celldetective 1.2.1__tar.gz → 1.2.2.post1__tar.gz

{celldetective-1.2.1 → celldetective-1.2.2.post1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.2.1
+Version: 1.2.2.post1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -12,14 +12,14 @@ Requires-Dist: wheel
 Requires-Dist: nbsphinx
 Requires-Dist: nbsphinx_link
 Requires-Dist: sphinx_rtd_theme
-Requires-Dist: sphinx==5.0.2
-Requires-Dist: jinja2<3.1
+Requires-Dist: sphinx
+Requires-Dist: jinja2
 Requires-Dist: ipykernel
 Requires-Dist: stardist
 Requires-Dist: cellpose<3
 Requires-Dist: scikit-learn
 Requires-Dist: btrack
-Requires-Dist: tensorflow<=2.12.1
+Requires-Dist: tensorflow~=2.15.0
 Requires-Dist: napari
 Requires-Dist: tqdm
 Requires-Dist: mahotas
@@ -32,10 +32,11 @@ Requires-Dist: seaborn
 Requires-Dist: opencv-python-headless==4.7.0.72
 Requires-Dist: liblapack
 Requires-Dist: gputools
-Requires-Dist: lmfit~=1.2.2
-Requires-Dist: superqt[cmap]>=0.6.1
+Requires-Dist: lmfit
+Requires-Dist: superqt[cmap]
 Requires-Dist: setuptools
 Requires-Dist: matplotlib_scalebar
+Requires-Dist: numpy==1.26.4
 
 # Celldetective
 
@@ -166,23 +167,25 @@ steps.
 
 To use the software, you must install python, *e.g.* through
 [Anaconda](https://www.anaconda.com/download). We developed and tested
-the software in Python 3.9.18.
+the software in Python 3.9 and more recently 3.11.
 
 # Installation
 
 ## Stable release
 
-Celldetective can be installed with `pip`:
+Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
+
+With the proper Python version, Celldetective can be directly installed with `pip`:
 
 ``` bash
 pip install celldetective
 ```
 
-We recommend that you create an environment to use Celldetective, *e.g.*
+We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
 with `conda`:
 
 ``` bash
-conda create -n celldetective python=3.9.18 pyqt
+conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
 pip install celldetective
 ```
@@ -208,6 +211,10 @@ will be immediately available in the python environment:
 git clone git://github.com/remyeltorro/celldetective.git
 cd celldetective
 
+# optional: create an environment
+conda create -n celldetective python=3.11 pyqt
+conda activate celldetective
+
 # install the celldetective package in editable/development mode
 pip install -r requirements.txt
 pip install -e .
@@ -230,10 +237,10 @@ with package requirements for other projects. Run the following lines to
 create an environment named \"celldetective\":
 
 ``` bash
-conda create -n celldetective python=3.9.18 pyqt
+conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
 pip install -r requirements.txt
-pip install .
+pip install -e .
 ```
 
 The installation of the dependencies will take a few minutes (up to half

{celldetective-1.2.1 → celldetective-1.2.2.post1}/README.md

@@ -127,23 +127,25 @@ steps.
 
 To use the software, you must install python, *e.g.* through
 [Anaconda](https://www.anaconda.com/download). We developed and tested
-the software in Python 3.9.18.
+the software in Python 3.9 and more recently 3.11.
 
 # Installation
 
 ## Stable release
 
-Celldetective can be installed with `pip`:
+Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
+
+With the proper Python version, Celldetective can be directly installed with `pip`:
 
 ``` bash
 pip install celldetective
 ```
 
-We recommend that you create an environment to use Celldetective, *e.g.*
+We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
 with `conda`:
 
 ``` bash
-conda create -n celldetective python=3.9.18 pyqt
+conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
 pip install celldetective
 ```
@@ -169,6 +171,10 @@ will be immediately available in the python environment:
 git clone git://github.com/remyeltorro/celldetective.git
 cd celldetective
 
+# optional: create an environment
+conda create -n celldetective python=3.11 pyqt
+conda activate celldetective
+
 # install the celldetective package in editable/development mode
 pip install -r requirements.txt
 pip install -e .
@@ -191,10 +197,10 @@ with package requirements for other projects. Run the following lines to
 create an environment named \"celldetective\":
 
 ``` bash
-conda create -n celldetective python=3.9.18 pyqt
+conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
 pip install -r requirements.txt
-pip install .
+pip install -e .
 ```
 
