celldetective 1.3.9.post5__py3-none-any.whl → 1.4.1__py3-none-any.whl

celldetective/gui/generic_signal_plot.py

@@ -1,5 +1,5 @@
 from PyQt5.QtWidgets import QMessageBox,QGridLayout, QButtonGroup, \
-	QCheckBox, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton, \
+	QCheckBox, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton, \
 	QRadioButton
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QDoubleValidator
@@ -18,13 +18,13 @@ import matplotlib.pyplot as plt
 plt.rcParams['svg.fonttype'] = 'none'
 from glob import glob
 from matplotlib.cm import tab10
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveWidget
 import matplotlib.cm as mcm
 import pandas as pd
 
 from lifelines.utils import qth_survival_times
 
-class GenericSignalPlotWidget(QWidget, Styles):
+class GenericSignalPlotWidget(CelldetectiveWidget):
 
 	def __init__(self, df = None, df_pos_info = None, df_well_info = None, feature_selected = None, parent_window=None, title='plot', *args, **kwargs):
 		
@@ -33,7 +33,6 @@ class GenericSignalPlotWidget(QWidget, Styles):
 
 		self.parent_window = parent_window
 		self.setWindowTitle(title)
-		self.setWindowIcon(self.celldetective_icon)
 
 		self.show_ci = False
 		self.legend_visible = True
@@ -60,8 +59,6 @@ class GenericSignalPlotWidget(QWidget, Styles):
 
 		self.fig.tight_layout()
 		self.setLayout(self.layout)
-		self.setAttribute(Qt.WA_DeleteOnClose)
-
 
 	def populate_widget(self):
 
@@ -170,7 +167,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		self.ci_btn.clicked.connect(self.switch_ci)
 		self.cell_lines_btn.clicked.connect(self.switch_cell_lines)
 
-		self.class_selection_widget = QWidget()
+		self.class_selection_widget = CelldetectiveWidget()
 
 		self.class_selection_lbl = QLabel('class of interest:')
 		class_hbox = QHBoxLayout()
@@ -197,7 +194,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		self.layout.addWidget(self.class_selection_widget) #Layout(class_hbox)
 
 		# Rescale 
-		self.rescale_widget = QWidget()
+		self.rescale_widget = CelldetectiveWidget()
 
 		scale_hbox = QHBoxLayout()
 		self.rescale_widget.setLayout(scale_hbox)
@@ -216,7 +213,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 
 
 		# Rescale 
-		self.cell_lines_alpha_wdg = QWidget()
+		self.cell_lines_alpha_wdg = CelldetectiveWidget()
 		alpha_hbox = QHBoxLayout()
 
 		self.alpha_slider = QLabeledDoubleSlider()
@@ -225,7 +222,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 										slider_initial_value=self.alpha_setting,
 										slider_range=(0,1),
 										decimal_option=True,
-										precision=1.0E-05,
+										precision=5,
 										)
 		self.alpha_slider.valueChanged.connect(self.submit_alpha)
 		self.cell_lines_alpha_wdg.setLayout(alpha_hbox)
@@ -343,7 +340,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		thresh = 20
 		self.well_name_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.usable_well_labels]
 
-		self.line_choice_widget = QWidget()
+		self.line_choice_widget = CelldetectiveWidget()
 		self.line_check_vbox = QGridLayout()
 		self.line_choice_widget.setLayout(self.line_check_vbox)
 
@@ -507,7 +504,8 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		# Spines
 		self.ax.spines['top'].set_visible(False)
 		self.ax.spines['right'].set_visible(False)
-
+		self.ax.grid(which='major', color='black', linestyle='-', linewidth=0.8, alpha=0.2)
+		self.ax.grid(which='minor', color='lightgray', linestyle='--', linewidth=0.5, alpha=0.1)
 		# Lims
 		safe_df = self.df.dropna(subset=self.feature_selected)
 		values = safe_df[self.feature_selected].values
@@ -828,7 +826,7 @@ class SurvivalPlotWidget(GenericSignalPlotWidget):
 
 	def set_table_options(self):
 
-		self.config_table_wg = QWidget()
+		self.config_table_wg = CelldetectiveWidget()
 		self.config_table_wg.setMinimumWidth(480)
 		self.config_table_wg.setWindowTitle('Survival data')
 		

celldetective/gui/gui_utils.py

@@ -1,23 +1,48 @@
-import numpy as np
-from PyQt5.QtWidgets import QGridLayout, QApplication, QMessageBox, QFrame, QSizePolicy, QWidget, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
+import os
+
+from PyQt5.QtWidgets import QGridLayout, QApplication, QMessageBox, QFrame, QSizePolicy, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
 	QPushButton, QLabel, QHBoxLayout, QCheckBox, QFileDialog, QToolButton, QMenu, QStylePainter, QStyleOptionComboBox, QStyle
 from PyQt5.QtCore import Qt, QSize, QAbstractTableModel, QEvent, pyqtSignal
 from PyQt5.QtGui import QDoubleValidator, QIntValidator, QStandardItemModel, QPalette
 
