cellects 0.1.2__py3-none-any.whl

cellects/gui/required_output.py

@@ -0,0 +1,232 @@
+#!/usr/bin/env python3
+"""
+This module contains the widget allowing the user to set which variables Cellects will compute during analysis.
+A first kind of variable is raw data: presence/absence coordinates of the specimens, network, oscillating pixels
+A second kind of variable describe the specimen at each time frame and for each arena of the image stack or video
+"""
+
+from PySide6 import QtWidgets, QtCore
+import logging
+from cellects.gui.custom_widgets import (
+    WindowType, PButton, Checkbox, FixedText)
+from cellects.image_analysis.shape_descriptors import descriptors_names_to_display
+
+
+class RequiredOutput(WindowType):
+    def __init__(self, parent, night_mode):
+        super().__init__(parent, night_mode)
+        self.setParent(parent)
+        # Create the main Title
+        self.true_init(night_mode)
+
+    def true_init(self, night_mode):
+
+        logging.info("Initialize RequiredOutput window")
+        self.title = FixedText('Required Output', police=30, night_mode=self.parent().po.all['night_mode'])
+        self.title.setAlignment(QtCore.Qt.AlignHCenter)
+        # Create the main layout
+        self.vlayout = QtWidgets.QVBoxLayout()
+        self.vlayout.addWidget(self.title) #
+        horzspaceItem = QtWidgets.QSpacerItem(1, 1, QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.MinimumExpanding)
+        self.vlayout.addItem(horzspaceItem) #
+
+        # Create the stylesheet for the boxes allowing to categorize required outputs.
+        boxstylesheet = \
+            ".QWidget {\n" \
+            + "border: 1px solid black;\n" \
+            + "border-radius: 20px;\n" \
+            + "}"
+
+        # I/ First box: Save presence coordinates
+        # I/A/ Title
+        self.save_presence_coordinates_label = FixedText('Save presence coordinates:', tip="Saved in the python numpy format: .npy",
+                                                 night_mode=self.parent().po.all['night_mode'])
+        self.vlayout.addWidget(self.save_presence_coordinates_label) #
+
+        # I/B/ Create the box
+        self.save_presence_coordinates_layout = QtWidgets.QGridLayout()
+        self.save_presence_coordinates_widget = QtWidgets.QWidget()
+        self.save_presence_coordinates_widget.setStyleSheet(boxstylesheet)
+
+        # I/C/ Create widgets
+        self.save_coord_specimen = Checkbox(self.parent().po.vars['save_coord_specimen'])
+        # self.save_coord_specimen.stateChanged.connect(self.save_coord_specimen_saving)
+        self.save_coord_specimen_label = FixedText('All pixels covered by the specimen(s)', tip="",
+                                           night_mode=self.parent().po.all['night_mode'])
+
+        self.save_coord_contour = Checkbox(self.parent().po.vars['save_coord_contour'])
+        # self.save_coord_contour.stateChanged.connect(self.save_coord_contour_saving)
+        self.save_coord_contour_label = FixedText('Contours of the specimen(s)', tip="",
+                                           night_mode=self.parent().po.all['night_mode'])
+        self.save_coord_thickening_slimming = Checkbox(self.parent().po.vars['save_coord_thickening_slimming'])
+        # self.save_coord_thickening_slimming.stateChanged.connect(self.save_coord_thickening_slimming_saving)
+        self.save_coord_thickening_slimming_label = FixedText('Thickening and slimming areas in the specimen(s)', tip="",
+                                           night_mode=self.parent().po.all['night_mode'])
+        self.save_coord_network = Checkbox(self.parent().po.vars['save_coord_network'])
