Merge pull request #1 from SarthakJariwala/lifetime_irf

Lifetime irf

Author: ltaing27

.gitignore

@@ -0,0 +1 @@
+*.pyc

PythonGUI_apps/DataBrowser.py

@@ -6,13 +6,18 @@
 """
 
 # system imports
+import sys
 from pathlib import Path
 
 import pyqtgraph as pg
 from pyqtgraph.Qt import QtGui
 
 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
 
 pg.mkQApp()
 pg.setConfigOption('background', 'w')
@@ -25,37 +30,49 @@
 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.select_comboBox.addItems(["Lifetime Analysis", "Spectrum Analysis", "UV-Vis Analysis"])
-        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()
-            
-        else:
-            print("not yet linked -- coming soon")
+	
+	def __init__(self):
+		TemplateBaseClass.__init__(self)
+		
+		# Create the main window
+		self.ui = WindowTemplate()
+		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"])
+		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_())
 
 def run():
-    win = MainWindow()
-    QtGui.QApplication.instance().exec_()
-    return
+	win = MainWindow()
+	QtGui.QApplication.instance().exec_()
+	return
 
 run()

PythonGUI_apps/DataBrowser.spec

@@ -0,0 +1,36 @@
+# -*- mode: python -*-
+
+block_cipher = None
+
+
+a = Analysis(['DataBrowser.py'],
+             pathex=['C:\\Users\\lindat18\\Dropbox\\Ginger_Lab\\Data_Analysis\\PythonGUI_apps'],
+             binaries=[],
+             datas=[],
+             hiddenimports=[],
+             hookspath=[],
+             runtime_hooks=[],
+             excludes=[],
+             win_no_prefer_redirects=False,
+             win_private_assemblies=False,
+             cipher=block_cipher,
+             noarchive=False)
+pyz = PYZ(a.pure, a.zipped_data,
+             cipher=block_cipher)
+exe = EXE(pyz,
+          a.scripts,
+          [],
+          exclude_binaries=True,
+          name='DataBrowser',
+          debug=False,
+          bootloader_ignore_signals=False,
+          strip=False,
+          upx=True,
+          console=True )
+coll = COLLECT(exe,
+               a.binaries,
+               a.zipfiles,
+               a.datas,
+               strip=False,
+               upx=True,
+               name='DataBrowser')

PythonGUI_apps/FLIM_analysis/FLIM_plot.py

@@ -0,0 +1,251 @@
+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
+# local modules
+ 
+pg.mkQApp()
+pg.setConfigOption('background', 'w')
+pg.setConfigOption('imageAxisOrder', 'row-major')
+
+base_path = Path(__file__).parent
+file_path = (base_path / "flim_plot_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)
+		
+		#set up ui signals
+		self.ui.load_scan_pushButton.clicked.connect(self.open_pkl_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.save_intensities_image)
+		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.show()
+
+	def open_pkl_file(self):
+		""" Open FLIM scan file """
+		try:
+			self.filename = QtWidgets.QFileDialog.getOpenFileName(self)
+			self.pkl_file = pickle.load(open(self.filename[0], 'rb'))
+		except Exception as err:
+			print(format(err))
+
+	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 plot_intensity_sums(self):
+		try:
+			data = self.pkl_file
+			self.numb_pixels_X = int((data['Scan Parameters']['X scan size (um)'])/(data['Scan Parameters']['X step size (um)']))
+			self.numb_pixels_Y = int((data['Scan Parameters']['Y scan size (um)'])/(data['Scan Parameters']['Y step size (um)']))
+			self.x_step_size = float(data['Scan Parameters']['X step size (um)'])
+			self.x_scan_size = float(data['Scan Parameters']['X scan size (um)'])
+			self.y_step_size = float(data['Scan Parameters']['Y step size (um)'])
+			self.y_scan_size = float(data['Scan Parameters']['Y scan size (um)'])
+
+			hist_data = data["Histogram data"]
+			hist_data = np.reshape(hist_data, newshape=(hist_data.shape[0], self.numb_pixels_X*self.numb_pixels_Y))
+			self.intensity_sums = np.sum(hist_data, axis=0) #sum intensities for each pixel
+			self.intensity_sums = np.reshape(self.intensity_sums, newshape=(self.numb_pixels_X, self.numb_pixels_Y))
+			self.ui.intensity_sums_viewBox.view.invertY(False) # stop y axis invert
+			self.ui.intensity_sums_viewBox.setImage(self.intensity_sums, scale=
+												  (data['Scan Parameters']['X step size (um)'],
+												   data['Scan Parameters']['Y step size (um)']))
+			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))
+		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.sum(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 plot_raw_scan(self):
+		try:
+			data = self.pkl_file
+			self.numb_pixels_X = int((data['Scan Parameters']['X scan size (um)'])/(data['Scan Parameters']['X step size (um)']))
+			self.numb_pixels_Y = int((data['Scan Parameters']['Y scan size (um)'])/(data['Scan Parameters']['Y step size (um)']))
+			self.x_step_size = float(data['Scan Parameters']['X step size (um)'])
+			self.x_scan_size = float(data['Scan Parameters']['X scan size (um)'])
+			self.y_step_size = float(data['Scan Parameters']['Y step size (um)'])
+			self.y_scan_size = float(data['Scan Parameters']['Y scan size (um)'])
+			# TODO test line scan plots
+			hist_data = data['Histogram data']
+			
+			self.hist_image = np.reshape(hist_data, newshape=(hist_data.shape[0],self.numb_pixels_X,self.numb_pixels_Y))
+			time_data = data['Time data']
+			self.times = 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=
+												(data['Scan Parameters']['X step size (um)'],
+												data['Scan Parameters']['Y step size (um)']), 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))
+			
+		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"):
+			self.roi2_plot.clear()
+		self.roi2_plot = self.ui.raw_hist_data_viewBox.getRoiPlot().plot(xvals, data, pen='r')
+
+	def save_intensities_image(self):
+		try:
+			filename_ext = os.path.basename(self.filename[0])
+			filename = os.path.splitext(filename_ext)[0] #get filename without extension
+			save_to = os.getcwd() + "\\" + filename + "_intensity_sums.png"
+			cpm.plot_confocal(self.intensity_sums, stepsize=np.abs(self.pkl_file['Scan Parameters']['X step size (um)']))
+			cpm.plt.savefig(save_to, bbox_inches='tight', dpi=300)
+		except:
+			pass
+
+	def save_intensities_array(self):
+		try:
+			filename_ext = os.path.basename(self.filename[0])
+			filename = os.path.splitext(filename_ext)[0] #get filename without extension
+			save_to = os.getcwd() + "\\" + 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
+
+"""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()