celldetective 1.3.3.post1__py3-none-any.whl → 1.3.4.post1__py3-none-any.whl

celldetective/gui/styles.py

@@ -23,6 +23,7 @@ class Styles(object):
 
 	def init_button_styles(self):
 
+
 		self.button_style_sheet = '''
 			QPushButton {
 				background-color: #1565c0;
@@ -147,6 +148,18 @@ class Styles(object):
 			}
 		'''
 
+		self.menu_check_style = '''
+			QCheckBox {
+				font-size: 10px;
+				padding-left: 10px;
+				padding-top: 5px;
+			}
+			QCheckBox::indicator:unchecked:hover {
+				background-color : rgba(189, 189, 189, 1);
+				opacity : 0.3;
+			}
+		'''
+
 		self.button_add = '''
 			QPushButton {
 				background-color: transparent;

celldetective/gui/survival_ui.py

@@ -39,8 +39,8 @@ class ConfigSurvival(QWidget, Styles):
 		self.float_validator = QDoubleValidator()
 		self.auto_close = False
 
-		self.well_option = self.parent_window.parent_window.well_list.currentIndex()
-		self.position_option = self.parent_window.parent_window.position_list.currentIndex()
+		self.well_option = self.parent_window.parent_window.well_list.getSelectedIndices()
+		self.position_option = self.parent_window.parent_window.position_list.getSelectedIndices()
 		self.interpret_pos_location()
 		#self.config_path = self.exp_dir + self.config_name
 
@@ -62,15 +62,10 @@ class ConfigSurvival(QWidget, Styles):
 
 		"""
 		
-		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.well_indices = self.parent_window.parent_window.well_list.getSelectedIndices()
+		self.position_indices = self.parent_window.parent_window.position_list.getSelectedIndices()
+		if self.position_indices==[]:
 			self.position_indices = None
-		else:
-			self.position_indices = np.array([self.position_option],dtype=int)
 
 
 	def populate_widget(self):
@@ -243,18 +238,10 @@ class ConfigSurvival(QWidget, Styles):
 
 		"""
 
-		self.well_option = self.parent_window.parent_window.well_list.currentIndex()
-		if self.well_option==len(self.wells):
-			wo = '*'
-		else:
-			wo = self.well_option
-		self.position_option = self.parent_window.parent_window.position_list.currentIndex()
-		if self.position_option==0:
-			po = '*'
-		else:
-			po = self.position_option - 1
+		self.well_option = self.parent_window.parent_window.well_list.getSelectedIndices()
+		self.position_option = self.parent_window.parent_window.position_list.getSelectedIndices()
 
-		self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=wo, position_option=po, population=self.cbs[0].currentText(), return_pos_info=True)
+		self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=self.well_option, position_option=self.position_option, population=self.cbs[0].currentText(), return_pos_info=True)
 		if self.df is None:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)

celldetective/gui/tableUI.py

@@ -1,5 +1,5 @@
 from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QMainWindow, QTableView, QAction, QMenu,QFileDialog, QLineEdit, QHBoxLayout, QWidget, QPushButton, QVBoxLayout, QComboBox, QLabel, QCheckBox, QMessageBox
-from PyQt5.QtCore import Qt, QAbstractTableModel
+from PyQt5.QtCore import Qt
 from PyQt5.QtGui import QBrush, QColor, QDoubleValidator
 import pandas as pd
 import matplotlib.pyplot as plt
@@ -17,7 +17,6 @@ from superqt import QColormapComboBox, QLabeledSlider, QSearchableComboBox
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from math import floor
-import re
 
 from matplotlib import colormaps
 

celldetective/gui/thresholds_gui.py

@@ -1,12 +1,6 @@
-import math
-
-import skimage
 from PyQt5.QtWidgets import QAction, QMenu, QMainWindow, QMessageBox, QLabel, QWidget, QFileDialog, QHBoxLayout, \
 	QGridLayout, QLineEdit, QScrollArea, QVBoxLayout, QComboBox, QPushButton, QApplication, QPushButton, QRadioButton, QButtonGroup
 from PyQt5.QtGui import QDoubleValidator, QIntValidator
-from matplotlib.patches import Circle
-from scipy import ndimage
-from skimage.morphology import disk
 
 from celldetective.filters import std_filter, gauss_filter
 from celldetective.gui.gui_utils import center_window, FigureCanvas, ListWidget, FilterChoice, color_from_class, help_generic

celldetective/gui/viewers.py

@@ -22,11 +22,7 @@ from fonticon_mdi6 import MDI6
 from matplotlib_scalebar.scalebar import ScaleBar
 import gc
 from celldetective.utils import mask_edges
-from scipy.ndimage import shift, grey_dilation
-from skimage.feature import blob_dog
-import math
-from skimage.morphology import disk
-from matplotlib.patches import Circle
+from scipy.ndimage import shift
 
 class StackVisualizer(QWidget, Styles):
 

celldetective/io.py

@@ -69,7 +69,7 @@ def collect_experiment_metadata(pos_path=None, well_path=None):
 	antibodies = get_experiment_antibodies(experiment)
 	pharmaceutical_agents = get_experiment_pharmaceutical_agents(experiment)
 	