+        # self.save_coord_network.stateChanged.connect(self.save_coord_network_saving)
+        self.save_coord_network_label = FixedText('Tubular network in the specimen(s)', tip="",
+                                           night_mode=self.parent().po.all['night_mode'])
+
+        # I/D/ Arrange widgets in the box
+        self.save_presence_coordinates_layout.addWidget(self.save_coord_specimen_label, 0, 0)
+        self.save_presence_coordinates_layout.addWidget(self.save_coord_specimen, 0, 1)
+        self.save_presence_coordinates_layout.addWidget(self.save_coord_contour_label, 1, 0)
+        self.save_presence_coordinates_layout.addWidget(self.save_coord_contour, 1, 1)
+
+        self.save_presence_coordinates_layout.addWidget(self.save_coord_thickening_slimming_label, 0, 2)
+        self.save_presence_coordinates_layout.addWidget(self.save_coord_thickening_slimming, 0, 3)
+        self.save_presence_coordinates_layout.addWidget(self.save_coord_network_label, 1, 2)
+        self.save_presence_coordinates_layout.addWidget(self.save_coord_network, 1, 3)
+
+        self.save_presence_coordinates_widget.setLayout(self.save_presence_coordinates_layout)
+        self.vlayout.addWidget(self.save_presence_coordinates_widget)
+
+        # II/ Second box: Save descriptors
+        # II/A/ Title
+        self.save_descriptors_label = FixedText('Save descriptors:',
+                                                         tip="Saved in .csv",
+                                                         night_mode=self.parent().po.all['night_mode'])
+        self.vlayout.addWidget(self.save_descriptors_label)  #
+
+        # II/B/ Create the box
+        self.save_descriptors_layout = QtWidgets.QGridLayout()
+        self.save_descriptors_widget = QtWidgets.QWidget()
+        self.save_descriptors_widget.setStyleSheet(boxstylesheet)
+
+        # II/C/ Create widgets
+
+        self.descriptor_widgets_list = []
+
+        # Create the table of the main output the user can select
+        self.create_check_boxes_table()
+        # II/D/ Set the layout
+        self.save_descriptors_widget.setLayout(self.save_descriptors_layout)
+        self.vlayout.addWidget(self.save_descriptors_widget)
+
+
+        # Create the last row layout that will contain a few more output and the ok button.
+        self.last_row_layout = QtWidgets.QHBoxLayout()
+        self.last_row_widget = QtWidgets.QWidget()
+
+        self.cancel = PButton('Cancel', night_mode=self.parent().po.all['night_mode'])
+        self.cancel.clicked.connect(self.cancel_is_clicked)
+        self.ok = PButton('Ok', night_mode=self.parent().po.all['night_mode'])
+        self.ok.clicked.connect(self.ok_is_clicked)
+        self.last_row_layout.addItem(self.horizontal_space)
+        self.last_row_layout.addWidget(self.cancel)
+        self.last_row_layout.addWidget(self.ok)
+
+        self.vlayout.addItem(horzspaceItem)
+        vertspaceItem = QtWidgets.QSpacerItem(1, 1, QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Maximum)
+
+        self.last_row_widget.setLayout(self.last_row_layout)
+        self.vlayout.addWidget(self.last_row_widget)
+
+        self.hlayout = QtWidgets.QHBoxLayout()
+        self.vwidget = QtWidgets.QWidget()
+        self.vwidget.setLayout(self.vlayout)
+        self.hlayout.addItem(vertspaceItem)
+        self.hlayout.addWidget(self.vwidget)
+        self.hlayout.addItem(vertspaceItem)
+        self.setLayout(self.hlayout)
+
+    def create_check_boxes_table(self):
+        """
+            Loop over all main outputs. An output is a variable allowing to describe the binary image
+            showing the presence/absence of the cell/colony at one time frame.
