - - - Import .pkl file - - - - - - 20 - 80 - 171 - 34 - - - - .pkl to .h5 - - - - - - - - - - ImageView - QGraphicsView -

pyqtgraph
- - - - - diff --git a/src/main/python/FLIM_analysis/step_size_labview_files.ui b/src/main/python/FLIM_analysis/step_size_labview_files.ui deleted file mode 100644 index 2078fb7..0000000 --- a/src/main/python/FLIM_analysis/step_size_labview_files.ui +++ /dev/null @@ -1,61 +0,0 @@ - - - Form - - - - 0 - 0 - 255 - 75 - - - - Form - - - - - - - 12 - - - - Step Size (um) - - - - - - - Done! - - - - - - - - 12 - - - - 4 - - - 100.000000000000000 - - - 0.100000000000000 - - - 0.100000000000000 - - - - - - - - diff --git a/src/main/python/H5_Pkl/h5_pkl_view.py b/src/main/python/H5_Pkl/h5_pkl_view.py deleted file mode 100644 index 7be99a5..0000000 --- a/src/main/python/H5_Pkl/h5_pkl_view.py +++ /dev/null @@ -1,124 +0,0 @@ -from __future__ import division, print_function, absolute_import -from ScopeFoundry import BaseApp -from ScopeFoundry.helper_funcs import load_qt_ui_file, sibling_path -from collections import OrderedDict -import os -from qtpy import QtCore, QtWidgets, QtGui -import pyqtgraph as pg -import pyqtgraph.dockarea as dockarea -import numpy as np -from ScopeFoundry.logged_quantity import LQCollection -from scipy.stats import spearmanr -import argparse -from .h5_tree import H5TreeSearchView -from .pkl_tree import PklTreeSearchView - -pg.setConfigOption('imageAxisOrder', 'row-major') - -class H5PklView(BaseApp): - - name = "h5_pkl_view" - - def __init__(self, argv): - BaseApp.__init__(self, argv) - self.setup() - parser = argparse.ArgumentParser() - for lq in self.settings.as_list(): - parser.add_argument("--" + lq.name) - args = parser.parse_args() - for lq in self.settings.as_list(): - if lq.name in args: - val = getattr(args,lq.name) - if val is not None: - lq.update_value(val) - - def setup(self): - self.ui_filename = sibling_path(__file__, "h5_pkl_view_gui.ui") - self.ui = load_qt_ui_file(self.ui_filename) - self.ui.show() - self.ui.raise_() - - self.views = OrderedDict() - - self.settings.New('data_filename', dtype='file') - self.settings.New('auto_select_view',dtype=bool, initial=True) - self.settings.New('view_name', dtype=str, initial='0', choices=('0',)) - - self.settings.data_filename.add_listener(self.on_change_data_filename) - - # UI Connections/ - self.settings.data_filename.connect_to_browse_widgets(self.ui.data_filename_lineEdit, - self.ui.data_filename_browse_pushButton) - - # set views - self.h5treeview = H5TreeSearchView(self) - self.load_view(self.h5treeview) - self.pkltreeview = PklTreeSearchView(self) - self.load_view(self.pkltreeview) - - self.settings.view_name.add_listener(self.on_change_view_name) - - self.current_view = None - - self.ui.show() - - def load_view(self, new_view): - # add to views dict - self.views[new_view.name] = new_view - - self.ui.dataview_page.layout().addWidget(new_view.ui) - new_view.ui.hide() - - # update choices for view_name - self.settings.view_name.change_choice_list(list(self.views.keys())) - return new_view - - def on_change_data_filename(self): - #Handle file change - try: - fname = self.settings.data_filename.val - if not self.settings['auto_select_view']: - self.current_view.on_change_data_filename(fname) - else: - view_name = self.auto_select_view(fname) - if self.current_view is None or view_name != self.current_view.name: - # update view (automatically calls on_change_data_filename) - self.settings['view_name'] = view_name - else: - # force update - if os.path.isfile(fname): - self.current_view.on_change_data_filename(fname) - except: - pass - - def on_change_view_name(self): - #Handle view change - happens when filetype changes - self.ui.dataview_placeholder.hide() - previous_view = self.current_view - - self.current_view = self.views[self.settings['view_name']] - # hide current view - # (handle the initial case where previous_view is None ) - if previous_view: - previous_view.ui.hide() - - # show new view - self.current_view.ui.show() - - # set datafile for new (current) view - fname = self.settings['data_filename'] - if os.path.isfile(fname): - self.current_view.on_change_data_filename(self.settings['data_filename']) - - def auto_select_view(self, fname): - #return the name of the last supported view for the given fname - for view_name, view in list(self.views.items())[::-1]: - if view.is_file_supported(fname): - return view_name - # return default file_info view if no others work - return "h5_tree_search" - -# if __name__ == '__main__': -# import sys -# app = H5PklView(sys.argv) -# sys.exit(app.exec_()) diff --git a/src/main/python/H5_Pkl/h5_pkl_view_gui.ui b/src/main/python/H5_Pkl/h5_pkl_view_gui.ui deleted file mode 100644 index d147ddc..0000000 --- a/src/main/python/H5_Pkl/h5_pkl_view_gui.ui +++ /dev/null @@ -1,89 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 856 - 925 - - - - H5/pkl View - - - - - - - Qt::Horizontal - - - - File - - - - - - - - - File: - - - - - - - Browse... - - - - - - - true - - - 0 - - - - Data View - - - - - - Once a file is loaded, data will show up here. - - - - - - - - - - - - - - - - - 0 - 0 - 856 - 21 - - - - - - - - diff --git a/src/main/python/H5_Pkl/h5_tree.py b/src/main/python/H5_Pkl/h5_tree.py deleted file mode 100644 index 6d82566..0000000 --- a/src/main/python/H5_Pkl/h5_tree.py +++ /dev/null @@ -1,100 +0,0 @@ -from ScopeFoundry.data_browser import DataBrowserView -from qtpy import QtWidgets -import h5py - -class H5TreeSearchView(DataBrowserView): - - name = 'h5_tree_search' - - def is_file_supported(self, fname): - return ('.h5' in fname) - - def setup(self): - #self.settings.New('search_text', dtype=str, initial="") - - self.ui = QtWidgets.QWidget() - self.ui.setLayout(QtWidgets.QVBoxLayout()) - self.search_lineEdit = QtWidgets.QLineEdit() - self.search_lineEdit.setPlaceholderText("Search") - self.tree_textEdit = QtWidgets.QTextEdit("") - - self.ui.layout().addWidget(self.search_lineEdit) - self.ui.layout().addWidget(self.tree_textEdit) - - #self.settings.search_text.connect_to_widget(self.search_lineEdit) - #self.settings.search_text.add_listener(self.on_new_search_text) - self.search_text = "" - - self.search_lineEdit.textChanged.connect(self.on_new_search_text) - - def on_change_data_filename(self, fname=None): - """ Handle file change """ - self.tree_textEdit.setText("loading {}".format(fname)) - try: - #if using h5_plot_and_view - if hasattr(self.databrowser.ui, "dataset_listWidget"): - self.dataset_dict = {} - self.databrowser.ui.dataset_listWidget.clear() - - self.fname = fname - self.f = h5py.File(fname, 'r') - self.on_new_search_text() - self.databrowser.ui.statusbar.showMessage("") - return self.f - - except Exception as err: - msg = "Failed to load %s:\n%s" %(fname, err) - self.databrowser.ui.statusbar.showMessage(msg) - self.tree_textEdit.setText(msg) - raise(err) - - def on_new_search_text(self, x=None): - if x is not None: - self.search_text = x.lower() - old_scroll_pos = self.tree_textEdit.verticalScrollBar().value() - self.tree_str = "" - self.f.visititems(self._visitfunc) - - self.tree_text_html = \ - """{}
-
- {} -
- """.format(self.fname, self.tree_str) - - self.tree_textEdit.setText(self.tree_text_html) - self.tree_textEdit.verticalScrollBar().setValue(old_scroll_pos) - - def _visitfunc(self, name, node): - level = len(name.split('/')) - indent = ' '*4*(level-1) - - #indent = ''.format(level*4) - localname = name.split('/')[-1] - - #search_text = self.settings['search_text'].lower() - search_text = self.search_text - if search_text and (search_text in localname.lower()): #highlight terms that contain search text - localname = """{}""".format(localname) - - if isinstance(node, h5py.Group): - self.tree_str += indent +"|> {}/
".format(localname) - elif isinstance(node, h5py.Dataset): - self.tree_str += indent +"|D {}: {} {}
".format(localname, node.shape, node.dtype) - - #if using h5_plot_and_view - if hasattr(self.databrowser.ui, "dataset_listWidget"): - item_name = "{}: {} {}".format(localname, node.shape, node.dtype) - self.databrowser.ui.dataset_listWidget.addItem(item_name) - if not hasattr(self, "dataset_dict"): - self.dataset_dict = {} - self.dataset_dict[item_name] = node - - - for key, val in node.attrs.items(): #highlight terms that contain search text - if search_text: - if search_text in str(key).lower(): - key = """{}""".format(key) - if search_text in str(val).lower(): - val = """{}""".format(val) - self.tree_str += indent+"     |- {} = {}
".format(key, val) \ No newline at end of file diff --git a/src/main/python/H5_Pkl/h5_view_and_plot.py b/src/main/python/H5_Pkl/h5_view_and_plot.py deleted file mode 100644 index 18f3635..0000000 --- a/src/main/python/H5_Pkl/h5_view_and_plot.py +++ /dev/null @@ -1,141 +0,0 @@ -from __future__ import division, print_function, absolute_import -from ScopeFoundry import BaseApp -from ScopeFoundry.helper_funcs import load_qt_ui_file, sibling_path -from collections import OrderedDict -import os -from qtpy import QtCore, QtWidgets, QtGui -import pyqtgraph as pg -import pyqtgraph.dockarea as dockarea -import numpy as np -from ScopeFoundry.logged_quantity import LQCollection -from scipy.stats import spearmanr -import argparse -from .h5_tree import H5TreeSearchView -from .pkl_tree import PklTreeSearchView - - - -class H5ViewPlot(BaseApp): - - name = "h5_view_plot" - - def __init__(self, argv): - pg.setConfigOption('imageAxisOrder', 'row-major') - BaseApp.__init__(self, argv) - self.setup() - parser = argparse.ArgumentParser() - for lq in self.settings.as_list(): - parser.add_argument("--" + lq.name) - args = parser.parse_args() - for lq in self.settings.as_list(): - if lq.name in args: - val = getattr(args,lq.name) - if val is not None: - lq.update_value(val) - - def setup(self): - self.ui_filename = sibling_path(__file__, "h5_view_and_plot_gui.ui") - self.ui = load_qt_ui_file(self.ui_filename) - self.ui.show() - self.ui.raise_() - - self.settings.New('data_filename', dtype='file') - - self.settings.data_filename.add_listener(self.on_change_data_filename) - - self.settings.New('view_name', dtype=str, initial='0', choices=('0',)) - - # UI Connections - self.settings.data_filename.connect_to_browse_widgets(self.ui.data_filename_lineEdit, - self.ui.data_filename_browse_pushButton) - self.ui.plot_pushButton.clicked.connect(self.plot_dataset) - self.ui.dataset_listWidget.currentItemChanged.connect(self.on_data_selection) - self.ui.plot_radioButton.toggled.connect(self.update_data_widget) - self.ui.image_radioButton.toggled.connect(self.update_data_widget) - - #set up image item for 2d array - self.data_img_layout = pg.GraphicsLayoutWidget() - self.ui.imageItem_page.layout().addWidget(self.data_img_layout) - self.data_img_layout = self.data_img_layout.addViewBox() - self.data_img = pg.ImageItem() - self.data_img_layout.addItem(self.data_img) - - #set up image view for 3d array - self.ui.data_imageView.getView().invertY(False) - - self.h5treeview = H5TreeSearchView(self) - self.ui.dataview_page.layout().addWidget(self.h5treeview.ui) - self.h5treeview.ui.hide() - self.ui.show() - - def on_change_data_filename(self): - """ Handle file change """ - try: - fname = self.settings.data_filename.val - if os.path.isfile(fname): - self.f = self.h5treeview.on_change_data_filename(fname) - self.ui.dataview_placeholder.hide() - self.h5treeview.ui.show() - except: - pass - - def plot_dataset(self): - """ Plot data set depending on dataset shape and plot type option. """ - self.plot = self.ui.data_plotWidget.getPlotItem() - self.plot.clear() - - data = self.dataset[()] - if self.dataset_shape == 1: - x_start = self.ui.plotWidget_x_start_spinBox.value() - x_end = self.ui.plotWidget_x_end_spinBox.value() - num_points = self.dataset.shape[0] - x_values = np.linspace(x_start, x_end, num_points) - self.plot.plot(x_values, data) - elif self.dataset_shape == 2 and self.ui.plot_radioButton.isChecked(): - self.plot.plot(data[0], data[1]) # TODO check and test this - elif self.dataset_shape == 2 and self.ui.image_radioButton.isChecked(): - self.data_img.setImage(data) - elif self.dataset_shape == 3: - if self.f['Cube/Info/Cube'].attrs['AcqMode'] == b'Hyperspectral Acquisition': # This works for our PhotonEtc. Hyperspectral Camera output - x_start = int(self.f['Cube/Info/Cube'].attrs['LowerWavelength']) - x_end = int(self.f['Cube/Info/Cube'].attrs['UpperWavelength']) - else: - x_start = self.ui.imageView_x_start_spinBox.value() - x_end = self.ui.imageView_x_end_spinBox.value() - num_points = self.dataset.shape[0] - x_values = np.linspace(x_start, x_end, num_points) #scale x axis - self.ui.data_imageView.setImage(data, xvals=x_values) - - def on_data_selection(self): - """ Handle dataset selection """ - try: - dataset_name = self.ui.dataset_listWidget.currentItem().text() - self.dataset = self.h5treeview.dataset_dict[dataset_name] - self.dataset_shape = len(self.dataset[()].shape) - self.update_data_widget() - if self.dataset_shape == 1: - self.ui.plot_type_groupBox.setEnabled(False) - self.ui.plot_radioButton.setChecked(True) - elif self.dataset_shape == 2: - self.ui.plot_type_groupBox.setEnabled(True) - elif self.dataset_shape == 3: - self.ui.plot_type_groupBox.setEnabled(False) - self.ui.image_radioButton.setChecked(True) - except: - pass - - def update_data_widget(self): - """ Decide which widget to display based on dataset shape and plot type option. """ - if self.dataset_shape == 1: - self.ui.data_stackedWidget.setCurrentIndex(0) - elif self.dataset_shape == 2 and self.ui.plot_radioButton.isChecked(): - self.ui.data_stackedWidget.setCurrentIndex(0) - elif self.dataset_shape == 2 and self.ui.image_radioButton.isChecked(): - self.ui.data_stackedWidget.setCurrentIndex(1) - elif self.dataset_shape == 3: - self.ui.data_stackedWidget.setCurrentIndex(2) - -# if __name__ == '__main__': -# import sys -# app = H5ViewPlot(sys.argv) -# sys.exit(app.exec_()) \ No newline at end of file diff --git a/src/main/python/H5_Pkl/h5_view_and_plot_gui.ui b/src/main/python/H5_Pkl/h5_view_and_plot_gui.ui deleted file mode 100644 index a7bcc01..0000000 --- a/src/main/python/H5_Pkl/h5_view_and_plot_gui.ui +++ /dev/null @@ -1,280 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 856 - 925 - - - - H5 View and Plot - - - - - - - Qt::Horizontal - - - - File - - - - - - - - - File: - - - - - - - Browse... - - - - - - - true - - - 0 - - - - Data View - - - - - - Once a file is loaded, data will show up here. - - - - - - - - true - - - Plot - - - - - - Datasets - - - - - - - - - - - - Plot data - - - - - - 0 - - - - - - - - - - - - - 203 - 16777215 - - - - 9999999.000000000000000 - - - 0.000000000000000 - - - - - - - X start - - - - - - - 9999999.000000000000000 - - - - - - - X end - - - - - - - - - - - - - - - - - - - - - 9999999.000000000000000 - - - - - - - - 203 - 16777215 - - - - 9999999.000000000000000 - - - 0.000000000000000 - - - - - - - X start - - - - - - - X end - - - - - - - - - - - - - Plot - - - - - - - true - - - Type - - - - - - true - - - Plot - - - true - - - - - - - true - - - Image - - - - - - - - - - - - - - - - - - - - - - - 0 - 0 - 856 - 21 - - - - - - - - PlotWidget - QGraphicsView -
pyqtgraph
- - - ImageView - QGraphicsView -
pyqtgraph
- - - - - diff --git a/src/main/python/H5_Pkl/pkl_tree.py b/src/main/python/H5_Pkl/pkl_tree.py deleted file mode 100644 index e60a85e..0000000 --- a/src/main/python/H5_Pkl/pkl_tree.py +++ /dev/null @@ -1,103 +0,0 @@ -from ScopeFoundry.data_browser import DataBrowserView -from qtpy import QtWidgets -import h5py -import pickle -import numpy as np -import lmfit - -class PklTreeSearchView(DataBrowserView): - - name = 'pkl_tree_search' - - def is_file_supported(self, fname): - return ('.pkl' in fname) - - def setup(self): - #self.settings.New('search_text', dtype=str, initial="") - - self.ui = QtWidgets.QWidget() - self.ui.setLayout(QtWidgets.QVBoxLayout()) - self.search_lineEdit = QtWidgets.QLineEdit() - self.search_lineEdit.setPlaceholderText("Search") - self.tree_textEdit = QtWidgets.QTextEdit("") - - self.ui.layout().addWidget(self.search_lineEdit) - self.ui.layout().addWidget(self.tree_textEdit) - - #self.settings.search_text.connect_to_widget(self.search_lineEdit) - #self.settings.search_text.add_listener(self.on_new_search_text) - self.search_text = "" - - self.search_lineEdit.textChanged.connect(self.on_new_search_text) - - def on_change_data_filename(self, fname=None): - """ Handle file change """ - self.tree_textEdit.setText("loading {}".format(fname)) - try: - self.fname = fname - #self.f = h5py.File(fname, 'r') - self.dictionary = pickle.load(open(self.fname, 'rb')) - self.on_new_search_text() - self.databrowser.ui.statusbar.showMessage("") - - except Exception as err: - msg = "Failed to load %s:\n%s" %(fname, err) - self.databrowser.ui.statusbar.showMessage(msg) - self.tree_textEdit.setText(msg) - raise(err) - - def on_new_search_text(self, x=None): - if x is not None: - self.search_text = x.lower() - old_scroll_pos = self.tree_textEdit.verticalScrollBar().value() - self.tree_str = "" - #self.f.visititems(self._visitfunc) - self.traverse_dict(self.dictionary, self.dictionary, 0) - - - self.tree_text_html = \ - """{}
-
- {} -
- """.format(self.fname, self.tree_str) - - self.tree_textEdit.setText(self.tree_text_html) - self.tree_textEdit.verticalScrollBar().setValue(old_scroll_pos) - - def traverse_dict(self, dictionary, previous_dict, level): - """ - Visit all values in the dictionary and its subdictionaries. - - dictionary -- dictionary to traverse - previous_dict -- dictionary one level up - level -- track how far to indent - """ - for key in dictionary: - if key not in previous_dict: - level -=1 - indent = " "*4*(level) - - if type(dictionary[key]) == dict: - print_string = key - if self.search_text and self.search_text in print_string: - self.tree_str += indent + """{}""".format(print_string) - else: - self.tree_str += indent + "|> {}/
".format(print_string) - level += 1 - previous_dict = dictionary[key] - self.traverse_dict(dictionary[key], previous_dict, level) - else: - value = dictionary[key] - if type(value) == np.ndarray or type(value)==np.memmap: - value = str(value.shape) + " " + str(value.dtype) - elif type(value) == lmfit.model.ModelResult: - value = "lmfit.model.ModelResult" - # if type(value) == list and len(value) > 5: ##account for data stored in lists - # value = str(np.asarray(value).shape) + " " + str(type(value[0])) - - print_string = key + " = " + str(value) - if self.search_text and self.search_text in print_string: - self.tree_str += indent + """{}""".format(print_string) - else: - self.tree_str += indent + "|- {}
".format(print_string) \ No newline at end of file diff --git a/src/main/python/Image_analysis/Image_analysis.py b/src/main/python/Image_analysis/Image_analysis.py deleted file mode 100644 index 50b2d1c..0000000 --- a/src/main/python/Image_analysis/Image_analysis.py +++ /dev/null @@ -1,222 +0,0 @@ -import sys -from pathlib import Path -import os.path -import pyqtgraph as pg -from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog -import numpy as np -import matplotlib.pyplot as plt -from PIL import Image - -# local modules - -pg.mkQApp() - - -base_path = Path(__file__).parent -file_path = (base_path / "image_analysis_gui.ui").resolve() - -uiFile = file_path - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -def updateDelay(scale, time): - """ Hack fix for scalebar inaccuracy""" - QtCore.QTimer.singleShot(time, scale.updateBar) - -class MainWindow(TemplateBaseClass): - - def __init__(self): - pg.setConfigOption('imageAxisOrder', 'col-major') - super(TemplateBaseClass, self).