celldetective 1.2.0__tar.gz → 1.2.1__tar.gz

{celldetective-1.2.0 → celldetective-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.2.0
+Version: 1.2.1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/gui/classifier_widget.py

@@ -279,9 +279,12 @@ class ClassifierWidget(QWidget, Styles):
 			try:
 				if cols_in_df:
 					self.selection = self.df.dropna(subset=cols).query(query).index
+					null_selection = self.df[self.df.loc[:,cols].isna().any(axis=1)].index
+					self.df.loc[null_selection, self.class_name] = np.nan
+					self.df.loc[self.selection, self.class_name] = 0
 				else:
-					self.selection = self.df.query(query).index
-				self.df.loc[self.selection, self.class_name] = 0
+					self.df.loc[:, self.class_name] = np.nan
+
 			except Exception as e:
 				print(e)
 				print(self.df.columns)
@@ -384,6 +387,7 @@ class ClassifierWidget(QWidget, Styles):
 								self.df.loc[indices, self.class_name_user] = 2
 								self.df.loc[indices, self.class_name_user.replace('class','t')] = -1
 				if self.irreversible_event_btn.isChecked():
+					self.df.loc[self.df[self.class_name_user]!=2, self.class_name_user.replace('class', 't')] = -1
 					self.estimate_time()
 		else:
 			self.group_name_user = 'group_' + self.name_le.text()
@@ -415,6 +419,7 @@ class ClassifierWidget(QWidget, Styles):
 		# reset
 		#self.init_class()
 		#self.update_props_scatter()
+		self.parent_window.parent_window.update_position_options()
 		self.close()
 
 	def switch_to_log(self, i):

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/gui/neighborhood_options.py

@@ -230,11 +230,12 @@ class ConfigNeighborhoods(QWidget, Styles):
 
 		status_layout = QHBoxLayout()
 
-		status_layout.addWidget(QLabel('status: '), 30)
+		#status_layout.addWidget(QLabel('status: '), 30)
 
 		status_sublayout = QHBoxLayout()
 		self.reference_population_status_cb = QComboBox()
 		self.reference_population_status_cb.setToolTip('Status of the reference population.')
+		self.reference_population_status_cb.hide()
 		status_sublayout.addWidget(self.reference_population_status_cb,95)
 
 		self.reference_switch_status_btn = QPushButton("")
@@ -243,6 +244,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 		self.reference_switch_status_btn.setIconSize(QSize(20, 20))
 		self.reference_switch_status_btn.clicked.connect(self.switch_not_reference)
 		self.reference_switch_status_btn.setToolTip('Invert status values.')
+		self.reference_switch_status_btn.hide()
 
 		status_sublayout.addWidget(self.reference_switch_status_btn, 5)
 

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/gui/signal_annotator.py

@@ -1361,10 +1361,10 @@ class MeasureAnnotator(SignalAnnotator):
 		self.locate_stack()
 
 		data, properties, graph, labels, _ = load_napari_data(self.pos, prefix=None, population=self.mode,return_stack=False)
-		if data is not None:
-			self.labels = relabel_segmentation(labels,data,properties)
-		else:
-			self.labels = labels
+		# if data is not None:
+		# 	self.labels = relabel_segmentation(labels,data,properties)
+		# else:
+		self.labels = labels
 
 		self.current_channel = 0
 

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/gui/signal_annotator2.py

@@ -1869,15 +1869,15 @@ class SignalAnnotator2(QMainWindow,Styles):
 
 
 		if self.df_targets is not None:
-			self.target_status_scatter = self.ax.scatter(self.target_positions[0][:,0], self.target_positions[0][:,1], marker="x", c=self.target_colors[0][:,1], s=50, picker=True, pickradius=10)
-			self.target_class_scatter = self.ax.scatter(self.target_positions[0][:,0], self.target_positions[0][:,1], marker='o', facecolors='none',edgecolors=self.target_colors[0][:,0], s=200)
+			self.target_status_scatter = self.ax.scatter(self.target_positions[0][:,0], self.target_positions[0][:,1], marker="x", c=self.target_colors[0][:,1], s=50, picker=True, pickradius=10, zorder=10)
+			self.target_class_scatter = self.ax.scatter(self.target_positions[0][:,0], self.target_positions[0][:,1], marker='o', facecolors='none',edgecolors=self.target_colors[0][:,0], s=200, zorder=10)
 		else:
 			self.target_status_scatter = self.ax.scatter([],[], marker="x", s=50, picker=True, pickradius=10)
 			self.target_class_scatter = self.ax.scatter([],[], marker='o', facecolors='none', s=200)
 