 The installation of the dependencies will take a few minutes (up to half

{celldetective-1.2.1 → celldetective-1.2.2.post1}/celldetective/__main__.py

@@ -27,10 +27,10 @@ class AppInitWindow(QMainWindow):
 
 		try:
 			subprocess.check_output('nvidia-smi')
-			print('Nvidia GPU detected')
+			print('NVIDIA GPU detected (activate or disable in Memory & Threads)...')
 			self.use_gpu = True
 		except Exception: # this command not being found can raise quite a few different errors depending on the configuration
-			print('No Nvidia GPU in system!')
+			print('No NVIDIA GPU detected...')
 			self.use_gpu = False
 			
 		self.soft_path = get_software_location()
@@ -170,13 +170,16 @@ class AppInitWindow(QMainWindow):
 
 		self.recentFileActs = []
 		self.threads_config_path = os.sep.join([self.soft_path,'celldetective','threads.json'])
+		print('Reading previous Memory & Threads settings...')
 		if os.path.exists(self.threads_config_path):
 			with open(self.threads_config_path, 'r') as f:
 				self.threads_config = json.load(f)
 			if 'use_gpu' in self.threads_config:
 				self.use_gpu = bool(self.threads_config['use_gpu'])
+				print(f'Use GPU: {self.use_gpu}...')
 			if 'n_threads' in self.threads_config:
 				self.n_threads = int(self.threads_config['n_threads'])
+				print(f'Number of threads: {self.n_threads}...')
 
 
 	def reload_previous_experiments(self):
@@ -250,9 +253,9 @@ class AppInitWindow(QMainWindow):
 			self.open_directory()
 
 	def load_recent_exp(self, path):
-		print('loading?')
-		print('you selected path ', path)
+		
 		self.experiment_path_selection.setText(path)
+		print(f'Attempt to load experiment folder: {path}...')
 		self.open_directory()
 
 	def open_about_window(self):
@@ -351,7 +354,7 @@ class AppInitWindow(QMainWindow):
 				print(f"Found {self.number_of_wells} wells...")
 			number_pos = []
 			for w in wells:
-				position_folders = glob(os.sep.join([w,f"{w.split(os.sep)[-2][1]}*", os.sep]))
+				position_folders = glob(os.sep.join([w,f"{w.split(os.sep)[-1][1]}*", os.sep]))
 				number_pos.append(len(position_folders))
 			print(f"Number of positions per well: {number_pos}")
 			
@@ -393,6 +396,7 @@ if __name__ == "__main__":
 	# myappid = 'mycompany.myproduct.subproduct.version' # arbitrary string
 	# ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
 	splash=True
+	print('Loading the libraries...')
 
 	App = QApplication(sys.argv)
 	#App.setWindowIcon(QIcon(os.sep.join([get_software_location(),'celldetective','icons','mexican-hat.png'])))
@@ -425,7 +429,10 @@ if __name__ == "__main__":
 	import psutil
 	import subprocess
 	import json
+	# import matplotlib
+	# matplotlib.rcParams.update({'font.size': 8})
 
+	print('Libraries successfully loaded...')
 
 	window = AppInitWindow(App)
 

{celldetective-1.2.1 → celldetective-1.2.2.post1}/celldetective/events.py

@@ -1,5 +1,5 @@
 import numpy as np
-
+from lifelines import KaplanMeierFitter
 
 def switch_to_events(classes, event_times, max_times, origin_times=None, left_censored=True, FrameToMin=None):
 	
@@ -104,4 +104,30 @@ def switch_to_events(classes, event_times, max_times, origin_times=None, left_ce
 	if FrameToMin is not None:
 		#print('convert to minutes!', FrameToMin)
 		survival_times = [s*FrameToMin for s in survival_times]
-	return events, survival_times
+	return events, survival_times
+
+def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMin=1):
+
+	cols = list(df.columns)
+	assert class_of_interest in cols,"The requested class cannot be found in the dataframe..."
+	assert t_event in cols,"The event time cannot be found in the dataframe..."
+	left_censored = False
+
+	classes = df.groupby(['position','TRACK_ID'])[class_of_interest].min().values
+	event_times = df.groupby(['position','TRACK_ID'])[t_event].min().values
+	max_times = df.groupby(['position','TRACK_ID'])['FRAME'].max().values
+
+	if t_reference is not None:
+		left_censored = True
+		assert t_reference in cols,"The reference time cannot be found in the dataframe..."
+		first_detections = df.groupby(['position','TRACK_ID'])[t_reference].max().values
+	
+	events, survival_times = switch_to_events(classes, event_times, max_times, origin_times=first_detections, left_censored=left_censored, FrameToMin=FrameToMin)
+	ks = KaplanMeierFitter()
+	if len(events)>0:
+		ks.fit(survival_times, event_observed=events)
+	else:
+		ks = None
+
+	return ks
+

{celldetective-1.2.1 → celldetective-1.2.2.post1}/celldetective/gui/about.py

@@ -2,7 +2,6 @@ from PyQt5.QtWidgets import QWidget, QVBoxLayout, QLabel
 from PyQt5.QtGui import QPixmap
 from PyQt5.QtCore import Qt
 from celldetective.utils import get_software_location
-import celldetective
 import os
 from celldetective.gui.gui_utils import center_window
 

{celldetective-1.2.1 → celldetective-1.2.2.post1}/celldetective/gui/analyze_block.py

@@ -1,25 +1,10 @@
-from PyQt5.QtWidgets import QFrame, QGridLayout, QComboBox, QLabel, QPushButton, QVBoxLayout, QHBoxLayout, QCheckBox, \
-    QMessageBox, QSpacerItem, QSizePolicy
+from PyQt5.QtWidgets import QFrame, QLabel, QPushButton, QVBoxLayout, \
+    QSpacerItem, QSizePolicy
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QIcon
-
-from superqt.fonticon import icon
-from fonticon_mdi6 import MDI6
-import gc
-
 from celldetective.gui.plot_measurements import ConfigMeasurementsPlot
-from celldetective.io import get_segmentation_models_list, control_segmentation_napari, get_signal_models_list, control_tracking_btrack
 from celldetective.gui import ConfigSurvival, ConfigSignalPlot
-from celldetective.gui.gui_utils import QHSeperationLine
-from celldetective.segmentation import segment_at_position, segment_from_threshold_at_position
-from celldetective.tracking import track_at_position
-from celldetective.measure import measure_at_position
-from celldetective.signals import analyze_signals_at_position
-import numpy as np
-from glob import glob
-from natsort import natsorted
 import os
-import pandas as pd
 from celldetective.gui import Styles
 
 class AnalysisPanel(QFrame, Styles):
@@ -94,7 +79,7 @@ class AnalysisPanel(QFrame, Styles):
 		self.configSurvival.show()
 
 	def configure_plot_signals(self):
-		print('plot signal analysis starting!!!')
+		print('Configure a signal collapse representation...')
 		self.ConfigSignalPlot = ConfigSignalPlot(self)
 		self.ConfigSignalPlot.show()
 

{celldetective-1.2.1 → celldetective-1.2.2.post1}/celldetective/gui/btrack_options.py

@@ -1,7 +1,7 @@
 from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas
-from superqt import QLabeledDoubleRangeSlider, QLabeledDoubleSlider,QLabeledSlider
+from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, help_generic
+from superqt import QLabeledDoubleSlider,QLabeledSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from celldetective.utils import extract_experiment_channels, get_software_location
@@ -47,8 +47,9 @@ class ConfigTracking(QMainWindow, Styles):
 
 		center_window(self)
 		self.setMinimumWidth(540)
-		self.setMinimumHeight(int(0.3*self.screen_height))
-		self.setMaximumHeight(int(0.8*self.screen_height))
+		self.minimum_height = 300
+		# self.setMinimumHeight(int(0.3*self.screen_height))
+		# self.setMaximumHeight(int(0.8*self.screen_height))
 		self.populate_widget()
 		self.load_previous_tracking_instructions()
 
@@ -116,7 +117,6 @@ class ConfigTracking(QMainWindow, Styles):
 		self.select_post_proc_btn = QPushButton()
 		self.select_post_proc_btn.clicked.connect(self.activate_post_proc_options)
 		self.select_post_proc_btn.setStyleSheet(self.button_select_all)
-		grid.addWidget(self.select_post_proc_btn, 0,0,1,4,alignment=Qt.AlignLeft)
 
 		self.post_proc_lbl = QLabel("POST-PROCESSING")
 		self.post_proc_lbl.setStyleSheet("""
@@ -125,19 +125,100 @@ class ConfigTracking(QMainWindow, Styles):
 			""")
 		grid.addWidget(self.post_proc_lbl, 0, 0, 1, 4, alignment=Qt.AlignCenter)
 
+		title_hbox = QHBoxLayout()
+
 		self.collapse_post_proc_btn = QPushButton()
 		self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 		self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
 		self.collapse_post_proc_btn.setStyleSheet(self.button_select_all)
-		grid.addWidget(self.collapse_post_proc_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+		#grid.addWidget(self.collapse_post_proc_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+
+		self.help_post_btn = QPushButton()
+		self.help_post_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_post_btn.setIconSize(QSize(20, 20))
+		self.help_post_btn.clicked.connect(self.help_post)
+		self.help_post_btn.setStyleSheet(self.button_select_all)
+		self.help_post_btn.setToolTip("Help.")
+
+		title_hbox.addWidget(self.select_post_proc_btn, 5)
+		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
+		title_hbox.addWidget(self.help_post_btn, 5)
+		title_hbox.addWidget(self.collapse_post_proc_btn, 5)
+		grid.addLayout(title_hbox, 0,0,1,4)
 
 		self.generate_post_proc_panel_contents()
 		grid.addWidget(self.ContentsPostProc, 1, 0, 1, 4, alignment=Qt.AlignTop)
 		self.collapse_post_proc_btn.clicked.connect(lambda: self.ContentsPostProc.setHidden(not self.ContentsPostProc.isHidden()))
-		# self.collapse_post_proc_btn.clicked.connect(self.collapse_features_advanced)
+		self.collapse_post_proc_btn.clicked.connect(self.collapse_post_advanced)
 		self.ContentsPostProc.hide()
 		self.uncheck_post_proc()
 
+	def collapse_post_advanced(self):
+
+		features_open = not self.ContentsFeatures.isHidden()
+		config_open = not self.ContentsConfig.isHidden()
+		post_open = not self.ContentsPostProc.isHidden()
+		is_open = np.array([features_open, config_open, post_open])
+
+		if self.ContentsPostProc.isHidden():
+			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
+			if len(is_open[is_open])==0:
+				self.scroll_area.setMinimumHeight(int(self.minimum_height))
+				self.adjustSize()
+		else:
+			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_up,color="black"))
+			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
+			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
+
+
+	def help_post(self):
+		
+		"""
+		Helper for track post-processing strategy.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','track-postprocessing.json'])
+
+		with open(dict_path) as f:
+			d = json.load(f)
+
+		suggestion = help_generic(d)
+		if isinstance(suggestion, str):
+			print(f"{suggestion=}")
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Information)
+			msgBox.setTextFormat(Qt.RichText)
+			msgBox.setText(rf"{suggestion}")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None		
+
+	def help_feature(self):
+		
+		"""
+		Helper for track post-processing strategy.
+		"""
+
+		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','feature-btrack.json'])
+
+		with open(dict_path) as f:
+			d = json.load(f)
+
+		suggestion = help_generic(d)
+		if isinstance(suggestion, str):
+			print(f"{suggestion=}")
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Information)
+			msgBox.setTextFormat(Qt.RichText)
+			msgBox.setText(rf"{suggestion}")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
 
 	def populate_features_frame(self):
 
@@ -146,12 +227,11 @@ class ConfigTracking(QMainWindow, Styles):
 		"""
 
 		grid = QGridLayout(self.features_frame)
-
+		title_hbox = QHBoxLayout()
+		
 		self.select_features_btn = QPushButton()
 		self.select_features_btn.clicked.connect(self.activate_feature_options)
 		self.select_features_btn.setStyleSheet(self.button_select_all)
-		grid.addWidget(self.select_features_btn, 0,0,1,4,alignment=Qt.AlignLeft)
-
 
 		self.feature_lbl = QLabel("FEATURES")
 		self.feature_lbl.setStyleSheet("""
@@ -164,7 +244,19 @@ class ConfigTracking(QMainWindow, Styles):
 		self.collapse_features_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 		self.collapse_features_btn.setIconSize(QSize(20, 20))
 		self.collapse_features_btn.setStyleSheet(self.button_select_all)
-		grid.addWidget(self.collapse_features_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+
+		self.help_feature_btn = QPushButton()
+		self.help_feature_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_feature_btn.setIconSize(QSize(20, 20))
+		self.help_feature_btn.clicked.connect(self.help_feature)
+		self.help_feature_btn.setStyleSheet(self.button_select_all)
+		self.help_feature_btn.setToolTip("Help.")
+
+		title_hbox.addWidget(self.select_features_btn, 5)
+		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
+		title_hbox.addWidget(self.help_feature_btn, 5)
+		title_hbox.addWidget(self.collapse_features_btn, 5)
+		grid.addLayout(title_hbox, 0,0,1,4)		
 
 		self.generate_feature_panel_contents()
 		grid.addWidget(self.ContentsFeatures, 1, 0, 1, 4, alignment=Qt.AlignTop)
@@ -179,16 +271,22 @@ class ConfigTracking(QMainWindow, Styles):
 		Switch the chevron icon and adjust the size for the FEATURES frame.
 		"""
 
+		features_open = not self.ContentsFeatures.isHidden()
+		config_open = not self.ContentsConfig.isHidden()
+		post_open = not self.ContentsPostProc.isHidden()
+		is_open = np.array([features_open, config_open, post_open])
+
 		if self.ContentsFeatures.isHidden():
 			self.collapse_features_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_features_btn.setIconSize(QSize(20, 20))
-			self.button_widget.adjustSize()
-			self.adjustSize()
+			if len(is_open[is_open])==0:
+				self.scroll_area.setMinimumHeight(int(self.minimum_height))
+				self.adjustSize()
 		else:
 			self.collapse_features_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_features_btn.setIconSize(QSize(20, 20))
-			self.button_widget.adjustSize()
-			self.adjustSize()	
+			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
+
 
 	def generate_post_proc_panel_contents(self):
 
@@ -273,7 +371,7 @@ class ConfigTracking(QMainWindow, Styles):
 		self.add_feature_btn.setToolTip("Add feature")
 		self.add_feature_btn.setIconSize(QSize(20, 20))		
 
-		self.features_list = ListWidget(self, FeatureChoice, initial_features=['area','intensity_mean',])
+		self.features_list = ListWidget(FeatureChoice, initial_features=['area','intensity_mean',])
 
 		self.del_feature_btn.clicked.connect(self.features_list.removeSel)
 		self.add_feature_btn.clicked.connect(self.features_list.addItem)
@@ -447,16 +545,22 @@ class ConfigTracking(QMainWindow, Styles):
 		Switch the chevron icon and adjust the size for the CONFIG frame.
 		"""
 
+		features_open = not self.ContentsFeatures.isHidden()
+		config_open = not self.ContentsConfig.isHidden()
+		post_open = not self.ContentsPostProc.isHidden()
+		is_open = np.array([features_open, config_open, post_open])
+
 		if self.ContentsConfig.isHidden():
 			self.collapse_config_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_config_btn.setIconSize(QSize(20, 20))
-			self.button_widget.adjustSize()
-			self.adjustSize()
+			if len(is_open[is_open])==0:
+				self.scroll_area.setMinimumHeight(int(self.minimum_height))
+				self.adjustSize()
 		else:
 			self.collapse_config_btn.setIcon(icon(MDI6.chevron_up,color="black"))
 			self.collapse_config_btn.setIconSize(QSize(20, 20))
-			self.button_widget.adjustSize()
-			self.adjustSize()	
+			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
+
 
 	def generate_config_panel_contents(self):
 		
@@ -884,7 +988,8 @@ class ConfigTracking(QMainWindow, Styles):
 			self.fig, self.ax = plt.subplots(1,1,figsize=(4,3))
 			self.hist_window = FigureCanvas(self.fig, title="Haralick: control digitized histogram")
 			self.ax.clear()
-			self.ax.hist(norm_img.flatten(), bins=self.haralick_options['n_intensity_bins'])
+			flat = norm_img.flatten()
+			self.ax.hist(flat[flat==flat], bins=self.haralick_options['n_intensity_bins'])
 			self.ax.set_xlabel('gray level value')
 			self.ax.set_ylabel('#')
 			plt.tight_layout()