celldetective 1.3.2__py3-none-any.whl → 1.3.4__py3-none-any.whl

celldetective/gui/measurement_options.py

@@ -10,7 +10,7 @@ from superqt import QLabeledDoubleSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
-from celldetective.gui.thresholds_gui import ThresholdSpot
+#from celldetective.gui.thresholds_gui import ThresholdSpot
 from celldetective.utils import extract_experiment_channels, get_software_location
 from celldetective.io import load_frames, auto_load_number_of_frames
 from celldetective.measure import compute_haralick_features
@@ -24,9 +24,8 @@ from glob import glob
 from natsort import natsorted
 from tifffile import imread
 from pathlib import Path
-import gc
 
-from celldetective.gui.viewers import CellEdgeVisualizer
+from celldetective.gui.viewers import CellEdgeVisualizer, SpotDetectionVisualizer
 from celldetective.gui.layouts import ProtocolDesignerLayout, BackgroundFitCorrectionLayout, LocalCorrectionLayout
 from celldetective.gui.gui_utils import ThresholdLineEdit
 from celldetective.gui import Styles
@@ -726,18 +725,10 @@ class ConfigMeasurements(QMainWindow, Styles):
 		else:
 			self.current_stack = movies[0]
 			self.stack_length = auto_load_number_of_frames(self.current_stack)
-			
-			if self.stack_length is None:
-				stack = imread(self.current_stack)
-				self.stack_length = len(stack)
-				del stack
-				gc.collect()
-			
 			self.mid_time = self.stack_length // 2
-			indices = self.mid_time + np.arange(len(self.channel_names))
+			indices = len(self.channel_names) * self.mid_time + np.arange(len(self.channel_names))
 			self.test_frame = load_frames(list(indices.astype(int)),self.current_stack, normalize_input=False)
 
-
 	def control_haralick_digitalization(self):
 
 		"""
@@ -746,9 +737,10 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		"""
 
-		self.locate_image()
+		self.locate_image() # pb here
 		self.extract_haralick_options()
 		if self.test_frame is not None:
+
 			digitized_img = compute_haralick_features(self.test_frame, np.zeros(self.test_frame.shape[:2]),
 													  channels=self.channel_names, return_digit_image_only=True,
 													  **self.haralick_options
@@ -951,51 +943,54 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		layout.addWidget(self.threshold_lbl, 4, 0)
 		layout.addWidget(self.threshold_value, 4, 1)
-		self.preview_spot = QPushButton('Preview')
-		self.preview_spot.clicked.connect(self.spot_preview)
-		self.preview_spot.setStyleSheet(self.button_style_sheet_2)
-		layout.addWidget(self.preview_spot, 5, 0, 1, 2)
-		self.spot_channel.setEnabled(False)
-		self.spot_channel_lbl.setEnabled(False)
-		self.diameter_value.setEnabled(False)
-		self.diameter_lbl.setEnabled(False)
-		self.threshold_value.setEnabled(False)
-		self.threshold_lbl.setEnabled(False)
-		self.preview_spot.setEnabled(False)
 
+		self.spot_viewer_btn = QPushButton()
+		self.spot_viewer_btn.clicked.connect(self.spot_preview)
+		self.spot_viewer_btn.setIcon(icon(MDI6.image_check, color="k"))
+		self.spot_viewer_btn.setStyleSheet(self.button_select_all)
+		self.spot_viewer_btn.setToolTip('Set detection parameters visually.')
+		layout.addWidget(self.spot_viewer_btn, 1, 1, 1, 1, alignment=Qt.AlignRight)
+
+		self.spot_detection_widgets = [self.spot_channel, self.spot_channel_lbl, self.diameter_value, self.diameter_lbl, self.threshold_value, self.threshold_lbl, self.spot_viewer_btn]
+		for wg in self.spot_detection_widgets:
+			wg.setEnabled(False)
 
 	def enable_spot_preview(self):
 
 		diam = self.diameter_value.text().replace(',','').replace('.','')
 		thresh = self.threshold_value.text().replace(',','').replace('.','')
 		if diam.isnumeric() and thresh.isnumeric():
-			self.preview_spot.setEnabled(True)
+			self.spot_viewer_btn.setEnabled(True)
 		else:
-			self.preview_spot.setEnabled(False)
+			self.spot_viewer_btn.setEnabled(False)
 