 		if self.df_effectors is not None:
-			self.effector_status_scatter = self.ax.scatter(self.effector_positions[0][:,0], self.effector_positions[0][:,1], marker="x", c=self.effector_colors[0][:,1], s=50, picker=True, pickradius=10)
-			self.effector_class_scatter = self.ax.scatter(self.effector_positions[0][:,0], self.effector_positions[0][:,1], marker='^', facecolors='none',edgecolors=self.effector_colors[0][:,0], s=200)
+			self.effector_status_scatter = self.ax.scatter(self.effector_positions[0][:,0], self.effector_positions[0][:,1], marker="x", c=self.effector_colors[0][:,1], s=50, picker=True, pickradius=10, zorder=10)
+			self.effector_class_scatter = self.ax.scatter(self.effector_positions[0][:,0], self.effector_positions[0][:,1], marker='^', facecolors='none',edgecolors=self.effector_colors[0][:,0], s=200, zorder=10)
 		else:
 			self.effector_status_scatter = self.ax.scatter([], [], marker="x", s=50, picker=True, pickradius=10)
 			self.effector_class_scatter = self.ax.scatter([],[], marker='^', facecolors='none', s=200)

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/gui/tableUI.py

@@ -5,7 +5,7 @@ import matplotlib.pyplot as plt
 from matplotlib.cm import viridis
 plt.rcParams['svg.fonttype'] = 'none'
 from celldetective.gui.gui_utils import FigureCanvas, center_window
-from celldetective.utils import differentiate_per_track
+from celldetective.utils import differentiate_per_track, collapse_trajectories_by_status
 import numpy as np
 import seaborn as sns
 import matplotlib.cm as mcm
@@ -335,7 +335,7 @@ class TableUI(QMainWindow, Styles):
 		self.tracks = False
 
 		if self.population=='pairs':
-			self.groupby_cols = ['position','reference_population', 'neighbor_population','REFERENCE_ID', 'NEIGHBOR_ID', 'FRAME']
+			self.groupby_cols = ['position','reference_population', 'neighbor_population','REFERENCE_ID', 'NEIGHBOR_ID']
 			self.tracks = True # for now
 		else:
 			if 'TRACK_ID' in data.columns:
@@ -959,7 +959,7 @@ class TableUI(QMainWindow, Styles):
 					pass
 			
 			if self.population=='pairs':
-				for col in self.groupby_cols[1:]: #['neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID']
+				for col in reversed(self.groupby_cols): #['neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID']
 					if col in group_table:
 						first_column = group_table.pop(col)
 						group_table.insert(0, col, first_column)				
@@ -1005,41 +1005,7 @@ class TableUI(QMainWindow, Styles):
 
 		elif self.per_status_option.isChecked():
 
-			status_of_interest = self.per_status_cb.currentText()
-			self.projection_mode = f'{self.status_operation.currentText()} per {status_of_interest}'
-			self.data = self.data.dropna(subset=status_of_interest,ignore_index=True)
-			unique_statuses = np.unique(self.data[status_of_interest].to_numpy())
-
-			df_sections = []
-			for s in unique_statuses:
-				subtab = self.data.loc[self.data[status_of_interest]==s,:]
-				op = getattr(subtab.groupby(self.groupby_cols), self.status_operation.currentText())
-				subtab_projected = op(subtab.groupby(self.groupby_cols))
-				frame_duration = subtab.groupby(self.groupby_cols).size().to_numpy()
-				for c in self.static_columns:
-					try:
-						subtab_projected[c] = subtab.groupby(self.groupby_cols)[c].apply(lambda x: x.unique()[0])
-					except Exception as e:
-						print(e)
-						pass
-				subtab_projected['duration_in_state'] = frame_duration
-				df_sections.append(subtab_projected)
-
-			group_table = pd.concat(df_sections,axis=0,ignore_index=True)
-
-			if self.population=='pairs':
-				for col in ['duration_in_state',status_of_interest, 'neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID']:
-					first_column = group_table.pop(col) 
-					group_table.insert(0, col, first_column)				
-			else:
-				for col in ['duration_in_state',status_of_interest,'TRACK_ID']:
-					first_column = group_table.pop(col) 
-					group_table.insert(0, col, first_column)
-
-			group_table.pop('FRAME')
-			group_table = group_table.sort_values(by=self.groupby_cols + [status_of_interest],ignore_index=True)
-			group_table = group_table.reset_index(drop=True)
-
+			group_table = collapse_trajectories_by_status(self.data, status=self.per_status_cb.currentText(),population=self.population, projection=self.status_operation.currentText(), groupby_columns=self.groupby_cols)
 
 		self.subtable = TableUI(group_table,f"Group by tracks: {self.projection_mode}", plot_mode="static")
 		self.subtable.show()

