From a1173e3d28aa0330a91870c7d07677024483154a Mon Sep 17 00:00:00 2001 From: laurentletg <48111184+laurentletg@users.noreply.github.com> Date: Thu, 11 Jul 2024 22:30:16 -0400 Subject: [PATCH 01/10] fixes #36 import missing packages. Removed PyQt5 import- all through qt --- SlicerCART/src/SlicerCART.py | 2364 --------------------- SlicerCART/src/resources/UI/SlicerCART.ui | 485 ----- 2 files changed, 2849 deletions(-) delete mode 100644 SlicerCART/src/SlicerCART.py delete mode 100644 SlicerCART/src/resources/UI/SlicerCART.ui diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py deleted file mode 100644 index 153cd50..0000000 --- a/SlicerCART/src/SlicerCART.py +++ /dev/null @@ -1,2364 +0,0 @@ -# To install a package in slicer python environment, use the following command: -# pip install --user package_name -import os -import logging -import qt, slicer -from PyQt5 import QtCore -from slicer.ScriptedLoadableModule import * -from slicer.util import VTKObservationMixin -from glob import glob -import re -import pandas as pd -import time -import slicerio # cannot install in slicer -import nrrd -import yaml -from pathlib import Path -from threading import RLock -from datetime import datetime -from bids_validator import BIDSValidator -import filecmp -import shutil -import nib -import numpy as np -import vtk -import random -import colorsys - - -INPUT_FILE_EXTENSION = '*.nii.gz' -INTERPOLATE_VALUE = 0 - -DEFAULT_VOLUMES_DIRECTORY = '' -DEFAULT_SEGMENTATION_DIRECTORY = '' - -REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT = False - -IS_CLASSIFICATION_REQUESTED = True -IS_SEGMENTATION_REQUESTED = True -IS_SEMI_AUTOMATIC_PHE_TOOL_REQUESTED = True - -MODALITY = 'CT' - -LABEL_CONFIG_FILE_PATH = os.path.join(Path(__file__).parent.resolve(), "label_config.yml") -KEYBOARD_SHORTCUTS_CONFIG_FILE_PATH = os.path.join(Path(__file__).parent.resolve(), "keyboard_shortcuts_config.yml") -CLASSIFICATION_CONFIG_FILE_PATH = os.path.join(Path(__file__).parent.resolve(), "classification_config.yml") -GENERAL_CONFIG_FILE_PATH = os.path.join(Path(__file__).parent.resolve(), "general_config.yml") - -TIMER_MUTEX = RLock() - -class LoadClassificationWindow(qt.QWidget): - def __init__(self, segmenter, classificationInformation_df, parent = None): - super(LoadClassificationWindow, self).__init__(parent) - - self.classificationInformation_df = classificationInformation_df - - self.segmenter = segmenter - - layout = qt.QVBoxLayout() - - self.versionTableView = qt.QTableWidget() - layout.addWidget(self.versionTableView) - - buttonLayout = qt.QHBoxLayout() - - versionLabel = qt.QLabel() - versionLabel.setText('Classification version to load: ') - versionLabel.setStyleSheet("font-weight: bold") - buttonLayout.addWidget(versionLabel) - - self.versionDropdown = qt.QComboBox() - buttonLayout.addWidget(self.versionDropdown) - - layout.addLayout(buttonLayout) - - if classificationInformation_df.shape[0] > 0: - available_versions = classificationInformation_df['Classification version'].to_list() - for v in available_versions: - self.versionDropdown.addItem(v) - - self.versionTableView.setRowCount(len(available_versions)) - self.versionTableView.setColumnCount(4) - self.versionTableView.horizontalHeader().setStretchLastSection(True) - self.versionTableView.horizontalHeader().setSectionResizeMode(qt.QHeaderView.Stretch) - - for index, row in classificationInformation_df.iterrows(): - cell = qt.QTableWidgetItem(row['Classification version']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 0, cell) - self.versionTableView.setHorizontalHeaderItem(0, qt.QTableWidgetItem('Version')) - - cell = qt.QTableWidgetItem(row['Annotator Name']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 1, cell) - self.versionTableView.setHorizontalHeaderItem(1, qt.QTableWidgetItem('Annotator')) - - cell = qt.QTableWidgetItem(row['Annotator degree']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 2, cell) - self.versionTableView.setHorizontalHeaderItem(2, qt.QTableWidgetItem('Degree')) - - cell = qt.QTableWidgetItem(row['Date and time']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 3, cell) - self.versionTableView.setHorizontalHeaderItem(3, qt.QTableWidgetItem('Date and Time')) - - self.loadButton = qt.QPushButton('Load') - self.loadButton.clicked.connect(self.pushLoad) - layout.addWidget(self.loadButton) - - self.cancelButton = qt.QPushButton('Cancel') - self.cancelButton.clicked.connect(self.pushCancel) - layout.addWidget(self.cancelButton) - - self.setLayout(layout) - self.setWindowTitle("Load Classification") - self.resize(800, 400) - - def pushLoad(self): - selected_version = self.versionDropdown.currentText - - selected_version_df = self.classificationInformation_df[self.classificationInformation_df['Classification version']==selected_version].reset_index(drop = True) - - for i, (objectName, label) in enumerate(self.segmenter.classification_config_yaml["checkboxes"].items()): - if selected_version_df.at[0, label] == 'Yes': - self.segmenter.checkboxWidgets[objectName].setChecked(True) - elif selected_version_df.at[0, label] == 'No': - self.segmenter.checkboxWidgets[objectName].setChecked(False) - - for i, (comboBoxName, options) in enumerate(self.segmenter.classification_config_yaml["comboboxes"].items()): - self.segmenter.comboboxWidgets[comboBoxName].setCurrentText(selected_version_df.at[0, comboBoxName.replace("_", " ").capitalize()]) - - for i, (freeTextBoxObjectName, label) in enumerate(self.segmenter.classification_config_yaml["freetextboxes"].items()): - saved_text = selected_version_df.at[0, label.capitalize()] - if str(saved_text) != 'nan': - self.segmenter.freeTextBoxes[freeTextBoxObjectName].setText(saved_text) - else: - self.segmenter.freeTextBoxes[freeTextBoxObjectName].setText("") - - self.close() - - def pushCancel(self): - self.close() - -class ShowSegmentVersionLegendWindow(qt.QWidget): - def __init__(self, segmenter, segmentationInformation_df, parent = None): - super(ShowSegmentVersionLegendWindow, self).__init__(parent) - - self.segmentationInformation_df = segmentationInformation_df - - self.segmenter = segmenter - - layout = qt.QVBoxLayout() - - informativeLabel = qt.QLabel() - informativeLabel.setText(f'Legend of [{self.segmenter.labelOfCompareSegmentVersions}] segment versions') - layout.addWidget(informativeLabel) - - self.versionTableView = qt.QTableWidget() - layout.addWidget(self.versionTableView) - - if segmentationInformation_df.shape[0] > 0: - - self.versionTableView.setRowCount(len(self.segmenter.colorsSelectedVersionFilePathsForCompareSegmentVersions)) - self.versionTableView.setColumnCount(5) - self.versionTableView.horizontalHeader().setStretchLastSection(True) - self.versionTableView.horizontalHeader().setSectionResizeMode(qt.QHeaderView.Stretch) - - for index, row in segmentationInformation_df.iterrows(): - currentColor = None - for (segment_name, color) in self.segmenter.colorsSelectedVersionFilePathsForCompareSegmentVersions.items(): - if row['Segmentation version'] in segment_name: - currentColor = color - - colorItem = qt.QTableWidgetItem() - colorItem.setBackground(qt.QBrush(qt.QColor(currentColor[0], currentColor[1], currentColor[2]))) - self.versionTableView.setItem(index, 0, colorItem) - self.versionTableView.setHorizontalHeaderItem(0, qt.QTableWidgetItem('Color')) - - cell = qt.QTableWidgetItem(row['Segmentation version']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 1, cell) - self.versionTableView.setHorizontalHeaderItem(1, qt.QTableWidgetItem('Version')) - - cell = qt.QTableWidgetItem(row['Annotator Name']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 2, cell) - self.versionTableView.setHorizontalHeaderItem(2, qt.QTableWidgetItem('Annotator')) - - cell = qt.QTableWidgetItem(row['Annotator degree']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 3, cell) - self.versionTableView.setHorizontalHeaderItem(3, qt.QTableWidgetItem('Degree')) - - cell = qt.QTableWidgetItem(row['Date and time']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 4, cell) - self.versionTableView.setHorizontalHeaderItem(4, qt.QTableWidgetItem('Date and Time')) - - self.cancelButton = qt.QPushButton('Done') - self.cancelButton.clicked.connect(self.pushCancel) - layout.addWidget(self.cancelButton) - - self.setLayout(layout) - self.setWindowTitle("Legend of Segment Versions") - self.resize(800, 200) - - def pushCancel(self): - self.close() - -class CompareSegmentVersionsWindow(qt.QWidget): - def __init__(self, segmenter, segmentationInformation_df, parent = None): - super(CompareSegmentVersionsWindow, self).