celldetective 1.1.1.post3__tar.gz → 1.1.1.post4__tar.gz

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.1.1.post3
+Version: 1.1.1.post4
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/celldetective/__main__.py

@@ -108,6 +108,10 @@ class AppInitWindow(QMainWindow):
 		OptionsMenu.addAction(self.MemoryAndThreadsAction)
 		menuBar.addMenu(OptionsMenu)
 
+		PluginsMenu = QMenu("Plugins", self)
+		PluginsMenu.addAction(self.CorrectAnnotationAction)
+		menuBar.addMenu(PluginsMenu)
+
 		helpMenu = QMenu("Help", self)
 		helpMenu.clear()
 		helpMenu.addAction(self.DocumentationAction)
@@ -130,6 +134,8 @@ class AppInitWindow(QMainWindow):
 
 		self.MemoryAndThreadsAction = QAction('Memory & Threads...')
 
+		self.CorrectAnnotationAction = QAction('Correct a segmentation annotation...')
+
 		self.newExpAction = QAction('New', self)
 		self.newExpAction.setShortcut("Ctrl+N")
 		self.newExpAction.setShortcutVisibleInContextMenu(True)
@@ -156,6 +162,7 @@ class AppInitWindow(QMainWindow):
 		self.openModels.triggered.connect(self.open_models_folder)
 		self.AboutAction.triggered.connect(self.open_about_window)
 		self.MemoryAndThreadsAction.triggered.connect(self.set_memory_and_threads)
+		self.CorrectAnnotationAction.triggered.connect(self.correct_seg_annotation)
 
 		self.DocumentationAction.triggered.connect(self.open_documentation)
 
@@ -186,6 +193,15 @@ class AppInitWindow(QMainWindow):
 			for r in self.recentFileActs:
 				r.triggered.connect(lambda checked, item=r: self.load_recent_exp(item.text()))
 
+	def correct_seg_annotation(self):
+		
+		self.filename,_ = QFileDialog.getOpenFileName(self,"Open Image", "/home/", "TIF Files (*.tif)")
+		if self.filename!='':
+			print('Opening ',self.filename,' in napari...')
+			correct_annotation(self.filename)
+		else:
+			return None
+
 	def set_memory_and_threads(self):
 		
 		print('setting memory and threads')
@@ -405,6 +421,7 @@ if __name__ == "__main__":
 	import subprocess
 	import os
 	from celldetective.gui.about import AboutWidget
+	from celldetective.io import correct_annotation
 	import psutil
 	import subprocess
 	import json

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/celldetective/gui/classifier_widget.py

@@ -12,6 +12,7 @@ from sklearn.metrics import r2_score
 from scipy.optimize import curve_fit
 from celldetective.gui import Styles
 from math import ceil
+from celldetective.utils import extract_cols_from_query
 
 def step_function(t, t_shift, dt):
 	return 1/(1+np.exp(-(t-t_shift)/dt))
@@ -263,17 +264,23 @@ class ClassifierWidget(QWidget, Styles):
 		self.propscanvas.canvas.draw_idle()
 
 	def apply_property_query(self):
+
 		query = self.property_query_le.text()
 		self.df[self.class_name] = 1
 
-		print(query, self.class_name)
+		cols = extract_cols_from_query(query) 
+		print(cols)
+		cols_in_df = np.all([c in list(self.df.columns) for c in cols], axis=0)
+		print(f'Testing if columns from query are in the dataframe: {cols_in_df}...')
 
 		if query=='':
 			print('empty query')
 		else:
 			try:
-				self.selection = self.df.query(query).index
-				print(self.selection)
+				if cols_in_df:
+					self.selection = self.df.dropna(subset=cols).query(query).index
+				else:
+					self.selection = self.df.query(query).index
 				self.df.loc[self.selection, self.class_name] = 0
 			except Exception as e:
 				print(e)

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/celldetective/gui/control_panel.py

@@ -16,6 +16,7 @@ import subprocess
 from celldetective.gui.viewers import StackVisualizer
 from celldetective.utils import extract_experiment_channels
 from celldetective.gui import Styles
+import pandas as pd
 
 class ControlPanel(QMainWindow, Styles):
 