-	return {"pos_path": pos_path, "pos_name": pos_name, "well_path": well_path, "well_name": well_name, "well_nbr": well_nbr, "experiment": experiment, "antibody": antibodies[idx], "concentration": concentrations[idx], "cell_type": cell_types[idx], "pharmaceutical_agent": pharmaceutical_agents[idx]}
+	return {"pos_path": pos_path, "position": pos_path, "pos_name": pos_name, "well_path": well_path, "well_name": well_name, "well_nbr": well_nbr, "experiment": experiment, "antibody": antibodies[idx], "concentration": concentrations[idx], "cell_type": cell_types[idx], "pharmaceutical_agent": pharmaceutical_agents[idx]}
 
 
 def get_experiment_wells(experiment):
@@ -691,7 +691,7 @@ def locate_stack(position, prefix='Aligned'):
 
 	return stack
 
-def locate_labels(position, population='target'):
+def locate_labels(position, population='target', frames=None):
 
 	"""
 
@@ -732,7 +732,33 @@ def locate_labels(position, population='target'):
 		label_path = natsorted(glob(position + os.sep.join(["labels_targets", "*.tif"])))
 	elif population.lower() == "effector" or population.lower() == "effectors":
 		label_path = natsorted(glob(position + os.sep.join(["labels_effectors", "*.tif"])))
-	labels = np.array([imread(i.replace('\\', '/')) for i in label_path])
+
+	label_names = [os.path.split(lbl)[-1] for lbl in label_path]
+
+	if frames is None:
+
+		labels = np.array([imread(i.replace('\\', '/')) for i in label_path])
+	
+	elif isinstance(frames, (int,float, np.int_)):
+
+		tzfill = str(int(frames)).zfill(4)
+		idx = label_names.index(f"{tzfill}.tif")
+		if idx==-1:
+			labels = None
+		else:
+			labels = np.array(imread(label_path[idx].replace('\\', '/')))
+
+	elif isinstance(frames, (list,np.ndarray)):
+		labels = []
+		for f in frames:
+			tzfill = str(int(f)).zfill(4)
+			idx = label_names.index(f"{tzfill}.tif")
+			if idx==-1:
+				labels.append(None)
+			else:
+				labels.append(np.array(imread(label_path[idx].replace('\\', '/'))))
+	else:
+		print('Frames argument must be None, int or list...')
 
 	return labels
 
@@ -783,7 +809,8 @@ def fix_missing_labels(position, population='target', prefix='Aligned'):
 		to_create = all_frames
 	to_create = [str(x).zfill(4)+'.tif' for x in to_create]
 	for file in to_create:
-		imwrite(os.sep.join([path, file]), template)
+		save_tiff_imagej_compatible(os.sep.join([path, file]), template.astype(np.int16), axes='YX')
+		#imwrite(os.sep.join([path, file]), template.astype(int))
 
 
 def locate_stack_and_labels(position, prefix='Aligned', population="target"):

celldetective/measure.py

@@ -25,8 +25,6 @@ from celldetective.extra_properties import *
 from inspect import getmembers, isfunction
 from skimage.morphology import disk
 
-import matplotlib.pyplot as plt
-
 abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0], 'celldetective'])
 
 def measure(stack=None, labels=None, trajectories=None, channel_names=None,
@@ -417,9 +415,10 @@ def measure_features(img, label, features=['area', 'intensity_mean'], channels=N
 	if haralick_options is not None:
 		try:
 			df_haralick = compute_haralick_features(img, label, channels=channels, **haralick_options)
-			df_haralick = df_haralick.rename(columns={"cell_id": "label"})
-			df_props = df_props.merge(df_haralick, how='outer', on='label', suffixes=('_delme', ''))
-			df_props = df_props[[c for c in df_props.columns if not c.endswith('_delme')]]
+			if df_haralick is not None:
+				df_haralick = df_haralick.rename(columns={"cell_id": "label"})
+				df_props = df_props.merge(df_haralick, how='outer', on='label', suffixes=('_delme', ''))
+				df_props = df_props[[c for c in df_props.columns if not c.endswith('_delme')]]
 		except Exception as e:
 			print(e)
 			pass
@@ -520,6 +519,10 @@ def compute_haralick_features(img, labels, channels=None, target_channel=0, scal
 	if len(img.shape)==3:
 		img = img[:,:,target_channel]
 