+            This function
+        """
+        descriptor_names = self.parent().po.all['descriptors']
+
+        for i, name in enumerate(descriptor_names):
+            label_index = i * 2
+            if i > 9:
+                row = i - 10 + 1 + 3
+                col = 4
+            else:
+                row = i + 1 + 3
+                col = 1
+            self.descriptor_widgets_list.append(FixedText(descriptors_names_to_display[i], 14, night_mode=self.parent().po.all['night_mode']))
+            self.save_descriptors_layout.addWidget(self.descriptor_widgets_list[label_index], row, col)
+            self.descriptor_widgets_list.append(Checkbox(self.parent().po.all['descriptors'][name]))
+            cb_index = label_index + 1
+
+            if name == 'fractal_analysis':# or name == 'network_analysis':
+                self.descriptor_widgets_list[label_index].setVisible(False)
+                self.descriptor_widgets_list[cb_index].setVisible(False)
+
+            self.save_descriptors_layout.addWidget(self.descriptor_widgets_list[cb_index], row, col + 1)
+
+    def cancel_is_clicked(self):
+        self.save_coord_specimen.setChecked(self.parent().po.vars['save_coord_specimen'])
+        self.save_coord_contour.setChecked(self.parent().po.vars['save_coord_contour'])
+        self.save_coord_thickening_slimming.setChecked(self.parent().po.vars['save_coord_thickening_slimming'])
+        self.save_coord_network.setChecked(self.parent().po.vars['save_coord_network'])
+
+        descriptor_names = self.parent().po.all['descriptors']
+        for i, name in enumerate(descriptor_names):
+            k = i * 2 + 1
+            if name == 'iso_digi_analysis':
+                self.descriptor_widgets_list[k].setChecked(self.parent().po.vars['iso_digi_analysis'])
+            elif name == 'oscilacyto_analysis':
+                self.descriptor_widgets_list[k].setChecked(self.parent().po.vars['oscilacyto_analysis'])
+            elif name == 'fractal_analysis':
+                self.descriptor_widgets_list[k].setChecked(self.parent().po.vars['fractal_analysis'])
+            elif name == 'network_analysis':
+                self.descriptor_widgets_list[k].setChecked(self.parent().po.vars['network_analysis'])
+            elif name == 'graph_extraction':
+                self.descriptor_widgets_list[k].setChecked(self.parent().po.vars['graph_extraction'])
+            else:
+                self.descriptor_widgets_list[k].setChecked(self.parent().po.all['descriptors'][name])
+
+        if self.parent().last_is_first:
+            self.parent().change_widget(0) # FirstWidget
+        else:
+            self.parent().change_widget(3) # ThirdWidget
+
+    def ok_is_clicked(self):
+        self.parent().po.vars['save_coord_specimen'] = self.save_coord_specimen.isChecked()
+        self.parent().po.vars['save_coord_contour'] = self.save_coord_contour.isChecked()
+        self.parent().po.vars['save_coord_thickening_slimming'] = self.save_coord_thickening_slimming.isChecked()
+        self.parent().po.vars['save_coord_network'] = self.save_coord_network.isChecked()
+        descriptor_names = self.parent().po.all['descriptors'].keys()
+        for i, name in enumerate(descriptor_names):
+            k = i * 2 + 1
+            checked_status = self.descriptor_widgets_list[k].isChecked()
+            self.parent().po.all['descriptors'][name] = checked_status
+            if name == 'iso_digi_analysis':
+                self.parent().po.vars['iso_digi_analysis'] = checked_status
+            if name == 'oscilacyto_analysis':
+                self.parent().po.vars['oscilacyto_analysis'] = checked_status
+            if name == 'fractal_analysis':
+                self.parent().po.vars['fractal_analysis'] = checked_status
+            if name == 'network_analysis':
+                self.parent().po.vars['network_analysis'] = checked_status
+            if name == 'graph_extraction':
+                self.parent().po.vars['graph_extraction'] = checked_status
+
+            # for j in [0, 1, 2]:
+            #     k = i * 4 + j + 1
+            #     self.parent().po.all['descriptors'][name][j] = self.descriptor_widgets_list[k].isChecked()
+        if not self.parent().thread['SaveAllVars'].isRunning():
+            self.parent().thread['SaveAllVars'].start()
+        self.parent().po.update_output_list()
+        if self.parent().last_is_first:
+            self.parent().change_widget(0) # FirstWidget
+        else:
+            self.parent().change_widget(3) # ThirdWidget
+
+    def closeEvent(self, event):
+        event.accept
+
+
+# if __name__ == "__main__":
+#     from cellects.gui.cellects import CellectsMainWidget
+#     import sys
+#
+#     app = QtWidgets.QApplication([])
+#     parent = CellectsMainWidget()
+#     session = RequiredOutput(parent, False)
+#     parent.insertWidget(0, session)
+#     parent.show()
+#     sys.exit(app.exec())