__init__() - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - - #setup image plot - self.image_plot_layout=pg.GraphicsLayoutWidget() - self.ui.image_groupBox.layout().addWidget(self.image_plot_layout) - self.image_plot = self.image_plot_layout.addPlot() - self.img_item = pg.ImageItem() - self.image_plot.addItem(self.img_item) - self.image_plot_view = self.image_plot.getViewBox() - - #setup lookup table - self.hist_lut = pg.HistogramLUTItem() - self.image_plot_layout.addItem(self.hist_lut) - - #region of interest - allows user to select scan area - self.roi = pg.ROI([0,0],[10, 10], movable=True) - self.roi.addScaleHandle([1, 1], [0, 0]) - self.roi.addRotateHandle([0, 0], [1, 1]) - self.roi.translateSnap = True - self.roi.scaleSnap = True - self.roi.sigRegionChanged.connect(self.line_profile_update_plot) - self.image_plot.addItem(self.roi) - - #setup rgb plot - self.rgb_plot_layout=pg.GraphicsLayoutWidget() - self.ui.rgb_plot_groupBox.layout().addWidget(self.rgb_plot_layout) - self.rgb_plot = self.rgb_plot_layout.addPlot() - - #set up ui signals - self.ui.load_image_pushButton.clicked.connect(self.load_image) - self.ui.custom_pixel_size_checkBox.stateChanged.connect(self.switch_custom_pixel_size) - self.ui.update_settings_pushButton.clicked.connect(self.reload_image) - self.ui.spot_radioButton.toggled.connect(self.update_camera) - - self.update_camera() #initialize camera pixel size - self.update_scaling_factor() #initialize scaling_factor - self.show() - - #row major. invert y false, rotate false - def load_image(self): - """ - Prompts the user to select a text file containing image data. - """ - try: - file = QtWidgets.QFileDialog.getOpenFileName(self, 'Open file', os.getcwd()) - self.original_image = Image.open(file[0]) - self.original_image = self.original_image.rotate(-90, expand=True) #correct image orientation - self.resize_to_scaling_factor(self.original_image) - except Exception as err: - print(format(err)) - - def resize_to_scaling_factor(self, image): - """ - Handles loading of image according to scaling_factor - """ - self.update_scaling_factor() - - if self.ui.spot_radioButton.isChecked() and self.ui.resize_image_checkBox.isChecked(): - image = self.original_image.resize((round(image.size[0]*self.scaling_factor), round(image.size[1]*self.scaling_factor))) - self.image_plot.getAxis("bottom").setScale(scale = 1) - self.image_plot.getAxis("left").setScale(scale = 1) - else: - image = self.original_image - self.image_plot.getAxis("bottom").setScale(scale = self.scaling_factor) - self.image_plot.getAxis("left").setScale(scale = self.scaling_factor) - - if self.ui.greyscale_checkBox.isChecked(): - image = image.convert("L") #convert to greyscale - - self.image_array = np.array(image) - width = self.image_array.shape[0] - height = self.image_array.shape[1] - - try: - #set image bounds with qrect - self.img_item_rect = QtCore.QRectF(0, 0, width, height) - self.img_item.setImage(image=self.image_array) - self.img_item.setRect(self.img_item_rect) - - # if self.ui.greyscale_checkBox.isChecked(): - # self.hist_lut.setImageItem(self.img_item) - - if self.ui.vertical_radioButton.isChecked(): - roi_height = self.scaling_factor * height - self.roi.setSize([width, roi_height]) - elif self.ui.horizontal_radioButton.isChecked(): - roi_height = self.scaling_factor * width - self.roi.setSize([roi_height, height]) - self.roi.setAngle(0) - self.roi.setPos(0, 0) - self.line_profile_update_plot() - except: - pass - - def line_profile_update_plot(self): - """ Handle line profile for intensity sum viewbox """ - self.rgb_plot.clear() - - # Extract image data from ROI - data, coords = self.roi.getArrayRegion(self.image_array, self.img_item, returnMappedCoords=True) - if data is None: - return - - if self.ui.vertical_radioButton.isChecked(): - x_values = coords[0,:,0] - elif self.ui.horizontal_radioButton.isChecked(): - x_values = coords[1,0,:] - - if self.ui.pixera_radioButton.isChecked() or (self.ui.spot_radioButton.isChecked() and not self.ui.resize_image_checkBox.isChecked()): - x_values = x_values * self.scaling_factor - - #calculate average along columns in region - if len(data.shape) <= 2: #if grayscale, average intensities - if self.ui.vertical_radioButton.isChecked(): - avg_to_plot = np.mean(data, axis=-1) - elif self.ui.horizontal_radioButton.isChecked(): - avg_to_plot = np.mean(data, axis=0) - try: - self.rgb_plot.plot(x_values, avg_to_plot) - except: - pass - elif len(data.shape) > 2: #if rgb arrays, plot individual components - r_values = data[:,:,0] - g_values = data[:,:,1] - b_values = data[:,:,2] - if self.ui.vertical_radioButton.isChecked(): - r_avg = np.mean(r_values, axis=-1) #average red values across columns - g_avg = np.mean(g_values, axis=-1) #average green values - b_avg = np.mean(b_values, axis=-1) #average blue values - elif self.ui.horizontal_radioButton.isChecked(): - r_avg = np.mean(r_values, axis=0) - g_avg = np.mean(g_values, axis=0) - b_avg = np.mean(b_values, axis=0) - try: - self.rgb_plot.plot(x_values, r_avg, pen='r') - self.rgb_plot.plot(x_values, g_avg, pen='g') - self.rgb_plot.plot(x_values, b_avg, pen='b') - except Exception as e: - pass - - def update_scaling_factor(self): - """ - Calculate scaling factor - """ - if self.ui.custom_pixel_size_checkBox.isChecked(): - self.camera_pixel_size = self.ui.custom_pixel_size_spinBox.value() - self.scaling_factor = self.camera_pixel_size - else: - self.scaling_factor = self.camera_pixel_size/int(self.ui.magnification_comboBox.currentText()) - self.roi.snapSize = self.scaling_factor #roi snaps to multiples of scaling_factor - - def reload_image(self): - if hasattr(self, "original_image"): - self.resize_to_scaling_factor(self.original_image) #resize image, sets up roi - - def switch_custom_pixel_size(self): - checked = self.ui.custom_pixel_size_checkBox.isChecked() - self.ui.custom_pixel_size_spinBox.setEnabled(checked) - self.ui.magnification_comboBox.setEnabled(not checked) - - def update_camera(self): - if self.ui.spot_radioButton.isChecked(): - self.camera_pixel_size = 7.4 - self.ui.greyscale_checkBox.setChecked(False) - self.ui.resize_image_checkBox.setEnabled(True) - self.update_scaling_factor() - elif self.ui.pixera_radioButton.isChecked(): - self.camera_pixel_size = 3 - self.ui.greyscale_checkBox.setChecked(True) - self.ui.resize_image_checkBox.setEnabled(False) - self.update_scaling_factor() - - def close_application(self): - choice = QtGui.QMessageBox.question(self, 'EXIT!', - "Do you want to exit the app?", - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if choice == QtGui.QMessageBox.Yes: - sys.exit() - else: - pass - -"""Run the Main Window""" -def run(): - win = MainWindow() - QtGui.QApplication.instance().exec_() - return win - -#Uncomment below if you want to run this as standalone -#run() \ No newline at end of file diff --git a/src/main/python/Image_analysis/image_analysis_gui.ui b/src/main/python/Image_analysis/image_analysis_gui.ui deleted file mode 100644 index 9fcffd9..0000000 --- a/src/main/python/Image_analysis/image_analysis_gui.ui +++ /dev/null @@ -1,208 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 1029 - 743 - - - - Image Analysis - - - QTabWidget::Triangular - - - - - - - Settings - - - - - - - - - - - - - Greyscale image - - - - - - - Load image - - - - - - - - 50 - - - - - 75 - - - - - 100 - - - - - 150 - - - - - - - - Magnification - - - - - - - Update settings - - - - - - - false - - - - - - - Custom pixel size (um) - - - - - - - Camera - - - - - - SPOT - - - true - - - - - - - Pixera - - - - - - - Resize image - - - - - - - - - - Direction to average pixels - - - - - - Vertical - - - true - - - - - - - Horizontal - - - - - - - - - - - - - - - - 0 - 0 - - - - - 600 - 0 - - - - Image - - - - - - - - RGB Plot - - - - - - - - - - 0 - 0 - 1029 - 31 - - - - - - - - diff --git a/src/main/python/Lifetime_analysis/Fit_functions.py b/src/main/python/Lifetime_analysis/Fit_functions.py deleted file mode 100644 index 7ad5c3e..0000000 --- a/src/main/python/Lifetime_analysis/Fit_functions.py +++ /dev/null @@ -1,132 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Fri Mar 29 11:21:59 2019 - -@author: Sarthak -""" - -import numpy as np -from scipy.optimize import differential_evolution -from scipy.special import gamma - -def stretch_exp_fit(TRPL, t, Tc = (0,1e5), Beta = (0,1), A = (0,1e6), noise=(0,1e6)): - - def exp_stretch(t, tc, beta, a, noise): - return ((a * np.exp(-((1.0 / tc) * t) ** beta)) + noise) - - def avg_tau_from_exp_stretch(tc, beta): - return (tc / beta) * gamma(1.0 / beta) - - def Diff_Ev_Fit_SE(TRPL): - TRPL = TRPL - - def residuals(params):#params are the parameters to be adjusted by differential evolution or leastsq, interp is the data to compare to the model. - #Variable Rates - tc = params[0] - beta = params[1] - a = params[2] - noise = params[3] - - PL_sim = exp_stretch(t,tc,beta,a, noise) - - Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) - return Resid #returns the difference between the PL data and simulated data - - bounds = [Tc, Beta, A, noise] - - result = differential_evolution(residuals, bounds) - return result.x - - p = Diff_Ev_Fit_SE(TRPL) - - tc = p[0] - beta = p[1] - a = p[2] - noise = p[3] - - PL_fit = exp_stretch(t,tc,beta,a, noise) - - avg_tau = avg_tau_from_exp_stretch(tc,beta) - - return tc, beta, a, avg_tau, PL_fit, noise - -def double_exp_fit(TRPL, t, tau1_bounds=(0,1000), a1_bounds=(0,1e6), tau2_bounds=(0,10000), a2_bounds=(0,1e5), noise=(0,1e6)): - - def single_exp(t, tau, a): - return (a * np.exp(-((1.0 / tau)*t))) - - def double_exp(t, tau1, a1, tau2, a2, noise): - return ((single_exp(t, tau1, a1)) + (single_exp(t, tau2, a2)) + noise) - - def avg_tau_from_double_exp(tau1, a1, tau2, a2): - return (((tau1*a1) + (tau2*a2))/(a1+a2)) - - def Diff_Ev_Fit_DE(TRPL): - TRPL = TRPL - - def residuals(params):#params are the parameters to be adjusted by differential evolution or leastsq, interp is the data to compare to the model. - #Variable Rates - tau1 = params[0] - a1 = params[1] - tau2 = params[2] - a2 = params[3] - noise = params[4] - - PL_sim = double_exp(t,tau1, a1, tau2, a2, noise) - - Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) - return Resid #returns the difference between the PL data and simulated data - - bounds = [tau1_bounds, a1_bounds, tau2_bounds, a2_bounds, noise] - - result = differential_evolution(residuals, bounds) - return result.x - - p = Diff_Ev_Fit_DE(TRPL) - - tau1 = p[0] - a1 = p[1] - tau2 = p[2] - a2 = p[3] - noise = p[4] - - PL_fit = double_exp(t, tau1, a1, tau2, a2, noise) - - avg_tau = avg_tau_from_double_exp(tau1, a1, tau2, a2) - - return tau1, a1, tau2, a2, avg_tau, PL_fit, noise - -def single_exp_fit(TRPL, t, tau_bounds=(0,10000), a_bounds=(0,1e6), noise=(0,1e6)): - - def single_exp(t, tau, a, noise): - return (a * np.exp(-((1.0 / tau)*t) ) + noise) - - def Diff_Ev_Fit_singleExp(TRPL): - TRPL = TRPL - - def residuals(params):#params are the parameters to be adjusted by differential evolution or leastsq, interp is the data to compare to the model. - #Variable Rates - tau = params[0] - a = params[1] - noise = params[2] - - PL_sim = single_exp(t, tau, a, noise) - - Resid= np.sum(((PL_sim-TRPL)**2)/(np.sqrt(TRPL)**2)) - return Resid #returns the difference between the PL data and simulated data - - bounds = [tau_bounds, a_bounds, noise] - - result = differential_evolution(residuals, bounds) - return result.x - - p = Diff_Ev_Fit_singleExp(TRPL) - - tau = p[0] - a = p[1] - noise = p[2] - - PL_fit = single_exp(t, tau, a, noise) - - return tau, a, PL_fit, noise - \ No newline at end of file diff --git a/src/main/python/Lifetime_analysis/Fit_functions_with_irf.py b/src/main/python/Lifetime_analysis/Fit_functions_with_irf.py deleted file mode 100644 index 5b454af..0000000 --- a/src/main/python/Lifetime_analysis/Fit_functions_with_irf.py +++ /dev/null @@ -1,329 +0,0 @@ -import numpy as np -import matplotlib.pyplot as plt -from scipy.optimize import fmin_tnc, differential_evolution -from scipy.special import gamma -from scipy.signal import fftconvolve -from scipy.integrate import odeint - - -"""Fit TCSPC data to a model by reconvolution with the IRF -Convolution is done in time domain with np.convolve() -Convolution can be done in the frequency domain of np.convolve() is replaced by scipy.signal.fftconvolve() - -For a good tutorial on numerical convolution, see section 13.1 of Numerical Recipes: - -Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P., -Numerical Recipes 3rd Edition: The Art of Scientific Computing. 3 ed.; -Cambridge University Press: New York, 2007 - -***Note that algorithm given in Numerical Recipes does convolution in the frequency -domain using the FFT. However the discussion of convolution in 13.1 applies to the time -domain and can be used to understand this Python code.*** - --MZ, 2/2017 -""" - -def convolve_sig_resp(signal_array, response_array, t_array, tstep): - - def normalize_response(response_array, t_array): - area = np.trapz(response_array, x = t_array) - return response_array / area - - def array_zeropad_neg(array, pad_length): - - return np.pad(array, (pad_length, 0), 'constant', constant_values = (0,0)) - - def array_zeropad_pos(array, pad_length): - return np.pad(array, (0, pad_length), 'constant', constant_values = (0,0)) - -# def array_symmetricpad_neg(array, pad_length): -# -# return np.pad(array, (pad_length, 0), 'symmetric') - - def signal_and_resp_forconv(signal_array, response_array): - resp_pad_negtime = array_zeropad_neg(normalize_response(response_array, t_array), len(response_array) - 1) - sig_pad_negtime = array_zeropad_neg(signal_array, len(signal_array) - 1) - sig_pad_postime = array_zeropad_pos(sig_pad_negtime, len(response_array)) - return [resp_pad_negtime, sig_pad_postime] - - resp, sig = signal_and_resp_forconv(signal_array, response_array) - convolution = tstep * fftconvolve(sig, resp, mode = 'same')#np.convolve(resp, sig, mode = 'same') - - return convolution[len(signal_array) - 1 : (2*len(signal_array)) - 1] - -def convolution_plusnoise(signal_array, response_array, t_array, tstep, noiselevel): - return convolve_sig_resp(signal_array, response_array, t_array, tstep) + noiselevel - -def herz_ode(t, n0, params): - a = params[0] - k1 = params[1] - k2 = params[2] - k3 = params[3] - def odefun(n, t, k1, k2, k3): - dndt = -(k1 * n) - (k2 * (n ** 2.0)) - (k3 * (n ** 3.0)) - return dndt - ode_sol = odeint(odefun, n0, t, args = (k1, k2, k3))[:,0] - pl = k2 * (ode_sol ** 2.0) - return a*pl - -def fit_herz_ode_global_3traces_fmin_tnc(t1, t2, t3, tstep, d1, d2, d3, irf, init_params, bounds, n0array): - time_array1 = t1 - time_array2 = t2 - time_array3 = t3 - data_array1 = d1 - data_array2 = d2 - data_array3 = d3 - n0 = n0array[0] - n1 = n0array[1] - n2 = n0array[2] - def min_fit_decay(params): - #Minimize chi-squre for data set with Poisson distribution () - - a0 = params[0] - a1 = params[1] - a2 = params[2] - k1 = params[3] - k2 = params[4] - k3 = params[5] - noise1 = params[6] - noise2 = params[7] - noise3 = params[8] - decaymodel1 = herz_ode(time_array1, n0, np.array([a0,k1,k2,k3])) - decaymodel2 = herz_ode(time_array2, n1, np.array([a1,k1,k2,k3])) - decaymodel3 = herz_ode(time_array3, n2, np.array([a2,k1,k2,k3])) - model1 = convolution_plusnoise(decaymodel1, irf, time_array1, tstep, noise1) - model2 = convolution_plusnoise(decaymodel2, irf, time_array2, tstep, noise2) - - model3 = convolution_plusnoise(decaymodel3, irf, time_array3, tstep, noise3) - - data_fit_idx1 = np.nonzero(data_array1) - data_fit_idx2 = np.nonzero(data_array2) - data_fit_idx3 = np.nonzero(data_array3) - data_array_fit1 = data_array1[data_fit_idx1] - data_array_fit2 = data_array2[data_fit_idx2] - data_array_fit3 = data_array3[data_fit_idx3] - - model_fit1 = model1[data_fit_idx1] - model_fit2 = model2[data_fit_idx2] - model_fit3 = model3[data_fit_idx3] - - min1 = np.sum(((data_array_fit1 - model_fit1)** 2.0) / (np.sqrt(data_array_fit1) ** 2.0)) - min2 = np.sum(((data_array_fit2 - model_fit2)** 2.0) / (np.sqrt(data_array_fit2) ** 2.0)) - min3 = np.sum(((data_array_fit3 - model_fit3)** 2.0) / (np.sqrt(data_array_fit3) ** 2.0)) - return np.sqrt((min1 ** 2.0) + (min2 ** 2.0) + (min3 ** 2.0)) - bestfit_params = fmin_tnc(min_fit_decay, init_params, approx_grad = True, bounds = bounds)[0] - def bestfit_decay(params): - a0 = params[0] - a1 = params[1] - a2 = params[2] - k1 = params[3] - k2 = params[4] - k3 = params[5] - noise1 = params[6] - # noise2 = params[7] - # noise3 = params[8] - decaymodel1 = herz_ode(time_array, n0, np.array([a0,k1,k2,k3])) - decaymodel2 = herz_ode(time_array, n1, np.array([a1,k1,k2,k3])) - decaymodel3 = herz_ode(time_array, n2, np.array([a2,k1,k2,k3])) - - model1 = convolution_plusnoise(decaymodel1, irf, time_array, tstep, noise1) - model2 = convolution_plusnoise(decaymodel2, irf, time_array, tstep, noise2) - model3 = convolution_plusnoise(decaymodel3, irf, time_array, tstep, noise3) - return [model1, model2, model3] - - bestfit_model = bestfit_decay(bestfit_params) - # plt.figure() - # plt.ylabel('PL Counts') - # plt.xlabel('Time (ns)') - # plt.semilogy(time_array1, data_array1,'b', label = 'Data') - # plt.semilogy(time_array1, bestfit_model[0], 'r', label = 'Fit') - # plt.semilogy(time_array2, data_array2,'b', label = 'Data') - # plt.semilogy(time_array2, bestfit_model[1], 'r', label = 'Fit') - # plt.semilogy(time_array3, data_array3,'b', label = 'Data') - # plt.semilogy(time_array3, bestfit_model[2], 'r', label = 'Fit') - # plt.legend(loc = 'best') - return bestfit_params, bestfit_model, data_array, time_array, irf - -def multi_exp(t, params, num_exp): - exp_array = np.empty((len(t), num_exp)) - - i = 0 - while (i - - MainWindow - - - - 0 - 0 - 2620 - 1676 - - - - Lifetime Analysis - - - - - - - - - true - - - - 10 - - - - Fitting Controls - - - false - - - - - - - - - 10 - - - - Fit with IRF - - - true - - - false - - - - - - - - 10 - - - - Fitting Function - - - - - - - - 10 - - - - - - - - true - - - - 10 - - - - Fitting method - - - - - - - - 10 - - - - - - - - - - - - - - - - - 0 - - - - - - - true - - - - 10 - - - - Bounds - - - - - - 4 - - - 9999999.000000000000000 - - - 1.100000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 0.900000000000000 - - - - - - - 4 - - - 1.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 10000.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - tc (ns) - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - beta - - - - - - - noise - - - - - - - 4 - - - 1.000000000000000 - - - 1.000000000000000 - - - - - - - a - - - - - - - 4 - - - 9999999.000000000000000 - - - 10000.000000000000000 - - - - - - - min - - - - - - - max - - - - - - - - - - false - - - - 10 - - - - Initial Guess - - - - - - a - - - - - - - noise - - - - - - - beta - - - - - - - tc (ns) - - - - - - - 4 - - - 9999999.000000000000000 - - - 5.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 1.000000000000000 - - - - - - - 4 - - - 1.000000000000000 - - - 0.500000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 0.100000000000000 - - - - - - - - - - - - - - Bounds - - - - - - min - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - max - - - - - - - a1 - - - - - - - - - - - - - - noise - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 300.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 10000.000000000000000 - - - - - - - tau2 (ns) - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 10000.000000000000000 - - - - - - - a2 - - - - - - - 4 - - - 9999999.000000000000000 - - - 10000.000000000000000 - - - - - - - tau1 (ns) - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 10.000000000000000 - - - - - - - - - - Initial Guess - - - - - - 4 - - - 9999999.000000000000000 - - - 1.000000000000000 - - - - - - - a1 - - - - - - - 4 - - - 9999999.000000000000000 - - - 1.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - 20.000000000000000 - - - - - - - a2 - - - - - - - 4 - - - 9999999.000000000000000 - - - 0.100000000000000 - - - - - - - tau2 (ns) - - - - - - - noise - - - - - - - tau1 (ns) - - - - - - - 4 - - - 9999999.000000000000000 - - - 1.000000000000000 - - - - - - - - - - - - - - Bounds - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - max - - - - - - - 4 - - - 9999999.000000000000000 - - - 10.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - - - - - - - - noise - - - - - - - a - - - - - - - 4 - - - 9999999.000000000000000 - - - 10000.000000000000000 - - - - - - - tau (ns) - - - - - - - 4 - - - 9999999.000000000000000 - - - 10000.000000000000000 - - - - - - - min - - - - - - - - - - Initial Guess - - - - - - 4 - - - 9999999.000000000000000 - - - 1.000000000000000 - - - - - - - a - - - - - - - tau (ns) - - - - - - - 4 - - - 9999999.000000000000000 - - - 1.000000000000000 - - - - - - - noise - - - - - - - 4 - - - 9999999.000000000000000 - - - 0.100000000000000 - - - - - - - - - - - - - - - - - - 10 - - - - Get Lifetime! - - - - - - - true - - - - 10 - - - - Calculate SRV - - - true - - - false - - - - - - Bulk Lifetime (ns) - - - - - - - Thickness (nm) - - - - - - - 100000.000000000000000 - - - 250.000000000000000 - - - - - - - 1000000.000000000000000 - - - 3.000000000000000 - - - - - - - 4 - - - 9999999.000000000000000 - - - - - - - 0 - - - - - - - 0 - - - - - - - SRV (cm/s) - - - - - - - 100000.000000000000000 - - - 8000.000000000000000 - - - - - - - Diffusion Coefficient (cm2/s) - - - - - - - Surface Lifetime (ns) - - - - - - - Average Lifetime (ns) - - - - - - - Calculate - - - - - - - SRV (cm/s) - - - - - - - 0 - - - - - - - - 75 - true - - - - SRV1 = SRV2 - - - - - - - - 75 - true - - - - SRV1 = 0 - - - - - - - - - - - - - 2 - 0 - - - - - - - - - 15 - - - - Settings - - - - - - - 12 - - - - Export Settings - - - - - - For Figure: - - - - - - - Export Fit Data - - - - - - - Clear Export Memory - - - - - - - - 12 - 50 - false - - - - Export figure - - - - - - - For Data: - - - - - - - Enter Legend Here... - - - - - - - Add trace to memory - - - - - - - - - - - 12 - - - - Plot Controls - - - - - - - 12 - 50 - false - - - - Plot - - - - - - - Y Axis Log - - - - - - - Plot color - - - - - - - - 12 - false - - - - Clear Plot - - - - - - - - - - - - Normalize - - - - - - - Clear plot everytime - - - - - - - - - - - 12 - - - - - - - - - 12 - - - - Resolution (ns) - - - - - - - false - - - - 12 - - - - true - - - - - - - - 12 - - - - 512 - - - 1 - - - - - - - - 12 - - - - IRF Channel No - - - - - - - - 12 - - - - Data Channel No - - - - - - - - 12 - - - - - - - - - 12 - - - - Load separate IRF file - - - - - - - - 12 - - - - Smooth Data - - - - - - - false - - - - 12 - - - - 1 - - - 1000 - - - - - - - - - - - - 0 - 0 - 2620 - 38 - - - - - File - - - - - - - - - - - - Open - - - - - Exit - - - - - Save - - - - - false - - - Open IRF File - - - - - - PlotWidget - QGraphicsView -
pyqtgraph
