celldetective 1.3.7.post2__py3-none-any.whl → 1.3.8.post1__py3-none-any.whl

celldetective/gui/tableUI.py

@@ -166,7 +166,7 @@ class DifferentiateColWidget(QWidget, Styles):
 		layout.addLayout(measurement_layout)
 
 		self.window_size_slider = QLabeledSlider()
-		self.window_size_slider.setRange(1,np.nanmax(self.parent_window.data.FRAME.to_numpy()))
+		self.window_size_slider.setRange(1,int(np.nanmax(self.parent_window.data.FRAME.to_numpy())))
 		self.window_size_slider.setValue(3)
 		window_layout = QHBoxLayout()
 		window_layout.addWidget(QLabel('window size: '), 25)
@@ -215,6 +215,108 @@ class DifferentiateColWidget(QWidget, Styles):
 		self.parent_window.table_view.setModel(self.parent_window.model)
 		self.close()
 
+
+
+class OperationOnColsWidget(QWidget, Styles):
+
+	def __init__(self, parent_window, column1=None, column2=None, operation='divide'):
+
+		super().__init__()
+		self.parent_window = parent_window
+		self.column1 = column1
+		self.column2 = column2
+		self.operation = operation
+
+		self.setWindowTitle(self.operation)
+		# Create the QComboBox and add some items
+		center_window(self)
+		
+		layout = QVBoxLayout(self)
+		layout.setContentsMargins(30,30,30,30)
+
+		self.col1_cb = QComboBox()
+		self.col1_cb.addItems(list(self.parent_window.data.columns))
+		if self.column1 is not None:
+			idx = self.col1_cb.findText(self.column1)
+			self.col1_cb.setCurrentIndex(idx)
+
+		numerator_layout = QHBoxLayout()
+		numerator_layout.addWidget(QLabel('column 1: '), 25)
+		numerator_layout.addWidget(self.col1_cb, 75)
+		layout.addLayout(numerator_layout)
+
+		self.col2_cb = QComboBox()
+		self.col2_cb.addItems(list(self.parent_window.data.columns))
+		if self.column2 is not None:
+			idx = self.col2_cb.findText(self.column2)
+			self.col2_cb.setCurrentIndex(idx)
+
+		denominator_layout = QHBoxLayout()
+		denominator_layout.addWidget(QLabel('column 2: '), 25)
+		denominator_layout.addWidget(self.col2_cb, 75)
+		layout.addLayout(denominator_layout)
+
+		self.submit_btn = QPushButton('Compute')
+		self.submit_btn.setStyleSheet(self.button_style_sheet)
+		self.submit_btn.clicked.connect(self.compute)
+		layout.addWidget(self.submit_btn, 30)
+
+		self.setAttribute(Qt.WA_DeleteOnClose)
+
+	def compute(self):
+
+		test = self._check_cols_before_operation()
+		if not test:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText(f"Operation could not be performed, one of the column types is object...")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+			else:
+				return None
+		else:
+			if self.operation=='divide':
+				name = f"{self.col1_txt}/{self.col2_txt}"
+				with np.errstate(divide='ignore', invalid='ignore'):
+					res = np.true_divide(self.col1, self.col2)
+					res[res == np.inf] = np.nan
+					res[self.col1!=self.col1] = np.nan
+					res[self.col2!=self.col2] = np.nan
+					self.parent_window.data[name] = res
+
+			elif self.operation=='multiply':
+				name = f"{self.col1_txt}*{self.col2_txt}"
+				res = np.multiply(self.col1, self.col2)
+
+			elif self.operation=='add':
+				name = f"{self.col1_txt}+{self.col2_txt}"
+				res = np.add(self.col1, self.col2)
+
+			elif self.operation=='subtract':
+				name = f"{self.col1_txt}-{self.col2_txt}"
+				res = np.subtract(self.col1, self.col2)				
+			
+			self.parent_window.data[name] = res
+			self.parent_window.model = PandasModel(self.parent_window.data)
+			self.parent_window.table_view.setModel(self.parent_window.model)
+			self.close()
+
+	def _check_cols_before_operation(self):
+
+		self.col1_txt = self.col1_cb.currentText()
+		self.col2_txt = self.col2_cb.currentText()
+		
+		self.col1 = self.parent_window.data[self.col1_txt].to_numpy()
+		self.col2 = self.parent_window.data[self.col2_txt].to_numpy()
+
+		test = np.all([self.col1.dtype!='O', self.col2.dtype!='O'])
+
+		return test
+
+
 class CalibrateColWidget(GenericOpColWidget):
 	