@@ -452,26 +453,32 @@ class ControlPanel(QMainWindow, Styles):
 					self.ProcessEffectors.check_tracking_result_btn.setEnabled(False)
 
 				if os.path.exists(os.sep.join([self.pos,'output','tables','trajectories_effectors.csv'])):
+					cols = pd.read_csv(os.sep.join([self.pos,'output','tables','trajectories_effectors.csv']), nrows=1).columns.tolist()
 					self.ProcessEffectors.check_measurements_btn.setEnabled(True)
-					self.ProcessEffectors.check_signals_btn.setEnabled(True)
+					if 'TRACK_ID' in cols:
+						self.ProcessEffectors.check_signals_btn.setEnabled(True)
 					#self.ProcessEffectors.signal_analysis_action.setEnabled(True)
 					self.ProcessEffectors.view_tab_btn.setEnabled(True)
-
+					self.ProcessEffectors.classify_btn.setEnabled(True)
 				else:
 					self.ProcessEffectors.check_measurements_btn.setEnabled(False)
 					self.ProcessEffectors.check_signals_btn.setEnabled(False)
 					#self.ProcessEffectors.signal_analysis_action.setEnabled(False)
 					self.ProcessEffectors.view_tab_btn.setEnabled(False)
+					self.ProcessEffectors.classify_btn.setEnabled(False)
 
 				if os.path.exists(os.sep.join([self.pos,'output','tables','trajectories_targets.csv'])):
+					cols = pd.read_csv(os.sep.join([self.pos,'output','tables','trajectories_targets.csv']), nrows=1).columns.tolist()
 					self.ProcessTargets.check_measurements_btn.setEnabled(True)
-					self.ProcessTargets.check_signals_btn.setEnabled(True)
+					if 'TRACK_ID' in cols:
+						self.ProcessTargets.check_signals_btn.setEnabled(True)
 					#self.ProcessTargets.signal_analysis_action.setEnabled(True)
 					self.ProcessTargets.view_tab_btn.setEnabled(True)
-
+					self.ProcessTargets.classify_btn.setEnabled(True)
 				else:
 					self.ProcessTargets.check_measurements_btn.setEnabled(False)
 					self.ProcessTargets.check_signals_btn.setEnabled(False)
 					#self.ProcessTargets.signal_analysis_action.setEnabled(False)
 					self.ProcessTargets.view_tab_btn.setEnabled(False)
+					self.ProcessTargets.classify_btn.setEnabled(False)
 

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/celldetective/gui/layouts.py

@@ -990,10 +990,12 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 											)
 		bg = bg[0]
 		bg = bg['bg']
-
-		self.viewer = StackVisualizer(
-									  stack=[bg],
-									  window_title='Reconstructed background',
-									  frame_slider = False,
-									 )
-		self.viewer.show()
+		print(bg)
+		if len(bg)>0:
+
+			self.viewer = StackVisualizer(
+										  stack=[bg],
+										  window_title='Reconstructed background',
+										  frame_slider = False,
+										 )
+			self.viewer.show()

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/celldetective/gui/neighborhood_options.py

@@ -319,16 +319,16 @@ class ConfigNeighborhoods(QWidget, Styles):
 	def fill_cbs_of_neighbor_population(self):
 
 		population = self.neighbor_population_cb.currentText()
-		class_cols, status_cols, time_cols = self.locate_population_specific_columns(population)
+		class_cols, status_cols, group_cols, time_cols = self.locate_population_specific_columns(population)
 		self.neighbor_population_status_cb.clear()
-		self.neighbor_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols)
+		self.neighbor_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols+group_cols)
 
 	def fill_cbs_of_reference_population(self):
 
 		population = self.reference_population_cb.currentText()
-		class_cols, status_cols, time_cols = self.locate_population_specific_columns(population)
+		class_cols, status_cols, group_cols, time_cols = self.locate_population_specific_columns(population)
 		self.reference_population_status_cb.clear()
-		self.reference_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols)
+		self.reference_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols+group_cols)
 		self.event_time_cb.addItems(['--', 't0']+time_cols)
 
 	def switch_not_reference(self):
@@ -364,6 +364,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 
 		class_idx = np.array([s.startswith('class_') for s in self.all_columns])
 		status_idx = np.array([s.startswith('status_') for s in self.all_columns])
+		group_idx = np.array([s.startswith('group_') for s in self.all_columns])		
 		time_idx = np.array([s.startswith('t_') for s in self.all_columns])
 
 		if len(class_idx)>0:
@@ -379,12 +380,17 @@ class ConfigNeighborhoods(QWidget, Styles):
 		else:
 			status_columns = []
 