- - - - - diff --git a/src/main/python/Lifetime_analysis/Lifetime_plot_fit.py b/src/main/python/Lifetime_analysis/Lifetime_plot_fit.py deleted file mode 100644 index 7967a1e..0000000 --- a/src/main/python/Lifetime_analysis/Lifetime_plot_fit.py +++ /dev/null @@ -1,653 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Wed Mar 27 16:50:26 2019 - -@author: Sarthak -""" - -# system imports -import sys -import os -from pathlib import Path - -# module imports -import pyqtgraph as pg -from pyqtgraph.Qt import QtCore, QtGui, QtWidgets -import numpy as np -import matplotlib.pyplot as plt - -sys.path.append(os.path.abspath('../Export_Windows')) -try: - from Export_window import ExportPlotWindow -except: - from Export_Windows.Export_window import ExportPlotWindow - -# local module imports -try: - from Lifetime_analysis.Fit_functions import stretch_exp_fit, double_exp_fit, single_exp_fit - from Lifetime_analysis.picoharp_phd import read_picoharp_phd - from Lifetime_analysis.Fit_functions_with_irf import fit_exp_stretch_diffev, fit_exp_stretch_fmin_tnc, fit_multi_exp_diffev, fit_multi_exp_fmin_tnc -except: - from Fit_functions import stretch_exp_fit, double_exp_fit, single_exp_fit - from Fit_functions_with_irf import fit_exp_stretch_diffev, fit_exp_stretch_fmin_tnc, fit_multi_exp_diffev, fit_multi_exp_fmin_tnc - from picoharp_phd import read_picoharp_phd - -"""Recylce params for plotting""" -plt.rc('xtick', labelsize = 20) -plt.rc('xtick.major', pad = 3) -plt.rc('ytick', labelsize = 20) -plt.rc('lines', lw = 2.5, markersize = 7.5) -plt.rc('legend', fontsize = 20) -plt.rc('axes', linewidth=3.5) - -pg.mkQApp() -pg.setConfigOption('background', 'w') -##pg.setConfigOption('crashWarning', True) - -base_path = Path(__file__).parent -file_path = (base_path / "Lifetime_analysis_gui_layout.ui").resolve() - -uiFile = file_path - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -class MainWindow(TemplateBaseClass): - - def __init__(self): - TemplateBaseClass.__init__(self) - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - self.ui.Res_comboBox.addItems(["0.004","0.008","0.016","0.032","0.064","0.128","0.256","0.512"]) - self.ui.FittingFunc_comboBox.addItems(["Stretched Exponential","Double Exponential", "Single Exponential"]) - self.ui.FittingMethod_comboBox.addItems(["diff_ev", "fmin_tnc"]) - - #set up file menu - self.ui.actionOpen.triggered.connect(self.open_file) - self.ui.actionOpen_IRF_File.triggered.connect(self.open_irf_file) - self.ui.actionSave.triggered.connect(self.save_file) - self.ui.actionExit.triggered.connect(self.close_application) - - #set up ui signals - self.ui.plot_pushButton.clicked.connect(self.plot) - self.ui.fit_pushButton.clicked.connect(self.call_fit_and_plot) - self.ui.clear_pushButton.clicked.connect(self.clear_plot) - self.ui.export_plot_pushButton.clicked.connect(self.export_window)#pub_ready_plot_export - self.ui.calculate_srv_pushButton.clicked.connect(self.calculate_srv) - - self.ui.log_checkBox.stateChanged.connect(self.make_semilog) - self.ui.fit_with_irf_checkBox.stateChanged.connect(self.switch_fit_settings) - self.ui.FittingFunc_comboBox.currentTextChanged.connect(self.switch_function_tab) - self.ui.FittingMethod_comboBox.currentTextChanged.connect(self.switch_init_params_groupBox) - self.ui.separate_irf_checkBox.stateChanged.connect(self.switch_open_irf) - self.ui.add_to_mem_pushButton.clicked.connect(self.add_trace_to_mem) - self.ui.export_data_pushButton.clicked.connect(self.export_data) - self.ui.clear_export_data_pushButton.clicked.connect(self.clear_export_data) - self.ui.smoothData_checkBox.stateChanged.connect(self.smooth_trace_enabled) - - #set up plot color button - self.plot_color_button = pg.ColorButton(color=(255,0,0)) - self.ui.plot_color_button_container.layout().addWidget(self.plot_color_button) - self.plot_color = self.plot_color_button.color() - self.plot_color_button.sigColorChanged.connect(self.plot_color_changed) - - self.file = None - self.out = None # output file after fitting - self.data_list = [] - self.fit_lifetime_called_w_irf = False - self.fit_lifetime_called_wo_irf = False - self.x_mem = [] # containers for adding x data to memory - self.y_mem = [] # containers for adding y data to memory - self.best_fit_mem = [] # containers for adding best fit data to memory - self.best_fit_mem_x = [] # containers for adding best fit data to memory - self.legend = [] # containers for adding legend to memory - - #variables accounting for data received from FLIM analysis - self.opened_from_flim = False #switched to True in FLIM_plot when "analyze lifetime" clicked - self.hist_data_from_flim = [] #container for flim roi data - - self.show() - - def open_file(self): - """ Open data file """ -# try: - self.filename = QtWidgets.QFileDialog.getOpenFileName(self) - try: - if ".csv" in self.filename[0] or ".txt" in self.filename[0]: #if txt or csv, prompt user to enter # of rows to skip - self.skip_rows_window = SkipRowsWindow() - self.skip_rows_window.skip_rows_signal.connect(self.open_with_skip_rows_window) - self.ui.Res_comboBox.setEnabled(True) - else: - self.file = read_picoharp_phd(self.filename[0]) - self.opened_from_flim = False - except: - pass - - def open_with_skip_rows_window(self): - """ Prompts user to enter how many rows to skip """ - skip_rows = self.skip_rows_window.ui.skip_rows_spinBox.value() - if ".txt" in self.filename[0]: - self.file = np.loadtxt(self.filename[0], skiprows=skip_rows) - elif ".csv" in self.filename[0]: - self.file = np.genfromtxt(self.filename[0], skip_header=skip_rows, delimiter=",") - - def open_irf_file(self): - """ Open file with irf - enabled if 'load separate irf' is checled """ - self.irf_filename = QtWidgets.QFileDialog.getOpenFileName(self) - try: - if ".txt" in self.irf_filename[0] or ".csv" in self.irf_filename[0]: - self.irf_skip_rows_window = SkipRowsWindow() - self.irf_skip_rows_window.skip_rows_signal.connect(self.open_irf_with_skip_rows_window) - self.ui.Res_comboBox.setEnabled(True) - else: - self.irf_file = read_picoharp_phd(self.irf_filename[0]) - except: - pass - - def open_irf_with_skip_rows_window(self): - irf_skip_rows = self.irf_skip_rows_window.ui.skip_rows_spinBox.value() - if ".txt" in self.irf_filename[0]: - self.irf_file = np.loadtxt(self.irf_filename[0], skiprows=irf_skip_rows) - elif ".csv" in self.irf_filename[0]: - self.irf_file = np.genfrontxt(self.irf_filename[0], skip_header=irf_skip_rows, delimiter=",") - - def save_file(self): - try: - filename = QtWidgets.QFileDialog.getSaveFileName(self) - np.savetxt(filename[0], self.out, fmt = '%.5f', header = 'Time, Raw_PL, Sim_PL', delimiter = ' ') - except: - pass - - def switch_open_irf(self): - """ Handle 'load separate irf' checkbox """ - self.ui.actionOpen_IRF_File.setEnabled(self.ui.separate_irf_checkBox.isChecked()) - - def switch_fit_settings(self): - """ Enable bounds/initial guess groupboxes only when 'Fit with IRF' is checked """ - checked = self.ui.fit_with_irf_checkBox.isChecked() - for func in "str de se".split(" "): - boundsGb = eval("self.ui."+func+"_bounds_groupBox") - #initGb = eval("self.ui."+func+"_init_groupBox") - boundsGb.setEnabled(checked) - #initGb.setEnabled(checked) - if checked == True: - self.switch_init_params_groupBox() - else: - initGb = eval("self.ui."+func+"_init_groupBox") - initGb.setEnabled(checked) - self.ui.FittingMethod_comboBox.setEnabled(checked) - - def switch_function_tab(self): - """ Switch bounds groupbox contents depending on selected fit function """ - fitting_func = self.ui.FittingFunc_comboBox.currentText() - if fitting_func == "Stretched Exponential": - self.ui.fitting_params_stackedWidget.setCurrentIndex(0) - elif fitting_func == "Double Exponential": - self.ui.fitting_params_stackedWidget.setCurrentIndex(1) - elif fitting_func == "Single Exponential": - self.ui.fitting_params_stackedWidget.setCurrentIndex(2) - - def switch_init_params_groupBox(self): - """ Enable initial guess groupbox only when fmin_tnc fit method selected """ - if self.ui.FittingMethod_comboBox.currentText() == "diff_ev": - for func in "str de se".split(" "): - initGb = eval("self.ui."+func+"_init_groupBox") - initGb.setEnabled(False) - #initGb.setEnabled(checked) - elif self.ui.FittingMethod_comboBox.currentText() == "fmin_tnc": - for func in "str de se".split(" "): - initGb = eval("self.ui."+func+"_init_groupBox") - initGb.setEnabled(True) - - def plot_color_changed(self): - """ Grab new plot_color when color button value is changed """ - self.plot_color = self.plot_color_button.color() - - def smooth_trace_enabled(self): - """Enable smooth spin box when smooth data is checked""" - if self.ui.smoothData_checkBox.isChecked(): - self.ui.smoothData_spinBox.setEnabled(True) - else: - self.ui.smoothData_spinBox.setEnabled(False) - - def acquire_settings(self, mode="data"): - """ - Acquire data or irf from channel specified in spinbox. - - mode -- string specifying whether to use data or irf channel (default "data") - """ - if mode == "data": - channel = int(self.ui.Data_channel_spinBox.value()) - elif mode == "irf": - channel = int(self.ui.irf_channel_spinBox.value()) - try: - try: # - if self.ui.separate_irf_checkBox.isChecked() and mode=="irf": #if separate irf, get from irf file - try: - y = self.irf_file[:,channel] - except: - y = self.irf_file.get_curve(channel)[1] - else: #otherwise, get data/irf from data file - y = self.file[:,channel] - - self.resolution = float(self.ui.Res_comboBox.currentText()) - except: - res, y = self.file.get_curve(channel) - time_window = int(np.floor(self.file.get_time_window_in_ns(channel))) - y = y[0:time_window] - self.resolution = res - - length = np.shape(y)[0] - x = np.arange(0, length*self.resolution, self.resolution, np.float) - - if self.ui.smoothData_checkBox.isChecked() and mode=="data": - y = np.convolve(y, np.ones(self.ui.smoothData_spinBox.value())/self.ui.smoothData_spinBox.value(), mode="same") - - if self.ui.normalize_checkBox.isChecked(): - y = y / np.amax(y) - - return x,y - - except Exception as e: - self.ui.Result_textBrowser.setText(str(e)) - - def plot(self): - try: - if self.opened_from_flim: - x, y = self.hist_data_from_flim - else: - x,y = self.acquire_settings() #get data - - self.ui.plot.plot(x, y, clear=self.ui.clear_plot_checkBox.isChecked(), pen=pg.mkPen(self.plot_color)) - self.fit_lifetime_called_w_irf = False - self.fit_lifetime_called_wo_irf = False - - try: - self.ui.Result_textBrowser.setText("Integral Counts :\n" "{:.2E}".format( - self.file.get_integral_counts(int(self.ui.Channel_spinBox.value())))) - except: - self.ui.Result_textBrowser.setText("Integral Counts :\n" "{:.2E}".format(np.sum(y))) - except: - pass - self.ui.plot.setLabel('left', 'Intensity', units='a.u.') - self.ui.plot.setLabel('bottom', 'Time (ns)') - - def make_semilog(self): - """ Switch y-log on/off """ - self.ui.plot.setLogMode(False,self.ui.log_checkBox.isChecked()) - - def clear_plot(self): - self.ui.plot.clear() - self.ui.Result_textBrowser.clear() - - def fit_and_plot(self): - """ Fit and plot without IRF """ - try: - if not hasattr(self, "file"): - self.ui.Result_textBrowser.setText("You need to load a data file.") - else: - if self.opened_from_flim: - x, y = self.hist_data_from_flim - else: - x,y = self.acquire_settings() #get data - y_norm = y/np.max(y) #normalized y - - # find the max intensity in the array and start things from there - find_max_int = np.nonzero(y_norm == 1) - y = y[np.asscalar(find_max_int[0]):] - x = x[np.asscalar(find_max_int[0]):] - - t = x - time_fit = t - TRPL_interp = np.interp(time_fit, t, y) - - fit_func = self.ui.FittingFunc_comboBox.currentText() - self.ui.plot.plot(t, y, clear=self.ui.clear_plot_checkBox.isChecked(), pen=pg.mkPen(self.plot_color)) - - if fit_func == "Stretched Exponential": #stretch exponential tab - tc, beta, a, avg_tau, PL_fit, noise = stretch_exp_fit(TRPL_interp, t) - self.out = np.empty((len(t), 3)) - self.out[:,0] = t #time - self.out[:,1] = TRPL_interp #Raw PL - self.out[:,2] = PL_fit # PL fit - self.ui.plot.plot(t, PL_fit, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') - self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Stretched Exponential" - "\nFit Method: " + "diff_ev" + #TODO : change when diff_ev and fmin_tnc implemented for non-irf - "\nAverage Lifetime = " + str(avg_tau)+ " ns" - "\nCharacteristic Tau = " + str(tc)+" ns" - "\nBeta = "+str(beta)+ - "\nNoise = "+ str(noise)) - self.ui.average_lifetime_spinBox.setValue(avg_tau) - - elif fit_func == "Double Exponential": #double exponential tab - tau1, a1, tau2, a2, avg_tau, PL_fit, noise = double_exp_fit(TRPL_interp, t) - self.out = np.empty((len(t), 3)) - self.out[:,0] = t #time - self.out[:,1] = TRPL_interp #Raw PL - self.out[:,2] = PL_fit # PL fit - self.ui.plot.plot(t, PL_fit, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') - self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Double Exponential" - "\nFit Method: " + "diff_ev" + - "\nAverage Lifetime = " + str(avg_tau)+ " ns" - "\nTau 1 = " + str(tau1)+" ns" - "\nA 1 = " + str(a1)+ - "\nTau 2 = " + str(tau2)+" ns" - "\nA 2 = " + str(a2)+ - "\nNoise = "+ str(noise)) - #TODO - once tau_avg implemented, set average lifetime spinbox to tau_avg value - - elif fit_func == "Single Exponential": #single exponential tab - tau, a, PL_fit, noise = single_exp_fit(TRPL_interp, t) - self.out = np.empty((len(t), 3)) - self.out[:,0] = t #time - self.out[:,1] = TRPL_interp #Raw PL - self.out[:,2] = PL_fit # PL fit - self.ui.plot.plot(t, PL_fit, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') - self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Single Exponential" - "\nFit Method: " + "diff_ev" + - "\nLifetime = " + str(tau)+ " ns" - "\nA = " + str(a)+ - "\nNoise = "+ str(noise)) - self.ui.average_lifetime_spinBox.setValue(tau) - - #add fit params to data_list - self.data_list.append("Data Channel: " + str(self.ui.Data_channel_spinBox.value()) + "\n" + self.ui.Result_textBrowser.toPlainText()) - self.fit_lifetime_called_wo_irf = True - self.fit_lifetime_called_w_irf = False - - self.ui.plot.setLabel('left', 'Intensity', units='a.u.') - self.ui.plot.setLabel('bottom', 'Time (ns)') - return self.out - - except Exception as e: - self.ui.Result_textBrowser.append(format(e)) - - def fit_and_plot_with_irf(self): - """ Fit and plot with IRF """ - try: - self.ui.Result_textBrowser.clear() - if not hasattr(self, "file"): - self.ui.Result_textBrowser.append("You need to load a data file.") - if not hasattr(self, "irf_file") and self.ui.separate_irf_checkBox.isChecked(): - self.ui.Result_textBrowser.append("You need to load an IRF file.") - else: - if self.opened_from_flim: - x,y = self.hist_data_from_flim - else: - x,y = self.acquire_settings() #get data - _, irf_counts = self.acquire_settings(mode="irf") #get irf counts - - #make sure Irf and data have the same length - if len(y) != len(irf_counts): - y = y[0:min(len(y), len(irf_counts))] - irf_counts = irf_counts[0:min(len(y), len(irf_counts))] - x = x[0:min(len(y), len(irf_counts))] - - y_norm = y/np.max(y) #normalized y - irf_norm = irf_counts/np.amax(irf_counts) #normalized irf - - t = x - time_fit = t - y = y_norm - irf_counts = irf_norm - - TRPL_interp = np.interp(time_fit, t, y) - - fit_func = self.ui.FittingFunc_comboBox.currentText() - self.ui.plot.plot(t, y, clear=self.ui.clear_plot_checkBox.isChecked(), pen=pg.mkPen(self.plot_color)) - if fit_func == "Stretched Exponential": #stretched exponential tab - tc_bounds = (self.ui.str_tc_min_spinBox.value(), self.ui.str_tc_max_spinBox.value()) #(0, 10000) - a_bounds = (self.ui.str_a_min_spinBox.value(), self.ui.str_a_max_spinBox.value())#(0.9, 1.1) - beta_bounds = (self.ui.str_beta_min_spinBox.value(), self.ui.str_beta_max_spinBox.value())#(0,1) - noise_bounds = (self.ui.str_noise_min_spinBox.value(), self.ui.str_noise_max_spinBox.value())#(0, 1e4) - stretch_exp_bounds = [tc_bounds, beta_bounds, a_bounds, noise_bounds] - stretch_exp_init_params = [self.ui.str_tc_init_spinBox.value(), self.ui.str_a_init_spinBox.value(), self.ui.str_beta_init_spinBox.value(), self.ui.str_noise_init_spinBox.value()] - - #tc, beta, a, avg_tau, PL_fit = stretch_exp_fit(TRPL_interp, t) - # resolution = float(self.ui.Res_comboBox.currentText()) - if self.ui.FittingMethod_comboBox.currentText() == "diff_ev": - bestfit_params, t_avg, bestfit_model, data_array, time_array, irf = fit_exp_stretch_diffev(t, self.resolution, TRPL_interp, irf_counts, stretch_exp_bounds) - else: #if fmin_tnc fitting method selected - bestfit_params, t_avg, bestfit_model, data_array, time_array, irf = fit_exp_stretch_fmin_tnc(t, self.resolution, TRPL_interp, irf_counts, stretch_exp_init_params, stretch_exp_bounds) - self.out = np.empty((len(t), 3)) - self.out[:,0] = t #time - self.out[:,1] = TRPL_interp #Raw PL - self.out[:,2] = bestfit_model # PL fit - self.ui.plot.plot(t, bestfit_model, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') - self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Stretched Exponential with IRF" - "\nFit Method: "+ self.ui.FittingMethod_comboBox.currentText() + - "\ntau_avg = %.5f ns" - "\nbeta = %.5f" - "\ntau_c = %.5f ns" - "\na = %.5f \nnoise = %.5f counts" %(t_avg, bestfit_params[1], bestfit_params[0], bestfit_params[2], bestfit_params[3])) - #self.effective_lifetime = t_avg - self.ui.average_lifetime_spinBox.setValue(t_avg) - - elif fit_func == "Double Exponential": #double exponential tab - a1_bounds = (self.ui.de_a1_min_spinBox.value(), self.ui.de_a1_max_spinBox.value()) - tau1_bounds = (self.ui.de_tau1_min_spinBox.value(), self.ui.de_tau1_max_spinBox.value()) - a2_bounds = (self.ui.de_a2_min_spinBox.value(), self.ui.de_a2_max_spinBox.value()) - tau2_bounds = (self.ui.de_tau2_min_spinBox.value(), self.ui.de_tau2_max_spinBox.value()) - noise_bounds = (self.ui.de_noise_min_spinBox.value(), self.ui.de_noise_max_spinBox.value()) - double_exp_bounds = [a1_bounds, tau1_bounds, a2_bounds, tau2_bounds, noise_bounds] - double_exp_init_params = [self.ui.de_a1_init_spinBox.value(), self.ui.de_tau1_init_spinBox.value(), self.ui.de_a2_init_spinBox.value(), - self.ui.de_tau2_init_spinBox.value(), self.ui.de_noise_init_spinBox.value()] - - if self.ui.FittingMethod_comboBox.currentText() == "diff_ev": - bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_diffev(t, self.resolution, TRPL_interp, irf_counts, double_exp_bounds, 2) - #bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_diffev(t, resolution, TRPL_interp, irf_counts, double_exp_init_bounds, 2) - else: - bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_fmin_tnc(t, self.resolution, TRPL_interp, irf_counts, double_exp_init_params, double_exp_bounds, 2) - self.out = np.empty((len(t), 3)) - self.out[:,0] = t #time - self.out[:,1] = TRPL_interp #Raw PL - self.out[:,2] = bestfit_model # PL fit - self.ui.plot.plot(t, bestfit_model, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') - self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Double Exponential with IRF" - "\nFit Method: "+ self.ui.FittingMethod_comboBox.currentText() + - "\na1 = %.5f" - "\ntau1 = %.5f ns" - "\na2 = %.5f" - "\ntau2 = %.5f ns" - "\nnoise = %.5f counts" %(bestfit_params[0], bestfit_params[1], bestfit_params[2], bestfit_params[3], bestfit_params[4])) - #TODO - once tau_avg implemented, set average lifetime spinbox to tau_avg value - if bestfit_params[3] > bestfit_params[1]: - self.ui.average_lifetime_spinBox.setValue(bestfit_params[3]) - elif bestfit_params[1] > bestfit_params[3]: - self.ui.average_lifetime_spinBox.setValue(bestfit_params[1]) - - elif fit_func == "Single Exponential": #single exponential tab - a_bounds = (self.ui.se_a_min_spinBox.value(), self.ui.se_a_max_spinBox.value()) - tau_bounds = (self.ui.se_tau_min_spinBox.value(), self.ui.se_tau_max_spinBox.value()) - noise_bounds = (self.ui.se_noise_min_spinBox.value(), self.ui.se_noise_max_spinBox.value()) - single_exp_bounds = [a_bounds, tau_bounds, noise_bounds] - single_exp_init_params = [self.ui.se_a_init_spinBox.value(), self.ui.se_tau_init_spinBox.value(), self.ui.se_noise_init_spinBox.value()] - - if self.ui.FittingMethod_comboBox.currentText() == "diff_ev": - bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_diffev(t, self.resolution, TRPL_interp, irf_counts, single_exp_bounds, 1) - else: - bestfit_params, bestfit_model, data_array, time_array, irf = fit_multi_exp_fmin_tnc(t, self.resolution, TRPL_interp, irf_counts, single_exp_init_params, single_exp_bounds, 1) - self.out = np.empty((len(t), 3)) - self.out[:,0] = t #time - self.out[:,1] = TRPL_interp #Raw PL - self.out[:,2] = bestfit_model # PL fit - self.ui.plot.plot(t, bestfit_model, clear=self.ui.clear_plot_checkBox.isChecked(), pen='k') - self.ui.Result_textBrowser.setText("Fit Results:\n\nFit Function: Single Exponential with IRF" - "\nFit Method: "+ self.ui.FittingMethod_comboBox.currentText() + - "\na = %.5f" - "\ntau = %.5f ns" - "\nnoise = %.5f counts" %(bestfit_params[0], bestfit_params[1], bestfit_params[2])) - self.ui.average_lifetime_spinBox.setValue(bestfit_params[1]) #set spinbox to tau value - - #add fit params to data_list - self.data_list.append("Data Channel: " + str(self.ui.Data_channel_spinBox.value()) + "\n" + self.ui.Result_textBrowser.toPlainText()) - self.fit_lifetime_called_w_irf = True - self.fit_lifetime_called_wo_irf = False - except Exception as e: - self.ui.Result_textBrowser.append(format(e)) - - def call_fit_and_plot(self): - if self.ui.fit_with_irf_checkBox.isChecked(): - self.fit_and_plot_with_irf() - else: - self.fit_and_plot() - if self.ui.calculate_srv_groupBox.isChecked(): - self.calculate_srv() #calculate srv on plot - self.data_list.append(self.get_srv_string()) #add srv params to data_list - - def calculate_surface_lifetime(self): - effective_lifetime = self.ui.average_lifetime_spinBox.value() - self.bulk_lifetime = self.ui.bulk_lifetime_spinBox.value() # in ns - self.surface_lifetime = (effective_lifetime * self.bulk_lifetime)/(self.bulk_lifetime - effective_lifetime) - self.ui.surface_lifetime_label.setText(str(self.surface_lifetime)) - - def calculate_srv (self): - self.calculate_surface_lifetime() - self.thickness = self.ui.thickness_spinBox.value()*1e-7 # convert to cm - self.diffusion_coeffecient = self.ui.diffusion_coefficient_spinBox.value() # in cm2/s - - self.srv1_srv2_equal = self.thickness / (2*((1e-9*self.surface_lifetime) - ((1/self.diffusion_coeffecient)*((self.thickness/np.pi)**2)) )) - self.srv1_zero = self.thickness / ((1e-9*self.surface_lifetime) - ((4/self.diffusion_coeffecient)*((self.thickness/np.pi)**2)) ) - - self.ui.srv1_srv2_equal_label.setText(str(self.srv1_srv2_equal)) - self.ui.srv1_zero_label.setText(str(self.srv1_zero)) - - def get_srv_string(self): - """ Get info from SRV Calculation groupbox as string """ - srv_string = "SRV Calculation:"\ - + "\nAverage Lifetime (ns): " + str(self.ui.average_lifetime_spinBox.value()) \ - + "\nBulk Lifetime (ns): " + str(self.ui.bulk_lifetime_spinBox.value()) \ - + "\nThickness (nm): " + str(self.ui.thickness_spinBox.value()) \ - + "\nDiffusion Coefficient (cm2/s): " + str(self.ui.diffusion_coefficient_spinBox.value()) - srv_string += "\nSurface Lifetime (ns): " + self.ui.surface_lifetime_label.text() - - srv_string += "\nSRV1 = SRV2"\ - + "\nSRV (cm/s): " + self.ui.srv1_srv2_equal_label.text() - - srv_string += "\nSRV1 = 0"\ - + "\nSRV (cm/s): " + self.ui.srv1_zero_label.text() - return srv_string - - def export_data(self): - """ Save fit params and srv calculations stored in data_list as .txt """ - folder = os.path.dirname(self.filename[0]) - filename_ext = os.path.basename(self.filename[0]) - filename = os.path.splitext(filename_ext)[0] #get filename without extension - - path = folder + "/" + filename + "_fit_results.txt" - if not os.path.exists(path): - file = open(path, "w+") - else: - file = open(path, "a+") - - for i in range(len(self.data_list)): - file.write(self.data_list[i] + "\n\n") - - self.data_list = [] - file.close() - - def clear_export_data(self): - self.data_list = [] - self.clean_up_after_fig_export() - - def clean_up_after_fig_export(self): - self.x_mem = [] - self.y_mem = [] - self.legend = [] - self.best_fit_mem = [] - self.best_fit_mem_x = [] - - def add_trace_to_mem(self): - try: - if self.fit_lifetime_called_w_irf == True: - self.x_mem.append(self.out[:,0]) - self.y_mem.append(self.out[:,1]) - self.best_fit_mem_x.append(self.out[:,0]) - self.best_fit_mem.append(self.out[:,2]) - elif self.fit_lifetime_called_wo_irf == True: - self.x_mem.append(self.acquire_settings()[0]) - self.y_mem.append(self.acquire_settings()[1]) - self.best_fit_mem_x.append(self.out[:,0]) - self.best_fit_mem.append(self.out[:,2]) - else: - self.x_mem.append(self.acquire_settings()[0]) - self.y_mem.append(self.acquire_settings()[1]) - self.legend.append(self.ui.lineEdit.text()) - except Exception as e: - print(e) - - def export_window(self): - self.exportplotwindow = ExportPlotWindow() - self.exportplotwindow.export_fig_signal.connect(self.pub_ready_plot_export) - - def pub_ready_plot_export(self): - try: - if self.x_mem == []: - self.ui.result_textBrowser.setText("Add traces to memory first!") - - else: - filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") - - plt.figure(figsize=(8,6)) - plt.tick_params(direction='out', length=8, width=3.5) - for i in range(len(self.x_mem)): - plt.plot(self.x_mem[i], self.y_mem[i], label=str(self.legend[i])) - if self.fit_lifetime_called_w_irf == True or self.fit_lifetime_called_wo_irf == True: - plt.plot(self.best_fit_mem_x[i], self.best_fit_mem[i],'k--') - - plt.yscale('log') - plt.xlabel("Time (ns)", fontsize=20, fontweight='bold') - plt.ylabel("Intensity (norm.)", fontsize=20, fontweight='bold') - plt.legend() - plt.tight_layout() - plt.xlim([self.exportplotwindow.ui.lowerX_spinBox.value(),self.exportplotwindow.ui.upperX_spinBox.value()]) - plt.ylim([self.exportplotwindow.ui.lowerY_spinBox.value(),self.exportplotwindow.ui.upperY_doubleSpinBox.value()]) - - plt.savefig(filename[0],bbox_inches='tight', dpi=300) - plt.close() - self.clean_up_after_fig_export() - - except Exception as e: - self.ui.Result_textBrowser.append(format(e)) - pass - - def close_application(self): - choice = QtGui.QMessageBox.question(self, 'EXIT!', - "Do you want to exit the app?", - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if choice == QtGui.QMessageBox.Yes: - sys.exit() - else: - pass - -"""Skip rows GUI""" -ui_file_path = (base_path / "skip_rows.ui").resolve() -skiprows_WindowTemplate, skiprows_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) - -class SkipRowsWindow(skiprows_TemplateBaseClass): - - skip_rows_signal = QtCore.pyqtSignal() #signal to help with pass info back to MainWindow - - def __init__(self): - skiprows_TemplateBaseClass.