code cleanup and documentation

Author: LAKESIDE\LindaT18

PythonGUI_apps/FLIM_analysis/FLIM_plot.py

@@ -12,8 +12,6 @@
 import customplotting.mscope as cpm
 # local modules
 
-
-
 pg.mkQApp()
 pg.setConfigOption('background', 'w')
 pg.setConfigOption('imageAxisOrder', 'row-major')
@@ -34,27 +32,29 @@ def __init__(self):
 		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()
 
-	"""Open Scan Files"""
 	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")
@@ -70,11 +70,10 @@ def plot_intensity_sums(self):
 			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"]
 			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)
+			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=
@@ -88,6 +87,7 @@ def plot_intensity_sums(self):
 			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()
@@ -144,10 +144,10 @@ def plot_raw_scan(self):
 
 	def switch_compare(self):
 		"""
-		Handles compare checkbox. If checked, show second ROI that user can use for comparison to first ROI.
+		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"):
+			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])
@@ -162,12 +162,13 @@ def switch_compare(self):
 			else:
 				self.roi2.hide()
 				self.roi2_plot.hide()
-		else:
+		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()
@@ -177,6 +178,7 @@ def update_roi2_plot(self):
 		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
@@ -199,7 +201,7 @@ def save_intensities_array(self):
 			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 transpoed intensity sums, as original array handles x in cols and y in rows
+			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
 
@@ -220,15 +222,15 @@ def pkl_to_h5(self):
 	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 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)
+				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]
+					h5_output.attrs[key] = dictionary[key] #if not dataset, create attribute
 
 	def close_application(self):
 		choice = QtGui.QMessageBox.question(self, 'EXIT!',

PythonGUI_apps/H5_Pkl/h5_tree.py

@@ -2,7 +2,6 @@
 from qtpy import QtWidgets
 import h5py
 
-
 class H5TreeSearchView(DataBrowserView):
 
     name = 'h5_tree_search'
@@ -29,6 +28,7 @@ def setup(self):
         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
@@ -65,7 +65,6 @@ def on_new_search_text(self, x=None):
         self.tree_textEdit.verticalScrollBar().setValue(old_scroll_pos)
 
     def _visitfunc(self, name, node):
-        
         level = len(name.split('/'))
         indent = ' '*4*(level-1)
 
@@ -74,7 +73,7 @@ def _visitfunc(self, name, node):
 
         #search_text = self.settings['search_text'].lower()
         search_text = self.search_text
-        if search_text and (search_text in localname.lower()):
+        if search_text and (search_text in localname.lower()): #highlight terms that contain search text
             localname = """<span style="color: red;">{}</span>""".format(localname)
 
         if isinstance(node, h5py.Group):
@@ -91,7 +90,7 @@ def _visitfunc(self, name, node):
                 self.dataset_dict[item_name] = node
 
 
-        for key, val in node.attrs.items():
+        for key, val in node.attrs.items(): #highlight terms that contain search text
             if search_text:
                 if search_text in str(key).lower(): 
                     key = """<span style="color: red;">{}</span>""".format(key)

PythonGUI_apps/H5_Pkl/h5_view_and_plot.py

@@ -68,7 +68,7 @@ def setup(self):
         self.ui.show()
 
     def on_change_data_filename(self):
-        #Handle file change
+        """ Handle file change """
         try:
             fname = self.settings.data_filename.val 
             if os.path.isfile(fname):
@@ -79,7 +79,7 @@ def on_change_data_filename(self):
             pass
 
     def plot_dataset(self):
-        #Plot data set depending on dataset shape and plot type option.
+        """ Plot data set depending on dataset shape and plot type option. """
         self.plot = self.ui.data_plotWidget.getPlotItem()
         self.plot.clear()
 
@@ -102,7 +102,7 @@ def plot_dataset(self):
             self.ui.data_imageView.setImage(data, xvals=x_values)
 
     def on_data_selection(self):
-        #Handle dataset selection
+        """ Handle dataset selection """
         try:
             dataset_name = self.ui.dataset_listWidget.currentItem().text()
             self.dataset = self.h5treeview.dataset_dict[dataset_name]
@@ -120,7 +120,7 @@ def on_data_selection(self):
             pass
 
     def update_data_widget(self):
-        #Decide which widget to display based on dataset shape and plot type option.
+        """ 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():

PythonGUI_apps/H5_Pkl/pkl_tree.py

@@ -30,6 +30,7 @@ def setup(self):
         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        
@@ -64,6 +65,13 @@ def on_new_search_text(self, x=None):
         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

PythonGUI_apps/Lifetime_analysis/Fit_functions_with_irf.py

@@ -40,7 +40,6 @@ def array_zeropad_pos(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)
@@ -52,8 +51,6 @@ def signal_and_resp_forconv(signal_array, response_array):
 
     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
 
@@ -147,8 +144,6 @@ def bestfit_decay(params):
     # 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))
 
@@ -242,9 +237,7 @@ def bestfit_decay(params):
     # plt.semilogy(time_array, data_array,'b', label = 'Data')
     # plt.semilogy(time_array, bestfit_model, 'r', label = 'Fit')
     # plt.legend(loc = 'best')
-    return bestfit_params, t_avg, bestfit_model, data_array, time_array, irf  
-
-
+    return bestfit_params, t_avg, bestfit_model, data_array, time_array, irf
 
 def fit_multi_exp_fmin_tnc(t, tstep, data, irf, init_params, bounds, n):
     time_array = t
@@ -290,7 +283,6 @@ def bestfit_decay(params):
     # plt.legend(loc = 'best')
     return bestfit_params, bestfit_model, data_array, time_array, irf  
 
-
 def fit_multi_exp_diffev(t, tstep, data, irf,  bounds, n):
     time_array = t
     data_array = data

PythonGUI_apps/Lifetime_analysis/Lifetime_analysis_gui_layout.ui

@@ -73,21 +73,6 @@
                <pointsize>10</pointsize>
               </font>
              </property>
-             <item>
-              <property name="text">
-               <string>Stretched Exponential</string>
-              </property>
-             </item>
-             <item>
-              <property name="text">
-               <string>Double Exponential</string>
-              </property>
-             </item>
-             <item>
-              <property name="text">
-               <string>Single Exponential</string>
-              </property>
-             </item>
             </widget>
            </item>
            <item row="2" column="0">
@@ -112,16 +97,6 @@
                <pointsize>10</pointsize>
               </font>
              </property>
-             <item>
-              <property name="text">
-               <string>diff_ev</string>
-              </property>
-             </item>
-             <item>
-              <property name="text">
-               <string>fmin_tnc</string>
-              </property>
-             </item>
             </widget>
            </item>
            <item row="0" column="1">