+		if len(group_idx)>0:
+			group_columns = list(self.all_columns[group_idx])
+		else:
+			group_columns = []
+
 		if len(time_idx)>0:
 			time_columns = list(self.all_columns[time_idx])
 		else:
 			time_columns = []
 
-		return class_columns, status_columns, time_columns
+		return class_columns, status_columns, group_columns, time_columns
 
 	def write_instructions(self):
 

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/celldetective/gui/signal_annotator.py

@@ -27,6 +27,7 @@ from matplotlib.cm import tab10
 import pandas as pd
 from sklearn.preprocessing import MinMaxScaler
 from celldetective.gui import Styles
+from celldetective.measure import contour_of_instance_segmentation
 
 class SignalAnnotator(QMainWindow, Styles):
 	"""
@@ -76,9 +77,9 @@ class SignalAnnotator(QMainWindow, Styles):
 
 		self.populate_widget()
 
-		self.setMinimumWidth(int(0.8 * self.screen_width))
+		#self.setMinimumWidth(int(0.8 * self.screen_width))
 		# self.setMaximumHeight(int(0.8*self.screen_height))
-		self.setMinimumHeight(int(0.8 * self.screen_height))
+		#self.setMinimumHeight(int(0.8 * self.screen_height))
 		# self.setMaximumHeight(int(0.8*self.screen_height))
 
 		self.setAttribute(Qt.WA_DeleteOnClose)
@@ -119,7 +120,6 @@ class SignalAnnotator(QMainWindow, Styles):
 
 		self.class_choice_cb.addItems(self.class_cols)
 		self.class_choice_cb.currentIndexChanged.connect(self.compute_status_and_colors)
-		self.class_choice_cb.setCurrentIndex(0)
 
 		class_hbox.addWidget(self.class_choice_cb, 70)
 
@@ -346,6 +346,8 @@ class SignalAnnotator(QMainWindow, Styles):
 		main_layout.addLayout(self.right_panel, 65)
 		self.button_widget.adjustSize()
 
+		self.compute_status_and_colors(0)
+
 		self.setCentralWidget(self.button_widget)
 		self.show()
 
@@ -462,6 +464,7 @@ class SignalAnnotator(QMainWindow, Styles):
 		self.newClassWidget.close()
 
 	def compute_status_and_colors(self, i):
+
 		self.class_name = self.class_choice_cb.currentText()
 		self.expected_status = 'status'
 		suffix = self.class_name.replace('class', '').replace('_', '', 1)
@@ -474,11 +477,15 @@ class SignalAnnotator(QMainWindow, Styles):
 		self.status_name = self.expected_status
 
 		print('selection and expected names: ', self.class_name, self.expected_time, self.expected_status)
+		cols = list(self.df_tracks.columns)
 
-		if self.time_name in self.df_tracks.columns and self.class_name in self.df_tracks.columns and not self.status_name in self.df_tracks.columns:
+		if self.time_name in cols and self.class_name in cols and not self.status_name in cols:
 			# only create the status column if it does not exist to not erase static classification results
 			self.make_status_column()
-		elif self.time_name in self.df_tracks.columns and self.class_name in self.df_tracks.columns:
+		elif self.time_name in cols and self.class_name in cols and self.df_tracks[self.status_name].isnull().all():
+			print('this is the case!', )
+			self.make_status_column()
+		elif self.time_name in cols and self.class_name in cols:
 			# all good, do nothing
 			pass
 		else:
@@ -855,7 +862,7 @@ class SignalAnnotator(QMainWindow, Styles):
 			self.cell_ax.legend()
 			self.cell_fcanvas.canvas.draw()
 		except Exception as e:
-			print(f"{e=}")
+			print(f"Plot signals: {e=}")
 
 	def extract_scatter_from_trajectories(self):
 
@@ -1109,7 +1116,7 @@ class SignalAnnotator(QMainWindow, Styles):
 			if len(min_values) > 0:
 				self.cell_ax.set_ylim(np.amin(min_values), np.amax(max_values))
 		except Exception as e:
-			print(e)
+			print('Ylim error:',e)
 
 	def draw_frame(self, framedata):
 