__init__(self) - - # Create the param window - self.ui = skiprows_WindowTemplate() - self.ui.setupUi(self) - self.ui.done_pushButton.clicked.connect(self.done) - self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False) - self.show() - - def done(self): - self.skip_rows_signal.emit() - self.close() - - -def run(): - win = MainWindow() - QtGui.QApplication.instance().exec_() - return win - -#Uncomment below if you want to run this as standalone -#run() \ No newline at end of file diff --git a/src/main/python/Lifetime_analysis/__init__.py b/src/main/python/Lifetime_analysis/__init__.py deleted file mode 100644 index b4011af..0000000 --- a/src/main/python/Lifetime_analysis/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from __future__ import absolute_import, division, print_function \ No newline at end of file diff --git a/src/main/python/Lifetime_analysis/picoharp_phd.py b/src/main/python/Lifetime_analysis/picoharp_phd.py deleted file mode 100644 index 455e1bc..0000000 --- a/src/main/python/Lifetime_analysis/picoharp_phd.py +++ /dev/null @@ -1,408 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Majority of this PicoHarp Parser was written by skyjur. -Check out the original code here --- -https://github.com/skyjur/picoharp300-curvefit-ui - -Modified by Sarthak --- -Created on Fri Apr 5 15:50:36 2019 - -@author: Sarthak -""" - -""" -PicoHarp 300 file parser -""" -import datetime -import numpy as np -from ctypes import c_uint, c_ulong, c_char, c_int, c_int64, c_float, \ - Structure, sizeof, memmove, addressof - -DISPCURVES = 8 -MAXCURVES = 512 -MAXCHANNELS = 65536 - - -class tParamStruct(Structure): - _pack_ = 4 - _fields_ = [ - ('Start', c_float), - ('Step', c_float), - ('End', c_float), - ] - - -class tCurveMapping(Structure): - _pack_ = 4 - _fields_ = [ - ('MapTo', c_int), - ('Show', c_int), - ] - - -class TxtHdr(Structure): - _pack_ = 4 - _fields_ = [ - ('Ident', c_char * 16), - ('FormatVersion', c_char * 6), - ('CreatorName', c_char * 18), - ('CreatorVersion', c_char * 12), - ('FileTime', c_char * 18), - ('CRLF', c_char * 2), - ('CommentField', c_char * 256), - ] - - -class BinHdr(Structure): - _pack_ = 4 - _fields_ = [ - ('Curves', c_int), - ('BitsPerHistoBin', c_int), - ('RoutingChannels', c_int), - ('NumberOfBoards', c_int), - ('ActiveCurve', c_int), - ('MeasMode', c_int), - ('SubMode', c_int), - ('RangeNo', c_int), - ('Offset', c_int), - ('Tacq', c_int), # in m - ('StopAt', c_int), - ('StopOnOvfl', c_int), - ('Restart', c_int), - ('DispLinLog', c_int), - ('DispTimeFrom', c_int), - ('DispTimeTo', c_int), - ('DispCountsFrom', c_int), - ('DispCountsTo', c_int), - ('DispCurves', tCurveMapping * DISPCURVES), - ('Params', tParamStruct * 3), - ('RepeatMode', c_int), - ('RepeatsPerCurve', c_int), - ('RepeatTime', c_int), - ('RepeatWaitTime', c_int), - ('ScriptName', c_char * 20), - ] - - -class BoardHdr(Structure): - _pack_ = 4 - _fields_ = [ - ('HardwareIdent', c_char * 16), - ('HardwareVersion', c_char * 8), - ('HardwareSerial', c_int), - ('SyncDivider', c_int), - ('CFDZeroCross0', c_int), - ('CFDLevel0', c_int), - ('CFDZeroCross1', c_int), - ('CFDLevel1', c_int), - ('Resolution', c_float), - ('RouterModelCode', c_int), - ('RouterEnabled', c_int), - ('RtChan1_InputType;', c_int), - ('RtChan1_InputLevel', c_int), - ('RtChan1_InputEdge', c_int), - ('RtChan1_CFDPresent', c_int), - ('RtChan1_CFDLevel', c_int), - ('RtChan1_CFDZeroCross', c_int), - ('RtChan2_InputType;', c_int), - ('RtChan2_InputLevel', c_int), - ('RtChan2_InputEdge', c_int), - ('RtChan2_CFDPresent', c_int), - ('RtChan2_CFDLevel', c_int), - ('RtChan2_CFDZeroCross', c_int), - ('RtChan3_InputType;', c_int), - ('RtChan3_InputLevel', c_int), - ('RtChan3_InputEdge', c_int), - ('RtChan3_CFDPresent', c_int), - ('RtChan3_CFDLevel', c_int), - ('RtChan3_CFDZeroCross', c_int), - ('RtChan4_InputType;', c_int), - ('RtChan4_InputLevel', c_int), - ('RtChan4_InputEdge', c_int), - ('RtChan4_CFDPresent', c_int), - ('RtChan4_CFDLevel', c_int), - ('RtChan4_CFDZeroCross', c_int), - ] - - -class CurveHdr(Structure): - _pack_ = 4 - _fields_ = [ - ('CurveIndex', c_int), - ('TimeOfRecording', c_ulong), - ('HardwareIdent', c_char * 16), - ('HardwareVersion', c_char * 8), - ('HardwareSerial', c_int), - ('SyncDivider', c_int), - ('CFDZeroCross0', c_int), - ('CFDLevel0', c_int), - ('CFDZeroCross1', c_int), - ('CFDLevel1', c_int), - ('Offset', c_int), - ('RoutingChannel', c_int), - ('ExtDevices', c_int), - ('MeasMode', c_int), - ('SubMode', c_int), - ('P1', c_float), - ('P2', c_float), - ('P3', c_float), - ('RangeNo', c_int), - ('Resolution', c_float), - ('Channels', c_int), - ('Tacq', c_int), - ('StopAfter', c_int), - ('StopReason', c_int), - ('InpRate0', c_int), - ('InpRate1', c_int), - ('HistCountRate', c_int), - ('IntegralCount', c_int64), - ('reserved', c_int), - ('DataOffset', c_int), - ('RouterModelCode', c_int), - ('RouterEnabled', c_int), - ('RtChan_InputType;', c_int), - ('RtChan_InputLevel', c_int), - ('RtChan_InputEdge', c_int), - ('RtChan_CFDPresent', c_int), - ('RtChan_CFDLevel', c_int), - ('RtChan_CFDZeroCross', c_int), - ] - - -class ParseError(Exception): pass - - -def _read(f, CType): - data = f.read(sizeof(CType)) - obj = CType() - memmove(addressof(obj), data, len(data)) - return obj - - -def _validate_header(header): - if not header.Ident == 'PicoHarp 300' or not header.FormatVersion == '2.0': - raise ParseError('Does not look like a PicoHarp 300 file.') - - -class Curve(object): - res = None - data = None - - def __repr__(self): - return 'Curve' % ( - self.res, - len(self.data) - ) - - -def timefmt(t): - d = datetime.datetime.fromtimestamp(t) - return d.strftime('%a %b %d %H:%M:%S %Y') - - -class PicoharpParser(object): - _ready = False - - def __init__(self, filename): - if isinstance(filename, (str)):#, unicode)): - filename = open(filename, mode='rb') - self.f = filename - self._prepare() - - def _prepare(self): - self.f.seek(0) - - header = self._header = _read(self.f, TxtHdr) - """SJ commented this --- it was giving ParseError""" -# _validate_header(header) - - bin_header = self._bin_header = _read(self.f, BinHdr) - - self._boards = [] - for i in range(bin_header.NumberOfBoards): - self._boards.append(_read(self.f, BoardHdr)) - - self._curves = [] - for i in range(bin_header.Curves): - self._curves.append(_read(self.f, CurveHdr)) - - def header(self): - return [(k, getattr(self._header, k)) for k, t in self._header._fields_] - - def no_of_curves(self): - return self._bin_header.Curves - - def get_curve(self, n): - header = self._curves[n] - res = header.Resolution - - self.f.seek(header.DataOffset) - array = np.fromfile(self.f, c_uint, header.Channels) - - return res, array - - def get_time_window_in_ns(self, curve_no): - curve = self._curves[curve_no] - rep_rate = curve.InpRate0 - res, _ = self.get_curve(curve_no) - time_window_s = (1/rep_rate)/res # in seconds - - return time_window_s * 1e9 # in nannoseconds - - def get_integral_counts(self, curve_no): - curve = self._curves[curve_no] - integral_counts = curve.IntegralCount - - return integral_counts - - def info(self): - txthdr = self._header - binhdr = self._bin_header - boards = self._boards - curves = self._curves - r = [] - w = r.append - yesno = lambda x: 'true' if x else 'false' - - w("Ident : %s" % txthdr.Ident) - w("Format Version : %s" % txthdr.FormatVersion) - w("Creator Name : %s" % txthdr.CreatorName) - w("Creator Version : %s" % txthdr.CreatorVersion) - w("Time of Creation : %s" % txthdr.FileTime) - w("File Comment : %s" % txthdr.CommentField) - - w("No of Curves : %s" % binhdr.Curves) - w("Bits per HistoBin: %s" % binhdr.BitsPerHistoBin) - w("RoutingChannels : %s" % binhdr.RoutingChannels) - w("No of Boards : %s" % binhdr.NumberOfBoards) - w("Active Curve : %s" % binhdr.ActiveCurve) - w("Measurement Mode : %s" % binhdr.MeasMode) - w("Sub-Mode : %s" % binhdr.SubMode) - w("Range No : %s" % binhdr.RangeNo) - w("Offset : %s" % binhdr.Offset) - w("AcquisitionTime : %s" % binhdr.Tacq) - w("Stop at : %s" % binhdr.StopAt) - w("Stop on Ovfl. : %s" % binhdr.StopOnOvfl) - w("Restart : %s" % binhdr.Restart) - w("DispLinLog : %s" % binhdr.DispLinLog) - w("DispTimeAxisFrom : %s" % binhdr.DispTimeFrom) - w("DispTimeAxisTo : %s" % binhdr.DispTimeTo) - w("DispCountAxisFrom: %s" % binhdr.DispCountsFrom) - w("DispCountAxisTo : %s" % binhdr.DispCountsTo) - - for i in range(DISPCURVES): - w("---------------------") - w("Curve No %s" % i) - w(" MapTo : %s" % binhdr.DispCurves[i].MapTo) - w(" Show : %s" % yesno(binhdr.DispCurves[i].Show)) - w("---------------------") - - for i in range(3): - w("---------------------") - w("Parameter No %s" % i) - w(" Start : %f" % binhdr.Params[i].Start) - w(" Step : %f" % binhdr.Params[i].Step) - w(" End : %f" % binhdr.Params[i].End) - w("---------------------") - - w("Repeat Mode : %d" % binhdr.RepeatMode) - w("Repeats per Curve: %d" % binhdr.RepeatsPerCurve) - w("Repeat Time : %d" % binhdr.RepeatTime) - w("Repeat wait Time : %d" % binhdr.RepeatWaitTime) - w("Script Name : %s" % binhdr.ScriptName) - - for i, board in enumerate(boards): - w("---------------------") - w("Board No %d" % i) - w(" HardwareIdent : %s" % board.HardwareIdent) - w(" HardwareVersion : %s" % board.HardwareVersion) - w(" HardwareSerial : %d" % board.HardwareSerial) - w(" SyncDivider : %d" % board.SyncDivider) - w(" CFDZeroCross0 : %d" % board.CFDZeroCross0) - w(" CFDLevel0 : %d" % board.CFDLevel0) - w(" CFDZeroCross1 : %d" % board.CFDZeroCross1) - w(" CFDLevel1 : %d" % board.CFDLevel1) - w(" Resolution : %.6f" % board.Resolution) - - if board.RouterModelCode: - w(" RouterModelCode : %d" % board.RouterModelCode) - w(" RouterEnabled : %d" % board.RouterEnabled) - - w(" RtChan1_InputType : %d" % board.RtChan1_InputType) - w(" RtChan1_InputLevel : %d" % board.RtChan1_InputLevel) - w(" RtChan1_InputEdge : %d" % board.RtChan1_InputEdge) - w(" RtChan1_CFDPresent : %d" % board.RtChan1_CFDPresent) - w(" RtChan1_CFDLevel : %d" % board.RtChan1_CFDLevel) - w(" RtChan1_CFDZeroCross : %d" % board.RtChan1_CFDZeroCross) - - w(" RtChan2_InputType : %d" % board.RtChan2_InputType) - w(" RtChan2_InputLevel : %d" % board.RtChan2_InputLevel) - w(" RtChan2_InputEdge : %d" % board.RtChan2_InputEdge) - w(" RtChan2_CFDPresent : %d" % board.RtChan2_CFDPresent) - w(" RtChan2_CFDLevel : %d" % board.RtChan2_CFDLevel) - w(" RtChan2_CFDZeroCross : %d" % board.RtChan2_CFDZeroCross) - - w(" RtChan3_InputType : %d" % board.RtChan3_InputType) - w(" RtChan3_InputLevel : %d" % board.RtChan3_InputLevel) - w(" RtChan3_InputEdge : %d" % board.RtChan3_InputEdge) - w(" RtChan3_CFDPresent : %d" % board.RtChan3_CFDPresent) - w(" RtChan3_CFDLevel : %d" % board.RtChan3_CFDLevel) - w(" RtChan3_CFDZeroCross : %d" % board.RtChan3_CFDZeroCross) - - w(" RtChan4_InputType : %d" % board.RtChan4_InputType) - w(" RtChan4_InputLevel : %d" % board.RtChan4_InputLevel) - w(" RtChan4_InputEdge : %d" % board.RtChan4_InputEdge) - w(" RtChan4_CFDPresent : %d" % board.RtChan4_CFDPresent) - w(" RtChan4_CFDLevel : %d" % board.RtChan4_CFDLevel) - w(" RtChan4_CFDZeroCross : %d" % board.RtChan4_CFDZeroCross) - - w("---------------------") - - for i, curve in enumerate(curves): - w("---------------------") - w("Curve Index : %d" % curve.CurveIndex) - w("Time of Recording : %s" % timefmt(curve.TimeOfRecording)) - w("HardwareIdent : %s" % curve.HardwareIdent) - w("HardwareVersion : %s" % curve.HardwareVersion) - w("HardwareSerial : %d" % curve.HardwareSerial) - w("SyncDivider : %d" % curve.SyncDivider) - w("CFDZeroCross0 : %d" % curve.CFDZeroCross0) - w("CFDLevel0 : %d" % curve.CFDLevel0 ) - w("CFDZeroCross1 : %d" % curve.CFDZeroCross1) - w("CFDLevel1 : %d" % curve.CFDLevel1) - w("Offset : %d" % curve.Offset) - w("RoutingChannel : %d" % curve.RoutingChannel) - w("ExtDevices : %d" % curve.ExtDevices) - w("Meas. Mode : %d" % curve.MeasMode) - w("Sub-Mode : %d" % curve.SubMode) - w("Par. 1 : %f" % curve.P1) - w("Par. 2 : %.6f" % curve.P2) - w("Par. 3 : %.6f" % curve.P3) - w("Range No : %d" % curve.RangeNo) - w("Resolution : %f" % curve.Resolution) - w("Channels : %d" % curve.Channels) - w("Acq. Time : %d" % curve.Tacq) - w("Stop after : %d" % curve.StopAfter) - w("Stop Reason : %d" % curve.StopReason) - w("InpRate0 : %d" % curve.InpRate0) - w("InpRate1 : %d" % curve.InpRate1) - w("HistCountRate : %d" % curve.HistCountRate) - w("IntegralCount : %d" % curve.IntegralCount) - w("reserved : %d" % curve.reserved) - w("dataoffset : %d" % curve.DataOffset) - - if curve.RouterModelCode: - w("RouterModelCode : %d" % curve.RouterModelCode) - w("RouterEnabled : %d" % curve.RouterEnabled) - w("RtChan_InputType : %d" % curve.RtChan_InputType) - w("RtChan_InputLevel : %d" % curve.RtChan_InputLevel) - w("RtChan_InputEdge : %d" % curve.RtChan_InputEdge) - w("RtChan_CFDPresent : %d" % curve.RtChan_CFDPresent) - w("RtChan_CFDLevel : %d" % curve.RtChan_CFDLevel) - w("RtChan_CFDZeroCross : %d" % curve.RtChan_CFDZeroCross) - - return '\n'.join(r) - -def read_picoharp_phd(datafile): - parser = PicoharpParser(datafile) - return parser \ No newline at end of file diff --git a/src/main/python/Lifetime_analysis/read_ph_phd.py b/src/main/python/Lifetime_analysis/read_ph_phd.py deleted file mode 100644 index 1d35203..0000000 --- a/src/main/python/Lifetime_analysis/read_ph_phd.py +++ /dev/null @@ -1,54 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Fri Apr 5 15:52:05 2019 - -@author: Sarthak -""" - -try: - from Lifetime_analysis import picoharp_phd -except: - import picoharp_phd -import numpy as np -import matplotlib.pyplot as plt -#import sys - -#datafile = "E:/Python code/APTES_APTMS.phd" - - -def read_picoharp_phd(datafile): - parser = picoharp_phd.PicoharpParser(datafile) - return parser - -#def phd_to_csv(datafile, return_df = False): -# parser = read_picoharp_phd(datafile) -# name, ext = datafile.rsplit('.', 1) -# -# total_curves = parser.no_of_curves() -# y = [] -# for i in range(total_curves): -# res, curve = parser.get_curve(i) -# time_window = int(np.floor(parser.get_time_window_in_ns(curve_no))) -# curve = curve[0:time_window] -# y.append(curve) -# -# df = pd.DataFrame(y) -# df.T.to_csv(name+".csv", index=False, header=False) -# if return_df == True: -# return df.T - -def smooth(curve, boxwidth): - sm_curve = np.convolve(curve, np.ones(boxwidth)/boxwidth, mode="same") - return sm_curve - -def get_x_y(curve_no, parser, smooth_trace = False, boxwidth = 3): - - assert type(parser) == picoharp_phd.PicoharpParser, 'must be picoharp parser' - res, curve = parser.get_curve(curve_no) - time_window = int(np.floor(parser.get_time_window_in_ns(curve_no))) - curve = curve[0:time_window] - size = len(curve) - x = np.arange(0, size*res, res, np.float) - if smooth_trace == True: - curve = smooth(curve, boxwidth=boxwidth) - return x,curve diff --git a/src/main/python/Lifetime_analysis/skip_rows.ui b/src/main/python/Lifetime_analysis/skip_rows.ui deleted file mode 100644 index 35a4e6b..0000000 --- a/src/main/python/Lifetime_analysis/skip_rows.ui +++ /dev/null @@ -1,42 +0,0 @@ - - - Form - - - - 0 - 0 - 413 - 94 - - - - Enter rows to skip - - - - - - Rows to skip - - - - - - - 10 - - - - - - - Done - - - - - - - - diff --git a/src/main/python/OceanOptics_acquire/OO_PZstageScan_acquire_gui.ui b/src/main/python/OceanOptics_acquire/OO_PZstageScan_acquire_gui.ui deleted file mode 100644 index 77dacb8..0000000 --- a/src/main/python/OceanOptics_acquire/OO_PZstageScan_acquire_gui.ui +++ /dev/null @@ -1,750 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 1219 - 901 - - - - MainWindow - - - - - - - - - - 15 - - - - Settings - - - - - - Stage Settings for Scan - - - - - - - 12 - - - - X Scan Size (um) - - - - - - - - 12 - - - - 5.000000000000000 - - - - - - - - 12 - - - - Initialize Piezo Stage - - - - - - - - 12 - - - - 0.100000000000000 - - - - - - - - 12 - - - - 5.000000000000000 - - - - - - - - 12 - - - - X Step (um) - - - - - - - - 12 - - - - 100.000000000000000 - - - 50.000000000000000 - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 12 - - - - Y Scan Size (um) - - - - - - - - 12 - - - - X Start (um) - - - - - - - - 12 - - - - 1.000000000000000 - - - 0.100000000000000 - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 12 - - - - Y Start (um) - - - - - - - - 12 - - - - Y Step (um) - - - - - - - - 12 - - - - Start X-Y Scan - - - - - - - - 12 - - - - Estimate Scan Time - - - - - - - - 12 - - - - 100.000000000000000 - - - 50.000000000000000 - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - - - - 15 - - - - OceanOptics Save Settings - - - - - - - 12 - - - - Save Every Spectrum - - - - - - - - 12 - - - - Save Single Spectrum - - - - - - - - - - Spectrometer Settings - - - - - - - 12 - - - - 1 - - - - - - - - 12 - - - - 3 - - - 3000 - - - 100 - - - - - - - - 12 - - - - Scans to Average - - - - - - - - 12 - - - - Intg. Time (ms) - - - - - - - - 12 - - - - Correct Dark Counts - - - true - - - - - - - - 12 - - - - Connect to Spectrometer - - - - - - - - 12 - - - - Live - - - - - - - - - - Scan Save Settings - - - - - - - 12 - - - - - - - - - 12 - - - - Sample Name: - - - - - - - - 12 - - - - Path to Folder - - - - - - - - - - - - - - - - - - 15 - - - - Independent Stage Movements - - - - - - - 12 - - - - Where is the stage? - - - - - - - - 12 - - - - Show Current Position - - - - - - - - 12 - - - - Center the Piezo Stage: - - - - - - - - 12 - - - - Center Stage - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 12 - - - - Absolute Movements - - - - - - - - 12 - - - - X (um) - - - - - - - - 12 - - - - - - - - - 12 - - - - Y (um) - - - - - - - - 12 - - - - - - - - - 12 - - - - OK - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 12 - - - - Relative Movements - - - - - - - - 12 - - - - X (um) - - - - - - - - 12 - - - - - - - - - 12 - - - - Y (um) - - - - - - - - 12 - - - - - - - - - 12 - - - - Ok - - - - - - - - - - - - - - 12 - - - - - - - - - 15 - - - - Information: - - - - - - - - 15 - - - - Scan Progress: - - - - - - - - 12 - - - - 0 - - - - - - - - - - - 0 - 0 - 1219 - 21 - - - - - - - - PlotWidget - QGraphicsView -
pyqtgraph
- - - - - diff --git a/src/main/python/OceanOptics_acquire/OO_acquire_gui.ui b/src/main/python/OceanOptics_acquire/OO_acquire_gui.ui deleted file mode 100644 index 33c8b19..0000000 --- a/src/main/python/OceanOptics_acquire/OO_acquire_gui.ui +++ /dev/null @@ -1,240 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 1206 - 668 - - - - MainWindow - - - - - - - - - - 15 - - - - Acquire Settings - - - - - - - 15 - - - - Save Settings - - - - - - - 12 - - - - Configure Folder to Save - - - - - - - - 12 - - - - Save Every Spectrum - - - - - - - - 12 - - - - Save Single Spectrum - - - - - - - - - - - 12 - - - - Correct Dark Counts - - - true - - - - - - - - 15 - - - - Close Connection - - - - - - - - 12 - - - - - - - - - 15 - - - - ALWAYS CLOSE CONNECTION!!! -BEFORE EXITING APP - - - - - - - - 12 - - - - Intg. Time (ms) - - - - - - - - 12 - - - - Scans to Average - - - - - - - - 10 - - - - 3 - - - 3000 - - - - - - - - 10 - - - - 1 - - - - - - - - 15 - - - - Live - - - - - - - - 12 - - - - Connect to Spectrometer - - - - - - - - - - - - - - - - - - - - - 0 - 0 - 1206 - 21 - - - - - - - - PlotWidget - QGraphicsView -
pyqtgraph