-from celldetective.gui import Styles
+from celldetective.gui import Styles, CelldetectiveWidget
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT
 import matplotlib.pyplot as plt
-import celldetective.extra_properties as extra_properties
+
+from celldetective.utils import get_software_location
+
+try:
+	import celldetective.extra_properties as extra_properties
+	extra_props = True
+except Exception as e:
+	print(f"The module extra_properties seems corrupted: {e}... Skip...")
+	extra_props = False
+
 from inspect import getmembers, isfunction
 from celldetective.filters import *
 from os import sep
 import json
 
 
+def generic_message(message, msg_type="warning"):
+	
+	print(message)
+	message_box = QMessageBox()
+	if msg_type=="warning":
+		message_box.setIcon(QMessageBox.Warning)
+	elif msg_type=="info":
+		message_box.setIcon(QMessageBox.Information)
+	elif msg_type=="critical":
+		message_box.setIcon(QMessageBox.Critical)
+	message_box.setText(message)
+	message_box.setWindowTitle(msg_type)
+	message_box.setStandardButtons(QMessageBox.Ok)
+	_ = message_box.exec()
+
 class PreprocessingLayout(QVBoxLayout, Styles):
 
 	"""
@@ -328,7 +353,7 @@ class PandasModel(QAbstractTableModel):
 		self.dataChanged.emit(ix, ix, (Qt.BackgroundRole,))
 
 
-class GenericOpColWidget(QWidget, Styles):
+class GenericOpColWidget(CelldetectiveWidget):
 
 	def __init__(self, parent_window, column=None, title=''):
 
@@ -415,7 +440,7 @@ class QuickSliderLayout(QHBoxLayout):
 		The slider widget that allows the user to select a value.
 	"""
 
-	def __init__(self, label=None, slider=None, layout_ratio=(0.25,0.75), slider_initial_value=1, slider_range=(0,1), slider_tooltip=None, decimal_option=True, precision=1.0E-03, *args):
+	def __init__(self, label=None, slider=None, layout_ratio=(0.25,0.75), slider_initial_value=1, slider_range=(0,1), slider_tooltip=None, decimal_option=True, precision=3, *args):
 		super().__init__(*args)
 
 		if label is not None and isinstance(label,str):
@@ -423,10 +448,11 @@ class QuickSliderLayout(QHBoxLayout):
 			self.addWidget(self.qlabel, int(100*layout_ratio[0]))
 
 		self.slider = slider
-		self.slider.setOrientation(1)
+		self.slider.setOrientation(Qt.Horizontal)
 		if decimal_option:
-			self.slider.setSingleStep(precision)
-			self.slider.setTickInterval(precision)
+			self.slider.setSingleStep(1.0*(10**(-precision)))
+			self.slider.setTickInterval(1.0*(10**(-precision)))
+			self.slider.setDecimals(precision)
 		else:
 			self.slider.setSingleStep(1)
 			self.slider.setTickInterval(1)
@@ -546,7 +572,7 @@ class QHSeperationLine(QFrame):
 		self.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Minimum)
 
 
-class FeatureChoice(QWidget, Styles):
+class FeatureChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()
@@ -575,10 +601,11 @@ class FeatureChoice(QWidget, Styles):
 								 "intensity_min",
 								 ]
 
-		members = getmembers(extra_properties, isfunction)
-		for o in members:
-			if isfunction(o[1]) and o[1].__module__=="celldetective.extra_properties":
-				standard_measurements.append(o[0])
+		if extra_props:
+			members = getmembers(extra_properties, isfunction)
+			for o in members:
+				if isfunction(o[1]) and o[1].__module__=="celldetective.extra_properties":
+					standard_measurements.append(o[0])
 
 		self.combo_box.addItems(standard_measurements)
 
@@ -599,7 +626,7 @@ class FeatureChoice(QWidget, Styles):
 		self.close()
 
 
-class FilterChoice(QWidget, Styles):
+class FilterChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 
@@ -626,6 +653,7 @@ class FilterChoice(QWidget, Styles):
 			'log_filter': {'blob_size': 30},
 			'tophat_filter': {'size': 4, 'connectivity': 4},
 			'otsu_filter': None,
+			'multiotsu_filter': {'classes': 3},
 			'local_filter': {'block_size': 73, 'method': 'mean', 'offset': 0},
 			'niblack_filter': {'window_size': 15, 'k': 0.2},
 			# 'sauvola_filter': {'window_size': 15, 'k': 0.2}
@@ -707,7 +735,7 @@ class FilterChoice(QWidget, Styles):
 				self.arguments_labels[i].setText('')
 
 
-class OperationChoice(QWidget):
+class OperationChoice(CelldetectiveWidget):
 	"""
 	Mini window to select an operation from numpy to apply on the ROI.
 