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/io.py

@@ -628,7 +628,7 @@ def locate_stack(position, prefix='Aligned'):
 
 	stack_path = glob(position + os.sep.join(['movie', f'{prefix}*.tif']))
 	assert len(stack_path) > 0, f"No movie with prefix {prefix} found..."
-	stack = imread(stack_path[0].replace('\\', '/'), is_mmstack=False)
+	stack = imread(stack_path[0].replace('\\', '/'))
 	if stack.ndim == 4:
 		stack = np.moveaxis(stack, 1, -1)
 	elif stack.ndim == 3:
@@ -1616,7 +1616,7 @@ def correct_annotation(filename):
 	def save_widget():
 		return export_labels()
 
-	img = imread(filename.replace('\\','/'),is_mmstack=False)
+	img = imread(filename.replace('\\','/'))
 	if img.ndim==3:
 		img = np.moveaxis(img, 0, -1)
 	elif img.ndim==2:

celldetective-1.2.1/celldetective/models/segmentation_effectors/ricm-bimodal/config_input.json

@@ -0,0 +1,130 @@
+{
+    "channels": [
+        "adhesion_channel",
+        "brightfield_channel"
+    ],
+    "diameter": 30.0,
+    "cellprob_threshold": 0.0,
+    "flow_threshold": 0.4,
+    "normalization_percentile": [
+        false,
+        true
+    ],
+    "normalization_clip": [
+        true,
+        true
+    ],
+    "normalization_values": [
+        [
+            0.75,
+            1.25
+        ],
+        [
+            1.0,
+            99.0
+        ]
+    ],
+    "model_type": "cellpose",
+    "spatial_calibration": 0.2,
+    "dataset": {
+        "train": [
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_100_0109.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_200_0057.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_200_0058.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_209_0022.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_2015_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0024.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_605_0037.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_102_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_200_0034.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_103_0011.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_701_0004.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_201_0035.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_100_0016.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_202_0020.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_303_0016.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_502_0000.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_201_0000.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0031.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_2012_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_608_0028.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_2012_0027.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_101_0021.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_302_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_104_0036.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_801_0036.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_502_0036.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_808_0173.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_5011_0006.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0019.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_302_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_400_0061.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_106_0117.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_402_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_305_0158.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_308_0191.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0050.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_500_0127.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_300_0009.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_701_0082.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0000.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_303_0019.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0002.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0009.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_701_0055.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_104_0019.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_600_0108.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0021.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_600_0193_roi_491_996_143_708.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_106_0000.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_2014_0038.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_604_0033.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_303_0025.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0038.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_201_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_406_0202.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0028.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_600_0172.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_600_0193.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_3011_0036.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_203_0024.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_209_0020.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_100_0181.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_201_0034.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_704_0010.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_2014_0034.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_303_0021.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0023.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_600_0019.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_808_0016.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_303_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_103_0034.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_101_0038.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_100_0007.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_607_0035.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_200_0006.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_206_0030.tif"
+        ],
+        "validation": [
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_6011_0026.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_100_0035.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_208_0020.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_102_0031.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_200_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_502_0150.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_304_0033.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_1015_0036.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_200_0061.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_5013_0000.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0025.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_801_0177.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_504_0016.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_301_0039.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_504_0037.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_305_0030.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_606_0036.tif",
+            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_300_0087.tif"
+        ]
+    }
+}

celldetective-1.2.1/celldetective/models/segmentation_effectors/ricm-bimodal/training_instructions.json

@@ -0,0 +1,37 @@
+{
+    "model_name": "ricm-bimodal",
+    "model_type": "cellpose",
+    "pretrained": null,
+    "spatial_calibration": 0.2,
+    "channel_option": [
+        "adhesion_channel",
+        "brightfield_channel"
+    ],
+    "normalization_percentile": [
+        false,
+        true
+    ],
+    "normalization_clip": [
+        true,
+        true
+    ],
+    "normalization_values": [
+        [
+            0.75,
+            1.25
+        ],
+        [
+            1.0,
+            99.0
+        ]
+    ],
+    "ds": [
+        "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined"
+    ],
+    "augmentation_factor": 3.0,
+    "validation_split": 0.2,
+    "learning_rate": 0.008,
+    "batch_size": 16,
+    "epochs": 3000,
+    "target_directory": "/home/kheya/Documents/torro-cinam/GitHub/celldetective/celldetective/models/segmentation_effectors"
+}