- - - - - diff --git a/src/main/python/OceanOptics_acquire/OceanOptics_acquire_plot.py b/src/main/python/OceanOptics_acquire/OceanOptics_acquire_plot.py deleted file mode 100644 index 8de85c0..0000000 --- a/src/main/python/OceanOptics_acquire/OceanOptics_acquire_plot.py +++ /dev/null @@ -1,297 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Wed Mar 27 16:50:26 2019 - -@author: Sarthak -""" - -import pyqtgraph as pg -from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog -import numpy as np -import pickle -import sys -import seabreeze.spectrometers as sb -from pipython import GCSDevice -import time - -pg.mkQApp() -pg.setConfigOption('background', 'w') - -#uiFile = "OO_acquire_gui.ui" "OO_PZstageScan_acquire_gui" -uiFile = "OO_PZstageScan_acquire_gui.ui" - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -class MainWindow(TemplateBaseClass): - - def __init__(self): - TemplateBaseClass.__init__(self) - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - - self.ui.connect_checkBox.stateChanged.connect(self._handle_spectrometer_connection) - self.ui.live_pushButton.clicked.connect(self.live) - - self.ui.path_to_folder_pushButton.clicked.connect(self.save_file_location) - self.ui.save_single_spec_pushButton.clicked.connect(self.save_single_spec) - - self.ui.init_stage_pushButton.clicked.connect(self.init_piezo_stage) - self.ui.show_curr_pos_pushButton.clicked.connect(self.current_piezo_stage_pos) - self.ui.center_stage_pushButton.clicked.connect(self.center_piezo) - self.ui.abs_mov_pushButton.clicked.connect(self.abs_mov) - self.ui.rel_mov_pushButton.clicked.connect(self.rel_mov) - self.ui.estimate_scan_time_pushButton.clicked.connect(self.estimate_scan_time) - self.ui.start_x_y_sacan_pushButton.clicked.connect(self.x_y_scan) - -# self.ui.clear_pushButton.clicked.connect(self.clear_plot) - self.pi_device = None - self.spec = None - - self.ui.status_textBrowser.setText("Welcome!\nGUI Initiated!") - - self.show() - - def _handle_spectrometer_connection(self): - if self.ui.connect_checkBox.isChecked(): - self.connect_spectrometer() - else: - self.close_connection() - - def connect_spectrometer(self): - if self.spec is None: - devices = sb.list_devices() - self.spec = sb.Spectrometer(devices[0]) - self.ui.status_textBrowser.append("Ocean Optics Device Connected!\n\n Device:\n\n"+str(sb.list_devices()[0])) - else: - self.ui.status_textBrowser.append("Already Connected") - - def init_piezo_stage(self): - if self.pi_device is None: - self.pi_device = GCSDevice("E-710") # Creates a Controller instant - self.pi_device.ConnectNIgpib(board=0,device=4) # Connect to GPIB board - self.ui.status_textBrowser.append('Connected: {}'.format(self.pi_device.qIDN().strip())) - # print('connected: {}'.format(self.pi_device.qIDN().strip())) - - self.axes = self.pi_device.axes[0:2] # selecting x and y axis of the stage - - self.pi_device.INI() - self.pi_device.REF(axes=self.axes) - - self.pi_device.SVO(axes=self.axes, values=[True,True]) # Turn on servo control for both axes - self.ui.status_textBrowser.append("Current Stage Position:\n{}".format(self.pi_device.qPOS(axes=self.axes))) - # print(self.pi_device.qPOS(axes=self.axes)) - else: - self.ui.status_textBrowser.append("Piezo Stage Is Already Initialized!") - - def center_piezo(self): - if self.pi_device is None: - self.init_piezo_stage() - self.pi_device.MOV(axes=self.axes, values=[50,50]) - self.ui.status_textBrowser.append("Piezo Stage Centered: [50x,50y]") - - def current_piezo_stage_pos(self): - if self.pi_device is None: - self.init_piezo_stage() - self.ui.status_textBrowser.append("Current Stage Position:\n{}".format(self.pi_device.qPOS(axes=self.axes))) - - def abs_mov(self): - if self.pi_device is None: - self.init_piezo_stage() - x_abs_pos = self.ui.x_abs_doubleSpinBox.value() - y_abs_pos = self.ui.y_abs_doubleSpinBox.value() - self.pi_device.MOV(axes=self.axes, values=[x_abs_pos,y_abs_pos]) - - def rel_mov(self): - if self.pi_device is None: - self.init_piezo_stage() - x_rel_pos = self.ui.x_rel_doubleSpinBox.value() - y_rel_pos = self.ui.y_rel_doubleSpinBox.value() - self.pi_device.MVR(axes=self.axes, values=[x_rel_pos,y_rel_pos]) - - def estimate_scan_time(self): - x_scan_size = self.ui.x_size_doubleSpinBox.value() - y_scan_size = self.ui.y_size_doubleSpinBox.value() - - x_step = self.ui.x_step_doubleSpinBox.value() - y_step = self.ui.y_step_doubleSpinBox.value() - - if y_scan_size == 0: - y_scan_size = 1 - - if x_scan_size == 0: - x_scan_size = 1 - - if y_step == 0: - y_step = 1 - - if x_step == 0: - x_step = 1 - - y_range = int(np.ceil(y_scan_size/y_step)) - x_range = int(np.ceil(x_scan_size/x_step)) - - total_points = x_range*y_range - - intg_time_ms = self.ui.intg_time_spinBox.value() - scans_to_avg = self.ui.scan_to_avg_spinBox.value() - - total_time = total_points*(intg_time_ms*1e-3)*(scans_to_avg) # in seconds - - self.ui.status_textBrowser.append("Estimated scan time: "+str(np.float16(total_time/60))+" mins") - - def x_y_scan(self): - if self.pi_device is None: - self.init_piezo_stage() - - if self.spec is None: - self.ui.status_textBrowser.append("Spectrometer not connected!\nForce connecting the spectrometer...") - self.connect_spectrometer() - - start_time = time.time() - x_start = self.ui.x_start_doubleSpinBox.value() - y_start = self.ui.y_start_doubleSpinBox.value() - - x_scan_size = self.ui.x_size_doubleSpinBox.value() - y_scan_size = self.ui.y_size_doubleSpinBox.value() - - x_step = self.ui.x_step_doubleSpinBox.value() - y_step = self.ui.y_step_doubleSpinBox.value() - - if y_scan_size == 0: - y_scan_size = 1 - - if x_scan_size == 0: - x_scan_size = 1 - - if y_step == 0: - y_step = 1 - - if x_step == 0: - x_step = 1 - - y_range = int(np.ceil(y_scan_size/y_step)) - x_range = int(np.ceil(x_scan_size/x_step)) - - # Define empty array for saving intensities - data_array = np.zeros(shape=(x_range*y_range,2048)) - - self.ui.status_textBrowser.append("Starting Scan...") - # Move to the starting position - self.pi_device.MOV(axes=self.axes, values=[x_start,y_start]) - - self.ui.status_textBrowser.append("Scan in Progress...") - - k = 0 - for i in range(y_range): - for j in range(x_range): -# print(self.pi_device.qPOS(axes=self.axes)) - - self._read_spectrometer() - data_array[k,:] = self.y - self.ui.plot.plot(self.spec.wavelengths(), self.y, pen='r', clear=True) - pg.QtGui.QApplication.processEvents() - - self.pi_device.MVR(axes=self.axes[0], values=[x_step]) - - self.ui.progressBar.setValue(100*((k+1)/(x_range*y_range))) - k+=1 - # TODO - # if statement needs to be modified to keep the stage at the finish y-pos for line scans in x, and same for y - if i == y_range-1: # this if statement is there to keep the stage at the finish position (in x) and not bring it back like we were doing during the scan - self.pi_device.MVR(axes=self.axes[1], values=[y_step]) - else: - self.pi_device.MVR(axes=self.axes, values=[-x_scan_size, y_step]) - - self.ui.status_textBrowser.append("Scan Complete!\nSaving Data...") - - save_dict = {"Wavelengths": self.spec.wavelengths(), "Intensities": data_array, - "Scan Parameters":{"X scan start (um)": x_start, "Y scan start (um)": y_start, - "X scan size (um)": x_scan_size, "Y scan size (um)": y_scan_size, - "X step size (um)": x_step, "Y step size (um)": y_step}, - "OceanOptics Parameters":{"Integration Time (ms)": self.ui.intg_time_spinBox.value(), - "Scans Averages": self.ui.scan_to_avg_spinBox.value(), - "Correct Dark Counts": self.ui.correct_dark_counts_checkBox.isChecked()} - } - - pickle.dump(save_dict, open(self.save_folder+"/"+self.ui.lineEdit.text()+"_raw_PL_spectra_data.pkl", "wb")) - - self.ui.status_textBrowser.append("Data saved!\nTotal time taken:"+str(np.float16((time.time()-start_time)/60))+" mins") - - def save_file_location(self): - self.save_folder = QtWidgets.QFileDialog.getExistingDirectory(self, caption="Select Folder") - - def save_single_spec(self): - save_array = np.zeros(shape=(2048,2)) - self._read_spectrometer() - save_array[:,1] = self.y - save_array[:,0] = self.spec.wavelengths() - - np.savetxt(self.save_folder+"/"+self.ui.lineEdit.text()+".txt", save_array, fmt = '%.5f', - header = 'Wavelength (nm), Intensity (counts)', delimiter = ' ') - - def live(self): - save_array = np.zeros(shape=(2048,2)) - - self.ui.plot.setLabel('left', 'Intensity', units='a.u.') - self.ui.plot.setLabel('bottom', 'Wavelength', units='nm') - j = 0 - while self.spec is not None:#self.ui.connect_checkBox.isChecked(): # this while loop works! - self._read_spectrometer() - save_array[:,1] = self.y - - self.ui.plot.plot(self.spec.wavelengths(), self.y, pen='r', clear=True) - - if self.ui.save_every_spec_checkBox.isChecked(): - save_array[:,0] = self.spec.wavelengths() - np.savetxt(self.save_folder+"/"+self.ui.lineEdit.text()+str(j)+".txt", save_array, fmt = '%.5f', - header = 'Wavelength (nm), Intensity (counts)', delimiter = ' ') - - pg.QtGui.QApplication.processEvents() - j += 1 - - def _read_spectrometer(self): - if self.spec is not None: - - intg_time_ms = self.ui.intg_time_spinBox.value() - self.spec.integration_time_micros(intg_time_ms*1e3) - - scans_to_avg = self.ui.scan_to_avg_spinBox.value() - Int_array = np.zeros(shape=(2048,scans_to_avg)) - - for i in range(scans_to_avg): #software average - data = self.spec.spectrum(correct_dark_counts=self.ui.correct_dark_counts_checkBox.isChecked()) - Int_array[:,i] = data[1] - self.y = np.mean(Int_array, axis=-1) - - else: - self.ui.status_textBrowser.append("Connect to Spectrometer!") - raise Exception("Must connect to spectrometer first!") - - - def close_connection(self): - if self.spec is not None: - self.spec.close() - self.ui.status_textBrowser.append("Ocean Optics Device Disconnected") - del self.spec - self.spec = None - - def close_application(self): - choice = QtGui.QMessageBox.question(self, 'EXIT!', - "Do you want to exit the app?", - QtGui.QMessageBox.Yes | QtGui.QMessageBox.No) - if choice == QtGui.QMessageBox.Yes: - sys.exit() - else: - pass - - -win = MainWindow() - - -## Start Qt event loop unless running in interactive mode or using pyside. -if __name__ == '__main__': - import sys - if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'): - QtGui.QApplication.instance().exec_() diff --git a/src/main/python/PLQE_analysis/column_selection_gui.ui b/src/main/python/PLQE_analysis/column_selection_gui.ui deleted file mode 100644 index c20125c..0000000 --- a/src/main/python/PLQE_analysis/column_selection_gui.ui +++ /dev/null @@ -1,107 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 800 - 600 - - - - Select number of columns - - - - - - - Data preview - - - - - - - - Select data columns - - - - - - - - Ref - - - - - - - Inpath - - - - - - - Outpath - - - - - - - 2 - - - - - - - 3 - - - - - - - 4 - - - - - - - Done - - - - - - - - - - - - - - - - - 0 - 0 - 800 - 31 - - - - - - - - diff --git a/src/main/python/PLQE_analysis/plqe_analysis.py b/src/main/python/PLQE_analysis/plqe_analysis.py deleted file mode 100644 index 3e42a4f..0000000 --- a/src/main/python/PLQE_analysis/plqe_analysis.py +++ /dev/null @@ -1,212 +0,0 @@ -# system imports -from pathlib import Path -import os.path -import pyqtgraph as pg -from pyqtgraph import exporters -from pyqtgraph.Qt import QtCore, QtGui, QtWidgets -import matplotlib.pyplot as plt -import numpy as np - -# local modules - -pg.mkQApp() -pg.setConfigOption('background', 'w') - -base_path = Path(__file__).parent -file_path = (base_path / "plqe_analysis_gui.ui").resolve() - -uiFile = file_path - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -"""params for plotting""" -plt.rc('xtick', labelsize = 20) -plt.rc('xtick.major', pad = 3) -plt.rc('ytick', labelsize = 20) -plt.rc('lines', lw = 1.5, markersize = 7.5) -plt.rc('legend', fontsize = 20) -plt.rc('axes', linewidth = 3.5) - -class MainWindow(TemplateBaseClass): - - def __init__(self): - super(TemplateBaseClass, self).__init__() - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - - #setup uv vis plot - self.plot = self.ui.plotWidget.getPlotItem() - self.plot.setTitle(title="Wavelength vs. Intensity") - self.plot.setLabel('bottom', 'Wavelength', unit='nm') - self.plot.setLabel('left', 'Intensity', unit='a.u.') - self.plot.setLogMode(x=None, y=1) - - #setup line rois for laser and emission - self.laser_region = pg.LinearRegionItem(brush=QtGui.QBrush(QtGui.QColor(255, 0, 0, 50))) - self.laser_region.sigRegionChanged.connect(self.update_laser_spinBoxes) - self.emission_region = pg.LinearRegionItem() - self.emission_region.sigRegionChanged.connect(self.update_emission_spinBoxes) - self.laser_region.setRegion((200, 400)) - self.emission_region.setRegion((700, 800)) - - #setup ui signals - self.ui.load_data_pushButton.clicked.connect(self.open_data_file) - self.ui.plot_pushButton.clicked.connect(self.plot_intensity) - self.ui.clear_pushButton.clicked.connect(self.clear) - self.ui.calculate_plqe_pushButton.clicked.connect(self.calculate_plqe) - self.ui.laser_start_spinBox.valueChanged.connect(self.update_laser_region) - self.ui.laser_stop_spinBox.valueChanged.connect(self.update_laser_region) - self.ui.emission_start_spinBox.valueChanged.connect(self.update_emission_region) - self.ui.emission_stop_spinBox.valueChanged.connect(self.update_emission_region) - - self.show() - - def open_data_file(self): - """ Open data file """ - try: - self.filename = QtWidgets.QFileDialog.getOpenFileName(self) - #self.data = np.loadtxt(self.filename[0], delimiter = '\t', skiprows = 1) - if ".txt" in self.filename[0]: - self.data = np.loadtxt(self.filename[0], delimiter = '\t', skiprows = 1) - elif ".csv" in self.filename[0]: - self.data = np.loadtxt(self.filename[0], delimiter = ',', skiprows = 1) - elif ".qua" in self.filename[0]:#TODO: Include a Pop-up window for input for skipping header - self.data = np.genfromtxt(self.filename[0], delimiter = '\t', skip_header = 28) - self.cs_window = ColSelectionWindow(self.data) - self.cs_window.col_selection_signal.connect(self.open_with_col_selection) - self.nm = np.copy(self.data[:,0]) - #self.ref_data = np.copy(self.data[:,1]) - #self.inpath_data = np.copy(self.data[:,2]) - #self.outpath_data = np.copy(self.data[:,3]) - except Exception as err: - print(format(err)) - - def open_with_col_selection(self): - ref_data_col = self.cs_window.ui.ref_spinBox.value() - 1 #subtract since spinboxes refer to column num and not index - inpath_data_col = self.cs_window.ui.inpath_spinBox.value() - 1 - outpath_data_col = self.cs_window.ui.outpath_spinBox.value() - 1 - self.ref_data = np.copy(self.data[:,ref_data_col]) - self.inpath_data = np.copy(self.data[:,inpath_data_col]) - self.outpath_data = np.copy(self.data[:,outpath_data_col]) - - def update_laser_spinBoxes(self): - """ Update laser spinboxes based on line rois """ - self.laser_start, self.laser_stop = self.laser_region.getRegion() - self.ui.laser_start_spinBox.setValue(self.laser_start) - self.ui.laser_stop_spinBox.setValue(self.laser_stop) - - - def update_emission_spinBoxes(self): - """ Update emission spinboxes based on line rois """ - self.emission_start, self.emission_stop = self.emission_region.getRegion() - self.ui.emission_start_spinBox.setValue(self.emission_start) - self.ui.emission_stop_spinBox.setValue(self.emission_stop) - - def update_laser_region(self): - """ Update laser line rois based on spinboxes """ - laser_start = self.ui.laser_start_spinBox.value() - laser_stop = self.ui.laser_stop_spinBox.value() - self.laser_region.setRegion((laser_start, laser_stop)) - - def update_emission_region(self): - """ Update emission line rois based on spinboxes """ - emission_start = self.ui.emission_start_spinBox.value() - emission_stop = self.ui.emission_stop_spinBox.value() - self.emission_region.setRegion((emission_start, emission_stop)) - - def plot_intensity(self): - try: - self.plot.plot(self.nm, self.inpath_data, pen='r') - self.plot.addItem(self.laser_region, ignoreBounds=True) - self.plot.addItem(self.emission_region, ignoreBounds=True) - except Exception as err: - print(format(err)) - - def find_nearest(self,array,value): - idx = (np.abs(array-value)).argmin() - return idx - - def calculate_plqe(self): - - nm_interp_step = 1 - nm_interp_start = np.ceil(self.nm[0] / nm_interp_step) * nm_interp_step - nm_interp_stop = np.floor(self.nm[len(self.nm) - 1] / nm_interp_step) * nm_interp_step - nm_interp = np.arange(nm_interp_start, nm_interp_stop + nm_interp_step, nm_interp_step) - - ref_interp = np.interp(nm_interp, self.nm, self.ref_data) - - - inpath_interp = np.interp(nm_interp, self.nm, self.inpath_data) - outpath_interp = np.interp(nm_interp, self.nm, self.outpath_data) - - - """L_x is area under laser profile for experiment x""" - """P_x_ is area under emission profile for experiment x""" - - - #plt.semilogy(nm, a1_outpath_data[:,1]) - - emission_start_idx = self.find_nearest(nm_interp, self.emission_start) - emission_stop_idx = self.find_nearest(nm_interp, self.emission_stop) - - laser_start_idx = self.find_nearest(nm_interp, self.laser_start) - laser_stop_idx = self.find_nearest(nm_interp, self.laser_stop) - - la = np.trapz(ref_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx]) - lb = np.trapz(outpath_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx]) - lc = np.trapz(inpath_interp[laser_start_idx: laser_stop_idx], x = nm_interp[laser_start_idx:laser_stop_idx]) - - pa = np.trapz(ref_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx]) - pb = np.trapz(outpath_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx]) - pc = np.trapz(inpath_interp[emission_start_idx:emission_stop_idx], x = nm_interp[emission_start_idx:emission_stop_idx]) - - absorb = 1.0 - (lc / lb) - - plqe = 100 * (pc - ((1.0 - absorb) * pb)) / (la * absorb) - #print('PLQE Percent = %.3f' %(plqe)) - #return plqe - self.ui.plqe_label.setText("%.3f" %(plqe)) - - def clear(self): - self.plot.clear() - -"""Table view GUI""" -ui_file_path = (base_path / "column_selection_gui.ui").resolve() -col_selection_WindowTemplate, col_selection_TemplateBaseClass = pg.Qt.loadUiType(ui_file_path) - -class ColSelectionWindow(col_selection_TemplateBaseClass): - - col_selection_signal = QtCore.pyqtSignal() #signal to help with pass info back to MainWindow - - def __init__(self, data): - col_selection_TemplateBaseClass.__init__(self) - # Create the param window - self.ui = col_selection_WindowTemplate() - self.ui.setupUi(self) - self.ui.done_pushButton.clicked.connect(self.done) - - self.table_widget = pg.TableWidget() - self.ui.data_preview_groupBox.layout().addWidget(self.table_widget) - - self.table_widget.setData(data) - - #self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False) - self.show() - - def done(self): - self.col_selection_signal.emit() - self.ui.textBrowser.setText("Data successfully loaded.") - #self.close() - - def closeEvent(self, event): - self.col_selection_signal.emit() - -"""Run the Main Window""" -def run(): - win = MainWindow() - QtGui.QApplication.instance().exec_() - return win - -#run() diff --git a/src/main/python/PLQE_analysis/plqe_analysis_gui.ui b/src/main/python/PLQE_analysis/plqe_analysis_gui.ui deleted file mode 100644 index 7720b49..0000000 --- a/src/main/python/PLQE_analysis/plqe_analysis_gui.ui +++ /dev/null @@ -1,150 +0,0 @@ - - - Form - - - - 0 - 0 - 575 - 524 - - - - PLQE Analysis - - - - - - PLQE - - - - - - Laser start - - - - - - - 9999.000000000000000 - - - 200.000000000000000 - - - - - - - Laser stop - - - - - - - 9999.000000000000000 - - - 400.000000000000000 - - - - - - - Emission start - - - - - - - 9999.000000000000000 - - - 700.000000000000000 - - - - - - - Emission stop - - - - - - - 9999.000000000000000 - - - 800.000000000000000 - - - - - - - PLQE Percent - - - - - - - 0 - - - - - - - Calculate PLQE - - - - - - - - - - Clear - - - - - - - Plot - - - - - - - Load data - - - - - - - - - - - PlotWidget - QGraphicsView -
pyqtgraph
