celldetective 1.3.0__tar.gz → 1.3.0.post1__tar.gz

{celldetective-1.3.0 → celldetective-1.3.0.post1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.0
+Version: 1.3.0.post1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.3.0.post1/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.0.post1"

{celldetective-1.3.0 → celldetective-1.3.0.post1}/celldetective/gui/classifier_widget.py

@@ -242,18 +242,20 @@ class ClassifierWidget(QWidget, Styles):
 
 	def update_props_scatter(self, feature_changed=True):
 
+		class_name = self.class_name
+
 		try:
 
 			if not self.project_times:
 				self.scat_props.set_offsets(self.df.loc[self.df['FRAME']==self.currentFrame,[self.features_cb[1].currentText(),self.features_cb[0].currentText()]].to_numpy())
-				colors = [color_from_status(c) for c in self.df.loc[self.df['FRAME']==self.currentFrame,self.class_name].to_numpy()]
+				colors = [color_from_status(c) for c in self.df.loc[self.df['FRAME']==self.currentFrame,class_name].to_numpy()]
 				self.scat_props.set_facecolor(colors)
 				self.scat_props.set_alpha(self.currentAlpha)
 				self.ax_props.set_xlabel(self.features_cb[1].currentText())
 				self.ax_props.set_ylabel(self.features_cb[0].currentText())
 			else:
 				self.scat_props.set_offsets(self.df[[self.features_cb[1].currentText(),self.features_cb[0].currentText()]].to_numpy())
-				colors = [color_from_status(c) for c in self.df[self.class_name].to_numpy()]
+				colors = [color_from_status(c) for c in self.df[class_name].to_numpy()]
 				self.scat_props.set_facecolor(colors)
 				self.scat_props.set_alpha(self.currentAlpha)
 				self.ax_props.set_xlabel(self.features_cb[1].currentText())
@@ -282,7 +284,8 @@ class ClassifierWidget(QWidget, Styles):
 	def apply_property_query(self):
 		
 		query = self.property_query_le.text()
-		self.df = classify_cells_from_query(self.df, self.class_name, query)
+		self.df = classify_cells_from_query(self.df, self.name_le.text(), query)
+		self.class_name = "status_"+self.name_le.text()
 		if self.df is None:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
@@ -292,7 +295,6 @@ class ClassifierWidget(QWidget, Styles):
 			returnValue = msgBox.exec()
 			if returnValue == QMessageBox.Ok:
 				return None
-
 		self.update_props_scatter()
 
 	def set_frame(self, value):
@@ -351,6 +353,7 @@ class ClassifierWidget(QWidget, Styles):
 					return None
 
 			name_map = {self.class_name: self.class_name_user}
+			print(f"{name_map=}")
 			self.df = self.df.drop(list(set(name_map.values()) & set(self.df.columns)), axis=1).rename(columns=name_map)
 			self.df.reset_index(inplace=True, drop=True)
 
@@ -379,6 +382,8 @@ class ClassifierWidget(QWidget, Styles):
 			#self.df[self.group_name_user] = self.df[self.group_name_user].replace({0: 1, 1: 0})
 			self.df.reset_index(inplace=True, drop=True)
 
+		if 'custom' in list(self.df.columns):
+			self.df = self.df.drop(['custom'],axis=1)
 
 		for pos,pos_group in self.df.groupby('position'):
 			pos_group.to_csv(pos+os.sep.join(['output', 'tables', f'trajectories_{self.mode}.csv']), index=False)

{celldetective-1.3.0 → celldetective-1.3.0.post1}/celldetective/io.py

@@ -766,6 +766,9 @@ def locate_stack_and_labels(position, prefix='Aligned', population="target"):
 	position = position.replace('\\', '/')
 	labels = locate_labels(position, population=population)
 	stack = locate_stack(position, prefix=prefix)
+	if len(labels) < len(stack):
+		fix_missing_labels(position, population=population, prefix=prefix)
+		labels = locate_labels(position, population=population)
 	assert len(stack) == len(
 		labels), f"The shape of the stack {stack.shape} does not match with the shape of the labels {labels.shape}"
 
@@ -1272,7 +1275,7 @@ def view_on_napari_btrack(data, properties, graph, stack=None, labels=None, rela
 	if stack is not None:
 		viewer.add_image(stack, channel_axis=-1, colormap=["gray"] * stack.shape[-1])
 	if labels is not None:
-		viewer.add_labels(labels, name='segmentation', opacity=0.4)
+		viewer.add_labels(labels.astype(int), name='segmentation', opacity=0.4)
 	viewer.add_points(vertices, size=4, name='points', opacity=0.3)
 	if data.shape[1]==4:
 		viewer.add_tracks(data, properties=properties, graph=graph, name='tracks')

{celldetective-1.3.0 → celldetective-1.3.0.post1}/celldetective/measure.py

@@ -1338,10 +1338,11 @@ def classify_cells_from_query(df, status_attr, query):
 	if not status_attr.startswith('status_'):
 		status_attr = 'status_'+status_attr
 
-	df[status_attr] = 0
+	df = df.copy()
+	df.loc[:,status_attr] = 0
+
 	cols = extract_cols_from_query(query)
 	cols_in_df = np.all([c in list(df.columns) for c in cols], axis=0)
-
 	if query=='':
 		print('The provided query is empty...')
 	else:
@@ -1354,11 +1355,10 @@ def classify_cells_from_query(df, status_attr, query):
 				df.loc[selection, status_attr] = 1
 			else:
 				df.loc[:, status_attr] = np.nan
-
 		except Exception as e:
-			print("The query could not be understood. No filtering was applied. {e}...")
+			print(f"The query could not be understood. No filtering was applied. {e}...")
 			return None
-	return df
+	return df.copy()
 
 def classify_tracks_from_query(df, event_name, query, irreversible_event=True, unique_state=False, r2_threshold=0.5, percentile_recovery=50):
 	

{celldetective-1.3.0 → celldetective-1.3.0.post1}/celldetective.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.0
+Version: 1.3.0.post1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.3.0/celldetective/_version.py

@@ -1 +0,0 @@
-__version__ = "1.3.0"