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/neighborhood.py

@@ -387,6 +387,8 @@ def compute_neighborhood_at_position(pos, distance, population=['targets', 'effe
 
 	df_A, path_A = get_position_table(pos, population=population[0], return_path=True)
 	df_B, path_B = get_position_table(pos, population=population[1], return_path=True)
+	if df_A is None or df_B is None:
+		return None
 
 	if clear_neigh:
 		if os.path.exists(path_A.replace('.csv','.pkl')):

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/signals.py

@@ -155,6 +155,7 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 	f = open(model_config_path)
 	config = json.load(f)
 	required_signals = config["channels"]
+	model_signal_length = config['model_signal_length']
 
 	try:
 		label = config['label']
@@ -190,6 +191,8 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 	trajectories_clean = clean_trajectories(trajectories, interpolate_na=interpolate_na, interpolate_position_gaps=interpolate_na, column_labels=column_labels)
 
 	max_signal_size = int(trajectories_clean[column_labels['time']].max()) + 2
+	assert max_signal_size <= model_signal_length,f'The current signals are longer ({max_signal_size}) than the maximum expected input ({model_signal_length}) for this signal analysis model. Abort...'
+
 	tracks = trajectories_clean[column_labels['track']].unique()
 	signals = np.zeros((len(tracks),max_signal_size, len(selected_signals)))
 

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective/utils.py

@@ -1289,16 +1289,27 @@ def _extract_channel_indices_from_config(config, channels_to_extract):
 	# V2
 	channels = []
 	for c in channels_to_extract:
-		if c!='None' and c is not None:
-			try:
-				c1 = int(ConfigSectionMap(config,"Channels")[c])
-				channels.append(c1)
-			except Exception as e:
-				print(f"Error {e}. The channel required by the model is not available in your data... Check the configuration file.")
-				channels = None
-				break
-		else:
+		try:
+			c1 = int(ConfigSectionMap(config,"Channels")[c])
+			channels.append(c1)
+		except Exception as e:
+			print(f"Warning... The channel {c} required by the model is not available in your data...")
 			channels.append(None)
+	if np.all([c is None for c in channels]):
+		channels = None
+
+	# channels = []
+	# for c in channels_to_extract:
+	# 	if c!='None' and c is not None:
+	# 		try:
+	# 			c1 = int(ConfigSectionMap(config,"Channels")[c])
+	# 			channels.append(c1)
+	# 		except Exception as e:
+	# 			print(f"Error {e}. The channel required by the model is not available in your data... Check the configuration file.")
+	# 			channels = None
+	# 			break
+	# 	else:
+	# 		channels.append(None)
 
 	# LEGACY
 	if channels is None:
@@ -2164,6 +2175,8 @@ def load_image_dataset(datasets, channels, train_spatial_calibration=None, mask_
 	- Spatial calibration adjustment involves rescaling the images and masks to match the `train_spatial_calibration`.
 	- Only images with a corresponding mask and a valid configuration file specifying channel indices and
 	  spatial calibration are loaded.
+	- The image samples must have at least one channel in common with the required channels to be accepted. The missing
+	  channels are passed as black frames.
 
 	Examples
 	--------
@@ -2202,24 +2215,29 @@ def load_image_dataset(datasets, channels, train_spatial_calibration=None, mask_
 					# Load config
 					with open(config_path, 'r') as f:
 						config = json.load(f)
-					try:
+
+					existing_channels = config['channels']
+					intersection = list(set(list(channels)) & set(list(existing_channels)))
+					print(f'{existing_channels=} {intersection=}')
+					if len(intersection)==0:
+						print(e,' channels could not be found in the config... Skipping image.')
+						continue
+					else:
 						ch_idx = []
 						for c in channels:
-							if c!='None':
-								idx = config['channels'].index(c)
+							if c in existing_channels:
+								idx = existing_channels.index(c)
 								ch_idx.append(idx)
 							else:
+								# For None or missing channel pass black frame
 								ch_idx.append(np.nan)
 						im_calib = config['spatial_calibration']
-					except Exception as e:
-						print(e,' channels and/or spatial calibration could not be found in the config... Skipping image.')
-						continue
 				
 				ch_idx = np.array(ch_idx)
 				ch_idx_safe = np.copy(ch_idx)
 				ch_idx_safe[ch_idx_safe!=ch_idx_safe] = 0
 				ch_idx_safe = ch_idx_safe.astype(int)
-				print(ch_idx_safe)
+				
 				image = image[ch_idx_safe]
 				image[np.where(ch_idx!=ch_idx)[0],:,:] = 0
 