- - - - - diff --git a/src/main/python/Spectrum_analysis/Spectra_fit_funcs.py b/src/main/python/Spectrum_analysis/Spectra_fit_funcs.py deleted file mode 100644 index a96f782..0000000 --- a/src/main/python/Spectrum_analysis/Spectra_fit_funcs.py +++ /dev/null @@ -1,241 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Sun Mar 31 15:46:54 2019 - -@author: Sarthak -""" - -# -*- coding: utf-8 -*- -""" -Created on Thu Jan 31 20:48:03 2019 - -@author: Sarthak -""" -import numpy as np -from lmfit.models import GaussianModel, LorentzianModel - -class Spectra_Fit(object): - """ - Fit a spectrum. - - Attributes: - data: spectrum data (x-axis and y-axis) - ref: reference spectrum (both x and y-axis) for background correction - """ - - def __init__(self, data, ref, wlref = None, fit_in_eV = True): - self.data = data - self.ref = ref - self.wlref = wlref - self.fit_in_eV = fit_in_eV - - def background_correction(self): - """Return the background corrected spectrum""" - x = self.data[:, 0] # wavelengths - y = self.data[:, 1] # intensity - yref = self.ref[:, 1] - y = y - yref # background correction - if self.wlref is not None: - wlref = self.wlref[:,1] - y = y/wlref - - if self.fit_in_eV is True: - x = np.sort(1240/self.data[:, 0]) # converting to eV and sorting in ascending order - y = [y[i] for i in np.argsort(1240/x)] # sorting argument of y acc to x sorting index - # need to do this because data is collected in wavelength - - return [x,y] - -class Single_Gaussian(Spectra_Fit): - """Fit a single gaussian to the spectrum - - Attributes: - data: spectrum data (x-axis and y-axis) - ref: reference spectrum (both x and y-axis) for background correction - """ - - def gaussian_model(self): - x,y = self.background_correction() - gmodel = GaussianModel(prefix = 'g1_') # calling gaussian model - pars = gmodel.guess(y, x=x) # parameters - center, width, height - result = gmodel.fit(y, pars, x=x, nan_policy='propagate') - return result - - # def gaussian_model_w_lims(self, center_initial_guess=None, sigma_initial_guess=None, center_min=None, center_max=None): - # x,y = self.background_correction() - # gmodel = GaussianModel(prefix = 'g1_') # calling gaussian model - # pars = gmodel.guess(y, x=x) # parameters - center, width, height - # pars['g1_center'].set(center_initial_guess, min=center_min, max=center_max) - # pars['g1_sigma'].set(sigma_initial_guess) - # result = gmodel.fit(y, pars, x=x, nan_policy='propagate') - # return result #770 760 780 sigma 15 - def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range): - x,y = self.background_correction() - if self.fit_in_eV is True: - peak_pos = 1240/peak_pos - sigma = 1240/sigma - min_max_range = np.sort(1240/np.asarray(min_max_range)) - gmodel = GaussianModel(prefix = 'g1_') # calling gaussian model - pars = gmodel.guess(y, x=x) # parameters - center, width, height - pars['g1_center'].set(peak_pos, min=min_max_range[0], max=min_max_range[1]) - pars['g1_sigma'].set(sigma) - result = gmodel.fit(y, pars, x=x, nan_policy='propagate') - return result - -class Single_Lorentzian(Spectra_Fit): - """Fit a single Lorentzian to the spectrum - - Attributes: - data: spectrum data (x-axis and y-axis) - ref: reference spectrum (both x and y-axis) for background correction - """ - - def lorentzian_model(self): - x,y = self.background_correction() - lmodel = LorentzianModel(prefix = 'l1_') # calling lorentzian model - pars = lmodel.guess(y, x=x) # parameters - center, width, height - result = lmodel.fit(y, pars, x=x, nan_policy='propagate') - return result - - def lorentzian_model_w_lims(self, peak_pos, sigma, min_max_range): - x,y = self.background_correction() - if self.fit_in_eV is True: - peak_pos = 1240/peak_pos - sigma = 1240/sigma - min_max_range = np.sort(1240/np.asarray(min_max_range)) - lmodel = LorentzianModel(prefix = 'l1_') # calling lorentzian model - pars = lmodel.guess(y, x=x) # parameters - center, width, height - pars['l1_center'].set(peak_pos, min = min_max_range[0], max = min_max_range[1]) - pars['l1_sigma'].set(sigma) - result = lmodel.fit(y, pars, x=x, nan_policy='propagate') - return result - -class Double_Gaussian(Spectra_Fit): - """Fit two gaussians to the spectrum - - Attributes: - data: spectrum data (x-axis and y-axis) - ref: reference spectrum (both x and y-axis) for background correction - """ - - def gaussian_model(self): - - x,y = self.background_correction() - gmodel_1 = GaussianModel(prefix='g1_') # calling gaussian model - pars = gmodel_1.guess(y, x=x) # parameters - center, width, height - - gmodel_2 = GaussianModel(prefix='g2_') - pars.update(gmodel_2.make_params()) # update parameters - center, width, height - - gmodel = gmodel_1 + gmodel_2 - result = gmodel.fit(y, pars, x=x, nan_policy='propagate') - return result - - def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range): - #center_initial_guesses - list containing initial guesses for peak centers. [center_guess1, center_guess2] - #sigma_initial_guesses - list containing initial guesses for sigma. [sigma1, sigma2] - #min_max_range - list containing lists of min and max for peak center. [ [min1, max1], [min2, max2] ] - - x,y = self.background_correction() - if self.fit_in_eV is True: - peak_pos = 1240/np.asarray(peak_pos) - sigma = 1240/np.asarray(sigma) - min_max_range = np.sort(1240/np.asarray(min_max_range)) - gmodel_1 = GaussianModel(prefix='g1_') # calling gaussian model - pars = gmodel_1.guess(y, x=x) # parameters - center, width, height - pars['g1_center'].set(peak_pos[0], min = min_max_range[0][0], max = min_max_range[0][1]) - pars['g1_sigma'].set(sigma[0]) - pars['g1_amplitude'].set(min=0) - - gmodel_2 = GaussianModel(prefix='g2_') - pars.update(gmodel_2.make_params()) # update parameters - center, width, height - pars['g2_center'].set(peak_pos[1], min = min_max_range[1][0], max = min_max_range[1][1]) - pars['g2_sigma'].set(sigma[1], min = pars['g1_sigma'].value) - pars['g2_amplitude'].set(min = 0) - - gmodel = gmodel_1 + gmodel_2 - result = gmodel.fit(y, pars, x=x, nan_policy='propagate') - return result - -class Multi_Gaussian(Spectra_Fit): - - # def __init__(self, data, ref, num_of_gaussians, peak_pos, sigma, min_max_range): - # Spectra_Fit.__init__(self, data, ref) - # self.num_of_gaussians = num_of_gaussians - # self.peak_pos = peak_pos - # self.min_max_range = min_max_range - def __init__(self, data, ref, num_of_gaussians, wlref=None, fit_in_eV = True): - Spectra_Fit.__init__(self, data, ref, wlref, fit_in_eV=True) - self.num_of_gaussians = num_of_gaussians - - def gaussian_model(self): - composite_model = None - composite_pars = None - - x,y = self.background_correction() - - for i in range(self.num_of_gaussians): - - model = GaussianModel(prefix='g'+str(i+1)+'_') - - if composite_pars is None: - composite_pars = model.guess(y, x=x) -# composite_pars = model.make_params() - - else: - composite_pars.update(model.make_params()) - - if composite_model is None: - composite_model = model - else: - composite_model += model - - result = composite_model.fit(y, composite_pars, x=x, nan_policy='propagate') - return result - - def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range): - self.peak_pos = peak_pos - self.sigma = sigma - self.min_max_range = min_max_range - - composite_model = None - composite_pars = None - - x,y = self.background_correction() - - assert self.num_of_gaussians == len(self.peak_pos), ("Number of gaussians must be equal to the number of peak positions") - assert len(self.min_max_range) == len(self.peak_pos), ("Number of bounds on the range must be equal to the number of peak positions") - - if self.fit_in_eV is True: - peak_pos = 1240/np.asarray(peak_pos) - sigma = 1240/np.asarray(sigma) - min_max_range = np.sort(1240/np.asarray(min_max_range)) - - - for i in range(self.num_of_gaussians): - - model = GaussianModel(prefix='g'+str(i+1)+'_') - - if composite_pars is None: - composite_pars = model.guess(y, x=x) -# composite_pars = model.make_params() - composite_pars['g'+str(i+1)+'_center'].set(self.peak_pos[i], - min = self.min_max_range[0][0], max = self.min_max_range[0][1]) - composite_pars['g'+str(i+1)+'_sigma'].set(self.sigma[i]) - composite_pars['g'+str(i+1)+'_amplitude'].set(min = 0) - - else: - composite_pars.update(model.make_params()) - composite_pars['g'+str(i+1)+'_center'].set(self.peak_pos[i], - min = self.min_max_range[i][0], max = self.min_max_range[i][1]) - composite_pars['g'+str(i+1)+'_sigma'].set(self.sigma[i], min = composite_pars['g1_sigma'].value) - composite_pars['g'+str(i+1)+'_amplitude'].set(min = 0) - - - if composite_model is None: - composite_model = model - else: - composite_model += model - - result = composite_model.fit(y, composite_pars, x=x, nan_policy='propagate') - return result \ No newline at end of file diff --git a/src/main/python/Spectrum_analysis/Spectra_plot_fit.py b/src/main/python/Spectrum_analysis/Spectra_plot_fit.py deleted file mode 100644 index 69f182b..0000000 --- a/src/main/python/Spectrum_analysis/Spectra_plot_fit.py +++ /dev/null @@ -1,1020 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Wed Mar 27 16:50:26 2019 - -@author: Sarthak -""" - -# system imports -import sys -import h5py -from pathlib import Path -import os.path -import pyqtgraph as pg -from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog -import numpy as np -import matplotlib.pyplot as plt -import matplotlib -import pickle -import lmfit -from lmfit.models import GaussianModel, LinearModel -from scipy import interpolate -import customplotting.mscope as cpm - -sys.path.append(os.path.abspath('../H5_Pkl')) -from H5_Pkl import h5_pkl_view -sys.path.append(os.path.abspath('../Export_Windows')) -try: - from Export_window import ExportFigureWindow, ExportPlotWindow -except: - from Export_Windows.Export_window import ExportFigureWindow, ExportPlotWindow -# local modules -try: - from Spectra_fit_funcs import Spectra_Fit, Single_Gaussian, Single_Lorentzian, Double_Gaussian, Multi_Gaussian - from pyqtgraph_MATPLOTLIBWIDGET import MatplotlibWidget -except: - from Spectrum_analysis.Spectra_fit_funcs import Spectra_Fit, Single_Gaussian, Single_Lorentzian, Double_Gaussian, Multi_Gaussian - from Spectrum_analysis.pyqtgraph_MATPLOTLIBWIDGET import MatplotlibWidget - -matplotlib.use('Qt5Agg') - -"""Recylce params for plotting""" -plt.rc('xtick', labelsize = 10) -plt.rc('xtick.major', pad = 1) -plt.rc('ytick', labelsize = 10) -plt.rc('lines', lw = 1.5, markersize = 3.5) -plt.rc('legend', fontsize = 10) -plt.rc('axes', linewidth=1.5) - -pg.mkQApp() -pg.setConfigOption('background', 'w') - - -base_path = Path(__file__).parent -file_path = (base_path / "Spectra_plot_fit_gui.ui").resolve() - -uiFile = file_path - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -def updateDelay(scale, time): - """ Hack fix for scalebar inaccuracy""" - QtCore.QTimer.singleShot(time, scale.updateBar) - -class MainWindow(TemplateBaseClass): - - def __init__(self): - pg.setConfigOption('imageAxisOrder', 'row-major') - super(TemplateBaseClass, self).__init__() - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - - # self.ui.fitFunc_comboBox.addItems(["Single Gaussian","Single Lorentzian", "Double Gaussian", "Multiple Gaussians"]) -# self.ui.actionExit.triggered.connect(self.close_application) - - ##setup ui signals - self.ui.importSpec_pushButton.clicked.connect(self.open_file) - self.ui.importBck_pushButton.clicked.connect(self.open_bck_file) - self.ui.importWLRef_pushButton.clicked.connect(self.open_wlref_file) - - self.ui.load_spectra_scan_pushButton.clicked.connect(self.open_spectra_scan_file) - self.ui.load_bck_file_pushButton.clicked.connect(self.open_spectra_bck_file) - self.ui.load_fitted_scan_pushButton.clicked.connect(self.open_fit_scan_file) - - self.ui.plot_pushButton.clicked.connect(self.plot) - self.ui.plot_fit_scan_pushButton.clicked.connect(self.plot_fit_scan) - self.ui.plot_raw_scan_pushButton.clicked.connect(self.plot_raw_scan) - self.ui.plot_intensity_sums_pushButton.clicked.connect(self.plot_intensity_sums) - - self.ui.fit_pushButton.clicked.connect(self.fit_and_plot) - self.ui.fit_scan_pushButton.clicked.connect(self.fit_and_plot_scan) - # self.ui.config_fit_params_pushButton.clicked.connect(self.configure_fit_params) - self.ui.clear_pushButton.clicked.connect(self.clear_plot) - self.ui.add_to_mem_pushButton.clicked.connect(self.add_trace_to_mem) - self.ui.export_single_figure_pushButton.clicked.connect(self.export_plot_window) - self.ui.export_scan_figure_pushButton.clicked.connect(self.export_window) - self.ui.analyze_spectra_fits_pushButton.clicked.connect(self.analyze_spectra_fits) - - self.ui.import_pkl_pushButton.clicked.connect(self.open_pkl_file) - self.ui.data_txt_pushButton.clicked.connect(self.pkl_data_to_txt) - self.ui.scan_params_txt_pushButton.clicked.connect(self.pkl_params_to_txt) - - self.ui.pkl_to_h5_pushButton.clicked.connect(self.pkl_to_h5) - - self.ui.tabWidget.currentChanged.connect(self.switch_overall_tab) - self.ui.fitFunc_comboBox.currentTextChanged.connect(self.switch_bounds_and_guess_tab) - self.ui.adjust_param_checkBox.stateChanged.connect(self.switch_adjust_param) - - self.ui.export_data_pushButton.clicked.connect(self.export_data) - self.ui.clear_export_data_pushButton.clicked.connect(self.clear_export_data) - - # for i in reversed(range(self.ui.bounds_groupBox.layout().count())): - # self.ui.bounds_groupBox.layout().itemAt(i).widget().deleteLater() - #self.ui.single_bounds_page.layout().addWidget(QtWidgets.QPushButton("test")) - - self.ui.plot = pg.PlotWidget() - self.ui.plot.setTitle(title="Spectrum Plot") - #self.ui.plot.show() - - self.file = None - self.bck_file = None - self.wlref_file = None - self.x = None - self.y = None - self.out = None # output file after fitting - - # Peak parameters if adjust params is selected - self.center_min = None - self.center_max = None - - #variables accounting for data received from FLIM analysis - self.opened_from_flim = False #switched to True in FLIM_plot when "analyze lifetime" clicked - self.sum_data_from_flim = [] - - # fit scan file variable set to None for analyze_spectra_fits - self.fit_scan_file = None - - #container for data to append to txt file - self.data_list = [] - - #for adding traces to memory for plotting/exporting all at once - self.x_mem = [] - self.y_mem = [] - self.best_fit_mem = [] - self.legend = [] - self.single_spec_fit_called = False - - self.show() - - """ Open Single Spectrum files """ - def open_file(self): - try: - self.single_spec_filename = QtWidgets.QFileDialog.getOpenFileName(self) - try: - try: - self.file = np.loadtxt(self.single_spec_filename[0], skiprows = 1, delimiter=" ") - except: - self.file = np.loadtxt(self.single_spec_filename[0], skiprows = 16, delimiter='\t') - except: - self.file = np.genfromtxt(self.single_spec_filename[0], skip_header=1, skip_footer=3, delimiter='\t') - self.opened_from_flim = False - except: - pass - - def open_bck_file(self): - try: - filename = QtWidgets.QFileDialog.getOpenFileName(self) - try: - try: - self.bck_file = np.loadtxt(filename[0], skiprows=1, delimiter=" ") - except: - self.bck_file = np.loadtxt(filename[0], skiprows = 16, delimiter='\t') - except: - self.bck_file = np.genfromtxt(filename[0], skip_header=1, skip_footer=3, delimiter='\t') - except Exception as e: - self.ui.result_textBrowser.append(str(e)) - pass - - def open_wlref_file(self): - try: - filename = QtWidgets.QFileDialog.getOpenFileName(self) - try: - try: - self.wlref_file = np.loadtxt(filename[0], skiprows=1, delimiter= " ") - except: - self.wlref_file = np.loadtxt(filename[0], skiprows = 16, delimiter='\t') - except: - self.wlref_file = np.genfromtxt(filename[0], skip_header=1, skip_footer=3, delimiter='\t') - except: - pass - - """Open Scan Files""" - def open_spectra_scan_file(self): - try: - filename = QtWidgets.QFileDialog.getOpenFileName(self, filter="Scan files (*.pkl *.h5)") - self.filename_for_viewer_launch = filename[0] - if ".pkl" in filename[0]: - self.spec_scan_file = pickle.load(open(filename[0], 'rb')) - if self.ui.launch_data_viewer_checkBox.isChecked(): - self.launch_h5_pkl_viewer() - self.scan_file_type = "pkl" - elif ".h5" in filename[0]: - self.spec_scan_file = h5py.File(filename[0], 'r') - if self.ui.launch_data_viewer_checkBox.isChecked(): - self.launch_h5_pkl_viewer() - self.scan_file_type = "h5" - self.get_data_params() - self.ui.result_textBrowser2.append("Done Loading - Spectra Scan File") - except Exception as e: - self.ui.result_textBrowser2.append(str(e)) - pass - - def open_spectra_bck_file(self): - try: - filename = QtWidgets.QFileDialog.getOpenFileName(self) - self.bck_file = np.loadtxt(filename[0])#, skiprows=1, delimiter=None) - self.ui.result_textBrowser2.append("Done Loading - Background File") - except Exception as e: - self.ui.result_textBrowser2.append(str(e)) - pass - - def open_fit_scan_file(self): - try: - filename = QtWidgets.QFileDialog.getOpenFileName(self) - with pg.BusyCursor(): - self.filename_for_viewer_launch = filename[0] - self.fit_scan_file = pickle.load(open(filename[0], 'rb')) - if self.ui.launch_data_viewer_checkBox.isChecked(): - self.launch_h5_pkl_viewer() # TODO Needs to implement reading the fit result datatype in PKL Viewer - self.ui.result_textBrowser2.append("Done Loading - Scan Fit File") - except Exception as e: - self.ui.result_textBrowser2.append(str(e)) - pass - - def open_pkl_file(self): - """ Open pkl file to convert to txt """ - try: - self.pkl_to_convert = QtWidgets.QFileDialog.getOpenFileNames(self) - files = self.pkl_to_convert[0] - for i in range(len(files)): - self.filename_for_viewer_launch = files[i] - if self.ui.launch_data_viewer_checkBox_2.isChecked(): - self.launch_h5_pkl_viewer() - except: - pass - - def launch_h5_pkl_viewer(self): - """ Launches H5/PKL viewer to give an insight into the data and its structure""" - viewer_window = h5_pkl_view.H5PklView(sys.argv) - viewer_window.settings['data_filename'] = self.filename_for_viewer_launch - - def analyze_spectra_fits(self): - """Analyze fits to the individual spectrum within a spectra scan fit file""" - if self.fit_scan_file is None: - self.open_fit_scan_file() - - #result_no = int(self.ui.result_spinBox.value()) - #self.matplotlibwidget = MatplotlibWidget(size=(12,8), dpi=300) - #self.fit_scan_file['result_'+str(0)].plot(fig=self.matplotlibwidget.getFigure().add_subplot(111)) - #self.matplotlibwidget.draw() - #self.matplotlibwidget.show() - analyze_window = Analyze(scan_fit_file=self.fit_scan_file) - analyze_window.run() - - def switch_overall_tab(self): - """ Enable/disable fit settings on right depending on current tab """ - if self.ui.tabWidget.currentIndex() == 0: - self.ui.fitting_settings_groupBox.setEnabled(True) - self.ui.fit_pushButton.setEnabled(True) - self.ui.fit_scan_pushButton.setEnabled(False) - self.ui.save_all_checkBox.setEnabled(False) - self.ui.scan_fit_settings_groupBox.setEnabled(False) - elif self.ui.tabWidget.currentIndex() == 1: - self.ui.fitting_settings_groupBox.setEnabled(False) - self.ui.fit_pushButton.setEnabled(False) - self.ui.fit_scan_pushButton.setEnabled(True) - self.ui.save_all_checkBox.setEnabled(True) - self.ui.scan_fit_settings_groupBox.setEnabled(True) - elif self.ui.tabWidget.currentIndex() == 2: - self.ui.fitting_settings_groupBox.setEnabled(False) - self.ui.fit_pushButton.setEnabled(False) - self.ui.fit_scan_pushButton.setEnabled(False) - self.ui.save_all_checkBox.setEnabled(False) - self.ui.scan_fit_settings_groupBox.setEnabled(False) - - """ Single spectrum functions """ - def switch_bounds_and_guess_tab(self): - """ Show the appropriate bounds and initial guess params based on fit function """ - fit_func = self.ui.fitFunc_comboBox.currentText() - if fit_func == "Single Gaussian" or fit_func == "Single Lorentzian": - self.ui.n_label.setEnabled(False) - self.ui.n_spinBox.setEnabled(False) - self.ui.bounds_stackedWidget.setCurrentIndex(0) - self.ui.guess_stackedWidget.setCurrentIndex(0) - self.ui.plot_components_checkBox.setEnabled(False) - self.ui.n_spinBox.setValue(1) - elif fit_func == "Double Gaussian": - self.ui.n_label.setEnabled(False) - self.ui.n_spinBox.setEnabled(False) - self.ui.bounds_stackedWidget.setCurrentIndex(1) - self.ui.guess_stackedWidget.setCurrentIndex(1) - self.ui.plot_components_checkBox.setEnabled(True) - self.ui.n_spinBox.setValue(2) - elif fit_func == "Triple Gaussian": - self.ui.n_label.setEnabled(False) - self.ui.n_spinBox.setEnabled(False) - self.ui.bounds_stackedWidget.setCurrentIndex(2) - self.ui.guess_stackedWidget.setCurrentIndex(2) - self.ui.plot_components_checkBox.setEnabled(True) - self.ui.n_spinBox.setValue(3) - - def switch_adjust_param(self): - """ Enable bounds and initial guess only when adjust parameters is checked """ - checked = self.ui.adjust_param_checkBox.isChecked() - self.ui.bounds_groupBox.setEnabled(checked) - self.ui.guess_groupBox.setEnabled(checked) - - def check_loaded_files(self): - """ - Check if 'subtract background' or 'white light correction' is checked - and if required files have been loaded. - """ - if self.ui.subtract_bck_radioButton.isChecked() and self.bck_file is None: - self.ui.result_textBrowser.setText("You need to load a background file.") - elif self.wlref_file is not None and self.ui.WLRef_checkBox.isChecked() == False: - self.ui.result_textBrowser.setText("You need to check the White Light Correction option!") - elif self.wlref_file is None and self.ui.WLRef_checkBox.isChecked(): - self.ui.result_textBrowser.setText("You need to load a White Light Ref file.") - else: - return True - - def plot(self): - try: - if self.opened_from_flim: - flim_data = self.sum_data_from_flim.T - interp = interpolate.interp1d(flim_data[:,0], flim_data[:,1]) - x_range = [flim_data[:,0][0], flim_data[:,0][-1]] - xnew = np.linspace(x_range[0], x_range[1], 100 ) - ynew = interp(xnew) - self.file = np.zeros((xnew.shape[0], 2)) - self.file[:,0] = xnew - self.file[:,1] = ynew - self.x = xnew - self.y = ynew - - elif self.file is None: #elif - self.ui.result_textBrowser.setText("You need to load a data file.") - else: - self.x = self.file[:,0] - self.y = self.file[:,1] - - self.check_loaded_files() - - if self.check_loaded_files() == True: #check the following conditions if all required files have been provided - if self.ui.subtract_bck_radioButton.isChecked() == True and self.ui.WLRef_checkBox.isChecked() == False: - bck_y = self.bck_file[:,1] - self.y = self.y - bck_y - elif self.ui.subtract_bck_radioButton.isChecked() == False and self.ui.WLRef_checkBox.isChecked() == True: - wlref_y = self.wlref_file[:,1] - self.y = (self.y)/wlref_y - - elif self.ui.subtract_bck_radioButton.isChecked() == True and self.ui.WLRef_checkBox.isChecked() == True: - bck_y = self.bck_file[:,1] - wlref_y = self.wlref_file[:,1] - self.y = (self.y-bck_y)/wlref_y - - - if self.ui.norm_checkBox.isChecked(): - self.normalize() - - self.check_eV_state() - self.ui.plot.show() - self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') - - except Exception as e: - self.ui.result_textBrowser.append(str(e)) - pass - self.ui.plot.setLabel('left', 'Intensity', units='a.u.') - if self.ui.fit_in_eV.isChecked(): - self.ui.plot.setLabel('bottom', 'Energy (eV)') - else: - self.ui.plot.setLabel('bottom', 'Wavelength (nm)') - - self.single_spec_fit_called = False - - def normalize(self): - self.y = (self.y) / np.amax(self.y) - - def check_eV_state(self): - if self.ui.fit_in_eV.isChecked(): - self.x = np.sort(1240/self.file[:,0]) - self.y = [self.y[i] for i in np.argsort(1240/self.file[:,0])] - else: - self.x = self.file[:,0] - self.y = self.file[:,1] - - def clear_plot(self): - self.ui.plot.clear() - self.ui.result_textBrowser.clear() - - def clear_check(self): - if self.ui.clear_checkBox.isChecked() == True: - return True - elif self.ui.clear_checkBox.isChecked() == False: - return False - - def fit_and_plot(self): - fit_func = self.ui.fitFunc_comboBox.currentText() - - try: - self.plot() - if self.opened_from_flim: - self.file = np.zeros((self.x.shape[0], 2)) - self.file[:,0] = self.x - self.file[:,1] = self.y - bck = lmfit.models.LinearModel(prefix='line_') - gmodel = GaussianModel(prefix='g1_') - pars = bck.make_params(intercept=self.y.min(), slope=0) - pars += gmodel.guess(self.y, x=self.x) - comp_model = gmodel + bck - self.result = comp_model.fit(self.y, pars, x=self.x, nan_policy='propagate') - self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') - self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') - self.ui.result_textBrowser.setText(self.result.fit_report()) - - - if