+	# Routine to skip black frames
+	if np.percentile(img.flatten(),99.9)==0.0:
+		return None
+
 	img = interpolate_nan(img)
 
 	# Rescale image and mask

celldetective/neighborhood.py

@@ -7,8 +7,6 @@ from celldetective.utils import contour_of_instance_segmentation, extract_identi
 from scipy.spatial.distance import cdist
 from celldetective.io import locate_labels, get_position_pickle, get_position_table
 
-import matplotlib.pyplot as plt
-
 abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0], 'celldetective'])
 
 

celldetective/scripts/measure_cells.py

@@ -5,7 +5,7 @@ Copright © 2022 Laboratoire Adhesion et Inflammation, Authored by Remy Torro.
 import argparse
 import os
 import json
-from celldetective.io import auto_load_number_of_frames, load_frames
+from celldetective.io import auto_load_number_of_frames, load_frames, fix_missing_labels, locate_labels
 from celldetective.utils import extract_experiment_channels, ConfigSectionMap, _get_img_num_per_channel, extract_experiment_channels
 from celldetective.utils import remove_redundant_features, remove_trajectory_measurements
 from celldetective.measure import drop_tonal_features, measure_features, measure_isotropic_intensity
@@ -16,7 +16,6 @@ import numpy as np
 import pandas as pd
 from natsort import natsorted
 from art import tprint
-from tifffile import imread
 import threading
 import datetime
 
@@ -165,6 +164,8 @@ else:
 	features += ['centroid']
 	do_iso_intensities = False
 
+# if 'centroid' not in features:
+# 	features += ['centroid']
 
 # if (features is not None) and (trajectories is not None):
 # 	features = remove_redundant_features(features, 
@@ -176,6 +177,12 @@ len_movie_auto = auto_load_number_of_frames(file)
 if len_movie_auto is not None:
 	len_movie = len_movie_auto
 
+if label_path is not None and file is not None:
+	test = len(label_path)==len_movie
+	if not test:
+		fix_missing_labels(pos, population=mode, prefix=movie_prefix)
+		label_path = natsorted(glob(os.sep.join([pos, label_folder, '*.tif'])))
+
 img_num_channels = _get_img_num_per_channel(channel_indices, len_movie, nbr_channels)
 
 
@@ -203,6 +210,8 @@ if trajectories is None:
 	if 'label' not in features:
 		features.append('label')
 
+if label_path is not None:
+	label_names = [os.path.split(lbl)[-1] for lbl in label_path]
 
 
 features_log=f'features: {features}'
@@ -228,7 +237,10 @@ def measure_index(indices):
 			img = load_frames(img_num_channels[:,t], file, scale=None, normalize_input=False)
 
 		if label_path is not None:
-			lbl = imread(label_path[t])
+			
+			lbl = locate_labels(pos, population=mode, frames=t)
+			if lbl is None:
+				continue
 
 		if trajectories is not None:
 
@@ -286,16 +298,16 @@ for th in threads:
 
 
 if len(timestep_dataframes)>0:
+	
 	df = pd.concat(timestep_dataframes)	
-	df.reset_index(inplace=True, drop=True)
 
-	if trajectories is None:
+	if trajectories is not None:
+		df = df.sort_values(by=[column_labels['track'],column_labels['time']])
+		df = df.dropna(subset=[column_labels['track']])
+	else:
 		df['ID'] = np.arange(len(df))
 
-	if column_labels['track'] in df.columns:
-		df = df.sort_values(by=[column_labels['track'], column_labels['time']])
-	else:
-		df = df.sort_values(by=column_labels['time'])
+	df = df.reset_index(drop=True)
 
 	df.to_csv(pos+os.sep.join(["output", "tables", table_name]), index=False)
 	print(f'Measurements successfully written in table {pos+os.sep.join(["output", "tables", table_name])}')

celldetective/signals.py

@@ -27,7 +27,7 @@ from natsort import natsorted
 from glob import glob
 import random
 from celldetective.utils import color_from_status, color_from_class
-from math import floor, ceil
+from math import floor
 from scipy.optimize import curve_fit
 import time
 import math
@@ -193,73 +193,74 @@ def analyze_signals(trajectories, model, interpolate_na=True,
 			signals[i,max(frames):,j] = signal[-1]
 
 	model = SignalDetectionModel(pretrained=complete_path)
+	if not model.pretrained is None:
 