@@ -2233,6 +2251,14 @@ def load_image_dataset(datasets, channels, train_spatial_calibration=None, mask_
 					
 			X.append(image)
 			Y.append(mask)
+
+			# fig,ax = plt.subplots(1,image.shape[-1]+1)
+			# for k in range(image.shape[-1]):
+			# 	ax[k].imshow(image[:,:,k],cmap='gray')
+			# ax[image.shape[-1]].imshow(mask)
+			# plt.pause(1)
+			# plt.close()
+
 			files.append(im)
 
 	assert len(X)==len(Y),'The number of images does not match with the number of masks... Abort.'
@@ -2367,4 +2393,46 @@ def interpolate_nan(img, method='nearest'):
 		interp_grid = griddata(points, values, (x_grid, y_grid), method=method)
 		return interp_grid
 	else:
-		return img
+		return img
+
+def collapse_trajectories_by_status(df, status=None, projection='mean', population='effectors', groupby_columns=['position','TRACK_ID']):
+	
+	static_columns = ['well_index', 'well_name', 'pos_name', 'position', 'well', 'status', 't0', 'class','cell_type','concentration', 'antibody', 'pharmaceutical_agent','TRACK_ID','position', 'neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID', 'FRAME']
+
+	if status is None or status not in list(df.columns):
+		print('invalid status selection...')
+		return None
+
+	df = df.dropna(subset=status,ignore_index=True)
+	unique_statuses = np.unique(df[status].to_numpy())
+
+	df_sections = []
+	for s in unique_statuses:
+		subtab = df.loc[df[status]==s,:]
+		op = getattr(subtab.groupby(groupby_columns), projection)
+		subtab_projected = op(subtab.groupby(groupby_columns))
+		frame_duration = subtab.groupby(groupby_columns).size().to_numpy()
+		for c in static_columns:
+			try:
+				subtab_projected[c] = subtab.groupby(groupby_columns)[c].apply(lambda x: x.unique()[0])
+			except Exception as e:
+				print(e)
+				pass
+		subtab_projected['duration_in_state'] = frame_duration
+		df_sections.append(subtab_projected)
+
+	group_table = pd.concat(df_sections,axis=0,ignore_index=True)
+	if population=='pairs':
+		for col in ['duration_in_state',status, 'neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID']:
+			first_column = group_table.pop(col) 
+			group_table.insert(0, col, first_column)				
+	else:
+		for col in ['duration_in_state',status,'TRACK_ID']:
+			first_column = group_table.pop(col) 
+			group_table.insert(0, col, first_column)
+
+	group_table.pop('FRAME')
+	group_table = group_table.sort_values(by=groupby_columns + [status],ignore_index=True)
+	group_table = group_table.reset_index(drop=True)
+
+	return group_table

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.2.0
+Version: 1.2.1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.2.0 → celldetective-1.2.1}/celldetective.egg-info/SOURCES.txt

@@ -65,6 +65,9 @@ celldetective/models/segmentation_effectors/blank
 celldetective/models/segmentation_effectors/primNK_cfse/config_input.json
 celldetective/models/segmentation_effectors/primNK_cfse/cp-cfse-transfer
 celldetective/models/segmentation_effectors/primNK_cfse/training_instructions.json
+celldetective/models/segmentation_effectors/ricm-bimodal/config_input.json
+celldetective/models/segmentation_effectors/ricm-bimodal/ricm-bimodal
+celldetective/models/segmentation_effectors/ricm-bimodal/training_instructions.json
 celldetective/models/segmentation_generic/blank
 celldetective/models/segmentation_targets/blank
 celldetective/models/signal_detection/blank

{celldetective-1.2.0 → celldetective-1.2.1}/setup.py

@@ -18,7 +18,7 @@ except:
     requirements = [str(ir.requirement) for ir in requirements]
 
 setup(name='celldetective',
-			version='1.2.0',
+			version='1.2.1',
 			description='description',
 			long_description=(this_directory / "README.md").read_text(),
 			#long_description=open('README.rst',encoding="utf8").read(),