self.ui.plot_without_bck_radioButton.isChecked(): #if plot w/o bck, create dummy bck_file - self.bck_file = np.zeros(shape=(self.file.shape[0], 2)) - self.bck_file[:,0] = self.file[:,0] - - # if self.ui.subtract_bck_radioButton.isChecked() == False: - # self.ui.result_textBrowser.setText("You need to check the subtract background option!") - if self.check_loaded_files is None: - pass - elif self.opened_from_flim: - pass - else: - self.check_eV_state() - if fit_func == "Single Gaussian": - single_gauss = Single_Gaussian(self.file, self.bck_file, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked()) - if self.ui.adjust_param_checkBox.isChecked(): - center1_min = self.ui.single_peakcenter1_min_spinBox.value() - center1_max = self.ui.single_peakcenter1_max_spinBox.value() - center1_guess = self.ui.single_peakcenter1_guess_spinBox.value() - sigma1_guess = self.ui.single_sigma1_guess_spinBox.value() - self.result = single_gauss.gaussian_model_w_lims(center1_guess, sigma1_guess, - [center1_min, center1_max]) - else: - self.result = single_gauss.gaussian_model() - #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') - self.plot() - self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') - self.ui.result_textBrowser.setText(self.result.fit_report()) - - elif fit_func == "Single Lorentzian": #and self.ui.subtract_bck_radioButton.isChecked() == True: - single_lorentzian = Single_Lorentzian(self.file, self.bck_file, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked()) - - if self.ui.adjust_param_checkBox.isChecked(): - center1_min = self.ui.single_peakcenter1_min_spinBox.value() - center1_max = self.ui.single_peakcenter1_max_spinBox.value() - center1_guess = self.ui.single_peakcenter1_guess_spinBox.value() - sigma1_guess = self.ui.single_sigma1_guess_spinBox.value() - self.result = single_lorentzian.lorentzian_model_w_lims(center1_guess, sigma1_guess, - [center1_min, center1_max]) - else: - self.result = single_lorentzian.lorentzian_model() - #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') - self.plot() - self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') - self.ui.result_textBrowser.setText(self.result.fit_report()) - - elif fit_func == "Double Gaussian": #and self.ui.subtract_bck_radioButton.isChecked() == True: - double_gauss = Double_Gaussian(self.file, self.bck_file, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked()) - if self.ui.adjust_param_checkBox.isChecked(): - center1_min = self.ui.double_peakcenter1_min_spinBox.value() - center1_max = self.ui.double_peakcenter1_max_spinBox.value() - center2_min = self.ui.double_peakcenter2_min_spinBox.value() - center2_max = self.ui.double_peakcenter2_max_spinBox.value() - center1_guess = self.ui.double_peakcenter1_guess_spinBox.value() - sigma1_guess = self.ui.double_sigma1_guess_spinBox.value() - center2_guess = self.ui.double_peakcenter2_guess_spinBox.value() - sigma2_guess = self.ui.double_sigma2_guess_spinBox.value() - - peak_pos = [center1_guess, center2_guess] - sigma = [sigma1_guess, sigma2_guess] - min_max_range = [ [center1_min, center1_max], [center2_min, center2_max] ] - self.result = double_gauss.gaussian_model_w_lims(peak_pos, sigma, min_max_range) - - else: - self.result = double_gauss.gaussian_model() - - #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') - self.plot() - self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') - if self.ui.plot_components_checkBox.isChecked(): - comps = self.result.eval_components(x=self.x) - self.ui.plot.plot(self.x, comps['g1_'], pen='b', clear=False) - self.ui.plot.plot(self.x, comps['g2_'], pen='g', clear=False) - - self.ui.result_textBrowser.setText(self.result.fit_report()) - - elif fit_func == "Triple Gaussian": #and self.ui.subtract_bck_radioButton.isChecked() == True: - #currently only works for triple gaussian (n=3) - multiple_gauss = Multi_Gaussian(self.file, self.bck_file, 3, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked()) - if self.ui.adjust_param_checkBox.isChecked(): - center1_min = self.ui.multi_peakcenter1_min_spinBox.value() - center1_max = self.ui.multi_peakcenter1_max_spinBox.value() - center2_min = self.ui.multi_peakcenter2_min_spinBox.value() - center2_max = self.ui.multi_peakcenter2_max_spinBox.value() - center3_min = self.ui.multi_peakcenter3_min_spinBox.value() - center3_max = self.ui.multi_peakcenter3_max_spinBox.value() - center1_guess = self.ui.multi_peakcenter1_guess_spinBox.value() - sigma1_guess = self.ui.multi_sigma1_guess_spinBox.value() - center2_guess = self.ui.multi_peakcenter2_guess_spinBox.value() - sigma2_guess = self.ui.multi_sigma2_guess_spinBox.value() - center3_guess = self.ui.multi_peakcenter3_guess_spinBox.value() - sigma3_guess = self.ui.multi_sigma3_guess_spinBox.value() -# num_gaussians = 3 - peak_pos = [center1_guess, center2_guess, center3_guess] - sigma = [sigma1_guess, sigma2_guess, sigma3_guess] - min_max_range = [ [center1_min, center1_max], [center2_min, center2_max], [center3_min, center3_max] ] - - self.result = multiple_gauss.gaussian_model_w_lims(peak_pos, sigma, min_max_range) - else: - self.result = multiple_gauss.gaussian_model() - - #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r') - self.plot() - self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k') - if self.ui.plot_components_checkBox.isChecked(): - comps = self.result.eval_components(x=self.x) - self.ui.plot.plot(self.x, comps['g1_'], pen='b', clear=False) - self.ui.plot.plot(self.x, comps['g2_'], pen='g', clear=False) - self.ui.plot.plot(self.x, comps['g3_'], pen='c', clear=False) - self.ui.result_textBrowser.setText(self.result.fit_report()) - - self.data_list.append(self.ui.result_textBrowser.toPlainText()) - self.single_spec_fit_called = True - - except Exception as e: - self.ui.result_textBrowser.append(str(e)) - - def export_window(self): - self.export_window = ExportImages() - self.export_window.export_fig_signal.connect(self.pub_ready_plot_export) - - def export_plot_window(self): - self.exportplotwindow = ExportPlotWindow() - self.exportplotwindow.export_fig_signal.connect(self.pub_ready_plot_export) - - def pub_ready_plot_export(self): - filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") - """Recylce params for plotting""" - plt.rc('xtick', labelsize = 20) - plt.rc('xtick.major', pad = 3) - plt.rc('ytick', labelsize = 20) - plt.rc('lines', lw = 1.5, markersize = 7.5) - plt.rc('legend', fontsize = 20) - plt.rc('axes', linewidth=3.5) - try: - try: - try: - data = self.spec_scan_file - except: - data = self.fit_scan_file - if self.export_window.ui.reverse_checkBox.isChecked(): - colormap = str(self.export_window.ui.cmap_comboBox.currentText())+"_r" - else: - colormap = str(self.export_window.ui.cmap_comboBox.currentText()) - if str(self.export_window.ui.dataChannel_comboBox.currentText()) == "Fitted": - param_selection = str(self.ui.comboBox.currentText()) - if param_selection == 'pk_pos': label = 'PL Peak Position (n.m.)' - elif param_selection == 'fwhm': label = 'PL FWHM (n.m.)' - cpm.plot_confocal(self.img, FLIM_adjust = False, stepsize = data['Scan Parameters']['X step size (um)'], cmap=colormap, cbar_label=label, - vmin=self.export_window.ui.vmin_spinBox.value(), vmax=self.export_window.ui.vmax_spinBox.value()) - elif str(self.export_window.ui.dataChannel_comboBox.currentText()) == "Raw": - cpm.plot_confocal(self.sums, FLIM_adjust = False, figsize=(10,10), stepsize = data['Scan Parameters']['X step size (um)'], cmap=colormap, - vmin=self.export_window.ui.vmin_spinBox.value(), vmax=self.export_window.ui.vmax_spinBox.value()) - plt.tick_params(direction='out', length=8, width=3.5) - plt.tight_layout() - plt.savefig(filename[0],bbox_inches='tight', dpi=300) - plt.close() - except: - if self.x_mem == []: - self.ui.result_textBrowser.setText("Add traces to memory first!") - else: - plt.figure(figsize=(8,6)) - plt.tick_params(direction='out', length=8, width=3.5) - for i in range(len(self.x_mem)): - plt.plot(self.x_mem[i], self.y_mem[i], label=str(self.legend[i])) - if self.single_spec_fit_called == True: - plt.plot(self.x_mem[i], self.best_fit_mem[i],'k') - - if self.ui.fit_in_eV.isChecked(): - plt.xlabel("Energy (eV)", fontsize=20, fontweight='bold') - else: - plt.xlabel("Wavelength (nm)", fontsize=20, fontweight='bold') - plt.ylabel("Intensity (a.u.)", fontsize=20, fontweight='bold') - plt.xlim([self.exportplotwindow.ui.lowerX_spinBox.value(),self.exportplotwindow.ui.upperX_spinBox.value()]) - plt.ylim([self.exportplotwindow.ui.lowerY_spinBox.value(),self.exportplotwindow.ui.upperY_doubleSpinBox.value()]) - plt.legend() - plt.tight_layout() - - plt.savefig(filename[0],bbox_inches='tight', dpi=300) - plt.close() - - except AttributeError: - self.ui.result_textBrowser.setText("Need to fit the data first!") - - def export_data(self): - """ Save fit params and srv calculations stored in data_list as .txt """ - folder = os.path.dirname(self.single_spec_filename[0]) - filename_ext = os.path.basename(self.single_spec_filename[0]) - filename = os.path.splitext(filename_ext)[0] #get filename without extension - - path = folder + "/" + filename + "_fit_results.txt" - if not os.path.exists(path): - file = open(path, "w+") - else: - file = open(path, "a+") - - for i in range(len(self.data_list)): - file.write(self.data_list[i] + "\n\n") - - self.data_list = [] - file.close() - - def clear_export_data(self): - self.data_list = [] - self.x_mem = [] - self.y_mem = [] - self.legend = [] - self.best_fit_mem = [] - - def add_trace_to_mem(self): - try: - self.x_mem.append(self.x) - self.y_mem.append(self.y) - if self.single_spec_fit_called == True: - self.best_fit_mem.append(self.result.best_fit) - self.legend.append(self.ui.lineEdit.text()) - except Exception as e: - print(e) - - - """ Scan spectra functions """ - def get_data_params(self): - data = self.spec_scan_file - if self.scan_file_type == "pkl": - self.intensities = data['Intensities'] - self.wavelengths = data['Wavelengths'] - # try: - self.x_scan_size = data['Scan Parameters']['X scan size (um)'] - self.y_scan_size = data['Scan Parameters']['Y scan size (um)'] - self.x_step_size = data['Scan Parameters']['X step size (um)'] - self.y_step_size = data['Scan Parameters']['Y step size (um)'] - # except: # TODO test and debug loading pkl file w/o scan parameters - # self.configure_scan_params() - # while not hasattr(self, "scan_params_entered"): - # pass - # self.x_scan_size = self.param_window.ui.x_scan_size_spinBox.value() - # self.y_scan_size = self.param_window.ui.y_scan_size_spinBox.value() - # self.x_step_size = self.param_window.ui.x_step_size_spinBox.value() - # self.y_step_size = self.param_window.ui.y_step_size_spinBox.value() - - else: #run this if scan file is h5 - self.x_scan_size = data['Scan Parameters'].attrs['X scan size (um)'] - self.y_scan_size = data['Scan Parameters'].attrs['Y scan size (um)'] - self.x_step_size = data['Scan Parameters'].attrs['X step size (um)'] - self.y_step_size = data['Scan Parameters'].attrs['Y step size (um)'] - self.intensities = data['Intensities'][()] #get dataset values - self.wavelengths = data['Wavelengths'][()] - - self.numb_x_pixels = int(np.ceil(self.x_scan_size/self.x_step_size)) - self.numb_y_pixels = int(np.ceil(self.y_scan_size/self.y_step_size)) - - """Open param window and get peak center range values and assign it to variables to use later""" - # def configure_scan_params(self): - # self.param_window = ParamWindow() - # self.param_window.peak_range.connect(self.peak_range) - - # def peak_range(self, peaks): - # self.center_min = peaks[0] - # self.center_max = peaks[1] - - def plot_fit_scan(self): - try: - if self.ui.use_raw_scan_settings.isChecked(): - num_x = self.numb_x_pixels - num_y =self.numb_y_pixels - else: - num_x = self.ui.num_x_spinBox.value() - num_y = self.ui.num_y_spinBox.value() - - numb_of_points = num_x * num_y #75*75 - - fwhm = np.zeros(shape=(numb_of_points,1)) - pk_pos = np.zeros(shape=(numb_of_points,1)) -# sigma = np.zeros(shape=(numb_of_points,1)) -# height = np.zeros(shape=(numb_of_points,1)) - - if type(self.fit_scan_file['result_0']) == dict: - for i in range(numb_of_points): - fwhm[i, 0] = 2.3548200*self.fit_scan_file['result_'+str(i)]['g1_sigma'] - pk_pos[i, 0] = self.fit_scan_file['result_'+str(i)]['g1_center'] -# sigma[i, 0] = self.fit_scan_file['result_'+str(i)]['g1_sigma'] -# height[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_height'] - - elif type(self.fit_scan_file['result_0']) == lmfit.model.ModelResult: - for i in range(numb_of_points): - fwhm[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_fwhm'] - pk_pos[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_center'] -# sigma[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_sigma'] -# height[i, 0] = self.fit_scan_file['result_'+str(i)].values['g1_height'] - - newshape = (num_x, num_y) - - param_selection = str(self.ui.comboBox.currentText()) - self.img = np.reshape(eval(param_selection), newshape) - - if num_y == 1: - x = np.linspace(0, self.x_scan_size, num_x) - self.graph_layout=pg.GraphicsLayoutWidget() - self.plot = self.graph_layout.addPlot(title="Line Scan") - self.plot.plot(x, self.img[:,0], pen="r") - self.graph_layout.show() - elif num_x == 1: - y = np.linspace(0, self.y_scan_size, num_y) - self.graph_layout=pg.GraphicsLayoutWidget() - self.plot = self.graph_layout.addPlot(title="Line Scan") - self.plot.plot(y, self.img[0,:], pen="r") - self.graph_layout.show() - - else: - self.fit_scan_viewbox = pg.ImageView() - if self.ui.use_raw_scan_settings.isChecked(): - self.fit_scan_viewbox.setImage(self.img, scale= - (self.x_step_size, - self.y_step_size)) - scale = pg.ScaleBar(size=2,suffix='um') - scale.setParentItem(self.fit_scan_viewbox.view) - scale.anchor((1, 1), (1, 1), offset=(-30, -30)) - self.fit_scan_viewbox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) - else: - self.fit_scan_viewbox.setImage(self.img) - - self.fit_scan_viewbox.view.invertY(False) - self.fit_scan_viewbox.show() - - except Exception as e: - self.ui.result_textBrowser2.append(str(e)) - pass - - def plot_raw_scan(self): - try: - # TODO test line scan plots - - intensities = self.intensities.T #this is only there because of how we are saving the data in the app - intensities = np.reshape(intensities, newshape=(2048,self.numb_x_pixels, self.numb_y_pixels)) - self.raw_scan_viewbox = pg.ImageView() - self.raw_scan_viewbox.setImage(intensities, scale= - (self.x_step_size, - self.y_step_size), xvals=self.wavelengths) - - #roi_plot = self.ui.raw_scan_viewBox.getRoiPlot() - #roi_plot.plot(data['Wavelengths'], intensities) - self.raw_scan_viewbox.view.invertY(False) - scale = pg.ScaleBar(size=2,suffix='um') - scale.setParentItem(self.raw_scan_viewbox.view) - scale.anchor((1, 1), (1, 1), offset=(-30, -30)) - self.raw_scan_viewbox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) - self.raw_scan_viewbox.show() - - except Exception as e: - self.ui.result_textBrowser2.append(str(e)) - - def plot_intensity_sums(self): - try: - # TODO test line scan plots - - #intensities = np.reshape(intensities, newshape=(2048, numb_pixels_X*numb_pixels_Y)) - - sums = np.sum(self.intensities, axis=-1) - self.sums = np.reshape(sums, newshape=(self.numb_x_pixels, self.numb_y_pixels)) - self.intensity_sums_viewBox = pg.ImageView() - - self.intensity_sums_viewBox.setImage(self.sums, scale= - (self.x_step_size, - self.y_step_size)) - self.intensity_sums_viewBox.view.invertY(False) - - scale = pg.ScaleBar(size=2,suffix='um') - scale.setParentItem(self.intensity_sums_viewBox.view) - scale.anchor((1, 1), (1, 1), offset=(-30, -30)) - self.intensity_sums_viewBox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10)) - self.intensity_sums_viewBox.show() - - except Exception as e: - self.ui.result_textBrowser2.append(str(e)) - - - def fit_and_plot_scan(self): -# self.ui.result_textBrowser.append("Starting Scan Fitting") - print("Starting Scan Fitting") - print("Using Single Gaussian to Fit\nThis is the only fitting functions implemented") - - with pg.BusyCursor(): - try: - """Define starting and stopping wavelength values here""" - start_nm = int(self.ui.start_nm_spinBox.value()) - stop_nm = int(self.ui.stop_nm_spinBox.value()) - - if self.bck_file is None: - print("Load Background file!") - ref = self.bck_file - index = (ref[:,0]>start_nm) & (ref[:,0]start_nm) & (x - - MainWindow - - - - 0 - 0 - 2115 - 1483 - - - - - 0 - 0 - - - - Spectral Analysis - - - - - - - - - - 12 - - - - Fit Settings - - - - - - false - - - - 10 - - - - n: - - - - - - - false - - - - 10 - - - - 1 - - - 1 - - - - - - - false - - - - 10 - - - - Plot components (>1 Gaussian) - - - true - - - - - - - false - - - - 10 - - - - Bounds - - - - - - 0 - - - - - - - - - - - - - - max - - - - - - - min - - - - - - - 9999.000000000000000 - - - 780.000000000000000 - - - - - - - 9999.000000000000000 - - - 760.000000000000000 - - - - - - - Peak Center 1 (nm) - - - - - - - - - - - - - - - - - - min - - - - - - - 9999.000000000000000 - - - 760.000000000000000 - - - - - - - 9999.000000000000000 - - - 820.000000000000000 - - - - - - - 9999.000000000000000 - - - 795.000000000000000 - - - - - - - Peak Center 2 (nm) - - - - - - - 9999.000000000000000 - - - 775.000000000000000 - - - - - - - max - - - - - - - Peak Center 1 (nm) - - - - - - - - - - - 9999.000000000000000 - - - 760.000000000000000 - - - - - - - 9999.000000000000000 - - - 820.000000000000000 - - - - - - - 9999.000000000000000 - - - 775.000000000000000 - - - - - - - 9999.000000000000000 - - - 755.000000000000000 - - - - - - - 9999.000000000000000 - - - 740.000000000000000 - - - - - - - Peak Center 1 (nm) - - - - - - - max - - - - - - - Peak Center 2 (nm) - - - - - - - Peak Center 3 (nm) - - - - - - - 9999.000000000000000 - - - 795.000000000000000 - - - - - - - min - - - - - - - - - - - - - - - - - - - - - - 10 - - - - Adjust Parameters - - - - - - - - 10 - - - - - Single Gaussian - - - - - Single Lorentzian - - - - - Double Gaussian - - - - - Triple Gaussian - - - - - - - - false - - - - 10 - - - - Initial Guess - - - - - - 0 - - - - - - - Sigma 1 (nm) - - - - - - - Peak Center 1 (nm) - - - - - - - 9999.000000000000000 - - - 770.000000000000000 - - - - - - - 15.000000000000000 - - - - - - - - - - - 9999.000000000000000 - - - 767.000000000000000 - - - - - - - 15.000000000000000 - - - - - - - Peak Center 1 (nm) - - - - - - - 9999.000000000000000 - - - 800.000000000000000 - - - - - - - Sigma 1 (nm) - - - - - - - Peak Center 2 (nm) - - - - - - - Sigma 2 (nm) - - - - - - - 15.000000000000000 - - - - - - - - - - - Peak Center 2 (nm) - - - - - - - Sigma 2 (nm) - - - - - - - Peak Center 3 (nm) - - - - - - - Sigma 3 (nm) - - - - - - - Peak Center 1 (nm) - - - - - - - Sigma 1 (nm) - - - - - - - 9999.000000000000000 - - - 800.000000000000000 - - - - - - - 15.000000000000000 - - - - - - - 9999.000000000000000 - - - 767.000000000000000 - - - - - - - 15.000000000000000 - - - - - - - 9999.000000000000000 - - - 750.000000000000000 - - - - - - - 15.000000000000000 - - - - - - - - - - - - - - - - - - 10 - - - - Fit/Plot in eV - - - true - - - - - - - - 10 - - - - Fit Single Spectrum - - - - - - - false - - - Save Entire Fit Model (File will be large and will take longer) - - - - - - - false - - - - 10 - - - - Fit Entire Scan - - - - - - - false - - - - 12 - - - - Scan Fit Settings - - - - - - - 10 - - - - Stop at (nm): - - - - - - - - 10 - - - - 300 - - - 1100 - - - 600 - - - - - - - - 10 - - - - Start at (nm): - - - - - - - - 10 - - - - Qt::ImhDigitsOnly - - - 300 - - - 1100 - - - 900 - - - - - - - - - - - - - 15 - - - - 0 - - - false - - - - Single Spectrum - - - - - - - 0 - 0 - - - - - 350 - 16777215 - - - - - 12 - - - - Load Settings - - - - - - - 10 - - - - Spectrum File - - - - - - - - 10 - - - - Export Figure - - - - - - - - 10 - - - - Clear Export Memory - - - - - - - - 10 - - - - Correct for White Light - - - - - - - - 10 - - - - White Light Ref File - - - - - - - - 10 - - - - Enter Legend Here... - - - - - - - - 10 - - - - For Single Spectrum - - - - - - - - 10 - - - - Subtract Background - - - true - - - - - - - - 10 - - - - Export Fit Data - - - - - - - - 10 - - - - Add Trace to Memory - - - - - - - - 10 - - - - Plot without Background - - - - - - - - 10 - 50 - false - - - - Plot - - - - - - - - 10 - - - - Background File - - - - - - - - 10 - - - - Clear Plots Everytime - - - true - - - - - - - - 10 - - - - Normalize - - - - - - - - 10 - false - - - - Clear Plot - - - - - - - Export Settings - - - - - - - For Data - - - - - - - For Figure - - - - - - - Plot Control - - - - - - - - - - - 10 - - - - - - - - - Scan Spectra Data - - - - - - - - - 210 - 16777215 - - - - - 12 - - - - Load Settings - - - - - - - 12 - - - - Spectra Scan -File - - - - - - - - 12 - - - - Background -File - - - - - - - - 12 - - - - Load Only - Fit File - - - - - - - - 12 - - - - For Scan Data - - - - - - - - - - - 12 - - - - - - - - - 12 - - - - Export Fitted -Scan - - - - - - - - 12 - - - - Launch Data Viewer - - - - - - - - 12 - - - - After Fitting Scan Data - - - - - - - - 12 - - - - Intensity Sums - - - - - - - - 12 - - - - For Raw Scan Data - - - - - - - - 12 - - - - Plot - - - - - - - - 12 - - - - Plot - - - - - - - - 12 - - - - - pk_pos - - - - - fwhm - - - - - - - - - 12 - - - - Plot - - - - - - - - 12 - - - - Export Settings - - - - - - - - 12 - - - - Analyze Spectra Fits - - - - - - - - 12 - - - - For Fit Scale - - - - - - - - 12 - - - - Use Raw Scan Settings - - - true - - - - - - - - 12 - - - - # X points - - - - - - - - 12 - - - - # Y points - - - - - - - 2000 - - - 100 - - - - - - - 2000 - - - 100 - - - - - - - - - - .pkl conversion - - - - - 10 - 70 - 351 - 251 - - - - txt - - - - - - - 12 - - - - Data to .txt - - - - - - - - 12 - - - - Scan params to .txt - - - - - - - - - 390 - 70 - 321 - 251 - - - - h5 - - - - - 50 - 80 - 221 - 41 - - - - - 12 - - - - .pkl to .h5 - - - - - - - 20 - 20 - 323 - 40 - - - - - 12 - - - - Import .pkl file - - - - - - 390 - 20 - 327 - 43 - - - - - 12 - - - - Launch Data Viewer - - - - - - - - - - - 0 - 0 - 2115 - 38 - - - - - - - - diff --git a/src/main/python/Spectrum_analysis/__init__.py b/src/main/python/Spectrum_analysis/__init__.py deleted file mode 100644 index b4011af..0000000 --- a/src/main/python/Spectrum_analysis/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from __future__ import absolute_import, division, print_function \ No newline at end of file diff --git a/src/main/python/Spectrum_analysis/analyze_fit_results.ui b/src/main/python/Spectrum_analysis/analyze_fit_results.ui deleted file mode 100644 index 7669c5a..0000000 --- a/src/main/python/Spectrum_analysis/analyze_fit_results.ui +++ /dev/null @@ -1,91 +0,0 @@ - - - Form - - - - 0 - 0 - 664 - 136 - - - - Analze Fit Results - - - - - - - - QFrame::StyledPanel - - - QFrame::Raised - - - - - - - 12 - - - - Check! - - - - - - - - 12 - - - - 1000000000 - - - - - - - - 12 - - - - Result number: - - - Qt::AlignCenter - - - - - - - - 15 - - - - Analyze Fit Results - - - Qt::AlignCenter - - - - - - - - - - - - - diff --git a/src/main/python/Spectrum_analysis/pyqtgraph_MATPLOTLIBWIDGET.py b/src/main/python/Spectrum_analysis/pyqtgraph_MATPLOTLIBWIDGET.py deleted file mode 100644 index ba2f59c..0000000 --- a/src/main/python/Spectrum_analysis/pyqtgraph_MATPLOTLIBWIDGET.py +++ /dev/null @@ -1,56 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Mon Sep 2 13:02:50 2019 - -@author: Sarthak -""" - -from pyqtgraph.Qt import QtGui, QtCore, USE_PYSIDE, USE_PYQT5 -import matplotlib - -#if not USE_PYQT5: -# if USE_PYSIDE: -# matplotlib.rcParams['backend.qt4']='PySide' -# -# from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas -# from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar -#else: -from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas -from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar - -from matplotlib.figure import Figure - -if matplotlib.get_backend() is not 'Qt5Agg': - matplotlib.use('Qt5Agg') - -class MatplotlibWidget(QtGui.QWidget): - """ - Implements a Matplotlib figure inside a QWidget. - Use getFigure() and redraw() to interact with matplotlib. - - Example:: - - mw = MatplotlibWidget() - subplot = mw.getFigure().add_subplot(111) - subplot.plot(x,y) - mw.draw() - """ - - def __init__(self, size=(5.0, 4.0), dpi=100): - QtGui.QWidget.