 	def __init__(self, *args, **kwargs):
@@ -563,12 +665,34 @@ class TableUI(QMainWindow, Styles):
 		self.log_action = QAction('&Log (decimal)...', self)
 		self.log_action.triggered.connect(self.take_log_of_selected_feature)
 		#self.derivative_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.log_action)						
+		self.mathMenu.addAction(self.log_action)
+
+
+		self.divide_action = QAction('&Divide...', self)
+		self.divide_action.triggered.connect(self.divide_signals)
+		#self.derivative_action.setShortcut("Ctrl+D")
+		self.mathMenu.addAction(self.divide_action)
+
+		self.multiply_action = QAction('&Multiply...', self)
+		self.multiply_action.triggered.connect(self.multiply_signals)
+		#self.derivative_action.setShortcut("Ctrl+D")
+		self.mathMenu.addAction(self.multiply_action)	
+
+		self.add_action = QAction('&Add...', self)
+		self.add_action.triggered.connect(self.add_signals)
+		#self.derivative_action.setShortcut("Ctrl+D")
+		self.mathMenu.addAction(self.add_action)	
+
+		self.subtract_action = QAction('&Subtract...', self)
+		self.subtract_action.triggered.connect(self.subtract_signals)
+		#self.derivative_action.setShortcut("Ctrl+D")
+		self.mathMenu.addAction(self.subtract_action)	
 
-		self.onehot_action = QAction('&One hot to categorical...', self)
-		self.onehot_action.triggered.connect(self.transform_one_hot_cols_to_categorical)
-		#self.onehot_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.onehot_action)		
+
+		# self.onehot_action = QAction('&One hot to categorical...', self)
+		# self.onehot_action.triggered.connect(self.transform_one_hot_cols_to_categorical)
+		# #self.onehot_action.setShortcut("Ctrl+D")
+		# self.mathMenu.addAction(self.onehot_action)		
 
 	def collapse_pairs_in_neigh(self):
 
@@ -734,6 +858,96 @@ class TableUI(QMainWindow, Styles):
 			pos_group.to_csv(pos[0]+os.sep.join(['output', 'tables', f'trajectories_{self.population}.csv']), index=False)
 		print("Done...")
 
+	def divide_signals(self):
+
+		x = self.table_view.selectedIndexes()
+		col_idx = np.unique(np.array([l.column() for l in x]))
+		if isinstance(col_idx, (list, np.ndarray)):
+			cols = np.array(list(self.data.columns))
+			if len(col_idx)>0:
+				selected_col1 = str(cols[col_idx[0]])
+				if len(col_idx)>1:
+					selected_col2 = str(cols[col_idx[1]])
+				else:
+					selected_col2 = None
+			else:
+				selected_col1 = None
+				selected_col2 = None
+		else:
+			selected_col1 = None
+			selected_col2 = None
+
+		self.divWidget = OperationOnColsWidget(self, column1=selected_col1, column2=selected_col2, operation='divide')
+		self.divWidget.show()
+
+
+	def multiply_signals(self):
+
+		x = self.table_view.selectedIndexes()
+		col_idx = np.unique(np.array([l.column() for l in x]))
+		if isinstance(col_idx, (list, np.ndarray)):
+			cols = np.array(list(self.data.columns))
+			if len(col_idx)>0:
+				selected_col1 = str(cols[col_idx[0]])
+				if len(col_idx)>1:
+					selected_col2 = str(cols[col_idx[1]])
+				else:
+					selected_col2 = None
+			else:
+				selected_col1 = None
+				selected_col2 = None
+		else:
+			selected_col1 = None
+			selected_col2 = None
+
+		self.mulWidget = OperationOnColsWidget(self, column1=selected_col1, column2=selected_col2, operation='multiply')
+		self.mulWidget.show()
+
+	def add_signals(self):
+
+		x = self.table_view.selectedIndexes()
+		col_idx = np.unique(np.array([l.column() for l in x]))
+		if isinstance(col_idx, (list, np.ndarray)):
+			cols = np.array(list(self.data.columns))
+			if len(col_idx)>0:
+				selected_col1 = str(cols[col_idx[0]])
+				if len(col_idx)>1:
+					selected_col2 = str(cols[col_idx[1]])
+				else:
+					selected_col2 = None
+			else:
+				selected_col1 = None
+				selected_col2 = None
+		else:
+			selected_col1 = None
+			selected_col2 = None
+
+		self.addiWidget = OperationOnColsWidget(self, column1=selected_col1, column2=selected_col2, operation='add')
+		self.addiWidget.show()
+
+	def subtract_signals(self):
+
+		x = self.table_view.selectedIndexes()
+		col_idx = np.unique(np.array([l.column() for l in x]))
+		if isinstance(col_idx, (list, np.ndarray)):
+			cols = np.array(list(self.data.columns))
+			if len(col_idx)>0:
+				selected_col1 = str(cols[col_idx[0]])
+				if len(col_idx)>1:
+					selected_col2 = str(cols[col_idx[1]])
+				else:
+					selected_col2 = None
+			else:
+				selected_col1 = None
+				selected_col2 = None
+		else:
+			selected_col1 = None
+			selected_col2 = None
+
+		self.subWidget = OperationOnColsWidget(self, column1=selected_col1, column2=selected_col2, operation='subtract')
+		self.subWidget.show()
+
+
 	def differenciate_selected_feature(self):
 		