 	def spot_preview(self):
 		self.locate_image()
 		if self.test_frame is not None:
 			self.locate_mask()
 			if self.test_mask is not None:
-				self.spot_visual = ThresholdSpot(current_channel=self.spot_channel.currentIndex(), img=self.test_frame,
-												 mask=self.test_mask, parent_window=self)
+				self.spot_visual = SpotDetectionVisualizer(frame_slider=True,
+														   contrast_slider=True,
+														   cell_type=self.mode,
+														   channel_cb=True,
+														   channel_names = self.channel_names,
+														   stack_path=self.current_stack,
+														   n_channels=len(self.channel_names),
+														   target_channel=self.spot_channel.currentIndex(),
+														   window_title='Detect spots',
+														   parent_channel_cb=self.spot_channel,
+														   parent_diameter_le=self.diameter_value,
+														   parent_threshold_le=self.threshold_value,
+														   PxToUm = 1,)
+				self.spot_visual.show()
+				#self.spot_visual = ThresholdSpot(current_channel=self.spot_channel.currentIndex(), img=self.test_frame,
+				#								 mask=self.test_mask, parent_window=self)
 
 	def enable_spot_detection(self):
-		if self.spot_check.isChecked():
-			self.spot_channel.setEnabled(True)
-			self.spot_channel_lbl.setEnabled(True)
-			self.diameter_value.setEnabled(True)
-			self.diameter_lbl.setEnabled(True)
-			self.threshold_value.setEnabled(True)
-			self.threshold_lbl.setEnabled(True)
-			self.preview_spot.setEnabled(True)
 
+		if self.spot_check.isChecked():
+			for wg in self.spot_detection_widgets:
+				wg.setEnabled(True)
 		else:
-			self.spot_channel.setEnabled(False)
-			self.spot_channel_lbl.setEnabled(False)
-			self.diameter_value.setEnabled(False)
-			self.diameter_lbl.setEnabled(False)
-			self.threshold_value.setEnabled(False)
-			self.threshold_lbl.setEnabled(False)
-			self.preview_spot.setEnabled(False)
+			for wg in self.spot_detection_widgets:
+				wg.setEnabled(False)

celldetective/gui/plot_measurements.py

@@ -56,8 +56,8 @@ class ConfigMeasurementsPlot(QWidget,Styles):
 
         print('Parent wells: ', self.wells)
 
-        self.well_option = self.parent_window.parent_window.well_list.currentIndex()
-        self.position_option = self.parent_window.parent_window.position_list.currentIndex()
+        self.well_option = self.parent_window.parent_window.well_list.getSelectedIndices()
+        self.position_option = self.parent_window.parent_window.position_list.getSelectedIndices()
         self.interpret_pos_location()
         # self.load_available_tables()
         # self.config_path = self.exp_dir + self.config_name
@@ -526,18 +526,10 @@ class ConfigMeasurementsPlot(QWidget,Styles):
 
         """
 
-        self.well_option = self.parent_window.parent_window.well_list.currentIndex()
-        if self.well_option == len(self.wells):
-            wo = '*'
-        else:
-            wo = self.well_option
-        self.position_option = self.parent_window.parent_window.position_list.currentIndex()
-        if self.position_option == 0:
-            po = '*'
-        else:
-            po = self.position_option - 1
+        self.well_option = self.parent_window.parent_window.well_list.getSelectedIndices()
+        self.position_option = self.parent_window.parent_window.position_list.getSelectedIndices()
 
-        self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=wo, position_option=po,
+        self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=self.well_option, position_option=self.position_option,
                                                            population=self.cbs[0].currentText(), return_pos_info=True)
 
         if self.df is None:

celldetective/gui/plot_signals_ui.py

@@ -47,8 +47,8 @@ class ConfigSignalPlot(QWidget, Styles):
 		self.ax2=None
 		self.auto_close = False
 
-		self.well_option = self.parent_window.parent_window.well_list.currentIndex()
-		self.position_option = self.parent_window.parent_window.position_list.currentIndex()
+		self.well_option = self.parent_window.parent_window.well_list.getSelectedIndices()
+		self.position_option = self.parent_window.parent_window.position_list.getSelectedIndices()
 		self.interpret_pos_location()
 
 		self.screen_height = self.parent_window.parent_window.parent_window.screen_height
@@ -67,15 +67,11 @@ class ConfigSignalPlot(QWidget, Styles):
 
 		"""
 		
-		if self.well_option==len(self.wells):
-			self.well_indices = np.arange(len(self.wells))
-		else:
-			self.well_indices = np.array([self.well_option],dtype=int)
-
-		if self.position_option==0:
+		self.well_indices = self.parent_window.parent_window.well_list.getSelectedIndices()
+		self.position_indices = self.parent_window.parent_window.position_list.getSelectedIndices()
+		if not self.parent_window.parent_window.position_list.isAnySelected():
 			self.position_indices = None
-		else:
-			self.position_indices = np.array([self.position_option],dtype=int)
+
 
 	def populate_widget(self):
 
@@ -188,11 +184,21 @@ class ConfigSignalPlot(QWidget, Styles):
 		if 't0' in self.all_columns:
 			time_columns.append('t0')
 		