__init__(self) - self.fig = Figure(size, dpi=dpi) - self.canvas = FigureCanvas(self.fig) - self.canvas.setParent(self) - self.toolbar = NavigationToolbar(self.canvas, self) - - self.vbox = QtGui.QVBoxLayout() - self.vbox.addWidget(self.toolbar) - self.vbox.addWidget(self.canvas) - - self.setLayout(self.vbox) - - def getFigure(self): - return self.fig - - def draw(self): - self.canvas.draw() \ No newline at end of file diff --git a/src/main/python/Spectrum_analysis/scan_params_input.ui b/src/main/python/Spectrum_analysis/scan_params_input.ui deleted file mode 100644 index 4df8d40..0000000 --- a/src/main/python/Spectrum_analysis/scan_params_input.ui +++ /dev/null @@ -1,68 +0,0 @@ - - - Form - - - - 0 - 0 - 542 - 211 - - - - Form - - - - - - X scan size - - - - - - - - - - Y scan size - - - - - - - - - - X step size - - - - - - - - - - Y step size - - - - - - - - - - Done - - - - - - - - diff --git a/src/main/python/Table/Table_widget.py b/src/main/python/Table/Table_widget.py deleted file mode 100644 index 4c7b447..0000000 --- a/src/main/python/Table/Table_widget.py +++ /dev/null @@ -1,145 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Mon Sep 2 17:04:49 2019 - -@author: Sarthak -""" - -from pathlib import Path -import pyqtgraph as pg -from pyqtgraph.python2_3 import asUnicode -from pyqtgraph.Qt import QtCore, QtGui - - -pg.mkQApp() -pg.setConfigOption('background', 'w') - - -base_path = Path(__file__).parent -file_path = (base_path / "Table_widget_gui.ui").resolve() - -uiFile = file_path - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -class MainWindow(TemplateBaseClass): - - def __init__(self): - super(TemplateBaseClass, self).__init__() - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - - self.clear() - - self.ui.clear_pushButton.clicked.connect(self.clear) - self.ui.add_row_pushButton.clicked.connect(self.add_row) - self.ui.add_column_pushButton.clicked.connect(self.add_column) - - """Saving and Copying --- implemented from pyqtgraph TableWidget""" - self.contextMenu = QtGui.QMenu() - self.contextMenu.addAction('Copy Selection').triggered.connect(self.copySel) - self.contextMenu.addAction('Copy All').triggered.connect(self.copyAll) - self.contextMenu.addAction('Save Selection').triggered.connect(self.saveSel) - self.contextMenu.addAction('Save All').triggered.connect(self.saveAll) - - self.show() - - def clear(self): - self.ui.tableWidget.clear() - self.verticalHeadersSet = False - self.horizontalHeadersSet = False - - def add_row(self): - row_position = self.ui.tableWidget.rowCount() - self.ui.tableWidget.insertRow(row_position) - - def add_column(self): - column_position = self.ui.tableWidget.columnCount() - self.ui.tableWidget.insertColumn(column_position) - - def save_table(self):# Needs to be implemented - print(self.ui.tableWidget.currentItem().text()) - - def serialize(self, useSelection=False): - """Convert entire table (or just selected area) into tab-separated text values""" - if useSelection: - selection = self.ui.tableWidget.selectedRanges()[0] - rows = list(range(selection.topRow(), - selection.bottomRow() + 1)) - columns = list(range(selection.leftColumn(), - selection.rightColumn() + 1)) - else: - rows = list(range(self.ui.tableWidget.rowCount())) - columns = list(range(self.ui.tableWidget.columnCount())) - - data = [] - if self.horizontalHeadersSet: - row = [] - if self.verticalHeadersSet: - row.append(asUnicode('')) - - for c in columns: - row.append(asUnicode(self.ui.tableWidget.horizontalHeaderItem(c).text())) - data.append(row) - - for r in rows: - row = [] - if self.verticalHeadersSet: - row.append(asUnicode(self.ui.tableWidget.verticalHeaderItem(r).text())) - for c in columns: - item = self.ui.tableWidget.item(r, c) - if item is not None: - row.append(asUnicode(item.text())) - else: - row.append(asUnicode('')) - data.append(row) - - s = '' - for row in data: - s += ('\t'.join(row) + '\n') - return s - - - def copySel(self): - """Copy selected data to clipboard.""" - QtGui.QApplication.clipboard().setText(self.serialize(useSelection=True)) - - def copyAll(self): - """Copy all data to clipboard.""" - QtGui.QApplication.clipboard().setText(self.serialize(useSelection=False)) - - - def saveSel(self): - """Save selected data to file.""" - self.save(self.serialize(useSelection=True)) - - - def saveAll(self): - """Save all data to file.""" - self.save(self.serialize(useSelection=False)) - - - def save(self, data): - fileName = QtGui.QFileDialog.getSaveFileName(self, "Save As..", "", "Tab-separated values (*.tsv)") - if fileName == '': - return - open(fileName[0], 'w').write(data) - - def contextMenuEvent(self, ev): - self.contextMenu.popup(ev.globalPos()) - - def keyPressEvent(self, ev): - if ev.key() == QtCore.Qt.Key_C and ev.modifiers() == QtCore.Qt.ControlModifier: - ev.accept() - self.copySel() -# else: -# QtGui.QTableWidget.keyPressEvent(self, ev) -"""Run the Main Window""" -def run(): - win = MainWindow() - QtGui.QApplication.instance().exec_() - return win - -#run() \ No newline at end of file diff --git a/src/main/python/Table/Table_widget_gui.ui b/src/main/python/Table/Table_widget_gui.ui deleted file mode 100644 index d5fae7e..0000000 --- a/src/main/python/Table/Table_widget_gui.ui +++ /dev/null @@ -1,70 +0,0 @@ - - - Form - - - - 0 - 0 - 658 - 438 - - - - TableWidget - - - - - - Add Row - - - - - - - Add Column - - - - - - - Clear - - - - - - - 12 - - - 6 - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/main/python/Table/__init__.py b/src/main/python/Table/__init__.py deleted file mode 100644 index 1a21e72..0000000 --- a/src/main/python/Table/__init__.py +++ /dev/null @@ -1,7 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Mon Sep 2 17:52:35 2019 - -@author: Sarthak -""" - diff --git a/src/main/python/UV_Vis_analysis/uv_vis_analysis.py b/src/main/python/UV_Vis_analysis/uv_vis_analysis.py deleted file mode 100644 index 6302a40..0000000 --- a/src/main/python/UV_Vis_analysis/uv_vis_analysis.py +++ /dev/null @@ -1,188 +0,0 @@ -# system imports -from pathlib import Path -import os.path -import pyqtgraph as pg -from pyqtgraph import exporters -from pyqtgraph.Qt import QtCore, QtGui, QtWidgets -import matplotlib.pyplot as plt - -import numpy as np -import time - -# local modules - -pg.mkQApp() -pg.setConfigOption('background', 'w') - -base_path = Path(__file__).parent -file_path = (base_path / "uv_vis_analysis_gui.ui").resolve() - -uiFile = file_path - -WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -"""params for plotting""" -plt.rc('xtick', labelsize = 20) -plt.rc('xtick.major', pad = 3) -plt.rc('ytick', labelsize = 20) -plt.rc('lines', lw = 1.5, markersize = 7.5) -plt.rc('legend', fontsize = 20) -plt.rc('axes', linewidth = 3.5) - -class MainWindow(TemplateBaseClass): - - def __init__(self): - super(TemplateBaseClass, self).__init__() - - # Create the main window - self.ui = WindowTemplate() - self.ui.setupUi(self) - - #setup uv vis plot - self.absorbance_plot_layout = pg.GraphicsLayoutWidget() - self.ui.absorbance_plot_container.layout().addWidget(self.absorbance_plot_layout) - self.absorbance_plot = self.absorbance_plot_layout.addPlot(title="Wavelengths vs. Absorbance") - self.absorbance_plot.setLabel('bottom', 'Wavelength', unit='nm') - self.absorbance_plot.setLabel('left', 'Absorbance', unit='a.u.') - - #setup correction region for uv vis - self.correction_region = pg.LinearRegionItem() - self.correction_region_min = 600 - self.correction_region_max = 900 - self.correction_region.setRegion((self.correction_region_min, self.correction_region_max)) - - #setup uv vis ui signals - self.ui.correct_for_scattering_checkBox.stateChanged.connect(self.scattering_checkBox_state) - self.scatter_corrected = False - self.ui.actionLoad_data.triggered.connect(self.open_data_file) - self.ui.plot_absorbance_pushButton.clicked.connect(self.plot_absorbance) - self.ui.clear_uvvis_pushButton.clicked.connect(self.clear_uvvis) - self.ui.export_uv_vis_pushButton.clicked.connect(self.export_uv_vis) - self.correction_region.sigRegionChanged.connect(self.update_correction_region) - - #setup tauc plot - self.tauc_plot_layout = pg.GraphicsLayoutWidget() - self.ui.tauc_plot_container.layout().addWidget(self.tauc_plot_layout) - self.tauc_plot = self.tauc_plot_layout.addPlot(title="Tauc plot fit") - self.tauc_plot.setLabel('bottom', 'hv', unit='ev') - y_label = '(ahv)' + chr(0x00B2) #char is superscripted 2 - self.tauc_plot.setLabel('left', y_label) - - #setup tauc ui signals - self.ui.plot_tauc_pushButton.clicked.connect(self.plot_tauc) - self.ui.clear_tauc_pushButton.clicked.connect(self.clear_tauc) - self.ui.export_tauc_pushButton.clicked.connect(self.export_tauc) - - self.show() - - def open_data_file(self): - try: - self.filename = QtWidgets.QFileDialog.getOpenFileName(self) - self.data = np.loadtxt(self.filename[0], delimiter = ',', skiprows = 2) - self.Wavelength = self.data[:,0] # in nm - self.Absorbance = self.data[:,1] - except Exception as err: - print(format(err)) - - def update_correction_region(self): - """ Update correction region variables from region """ - self.correction_region_min, self.correction_region_max = self.correction_region.getRegion() - - def scattering_checkBox_state(self): - if self.ui.correct_for_scattering_checkBox.isChecked(): - self.scatter_corrected = True - self.ui.mean_radioButton.setEnabled(True) - self.ui.fourth_orderpoly_radioButton.setEnabled(True) - else: - self.scatter_corrected = False - self.ui.mean_radioButton.setEnabled(False) - self.ui.fourth_orderpoly_radioButton.setEnabled(False) - - def plot_absorbance(self): - try: - self.plotted_absorbance = self.Absorbance #by default set to original absorbance data - if self.scatter_corrected == True: - if self.ui.fourth_orderpoly_radioButton.isChecked(): - p = (np.polyfit(self.Wavelength[(self.Wavelength>self.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelengthself.correction_region_min) & (self.Wavelength self.hv_min) & (self.hv < self.hv_max) - model = np.polyfit(self.hv[self.index], self.Alpha_hv[self.index], 1) - self.Alpha_hv_fit = self.hv * model[0] + model[1] #This is the linear fit - self.tauc_plot.plot(self.hv, self.Alpha_hv, pen='r') - self.tauc_plot.plot(self.hv, self.Alpha_hv_fit, pen='k') - self.tauc_plot.setXRange(1,2) - self.tauc_plot.setYRange(0, np.max(self.Alpha_hv[self.index]) + 1) - - self.Eg = - model[1]/model[0] - self.ui.bandgap_label.setText(str(self.Eg)) - except: - pass - - def clear_tauc(self): - self.tauc_plot.clear() - - def export_uv_vis(self): - """ Export publication ready uv vis figure """ - try: - filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") - plt.figure(figsize=(8,6)) - plt.tick_params(direction='out', length=8, width=3.5) - plt.plot(self.Wavelength, self.plotted_absorbance, linewidth = 3, color = 'r') - if self.scatter_corrected: - plt.xlim(self.correction_region_min, self.correction_region_max) - plt.ylim(0, np.max(self.plotted_absorbance[(self.Wavelength>self.correction_region_min)]) +0.5) - else: - plt.xlim(self.correction_region_min, self.correction_region_max) - plt.ylim(0, np.max(self.plotted_absorbance[(self.Wavelength>self.correction_region_min)] +0.5)) - plt.xlabel('Wavelength (nm)', fontsize = 20) - plt.ylabel('Absorbance (a.u.)', fontsize = 20) - plt.savefig(filename[0],bbox_inches='tight', dpi=300) - plt.close() - except: - pass - - def export_tauc(self): - """ Export publication ready tauc figure""" - try: - filename = QtWidgets.QFileDialog.getSaveFileName(self,caption="Filename with EXTENSION") - plt.figure(figsize=(8,6)) - plt.tick_params(direction='out', length=8, width=3.5) - plt.plot(self.hv, self.Alpha_hv, linewidth = 3, color = 'r') - plt.plot(self.hv, self.Alpha_hv_fit, linewidth = 2, color = 'black') - plt.xlim(1,2) - plt.ylim(0, np.max(self.Alpha_hv[self.index]) + 1) - plt.xlabel('h$\\nu$ (eV)', fontsize = 20) - plt.ylabel('($\\alpha$h$\\nu$)$^2$', fontsize = 20) - #plt.title(Plot_title, fontsize = 20) - - plt.text(1.2, 1.2, r'E$_{g}$ = %.2f eV'%self.Eg, fontsize = 15) - plt.tight_layout() - plt.savefig(filename[0],bbox_inches='tight', dpi=300) - plt.close() - except: - pass - -"""Run the Main Window""" -def run(): - win = MainWindow() - QtGui.QApplication.instance().exec_() - return win \ No newline at end of file diff --git a/src/main/python/UV_Vis_analysis/uv_vis_analysis_gui.ui b/src/main/python/UV_Vis_analysis/uv_vis_analysis_gui.ui deleted file mode 100644 index 85bd935..0000000 --- a/src/main/python/UV_Vis_analysis/uv_vis_analysis_gui.ui +++ /dev/null @@ -1,268 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 742 - 924 - - - - UV-Vis Analysis - - - - - - - UV-Vis plot - - - - - - - - Scattering Correction - - - - - - - Plot - - - - - - - false - - - 4th Order Polynomial - - - true - - - - - - - Clear - - - - - - - Correct for scattering - - - - - - - false - - - Simple Mean - - - - - - - - - - 0 - 0 - - - - - - - - - Export UV-Vis plot - - - - - - - - - - Tauc plot - - - true - - - false - - - - - - - - hv min (ev) - - - - - - - - 180 - 0 - - - - -9999999.000000000000000 - - - 9999999.000000000000000 - - - 0.010000000000000 - - - 1.500000000000000 - - - - - - - - 180 - 0 - - - - -9999999.000000000000000 - - - 9999999.000000000000000 - - - 0.010000000000000 - - - 1.800000000000000 - - - - - - - hv max (ev) - - - - - - - Plot - - - - - - - Clear - - - - - - - - - - 0 - 0 - - - - - - - - - - - Bandgap (ev): - - - - - - - 0 - - - - - - - - 16777215 - 16777215 - - - - Export tauc plot - - - - - - - - - - - - - - - - - - - - - 0 - 0 - 742 - 21 - - - - - File - - - - - - - - - Load data - - - - - - diff --git a/src/main/python/__init__.py b/src/main/python/__init__.py deleted file mode 100644 index 8b13789..0000000 --- a/src/main/python/__init__.py +++ /dev/null @@ -1 +0,0 @@ - diff --git a/src/main/python/main.py b/src/main/python/main.py deleted file mode 100644 index 63b241d..0000000 --- a/src/main/python/main.py +++ /dev/null @@ -1,111 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Wed Apr 10 14:41:08 2019 - -@author: Sarthak -""" - -# system imports -import sys -from pathlib import Path - -import pyqtgraph as pg -from pyqtgraph.Qt import QtGui, QtCore - -from fbs_runtime.application_context.PyQt5 import ApplicationContext, cached_property -from PyQt5.QtWidgets import QMainWindow -from PyQt5 import uic - -from Lifetime_analysis import Lifetime_plot_fit -from Spectrum_analysis import Spectra_plot_fit -from FLIM_analysis import FLIM_plot -from UV_Vis_analysis import uv_vis_analysis -from PLQE_analysis import plqe_analysis -from H5_Pkl import h5_pkl_view, h5_view_and_plot -from Image_analysis import Image_analysis -from Table import Table_widget -from Export_Windows import Multi_Trace_Exporter - -class AppContext(ApplicationContext): - def run(self): - self.main_window.show() - return self.app.exec_() - - def get_main_ui(self): - qtCreatorFile = self.get_resource("DataBrowser_GUI.ui") - return qtCreatorFile - - @cached_property - def main_window(self): - return MainWindow(self.get_main_ui()) - -# pg.mkQApp() -# #pg.setConfigOption('background', 'w') - -# base_path = Path(__file__).parent -# file_path = (base_path / "DataBrowser_GUI.ui").resolve() - -# uiFile = file_path - -# WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile) - -class MainWindow(QMainWindow): - - def __init__(self, uiFile): - super(MainWindow, self).__init__() - - # Create the main window - self.ui = uic.loadUi(uiFile, self) - # self.ui.setupUi(self) - self.ui.select_comboBox.addItems(["Lifetime Analysis", "Spectrum Analysis", "FLIM Analysis", - "UV-Vis Analysis", "PLQE Analysis", "H5 View/Plot", "H5/PKL Viewer", "Image Analysis", "Table View", - "Mulit-Trace Exporter"]) - self.ui.load_pushButton.clicked.connect(self.load_app) - - self.show() - - - def load_app(self): - - analysis_software = self.ui.select_comboBox.currentText() - - if analysis_software == "Lifetime Analysis": - self.lifetime_window = Lifetime_plot_fit.MainWindow() - self.lifetime_window.show() - elif analysis_software == "Spectrum Analysis": - self.spectrum_window = Spectra_plot_fit.MainWindow() - self.spectrum_window.show() - elif analysis_software == "FLIM Analysis": - self.flim_window = FLIM_plot.MainWindow() - self.flim_window.show() - elif analysis_software == "UV-Vis Analysis": - self.uv_vis_window = uv_vis_analysis.MainWindow() - self.uv_vis_window.show() - elif analysis_software == "PLQE Analysis": - self.plqe_window = plqe_analysis.MainWindow() - self.plqe_window.show() - elif analysis_software == "H5 View/Plot": - app = h5_view_and_plot.H5ViewPlot(sys.argv) - #sys.exit(app.exec_()) - elif analysis_software == "H5/PKL Viewer": - app = h5_pkl_view.H5PklView(sys.argv) - #sys.exit(app.exec_()) - elif analysis_software == "Image Analysis": - self.image_window = Image_analysis.MainWindow() - self.image_window.show() - elif analysis_software == "Table View": - self.table_widget = Table_widget.MainWindow() - self.table_widget.show() - elif analysis_software == "Mulit-Trace Exporter": - self.trace_exporter = Multi_Trace_Exporter.MainWindow() - self.trace_exporter.show() - - -def run(): - appctxt = AppContext() # 1. Instantiate ApplicationContext - appctxt.app.setStyle("Fusion") - exit_code = appctxt.run() - sys.exit(exit_code) # 2. Invoke appctxt.app.exec_() - -if __name__ == '__main__': - run() \ No newline at end of file diff --git a/src/main/python/main_0.py b/src/main/python/main_0.py deleted file mode 100644 index 4038d57..0000000 --- a/src/main/python/main_0.py +++ /dev/null @@ -1,15 +0,0 @@ -from fbs_runtime.application_context.PyQt5 import ApplicationContext -from PyQt5.QtWidgets import QMainWindow - -import sys - -class AppContext(ApplicationContext): - pass - -if __name__ == '__main__': - appctxt = AppContext() # 1. Instantiate ApplicationContext - window = QMainWindow() - window.resize(250, 150) - window.show() - exit_code = appctxt.app.exec_() # 2. Invoke appctxt.app.exec_() - sys.exit(exit_code) \ No newline at end of file diff --git a/src/main/resources/base/DataBrowser_GUI.ui b/src/main/resources/base/DataBrowser_GUI.ui deleted file mode 100644 index 054b4ef..0000000 --- a/src/main/resources/base/DataBrowser_GUI.ui +++ /dev/null @@ -1,97 +0,0 @@ - - - MainWindow - - - - 0 - 0 - 435 - 221 - - - - GLabViz - DataBrowser - - - - - - - - 30 - 75 - true - - - - GLabViz - - - Qt::AlignCenter - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 15 - - - - Analysis Tool : - - - - - - - - 15 - - - - - - - - - 15 - - - - Load - - - - - - - - - 0 - 0 - 435 - 21 - - - - - - - - From ee8b496b014ccde2520f921436e72a5efbeb444f Mon Sep 17 00:00:00 2001 From: SarthakJariwala Date: Wed, 3 Mar 2021 13:57:29 -0800 Subject: [PATCH 09/10] new screenshots --- Screenshots/GLabViz_Lifetime_analysis_2.png | Bin 115272 -> 67330 bytes Screenshots/GLabViz_interface_1.png | Bin 8358 -> 5603 bytes 2 files changed, 0 insertions(+), 0 deletions(-) diff 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zW5o_EP{{m`R0w-NhKp}$aEF)5>^Jf1;fE@rCrjDF+$x%rese5M4I69wa2sx~&wzsH zv--QwP#e!S`koqbHk5311AN3kP+j=^9fOiCkd=B3Ba8(KSpi<{xXp#37oPPGU+oyV z3vFCxEk5yFxmR;u;+%z!=jk=uUSnvTz%amB;8Vt=w^}j9>O5JY#u3CAOd(!939uTP zi^x5qZuncY`pJ#+>s`q0JCXN#U>*P{y%39gahWO%1L*bS3B&%SnjR^!{bwu_!iL36 z_q_!G{Aq~SQW*CFK+I{0i>)amJp3%7k^M`M*yBIrFvV5W$8VQ z^*N8saR^X-nxu+3(>*@n?qIL+tHi!DDL#GSp#mN~_h-7{@v2_zb{!~XxNc{*kPfx3Ka^HFGpTFcA0Eewqi&2aOc#QG1V_Bu zwN!b6)4YY@t6Mwk`tv*}kmb9gdtkfni#P=~vm|diJ Date: Fri, 19 Mar 2021 13:28:16 +0000 Subject: [PATCH 10/10] Bump pillow from 7.1.0 to 8.1.1 Bumps [pillow](https://github.com/python-pillow/Pillow) from 7.1.0 to 8.1.1. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/master/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/7.1.0...8.1.1) Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index f74b5d1..b935d2e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -61,7 +61,7 @@ parso==0.5.1 partd==1.0.0 pefile==2019.4.18 pickleshare==0.7.5 -Pillow==7.1.0 +Pillow==8.1.1 pkginfo==1.4.2 prometheus-client==0.7.1 prompt-toolkit==2.0.9