 		# check only one col selected and assert is numerical
@@ -742,9 +956,12 @@ class TableUI(QMainWindow, Styles):
 		
 		x = self.table_view.selectedIndexes()
 		col_idx = np.unique(np.array([l.column() for l in x]))
-		if col_idx!=0:
+		if isinstance(col_idx, (list, np.ndarray)):
 			cols = np.array(list(self.data.columns))
-			selected_col = str(cols[col_idx][0])
+			if len(col_idx)>0:
+				selected_col = str(cols[col_idx[0]])
+			else:
+				selected_col = None
 		else:
 			selected_col = None
 
@@ -759,9 +976,12 @@ class TableUI(QMainWindow, Styles):
 		
 		x = self.table_view.selectedIndexes()
 		col_idx = np.unique(np.array([l.column() for l in x]))
-		if col_idx!=0:
+		if isinstance(col_idx, (list, np.ndarray)):
 			cols = np.array(list(self.data.columns))
-			selected_col = str(cols[col_idx][0])
+			if len(col_idx)>0:
+				selected_col = str(cols[col_idx[0]])
+			else:
+				selected_col = None
 		else:
 			selected_col = None
 
@@ -772,9 +992,12 @@ class TableUI(QMainWindow, Styles):
 		
 		x = self.table_view.selectedIndexes()
 		col_idx = np.unique(np.array([l.column() for l in x]))
-		if col_idx!=0:
+		if isinstance(col_idx, (list, np.ndarray)):
 			cols = np.array(list(self.data.columns))
-			selected_col = str(cols[col_idx][0])
+			if len(col_idx)>0:
+				selected_col = str(cols[col_idx[0]])
+			else:
+				selected_col = None
 		else:
 			selected_col = None
 
@@ -790,9 +1013,12 @@ class TableUI(QMainWindow, Styles):
 		
 		x = self.table_view.selectedIndexes()
 		col_idx = np.unique(np.array([l.column() for l in x]))
-		if col_idx!=0:
+		if isinstance(col_idx, (list, np.ndarray)):
 			cols = np.array(list(self.data.columns))
-			selected_col = str(cols[col_idx][0])
+			if len(col_idx)>0:
+				selected_col = str(cols[col_idx[0]])
+			else:
+				selected_col = None
 		else:
 			selected_col = None
 
@@ -804,11 +1030,14 @@ class TableUI(QMainWindow, Styles):
 
 		x = self.table_view.selectedIndexes()
 		col_idx = np.unique(np.array([l.column() for l in x]))
-		if list(col_idx):
+		if isinstance(col_idx, (list, np.ndarray)):
 			cols = np.array(list(self.data.columns))
-			selected_cols = cols[col_idx]
+			if len(col_idx)>0:
+				selected_col = str(cols[col_idx[0]])
+			else:
+				selected_col = None
 		else:
-			selected_cols = None
+			selected_col = None
 
 		self.mergewidget = MergeOneHotWidget(self, selected_columns=selected_cols)
 		self.mergewidget.show()
@@ -874,7 +1103,7 @@ class TableUI(QMainWindow, Styles):
 		self.projection_option.setChecked(True)
 		self.projection_option.toggled.connect(self.enable_projection_options)
 		self.projection_op_cb = QComboBox()
-		self.projection_op_cb.addItems(['mean','median','min','max', 'prod', 'sum'])
+		self.projection_op_cb.addItems(['mean','median','min','max','first','last','prod','sum'])
 
 		projection_layout = QHBoxLayout()
 		projection_layout.addWidget(self.projection_option, 33)
@@ -1044,8 +1273,11 @@ class TableUI(QMainWindow, Styles):
 		all_cms = list(colormaps)
 		for cm in all_cms:
 			if hasattr(matplotlib.cm, str(cm).lower()):
-				self.cmap_cb.addColormap(cm.lower())
-		
+				try:
+					self.cmap_cb.addColormap(cm.lower())
+				except:
+					pass
+					
 		hbox = QHBoxLayout()
 		hbox.addWidget(QLabel('colormap: '), 33)
 		hbox.addWidget(self.cmap_cb, 66)

celldetective/gui/viewers.py

@@ -932,7 +932,7 @@ class CellSizeViewer(StackVisualizer):
 	  with interactive sliders for diameter adjustment and circle display.
 	"""
 