@@ -738,7 +766,7 @@ class OperationChoice(QWidget):
 		self.close()
 
 
-class GeometryChoice(QWidget):
+class GeometryChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 
@@ -802,7 +830,7 @@ class GeometryChoice(QWidget):
 		self.close()
 
 
-class DistanceChoice(QWidget):
+class DistanceChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()
@@ -836,7 +864,7 @@ class DistanceChoice(QWidget):
 		self.close()
 
 
-class ListWidget(QWidget):
+class ListWidget(CelldetectiveWidget):
 
 	"""
 	A customizable widget for displaying and managing a list of items, with the 
@@ -963,7 +991,7 @@ class ListWidget(QWidget):
 				del self.items[idx]
 
 
-class FigureCanvas(QWidget):
+class FigureCanvas(CelldetectiveWidget):
 	"""
 	Generic figure canvas.
 	"""
@@ -1183,8 +1211,9 @@ def color_from_state(state, recently_modified=False):
 	"""
 
 	unique_values = np.unique(state)
-	color_map={}
+	color_map = {}
 	for value in unique_values:
+
 		if np.isnan(value):
 			value = "nan"
 			color_map[value] = 'k'
@@ -1192,8 +1221,10 @@ def color_from_state(state, recently_modified=False):
 			color_map[value] = 'tab:blue'
 		elif value==1:
 			color_map[value] = 'tab:red'
+		elif value==99:
+			color_map[value] = 'k'
 		else:
-			color_map[value] = plt.cm.tab10(value)
+			color_map[value] = plt.cm.tab20(value/20.0)
 
 	return color_map
 
@@ -1219,7 +1250,7 @@ def color_from_class(cclass, recently_modified=False):
 			return 'k'
 
 
-class ChannelChoice(QWidget):
+class ChannelChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()

celldetective/gui/help/neighborhood.json

@@ -3,13 +3,13 @@
     "yes": {
       "Do you have the complete shape information for both populations?": {
         "yes": "You can calculate a mask-contact neighborhood. Define the reference and neighbor populations. Adjust the tolerance parameter to control how sensitive the analysis is to contact between reference and neighbor cells.",
-        "no": "You can use an isotropic distance threshold. Define the reference and neighbor populations. Set a radius \( r > (R_{\text{ref}} + 0.5 \times R_{\text{neigh}}) \), where \( R_{\text{ref}} \) is the average radius of reference cells and \( R_{\text{neigh}} \) is the average radius of neighbor cells."
+        "no": "You can use an isotropic distance threshold. Define the reference and neighbor populations. Set a radius ( r > (R_{\text{ref}} + 0.5 \times R_{\text{neigh}}) ), where ( R_{\text{ref}} ) is the average radius of reference cells and ( R_{\text{neigh}} ) is the average radius of neighbor cells."
       }
     },
     "no": {
       "Do you have the complete shape information for the population of interest?": {
         "yes": "You can calculate a mask-contact neighborhood. Use the same population as both the reference and neighbor. Adjust the tolerance parameter to control sensitivity to cell-cell contact.",
-        "no": "You can use an isotropic distance threshold. Use the same population as both the reference and neighbor. Set a radius \( r > 1.5 \times R \), where \( R \) is the average cell radius."
+        "no": "You can use an isotropic distance threshold. Use the same population as both the reference and neighbor. Set a radius ( r > 1.5 \times R ), where ( R ) is the average cell radius."
       }
     }
   }

celldetective/gui/json_readers.py

@@ -1,10 +1,11 @@
 import configparser
-from PyQt5.QtWidgets import QWidget, QVBoxLayout, QScrollArea, QLabel, QHBoxLayout, QLineEdit, QPushButton
+from PyQt5.QtWidgets import QVBoxLayout, QScrollArea, QLabel, QHBoxLayout, QLineEdit, QPushButton
 from PyQt5.QtCore import Qt
 import configparser
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveWidget
 
-class ConfigEditor(QWidget, Styles):
+
+class ConfigEditor(CelldetectiveWidget):
     
     def __init__(self, parent_window):
 
@@ -27,7 +28,7 @@ class ConfigEditor(QWidget, Styles):
         # Create a scroll area to contain the main layout
         scroll = QScrollArea()
         scroll.setWidgetResizable(True)
-        scroll_content = QWidget()
+        scroll_content = CelldetectiveWidget()
         self.scroll_layout = QVBoxLayout(scroll_content)
         scroll_content.setLayout(self.scroll_layout)
         scroll.setWidget(scroll_content)