@@ -1301,7 +1308,9 @@ class SignalAnnotator(QMainWindow, Styles):
 
 
 class MeasureAnnotator(SignalAnnotator):
+
 	def __init__(self, parent_window=None):
+
 		QMainWindow.__init__(self)
 		self.parent_window = parent_window
 		self.setWindowTitle("Signal annotator")
@@ -1315,11 +1324,11 @@ class MeasureAnnotator(SignalAnnotator):
 		self.int_validator = QIntValidator()
 		self.current_alpha=0.5
 		if self.mode == "targets":
-			self.instructions_path = self.exp_dir + "configs/signal_annotator_config_targets.json"
-			self.trajectories_path = self.pos + 'output/tables/trajectories_targets.csv'
+			self.instructions_path = self.exp_dir + os.sep.join(['configs','signal_annotator_config_targets.json'])
+			self.trajectories_path = self.pos + os.sep.join(['output','tables','trajectories_targets.csv'])
 		elif self.mode == "effectors":
-			self.instructions_path = self.exp_dir + "configs/signal_annotator_config_effectors.json"
-			self.trajectories_path = self.pos + 'output/tables/trajectories_effectors.csv'
+			self.instructions_path = self.exp_dir + os.sep.join(['configs','signal_annotator_config_effectors.json'])
+			self.trajectories_path = self.pos + os.sep.join(['output','tables','trajectories_effectors.csv'])
 
 		self.screen_height = self.parent_window.parent_window.parent_window.screen_height
 		self.screen_width = self.parent_window.parent_window.parent_window.screen_width
@@ -1330,8 +1339,13 @@ class MeasureAnnotator(SignalAnnotator):
 		center_window(self)
 
 		self.locate_stack()
+
 		data, properties, graph, labels, _ = load_napari_data(self.pos, prefix=None, population=self.mode,return_stack=False)
-		self.labels = relabel_segmentation(labels,data,properties)
+		if data is not None:
+			self.labels = relabel_segmentation(labels,data,properties)
+		else:
+			self.labels = labels
+
 		self.current_channel = 0
 
 		self.locate_tracks()
@@ -1577,8 +1591,10 @@ class MeasureAnnotator(SignalAnnotator):
 		self.class_choice_cb = QComboBox()
 
 		cols = np.array(self.df_tracks.columns)
-		self.class_cols = np.array([c.startswith('group') for c in list(self.df_tracks.columns)])
+		self.class_cols = np.array([c.startswith('group') or c.startswith('status') for c in list(self.df_tracks.columns)])
 		self.class_cols = list(cols[self.class_cols])
+		print(self.class_cols)
+
 		try:
 			self.class_cols.remove('group_id')
 		except Exception:
@@ -1711,6 +1727,14 @@ class MeasureAnnotator(SignalAnnotator):
 		btn_hbox.addWidget(self.save_btn, 90)
 		self.left_panel.addLayout(btn_hbox)
 
+		self.export_btn = QPushButton('')
+		self.export_btn.setStyleSheet(self.button_select_all)
+		self.export_btn.clicked.connect(self.export_measurements)
+		self.export_btn.setIcon(icon(MDI6.export, color="black"))
+		self.export_btn.setIconSize(QSize(25, 25))
+		btn_hbox.addWidget(self.export_btn, 10)
+		self.left_panel.addLayout(btn_hbox)
+
 		# Animation
 		animation_buttons_box = QHBoxLayout()
 
@@ -1810,6 +1834,28 @@ class MeasureAnnotator(SignalAnnotator):
 		# del self.img
 		gc.collect()
 
+
+	def export_measurements(self):
+
+		auto_dataset_name = self.pos.split(os.sep)[-4] + '_' + self.pos.split(os.sep)[-2] + f'_{str(self.current_frame).zfill(3)}' + f'_{self.status_name}.npy'
+
+		if self.normalized_signals:
+			self.normalize_features_btn.click()
+
+		subdf = self.df_tracks.loc[self.df_tracks['FRAME']==self.current_frame,:]
+		subdf['class'] = subdf[self.status_name]
+		dico = subdf.to_dict('records')
+
+		pathsave = QFileDialog.getSaveFileName(self, "Select file name", self.exp_dir + auto_dataset_name, ".npy")[0]
+		if pathsave != '':
+			if not pathsave.endswith(".npy"):
+				pathsave += ".npy"
+			try:
+				np.save(pathsave, dico)
+				print(f'File successfully written in {pathsave}.')
+			except Exception as e:
+				print(f"Error {e}...")
+
 	def set_next_frame(self):
 
 		self.current_frame = self.current_frame + 1
@@ -1887,13 +1933,17 @@ class MeasureAnnotator(SignalAnnotator):
 
 	def give_cell_information(self):
 
-		cell_selected = f"cell: {self.track_of_interest}\n"
-		if 'TRACK_ID' in self.df_tracks.columns:
-			cell_status = f"phenotype: {self.df_tracks.loc[self.df_tracks['TRACK_ID'] == self.track_of_interest, self.status_name].to_numpy()[0]}\n"
-		else:
-			cell_status = f"phenotype: {self.df_tracks.loc[self.df_tracks['ID'] == self.track_of_interest, self.status_name].to_numpy()[0]}\n"
-		self.cell_info.setText(cell_selected + cell_status)
-
+		try:
+			cell_selected = f"cell: {self.track_of_interest}\n"
+			if 'TRACK_ID' in self.df_tracks.columns:
+				cell_status = f"phenotype: {self.df_tracks.loc[self.df_tracks['TRACK_ID'] == self.track_of_interest, self.status_name].to_numpy()[0]}\n"
+			else:
+				cell_status = f"phenotype: {self.df_tracks.loc[self.df_tracks['ID'] == self.track_of_interest, self.status_name].to_numpy()[0]}\n"
+			self.cell_info.setText(cell_selected + cell_status)
+		except Exception as e:
+			print('Cell info:',e)
+			print(self.track_of_interest, self.status_name)
+			
 	def create_new_event_class(self):
 
 		# display qwidget to name the event
@@ -1978,8 +2028,14 @@ class MeasureAnnotator(SignalAnnotator):
 		self.frame_lbl.setText(f'position: {self.framedata}')
 		self.im.set_array(self.img)
 		self.status_scatter.set_offsets(self.positions[self.framedata])
-		self.status_scatter.set_edgecolors(self.colors[self.framedata][:, 0])
+		try:
+			self.status_scatter.set_edgecolors(self.colors[self.framedata][:, 0])
+		except Exception as e:
+			print('L1993: ',e)
+
 		self.current_label = self.labels[self.current_frame]
+		self.current_label = contour_of_instance_segmentation(self.current_label, 5)
+
 		self.im_mask.remove()
 		self.im_mask = self.ax.imshow(np.ma.masked_where(self.current_label == 0, self.current_label),
 											   cmap='viridis', interpolation='none',alpha=self.current_alpha,vmin=0,vmax=np.nanmax(self.labels.flatten()))
@@ -2108,9 +2164,9 @@ class MeasureAnnotator(SignalAnnotator):
 
 			self.extract_scatter_from_trajectories()
 			if 'TRACK_ID' in self.df_tracks.columns:
-				self.track_of_interest = self.df_tracks['TRACK_ID'].min()
+				self.track_of_interest = self.df_tracks.dropna(subset='TRACK_ID')['TRACK_ID'].min()
 			else:
-				self.track_of_interest = self.df_tracks['ID'].min()
+				self.track_of_interest = self.df_tracks.dropna(subset='ID')['ID'].min()
 
 			self.loc_t = []
 			self.loc_idx = []
@@ -2172,9 +2228,13 @@ class MeasureAnnotator(SignalAnnotator):
 		"""
 		self.current_frame = self.frame_slider.value()
 		self.reload_frame()
-		if 'ID' in self.df_tracks.columns:
+		if 'TRACK_ID' in list(self.df_tracks.columns):
+			pass
+		elif 'ID' in list(self.df_tracks.columns):
+			print('ID in cols... change class of interest... ')
 			self.track_of_interest = self.df_tracks[self.df_tracks['FRAME'] == self.current_frame]['ID'].min()
 			self.modify()
+
 		self.draw_frame(self.current_frame)
 		self.fcanvas.canvas.draw()
 		self.plot_signals()
@@ -2302,7 +2362,7 @@ class MeasureAnnotator(SignalAnnotator):
 		try:
 			self.selection.pop(0)
 		except Exception as e:
-			print(e)
+			print('Cancel selection: ',e)
 
 		try:
 			for k, (t, idx) in enumerate(zip(self.loc_t, self.loc_idx)):

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/celldetective/gui/tableUI.py

@@ -65,9 +65,9 @@ class QueryWidget(QWidget):
 
 	def filter_table(self):
 		try:
-			query_text = self.query_le.text().replace('class', '`class`')
+			query_text = self.query_le.text() #.replace('class', '`class`')
 			tab = self.parent_window.data.query(query_text)
-			self.subtable = TableUI(tab, query_text, plot_mode="scatter")
+			self.subtable = TableUI(tab, query_text, plot_mode="static")
 			self.subtable.show()
 			self.close()
 		except Exception as e:
@@ -268,7 +268,6 @@ class RenameColWidget(QWidget):
 		old_name = self.column
 		new_name = self.new_col_name.text()
 		self.parent_window.data = self.parent_window.data.rename(columns={old_name: new_name})
-		print(self.parent.data.columns)
 
 		self.parent_window.model = PandasModel(self.parent_window.data)
 		self.parent_window.table_view.setModel(self.parent_window.model)
@@ -583,18 +582,20 @@ class TableUI(QMainWindow, Styles):
 		layout.addWidget(QLabel('Representations: '))
 		self.hist_check = QCheckBox('histogram')
 		self.kde_check = QCheckBox('KDE plot')
-		self.count_check = QCheckBox('Countplot')
+		self.count_check = QCheckBox('countplot')
 		self.ecdf_check = QCheckBox('ECDF plot')
+		self.scat_check = QCheckBox('scatter plot')
 		self.swarm_check = QCheckBox('swarm')
 		self.violin_check = QCheckBox('violin')
 		self.strip_check = QCheckBox('strip')
-		self.box_check = QCheckBox('Boxplot')
-		self.boxenplot_check = QCheckBox('Boxenplot')
+		self.box_check = QCheckBox('boxplot')
+		self.boxenplot_check = QCheckBox('boxenplot')
 
 		layout.addWidget(self.hist_check)
 		layout.addWidget(self.kde_check)
 		layout.addWidget(self.count_check)
 		layout.addWidget(self.ecdf_check)
+		layout.addWidget(self.scat_check)
 		layout.addWidget(self.swarm_check)
 		layout.addWidget(self.violin_check)
 		layout.addWidget(self.strip_check)
@@ -707,6 +708,14 @@ class TableUI(QMainWindow, Styles):
 		if self.ecdf_check.isChecked():
 			sns.ecdfplot(data=self.data, x=self.x, hue=hue_variable, legend=legend, ax=self.ax, palette=colors)
 			legend = False
+		
+		if self.scat_check.isChecked():
+			if self.x_option:
+				sns.scatterplot(data=self.data, x=self.x,y=self.y, hue=hue_variable,legend=legend, ax=self.ax, palette=colors)
+				legend = False
+			else:
+				print('please provide a -x variable...')
+				pass
 
 		if self.swarm_check.isChecked():
 			if self.x_option:

{celldetective-1.1.1.post3 → celldetective-1.1.1.post4}/celldetective/io.py

@@ -26,6 +26,7 @@ from stardist import fill_label_holes
 from celldetective.utils import interpolate_nan
 from scipy.interpolate import griddata
 
+
 def get_experiment_wells(experiment):
 	
 	"""
@@ -801,6 +802,10 @@ def auto_load_number_of_frames(stack_path):
 	"""
 
 	# Try to estimate automatically # frames
+	
+	if stack_path is None:
+		return None
+
 	stack_path = stack_path.replace('\\','/')
 
 	with TiffFile(stack_path) as tif:
@@ -1370,6 +1375,14 @@ def control_segmentation_napari(position, prefix='Aligned', population="target",
 		exp_name = os.path.split(expfolder)[-1]
 		print(exp_name)
 
+		wells = get_experiment_wells(expfolder)
+		well_idx = list(wells).index(str(parent1)+os.sep)
+		ab = get_experiment_antibodies(expfolder)[well_idx]
+		conc = get_experiment_concentrations(expfolder)[well_idx]
+		ct = get_experiment_cell_types(expfolder)[well_idx]
+		pa = get_experiment_pharmaceutical_agents(expfolder)[well_idx]
+
+
 		spatial_calibration = float(ConfigSectionMap(config,"MovieSettings")["pxtoum"])
 		channel_names, channel_indices = extract_experiment_channels(config)
 
@@ -1424,7 +1437,7 @@ def control_segmentation_napari(position, prefix='Aligned', population="target",
 				multichannel = np.array(multichannel)        
 				save_tiff_imagej_compatible(annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}_roi_{xmin}_{xmax}_{ymin}_{ymax}_labelled.tif", labels_layer[xmin:xmax,ymin:ymax].astype(np.int16), axes='YX')
 				save_tiff_imagej_compatible(annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}_roi_{xmin}_{xmax}_{ymin}_{ymax}.tif", multichannel, axes='CYX')
-				info = {"spatial_calibration": spatial_calibration, "channels": list(channel_names)}
+				info = {"spatial_calibration": spatial_calibration, "channels": list(channel_names), 'cell_type': ct, 'antibody': ab, 'concentration': conc, 'pharmaceutical_agent': pa}
 				info_name = annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}_roi_{xmin}_{xmax}_{ymin}_{ymax}.json"
 				with open(info_name, 'w') as f:
 					json.dump(info, f, indent=4)
@@ -1441,7 +1454,7 @@ def control_segmentation_napari(position, prefix='Aligned', population="target",
 			multichannel = np.array(multichannel)		
 			save_tiff_imagej_compatible(annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}_labelled.tif", labels_layer, axes='YX')
 			save_tiff_imagej_compatible(annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}.tif", multichannel, axes='CYX')
-			info = {"spatial_calibration": spatial_calibration, "channels": list(channel_names)}
+			info = {"spatial_calibration": spatial_calibration, "channels": list(channel_names), 'cell_type': ct, 'antibody': ab, 'concentration': conc, 'pharmaceutical_agent': pa}
 			info_name = annotation_folder + f"{exp_name}_{position.split(os.sep)[-2]}_{str(t).zfill(4)}.json"
 			with open(info_name, 'w') as f:
 				json.dump(info, f, indent=4)
@@ -1481,6 +1494,59 @@ def control_segmentation_napari(position, prefix='Aligned', population="target",
 		del labels
 		gc.collect()
 
+def correct_annotation(filename):
+
+	"""
+	New function to reannotate an annotation image in post, using napari and save update inplace.
+	"""
+	
+	def export_labels():
+		labels_layer = viewer.layers['segmentation'].data
+		for t,im in enumerate(tqdm(labels_layer)):
+
+			try:
+				im = auto_correct_masks(im)
+			except Exception as e:
+				print(e)
+
+			save_tiff_imagej_compatible(existing_lbl, im.astype(np.int16), axes='YX')
+		print("The labels have been successfully rewritten.")
+
+	@magicgui(call_button='Save the modified labels')
+	def save_widget():
+		return export_labels()
+	
+	img = imread(filename.replace('\\','/'))
+	if img.ndim==3:
+		img = np.moveaxis(img, 0, -1)
+	elif img.ndim==2:
+		img = img[:,:,np.newaxis]
+		
+	existing_lbl = filename.replace('.tif','_labelled.tif')
+	if os.path.exists(existing_lbl):
+		labels = imread(existing_lbl)[np.newaxis,:,:].astype(int)
+	else:
+		labels = np.zeros_like(img[:,:,0]).astype(int)[np.newaxis,:,:]
+		
+	stack = img[np.newaxis,:,:,:]
+	
+	viewer = napari.Viewer()
+	viewer.add_image(stack,channel_axis=-1,colormap=["gray"]*stack.shape[-1])
+	viewer.add_labels(labels, name='segmentation',opacity=0.4)
+	viewer.window.add_dock_widget(save_widget, area='right')
+	viewer.show(block=True)    
+
+	# temporary fix for slight napari memory leak
+	for i in range(100):
+		try:
+			viewer.layers.pop()
+		except:
+			pass
+	del viewer
+	del stack
+	del labels
+	gc.collect()
+
 
 def _view_on_napari(tracks=None, stack=None, labels=None):
 	
@@ -1628,7 +1694,7 @@ def locate_segmentation_model(name):
 	"""
 
 	main_dir = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0],"celldetective"])
-	modelpath = os.sep.join([main_dir, "models", "segmentation*", os.sep])
+	modelpath = os.sep.join([main_dir, "models", "segmentation*"]) + os.sep
 	print(f'Looking for {name} in {modelpath}')
 	models = glob(modelpath+f'*{os.sep}')