-	def __init__(self, initial_diameter=40, set_radius_in_list=False, diameter_slider_range=(0,200), parent_le=None, parent_list_widget=None, *args, **kwargs):
+	def __init__(self, initial_diameter=40, set_radius_in_list=False, diameter_slider_range=(0,500), parent_le=None, parent_list_widget=None, *args, **kwargs):
 		# Initialize the widget and its attributes
 		
 		super().__init__(*args, **kwargs)

celldetective/io.py

@@ -16,7 +16,7 @@ import concurrent.futures
 from csbdeep.utils import normalize_mi_ma
 from csbdeep.io import save_tiff_imagej_compatible
 
-import skimage.io as skio
+import imageio.v2 as imageio
 from skimage.measure import regionprops_table, label
 
 from btrack.datasets import cell_config
@@ -400,6 +400,23 @@ def get_experiment_metadata(experiment):
 	metadata = ConfigSectionMap(config, "Metadata")
 	return metadata
 
+def get_experiment_labels(experiment):
+
+	config = get_config(experiment)
+	wells = get_experiment_wells(experiment)
+	nbr_of_wells = len(wells)
+
+	labels = ConfigSectionMap(config, "Labels")
+	for k in list(labels.keys()):
+		values = labels[k].split(',')
+		if nbr_of_wells != len(values):
+			values = [str(s) for s in np.linspace(0, nbr_of_wells - 1, nbr_of_wells)]
+		if np.all([s.isnumeric() for s in values]):
+			values = [float(s) for s in values]
+		labels.update({k: values})
+
+	return labels
+
 
 def get_experiment_concentrations(experiment, dtype=str):
 	
@@ -982,10 +999,8 @@ def load_experiment_tables(experiment, population='targets', well_option='*', po
 	wells = get_experiment_wells(experiment)
 
 	movie_prefix = ConfigSectionMap(config, "MovieSettings")["movie_prefix"]
-	concentrations = get_experiment_concentrations(experiment, dtype=float)
-	cell_types = get_experiment_cell_types(experiment)
-	antibodies = get_experiment_antibodies(experiment)
-	pharmaceutical_agents = get_experiment_pharmaceutical_agents(experiment)
+
+	labels = get_experiment_labels(experiment)
 	metadata = get_experiment_metadata(experiment) # None or dict of metadata
 	well_labels = _extract_labels_from_config(config, len(wells))
 
@@ -1001,14 +1016,8 @@ def load_experiment_tables(experiment, population='targets', well_option='*', po
 
 		well_name, well_number = extract_well_name_and_number(well_path)
 		widx = well_indices[k]
-
 		well_alias = well_labels[widx]
 
-		well_concentration = concentrations[widx]
-		well_antibody = antibodies[widx]
-		well_cell_type = cell_types[widx]
-		well_pharmaceutical_agent = pharmaceutical_agents[widx]
-
 		positions = get_positions_in_well(well_path)
 		if position_indices is not None:
 			try:
@@ -1037,10 +1046,13 @@ def load_experiment_tables(experiment, population='targets', well_option='*', po
 				df_pos['well_name'] = well_name
 				df_pos['pos_name'] = pos_name
 
-				df_pos['concentration'] = well_concentration
-				df_pos['antibody'] = well_antibody
-				df_pos['cell_type'] = well_cell_type
-				df_pos['pharmaceutical_agent'] = well_pharmaceutical_agent
+				for k in list(labels.keys()):
+					values = labels[k]
+					try:
+						df_pos[k] = values[widx]
+					except Exception as e:
+						print(f"{e=}")
+
 				if metadata is not None:
 					keys = list(metadata.keys())
 					for k in keys:
@@ -1052,10 +1064,6 @@ def load_experiment_tables(experiment, population='targets', well_option='*', po
 				pos_dict = {'pos_path': pos_path, 'pos_index': real_pos_index, 'pos_name': pos_name, 'table_path': table,
 					 'stack_path': stack_path,'well_path': well_path, 'well_index': real_well_index, 'well_name': well_name,
 					 'well_number': well_number, 'well_alias': well_alias}
-				# if metadata is not None:
-				# 	keys = list(metadata.keys())
-				# 	for k in keys:
-				# 		pos_dict.update({k: metadata[k]})
 
 				df_pos_info.append(pos_dict)
 
@@ -3335,7 +3343,7 @@ def load_frames(img_nums, stack_path, scale=None, normalize_input=True, dtype=fl
 	"""
 
 	try:
-		frames = skio.imread(stack_path, key=img_nums, plugin="tifffile")
+		frames = imageio.imread(stack_path, key=img_nums)
 	except Exception as e:
 		print(
 			f'Error in loading the frame {img_nums} {e}. Please check that the experiment channel information is consistent with the movie being read.')