+		self.class_columns = np.unique(class_columns)
+		self.time_columns = np.unique(time_columns)
+		thresh = 18
+		self.class_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.class_columns]
+		self.time_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.time_columns]
+
 		self.cbs[2].clear()
-		self.cbs[2].addItems(np.unique(self.cb_options[2]+time_columns))
+		self.cbs[2].addItems(self.time_truncated)
+		for i in range(len(self.time_columns)):
+			self.cbs[2].setItemData(i, self.time_columns[i], Qt.ToolTipRole)
 
 		self.cbs[1].clear()
-		self.cbs[1].addItems(np.unique(self.cb_options[1]+class_columns))
+		self.cbs[1].addItems(self.class_truncated)
+		for i in range(len(self.class_columns)):
+			self.cbs[1].setItemData(i, self.class_columns[i], Qt.ToolTipRole)
 
 	def ask_for_feature(self):
 
@@ -273,7 +279,8 @@ class ConfigSignalPlot(QWidget, Styles):
 
 		# read instructions from combobox options
 		self.load_available_tables()
-		class_col = self.cbs[1].currentText()	
+		class_col = self.class_columns[self.cbs[1].currentIndex()]
+		print(f"{class_col=}")	
 
 		if self.df is not None:
 
@@ -300,18 +307,10 @@ class ConfigSignalPlot(QWidget, Styles):
 
 		"""
 
-		self.well_option = self.parent_window.parent_window.well_list.currentIndex()
-		if self.well_option==len(self.wells):
-			wo = '*'
-		else:
-			wo = self.well_option
-		self.position_option = self.parent_window.parent_window.position_list.currentIndex()
-		if self.position_option==0:
-			po = '*'
-		else:
-			po = self.position_option - 1
+		self.well_option = self.parent_window.parent_window.well_list.getSelectedIndices()		
+		self.position_option = self.parent_window.parent_window.position_list.getSelectedIndices()
 
-		self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=wo, position_option=po, population=self.cbs[0].currentText(), return_pos_info=True)
+		self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=self.well_option, position_option=self.position_option, population=self.cbs[0].currentText(), return_pos_info=True)
 
 		if self.df is None:
 			
@@ -337,8 +336,8 @@ class ConfigSignalPlot(QWidget, Styles):
 
 		# Per position signal
 		max_time = int(self.df.FRAME.max()) + 1
-		class_col = self.cbs[1].currentText()
-		time_col = self.cbs[2].currentText()
+		class_col = self.class_columns[self.cbs[1].currentIndex()]
+		time_col = self.time_columns[self.cbs[2].currentIndex()]
 		if self.abs_time_checkbox.isChecked():
 			time_col = self.frame_slider.value()
 
@@ -375,6 +374,9 @@ class ConfigSignalPlot(QWidget, Styles):
 		if isinstance(cclass,int):
 			cclass = [cclass]
 
+		class_col = self.class_columns[self.cbs[1].currentIndex()]
+		time_col = self.time_columns[self.cbs[2].currentIndex()]
+
 		n_cells = len(well_group.groupby(['position','TRACK_ID']))
 		depth = int(2*max_time + 3)
 		matrix = np.zeros((n_cells, depth))
@@ -382,14 +384,14 @@ class ConfigSignalPlot(QWidget, Styles):
 		mapping = np.arange(-max_time-1, max_time+2)
 		cid=0
 		for block,movie_group in well_group.groupby('position'):
-			for tid,track_group in movie_group.loc[movie_group[self.cbs[1].currentText()].isin(cclass)].groupby('TRACK_ID'):
+			for tid,track_group in movie_group.loc[movie_group[class_col].isin(cclass)].groupby('TRACK_ID'):
 				try:
 					timeline = track_group['FRAME'].to_numpy().astype(int)
 					feature = track_group[feature_selected].to_numpy()
 					if self.checkBox_feature.isChecked():
 						second_feature=track_group[self.second_feature_selected].to_numpy()
 					if self.cbs[2].currentText().startswith('t') and not self.abs_time_checkbox.isChecked():
-						t0 = math.floor(track_group[self.cbs[2].currentText()].to_numpy()[0])
+						t0 = math.floor(track_group[time_col].to_numpy()[0])
 						timeline -= t0
 					elif self.cbs[2].currentText()=='first detection' and not self.abs_time_checkbox.isChecked():
 
@@ -401,7 +403,6 @@ class ConfigSignalPlot(QWidget, Styles):
 
 						first_detection = timeline[feat==feat][0]
 						timeline -= first_detection
-						print(first_detection, timeline)
 
 					elif self.abs_time_checkbox.isChecked():
 						timeline -= int(self.frame_slider.value())
@@ -410,7 +411,6 @@ class ConfigSignalPlot(QWidget, Styles):
 					matrix[cid,loc_t] = feature
 					if second_feature:
 						matrix[cid,loc_t+1]=second_feature
-					print(timeline, loc_t)
 
 					cid+=1
 				except: