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

celldetective/__main__.py

@@ -5,6 +5,7 @@ from PyQt5.QtGui import QPixmap
 from os import sep
 from celldetective.utils import get_software_location
 from time import time, sleep
+
 #os.environ['QT_DEBUG_PLUGINS'] = '1'
 
 if __name__ == "__main__":
@@ -15,9 +16,11 @@ if __name__ == "__main__":
 	App = QApplication(sys.argv)
 	App.setStyle("Fusion")
 
+	software_location = get_software_location()
+
 	if splash:
 		start = time()
-		splash_pix = QPixmap(sep.join([get_software_location(),'celldetective','icons','splash.png']))
+		splash_pix = QPixmap(sep.join([software_location,'celldetective','icons','splash.png']))
 		splash = QSplashScreen(splash_pix)
 		splash.setMask(splash_pix.mask())
 		splash.show()
@@ -26,13 +29,36 @@ if __name__ == "__main__":
 			sleep(0.001)
 			App.processEvents()
 
-	from PyQt5.QtWidgets import QFileDialog, QWidget, QVBoxLayout, QCheckBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QMessageBox, QMenu, QAction
-	from PyQt5.QtGui import QIcon, QDesktopServices, QIntValidator
+	try:
+		
+		import requests
+		import re
+		from celldetective import __version__
+
+		package = 'celldetective'
+		response = requests.get(f'https://pypi.org/pypi/{package}/json')
+		latest_version = response.json()['info']['version']
+
+		latest_version_num = re.sub('[^0-9]','', latest_version)
+		current_version_num = re.sub('[^0-9]','',__version__)
+
+		if len(latest_version_num)!=len(current_version_num):
+			max_length = max([len(latest_version_num),len(current_version_num)])
+			latest_version_num = int(latest_version_num.zfill(max_length - len(latest_version_num)))
+			current_version_num = int(current_version_num.zfill(max_length - len(current_version_num)))
+
+		if latest_version_num > current_version_num:
+			print('Update is available...\nPlease update using `pip install --upgrade celldetective`...')
+	
+	except Exception as e:
+
+		print(f"{e=}")
+
 	from celldetective.gui.InitWindow import AppInitWindow
 
 	print('Libraries successfully loaded...')
 
-	window = AppInitWindow(App)
+	window = AppInitWindow(App, software_location=software_location)
 
 	if splash:
 		splash.finish(window)

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.3.3.post1"
+__version__ = "1.3.4.post1"

celldetective/extra_properties.py

@@ -29,6 +29,27 @@ from celldetective.utils import interpolate_nan, contour_of_instance_segmentatio
 
 # Percentiles
 
+def custom_area(regionmask):
+	return np.sum(regionmask)
+
+def intensity_area_under_one(regionmask, intensity_image):
+	
+	subregion = regionmask[intensity_image<1]
+	if len(subregion)>0:
+		return np.sum(subregion)
+	else:
+		return 0.0
+
+def intensity_fraction_of_area_under_one(regionmask, intensity_image):
+
+	subregion = regionmask[intensity_image<1]
+	area = np.sum(regionmask)
+
+	if len(subregion) > 0:
+		return float(np.sum(subregion)) / float(area)
+	else:
+		return 0.0
+
 def intensity_percentile_ninety_nine(regionmask, intensity_image):
 	return np.nanpercentile(intensity_image[regionmask],99)
 

celldetective/filters.py

@@ -4,15 +4,19 @@ import scipy.ndimage as snd
 import numpy as np
 
 def gauss_filter(img, sigma, interpolate=True, *kwargs):
+
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
+
 	return snd.gaussian_filter(img.astype(float), sigma, *kwargs)
 
 def median_filter(img, size, interpolate=True, *kwargs):
+
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
 
 	size = int(size)
+	
 	return snd.median_filter(img, size, *kwargs)
 
 def maximum_filter(img, size, interpolate=True, *kwargs):
@@ -65,13 +69,17 @@ def std_filter(img, size, interpolate=True):
 
 	if interpolate:
 		img = interpolate_nan(img.astype(float))
+	
 	size = int(size)
 	img = img.astype(float)
+	
 	win_mean = snd.uniform_filter(img, (size,size), mode='wrap')
 	win_sqr_mean = snd.uniform_filter(img**2, (size, size), mode='wrap')
-	win_sqr_mean[win_sqr_mean!=win_sqr_mean] = 0.
 	win_sqr_mean[win_sqr_mean<=0.] = 0. # add this to prevent sqrt from breaking
-	img = np.sqrt(win_sqr_mean - win_mean**2)
+	
+	sub = np.subtract(win_sqr_mean,win_mean**2)
+	sub[sub<=0.] = 0.
+	img = np.sqrt(sub)
 
 	return img
 
@@ -96,16 +104,21 @@ def local_filter(img, *kwargs):
 	return binary.astype(float)
 
 def niblack_filter(img, *kwargs):
+
 	thresh = threshold_niblack(img, *kwargs)
 	binary = img >= thresh
 	return binary.astype(float)
 
 def sauvola_filter(img, *kwargs):
+
 	thresh = threshold_sauvola(img, *kwargs)
 	binary = img >= thresh
 	return binary.astype(float)
 
 def log_filter(img, sigma, *kwargs):
+
+	if interpolate:
+		img = interpolate_nan(img.astype(float))
 	return snd.gaussian_laplace(img.astype(float), sigma, *kwargs)
 
 def tophat_filter(img, size, connectivity=4, interpolate=True, *kwargs):

celldetective/gui/InitWindow.py

@@ -1,48 +1,49 @@
-from PyQt5.QtWidgets import QApplication, QMainWindow
-from celldetective.utils import get_software_location, download_zenodo_file
 import os
+
+from PyQt5.QtWidgets import QApplication, QMainWindow
 from PyQt5.QtWidgets import QFileDialog, QWidget, QVBoxLayout, QCheckBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QMessageBox, QMenu, QAction
 from PyQt5.QtCore import Qt, QUrl
 from PyQt5.QtGui import QIcon, QDesktopServices, QIntValidator
+
 from glob import glob
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
-import gc
-from celldetective.gui import Styles, ControlPanel, ConfigNewExperiment
-from celldetective.gui.gui_utils import center_window
-import subprocess
-import os
+
 from celldetective.gui.about import AboutWidget
 from celldetective.io import correct_annotation
-import psutil
-import subprocess
+from celldetective.utils import download_zenodo_file
+from celldetective.gui.gui_utils import center_window
+from celldetective.gui import Styles, ControlPanel, ConfigNewExperiment
+
+import gc
+from subprocess import check_output, Popen
+from psutil import cpu_count
 import json
 
-class AppInitWindow(QMainWindow):
+class AppInitWindow(QMainWindow, Styles):
 
 	"""
 	Initial window to set the experiment folder or create a new one.
 	"""
 
-	def __init__(self, parent_window=None):
+	def __init__(self, parent_window=None, software_location=None):
+
 		super().__init__()
 
 		self.parent_window = parent_window
-		self.Styles = Styles()
-		self.init_styles()
 		self.setWindowTitle("celldetective")
 
-		self.n_threads = min([1,psutil.cpu_count()])
+		self.n_threads = min([1,cpu_count()])
 
 		try:
-			subprocess.check_output('nvidia-smi')
+			check_output('nvidia-smi')
 			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 detected...')
 			self.use_gpu = False
-			
-		self.soft_path = get_software_location()
+		
+		self.soft_path = software_location
 		self.onlyInt = QIntValidator()
 		self.setWindowIcon(QIcon(os.sep.join([self.soft_path,'celldetective','icons','logo.png'])))
 		center_window(self)
@@ -65,6 +66,7 @@ class AppInitWindow(QMainWindow):
 		self.show()
 	
 	def closeEvent(self, event):
+
 		QApplication.closeAllWindows()
 		event.accept()
 		gc.collect()
@@ -188,6 +190,9 @@ class AppInitWindow(QMainWindow):
 	def download_spreading_assay_demo(self):
 		
 		self.target_dir = str(QFileDialog.getExistingDirectory(self, 'Select Folder for Download'))
+		if self.target_dir=='':
+			return None
+		
 		if not os.path.exists(os.sep.join([self.target_dir,'demo_ricm'])):
 			download_zenodo_file('demo_ricm', self.target_dir)
 		self.experiment_path_selection.setText(os.sep.join([self.target_dir, 'demo_ricm']))
@@ -196,6 +201,9 @@ class AppInitWindow(QMainWindow):
 	def download_cytotoxicity_assay_demo(self):
 		
 		self.target_dir = str(QFileDialog.getExistingDirectory(self, 'Select Folder for Download'))
+		if self.target_dir=='':
+			return None
+
 		if not os.path.exists(os.sep.join([self.target_dir,'demo_adcc'])):
 			download_zenodo_file('demo_adcc', self.target_dir)
 		self.experiment_path_selection.setText(os.sep.join([self.target_dir, 'demo_adcc']))
@@ -302,9 +310,10 @@ class AppInitWindow(QMainWindow):
 		QDesktopServices.openUrl(doc_url)
 
 	def open_models_folder(self):
+		
 		path = os.sep.join([self.soft_path,'celldetective','models',os.sep])
 		try:
-			subprocess.Popen(f'explorer {os.path.realpath(path)}')
+			Popen(f'explorer {os.path.realpath(path)}')
 		except:
 
 			try:
@@ -312,9 +321,6 @@ class AppInitWindow(QMainWindow):
 			except:
 				return None
 
-
-		#os.system(f'start {os.path.realpath(path)}')
-
 	def create_buttons_hbox(self):
 
 		self.buttons_layout = QHBoxLayout()
@@ -344,18 +350,6 @@ class AppInitWindow(QMainWindow):
 		else:
 			self.validate_button.setEnabled(False)
 
-	def init_styles(self):
-
-		"""
-		Initialize styles.
-		"""
-		
-		self.qtab_style = self.Styles.qtab_style
-		self.button_style_sheet = self.Styles.button_style_sheet
-		self.button_style_sheet_2 = self.Styles.button_style_sheet_2
-		self.button_style_sheet_2_not_done = self.Styles.button_style_sheet_2_not_done
-		self.button_style_sheet_3 = self.Styles.button_style_sheet_3
-		self.button_select_all = self.Styles.button_select_all
 
 	def set_experiment_path(self, path):
 		self.experiment_path_selection.setText(path)
@@ -414,7 +408,7 @@ class AppInitWindow(QMainWindow):
 			self.experiment_path_selection.setText(self.foldername)
 		else:
 			return None
-		if not os.path.exists(self.foldername+"/config.ini"):
+		if not os.path.exists(os.sep.join([self.foldername,"config.ini"])):
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
 			msgBox.setText("No configuration can be found in the selected folder...")