-	classes = model.predict_class(signals)
-	times_recast = model.predict_time_of_interest(signals)
+		classes = model.predict_class(signals)
+		times_recast = model.predict_time_of_interest(signals)
 
-	if label is None:
-		class_col = 'class'
-		time_col = 't0'
-		status_col = 'status'
-	else:
-		class_col = 'class_'+label
-		time_col = 't_'+label
-		status_col = 'status_'+label
+		if label is None:
+			class_col = 'class'
+			time_col = 't0'
+			status_col = 'status'
+		else:
+			class_col = 'class_'+label
+			time_col = 't_'+label
+			status_col = 'status_'+label
 
-	for i,(tid,group) in enumerate(trajectories.groupby(column_labels['track'])):
-		indices = group.index
-		trajectories.loc[indices,class_col] = classes[i]
-		trajectories.loc[indices,time_col] = times_recast[i]
-	print('Done.')
+		for i,(tid,group) in enumerate(trajectories.groupby(column_labels['track'])):
+			indices = group.index
+			trajectories.loc[indices,class_col] = classes[i]
+			trajectories.loc[indices,time_col] = times_recast[i]
+		print('Done.')
 
-	for tid, group in trajectories.groupby(column_labels['track']):
-		
-		indices = group.index
-		t0 = group[time_col].to_numpy()[0]
-		cclass = group[class_col].to_numpy()[0]
-		timeline = group[column_labels['time']].to_numpy()
-		status = np.zeros_like(timeline)
-		if t0 > 0:
-			status[timeline>=t0] = 1.
-		if cclass==2:
-			status[:] = 2
-		if cclass>2:
-			status[:] = 42
-		status_color = [color_from_status(s) for s in status]
-		class_color = [color_from_class(cclass) for i in range(len(status))]
-
-		trajectories.loc[indices, status_col] = status
-		trajectories.loc[indices, 'status_color'] = status_color
-		trajectories.loc[indices, 'class_color'] = class_color
-
-	if plot_outcome:
-		fig,ax = plt.subplots(1,len(selected_signals), figsize=(10,5))
-		for i,s in enumerate(selected_signals):
-			for k,(tid,group) in enumerate(trajectories.groupby(column_labels['track'])):
-				cclass = group[class_col].to_numpy()[0]
-				t0 = group[time_col].to_numpy()[0]
-				timeline = group[column_labels['time']].to_numpy()
-				if cclass==0:
-					if len(selected_signals)>1:
-						ax[i].plot(timeline - t0, group[s].to_numpy(),c='tab:blue',alpha=0.1)
-					else:
-						ax.plot(timeline - t0, group[s].to_numpy(),c='tab:blue',alpha=0.1)
-		if len(selected_signals)>1:				
-			for a,s in zip(ax,selected_signals):
-				a.set_title(s)
-				a.set_xlabel(r'time - t$_0$ [frame]')
-				a.spines['top'].set_visible(False)
-				a.spines['right'].set_visible(False)
-		else:
-			ax.set_title(s)
-			ax.set_xlabel(r'time - t$_0$ [frame]')
-			ax.spines['top'].set_visible(False)
-			ax.spines['right'].set_visible(False)			
-		plt.tight_layout()
-		if output_dir is not None:
-			plt.savefig(output_dir+'signal_collapse.png',bbox_inches='tight',dpi=300)
-		plt.pause(3)
-		plt.close()
+		for tid, group in trajectories.groupby(column_labels['track']):
+			
+			indices = group.index
+			t0 = group[time_col].to_numpy()[0]
+			cclass = group[class_col].to_numpy()[0]
+			timeline = group[column_labels['time']].to_numpy()
+			status = np.zeros_like(timeline)
+			if t0 > 0:
+				status[timeline>=t0] = 1.
+			if cclass==2:
+				status[:] = 2
+			if cclass>2:
+				status[:] = 42
+			status_color = [color_from_status(s) for s in status]
+			class_color = [color_from_class(cclass) for i in range(len(status))]
+
+			trajectories.loc[indices, status_col] = status
+			trajectories.loc[indices, 'status_color'] = status_color
+			trajectories.loc[indices, 'class_color'] = class_color
+
+		if plot_outcome:
+			fig,ax = plt.subplots(1,len(selected_signals), figsize=(10,5))
+			for i,s in enumerate(selected_signals):
+				for k,(tid,group) in enumerate(trajectories.groupby(column_labels['track'])):
+					cclass = group[class_col].to_numpy()[0]
+					t0 = group[time_col].to_numpy()[0]
+					timeline = group[column_labels['time']].to_numpy()
+					if cclass==0:
+						if len(selected_signals)>1:
+							ax[i].plot(timeline - t0, group[s].to_numpy(),c='tab:blue',alpha=0.1)
+						else:
+							ax.plot(timeline - t0, group[s].to_numpy(),c='tab:blue',alpha=0.1)
+			if len(selected_signals)>1:				
+				for a,s in zip(ax,selected_signals):
+					a.set_title(s)
+					a.set_xlabel(r'time - t$_0$ [frame]')
+					a.spines['top'].set_visible(False)
+					a.spines['right'].set_visible(False)
+			else:
+				ax.set_title(s)
+				ax.set_xlabel(r'time - t$_0$ [frame]')
+				ax.spines['top'].set_visible(False)
+				ax.spines['right'].set_visible(False)			
+			plt.tight_layout()
+			if output_dir is not None:
+				plt.savefig(output_dir+'signal_collapse.png',bbox_inches='tight',dpi=300)
+			plt.pause(3)
+			plt.close()
 
 	return trajectories
 
@@ -800,8 +801,12 @@ class SignalDetectionModel(object):
 
 
 		if self.pretrained is not None:
-			print(f"Load pretrained models from {path}...")
-			self.load_pretrained_model()
+			print(f"Load pretrained models from {pretrained}...")
+			test = self.load_pretrained_model()
+			if test is None:
+				self.pretrained = None
+				print('Pretrained model could not be loaded. Check the log for error. Abort...')
+				return None
 		else:
 			print("Create models from scratch...")
 			self.create_models_from_scratch()
@@ -828,6 +833,9 @@ class SignalDetectionModel(object):
 		- The configuration file is expected to be named "config_input.json" and located in the same directory as the models.
 		"""
 
+		if self.pretrained.endswith(os.sep):
+			self.pretrained = os.sep.join(self.pretrained.split(os.sep)[:-1])
+
 		try:
 			self.model_class = load_model(os.sep.join([self.pretrained,"classifier.h5"]),compile=False)
 			self.model_class.load_weights(os.sep.join([self.pretrained,"classifier.h5"]))
@@ -843,6 +851,9 @@ class SignalDetectionModel(object):
 			print(f"Error {e}...")
 			self.model_reg = None
 
+		if self.model_class is None and self.model_reg is None:
+			return None
+
 		# load config
 		with open(os.sep.join([self.pretrained,"config_input.json"])) as config_file:
 			model_config = json.load(config_file)
@@ -867,6 +878,7 @@ class SignalDetectionModel(object):
 
 		assert self.model_class.layers[0].input_shape[0] == self.model_reg.layers[0].input_shape[0], f"mismatch between input shape of classification: {self.model_class.layers[0].input_shape[0]} and regression {self.model_reg.layers[0].input_shape[0]} models... Error."
 
+		return True
 
 	def create_models_from_scratch(self):
 

celldetective/tracking.py

@@ -959,22 +959,28 @@ def write_first_detection_class(tab, column_labels={'track': "TRACK_ID", 'time':
 		indices = track_group.index
 		detection = track_group[column_labels['x']].values
 		timeline = track_group[column_labels['time']].values
-		if len(timeline)>2:
-			dt = timeline[1] - timeline[0]
-			if np.any(detection==detection):
-				t_first = timeline[detection==detection][0]
-				cclass = 0
-				if t_first<=0:
-					t_first = -1
-					cclass = 2
-				else:
-					t_first =  float(t_first) - float(dt)
-			else:
+		dt = 1
+		
+		# Initialize
+		cclass = 2; t_first = np.nan;
+
+		if np.any(detection==detection):
+			t_first = timeline[detection==detection][0]
+			cclass = 0
+			if t_first<=0:
 				t_first = -1
 				cclass = 2
+			else:
+				t_first =  float(t_first) - float(dt)
+				if t_first==0:
+					t_first += 0.01
+		else:
+			t_first = -1
+			cclass = 2
+
+		tab.loc[indices, 'class_firstdetection'] = cclass
+		tab.loc[indices, 't_firstdetection'] = t_first
 
-			tab.loc[indices, 'class_firstdetection'] = cclass
-			tab.loc[indices, 't_firstdetection'] = t_first
 	return tab
 
 

{celldetective-1.3.3.post1.dist-info → celldetective-1.3.4.post1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.3.post1
+Version: 1.3.4.post1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -41,6 +41,7 @@ Requires-Dist: pytest
 Requires-Dist: pytest-qt
 Requires-Dist: h5py
 Requires-Dist: cliffs_delta
+Requires-Dist: requests
 
 # Celldetective