celldetective 1.3.2__py3-none-any.whl → 1.3.3.post1__py3-none-any.whl

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.3.2"
+__version__ = "1.3.3.post1"

celldetective/gui/control_panel.py

@@ -450,8 +450,8 @@ class ControlPanel(QMainWindow, Styles):
 			self.view_stack_btn.setEnabled(False)
 			self.ProcessEffectors.signal_analysis_action.setEnabled(True)
 			self.ProcessTargets.signal_analysis_action.setEnabled(True)
-
-			self.delete_tracks_btn.hide()
+			if hasattr(self,'delete_tracks_btn'):
+				self.delete_tracks_btn.hide()
 			self.ProcessTargets.delete_tracks_btn.hide()
 			self.ProcessEffectors.delete_tracks_btn.hide()
 		else:

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
@@ -26,7 +26,7 @@ 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
@@ -951,51 +951,54 @@ 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/process_block.py

@@ -291,6 +291,7 @@ class ProcessPanel(QFrame, Styles):
 		self.signal_models_list.addItems(signal_models)
 
 	def generate_tracking_options(self):
+		
 		grid_track = QHBoxLayout()
 
 		self.track_action = QCheckBox("TRACK")
@@ -303,16 +304,6 @@ class ProcessPanel(QFrame, Styles):
 			padding-top: 5px;
 			""")
 		grid_track.addWidget(self.track_action, 75)
-		#self.to_disable.append(self.track_action_tc)
-
-		# self.show_track_table_btn = QPushButton()
-		# self.show_track_table_btn.setIcon(icon(MDI6.table,color="black"))
-		# self.show_track_table_btn.setIconSize(QSize(20, 20))
-		# self.show_track_table_btn.setToolTip("Show trajectories table.")
-		# self.show_track_table_btn.setStyleSheet(self.button_select_all)
-		# #self.show_track_table_btn.clicked.connect(self.display_trajectory_table)
-		# self.show_track_table_btn.setEnabled(False)
-		# grid_track.addWidget(self.show_track_table_btn, 6)  #4,3,1,1, alignment=Qt.AlignLeft
 
 		self.delete_tracks_btn = QPushButton()
 		self.delete_tracks_btn.setIcon(icon(MDI6.trash_can,color="black"))
@@ -640,25 +631,6 @@ class ProcessPanel(QFrame, Styles):
 
 		self.seg_model_list.insertSeparator(len(self.models_truncated))
 
-
-		#if ("live_nuclei_channel" in self.exp_channels)*("dead_nuclei_channel" in self.exp_channels):
-		# 	print("both channels found")
-		# 	index = self.tc_seg_model_list.findText("MCF7_Hoescht_PI_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" in self.exp_channels)*("dead_nuclei_channel" not in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("MCF7_Hoescht_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" not in self.exp_channels)*("dead_nuclei_channel" in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("MCF7_PI_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" not in self.exp_channels)*("dead_nuclei_channel" not in self.exp_channels)*("adhesion_channel" in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("RICM", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-
 	def tick_all_actions(self):
 		self.switch_all_ticks_option()
 		if self.all_ticked:
@@ -884,28 +856,7 @@ class ProcessPanel(QFrame, Styles):
 		if self.segment_action.isChecked():
 			self.segment_action.setChecked(False)
 
-		# QApplication.restoreOverrideCursor()
-		# self.unfreeze()
-
-	# def view_current_stack_with_scale_bar(self):
-
-	# 	self.parent_window.locate_image()
-	# 	if self.parent_window.current_stack is not None:
-	# 		self.viewer = CellSizeViewer(
-	# 									  initial_diameter = float(self.diameter_le.text().replace(',', '.')),
-	# 			parent_le = self.diameter_le,
-	# 									  stack_path=self.parent_window.current_stack,
-	# 									  window_title=f'Position {self.parent_window.position_list.currentText()}',
-	# 									  frame_slider = True,
-	# 									  contrast_slider = True,
-	# 									  channel_cb = True,
-	# 									  channel_names = self.parent_window.exp_channels,
-	# 									  n_channels = self.parent_window.nbr_channels,
-	# 									  PxToUm = 1,
-	# 									 )
-	# 		self.viewer.show()
-
-
+		self.cellpose_calibrated = False
 
 	def open_napari_tracking(self):
 		print(f'View the tracks before post-processing for position {self.parent_window.pos} in napari...')
@@ -933,24 +884,6 @@ class ProcessPanel(QFrame, Styles):
 			if returnValue == QMessageBox.Ok:
 				return None
 
-	# def interpret_pos_location(self):
-
-	# 	"""
-	# 	Read the well/position selection from the control panel to decide which data to load
-	# 	Set position_indices to None if all positions must be taken
-
-	# 	"""
-
-	# 	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.position_indices = None
-	# 	else:
-	# 		self.position_indices = np.array([self.position_option],dtype=int)
-
 	def load_available_tables(self):
 
 		"""
@@ -1016,6 +949,7 @@ class ProcessPanel(QFrame, Styles):
 		self.process_population()
 
 
+
 class NeighPanel(QFrame, Styles):
 	def __init__(self, parent_window):
 
@@ -1523,35 +1457,12 @@ class NeighPanel(QFrame, Styles):
 					rel_measure_at_position(self.pos)
 
 				if self.signal_analysis_action.isChecked():
-					
-					# df_targets = get_position_pickle(self.pos, population='targets')
-					# df_effectors = get_position_pickle(self.pos, population='effectors')
-					# self.dataframes = {
-					# 	'targets': df_targets,
-					# 	'effectors': df_effectors,
-					# }
-
-					# df_pairs = get_position_table(self.pos, population='pairs')
-
-					# # Need to identify expected reference / neighbor tables
-					# model_path = locate_signal_model(self.pair_signal_models_list.currentText(), pairs=True)
-					# print(f'Looking for model in {model_path}...')
-					# complete_path = model_path
-					# complete_path = rf"{complete_path}"
-					# model_config_path = os.sep.join([complete_path, 'config_input.json'])
-					# model_config_path = rf"{model_config_path}"
-					# f = open(model_config_path)
-					# model_config_path = json.load(f)
-
-					# reference_population = model_config_path['reference_population']
-					# neighbor_population = model_config_path['neighbor_population']
-
-					# analyze_pair_signals(df_pairs, self.dataframes[reference_population], self.dataframes[neighbor_population], model=self.pair_signal_models_list.currentText())
+
 					analyze_pair_signals_at_position(self.pos, self.pair_signal_models_list.currentText(), use_gpu=self.parent_window.parent_window.use_gpu)
+
 		self.parent_window.update_position_options()
 		print('Done.')
 
-
 	def check_signals2(self):
 
 		test = self.parent_window.locate_selected_position()

celldetective/gui/retrain_segmentation_model_options.py

@@ -616,4 +616,6 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		
 		train_segmentation_model(model_folder+"training_instructions.json", use_gpu=self.parent_window.parent_window.parent_window.use_gpu)
 
-		# self.parent.refresh_signal_models()
+		self.parent_window.init_seg_model_list()
+		idx = self.parent_window.seg_model_list.findText(model_name)
+		self.parent_window.seg_model_list.setCurrentIndex(idx)