__init__(parent) - - self.segmentationInformation_df = segmentationInformation_df - - self.segmenter = segmenter - - layout = qt.QVBoxLayout() - - informativeLabel = qt.QLabel() - informativeLabel.setText('READ ONLY feature. Please use the Load Segmentation button to modify an existing segmentation.') - layout.addWidget(informativeLabel) - - self.versionTableView = qt.QTableWidget() - layout.addWidget(self.versionTableView) - - buttonLayout = qt.QHBoxLayout() - - labelLabel = qt.QLabel() - labelLabel.setText('Label of interest for comparison ') - labelLabel.setStyleSheet("font-weight: bold") - buttonLayout.addWidget(labelLabel) - - self.labelDropdown = qt.QComboBox() - for label in self.segmenter.label_config_yaml['labels']: - self.labelDropdown.addItem(label['name']) - buttonLayout.addWidget(self.labelDropdown) - - layout.addLayout(buttonLayout) - - self.versionCheckboxWidgets = {} - - if segmentationInformation_df.shape[0] > 0: - available_versions = segmentationInformation_df['Segmentation version'].to_list() - - self.versionTableView.setRowCount(len(available_versions)) - self.versionTableView.setColumnCount(5) - self.versionTableView.horizontalHeader().setStretchLastSection(True) - self.versionTableView.horizontalHeader().setSectionResizeMode(qt.QHeaderView.Stretch) - - for index, row in segmentationInformation_df.iterrows(): - checkboxItem = qt.QTableWidgetItem() - checkboxItem.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled) - checkboxItem.setCheckState(QtCore.Qt.Unchecked) - checkboxItem.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 0, checkboxItem) - self.versionTableView.setHorizontalHeaderItem(0, qt.QTableWidgetItem('Select')) - self.versionCheckboxWidgets[index] = checkboxItem - - cell = qt.QTableWidgetItem(row['Segmentation version']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 1, cell) - self.versionTableView.setHorizontalHeaderItem(1, qt.QTableWidgetItem('Version')) - - cell = qt.QTableWidgetItem(row['Annotator Name']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 2, cell) - self.versionTableView.setHorizontalHeaderItem(2, qt.QTableWidgetItem('Annotator')) - - cell = qt.QTableWidgetItem(row['Annotator degree']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 3, cell) - self.versionTableView.setHorizontalHeaderItem(3, qt.QTableWidgetItem('Degree')) - - cell = qt.QTableWidgetItem(row['Date and time']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 4, cell) - self.versionTableView.setHorizontalHeaderItem(4, qt.QTableWidgetItem('Date and Time')) - - self.viewSegmentsButton = qt.QPushButton('Compare') - self.viewSegmentsButton.clicked.connect(self.pushViewSegmentsButton) - layout.addWidget(self.viewSegmentsButton) - - self.cancelButton = qt.QPushButton('Cancel') - self.cancelButton.clicked.connect(self.pushCancel) - layout.addWidget(self.cancelButton) - - self.setLayout(layout) - self.setWindowTitle("[READ ONLY] Compare Segment Versions") - self.resize(800, 400) - - def pushViewSegmentsButton(self): - selected_label = self.labelDropdown.currentText - selected_version_file_paths = {} - - segmentation_file_extension = "" - if "nii" in INPUT_FILE_EXTENSION: - segmentation_file_extension = ".nii.gz" - elif "nrrd" in INPUT_FILE_EXTENSION: - segmentation_file_extension = ".seg.nrrd" - - for index, row in self.segmentationInformation_df.iterrows(): - if self.versionCheckboxWidgets[index].checkState() > 0: - selected_version = row['Segmentation version'] - absolute_path_to_segmentation = f'{self.segmenter.currentOutputPath}{os.sep}{self.segmenter.currentVolumeFilename}_{selected_version}{segmentation_file_extension}' - selected_version_file_paths[f"{selected_label}_{selected_version}_{row['Annotator Name']}"] = absolute_path_to_segmentation - - self.segmenter.compareSegmentVersions(selected_label, selected_version_file_paths) - - self.close() - - def pushCancel(self): - self.close() - -class LoadSegmentationsWindow(qt.QWidget): - def __init__(self, segmenter, segmentationInformation_df, parent = None): - super(LoadSegmentationsWindow, self).__init__(parent) - - self.segmentationInformation_df = segmentationInformation_df - - self.segmenter = segmenter - - layout = qt.QVBoxLayout() - - self.versionTableView = qt.QTableWidget() - layout.addWidget(self.versionTableView) - - buttonLayout = qt.QHBoxLayout() - - versionLabel = qt.QLabel() - versionLabel.setText('Segmentation version to load: ') - versionLabel.setStyleSheet("font-weight: bold") - buttonLayout.addWidget(versionLabel) - - self.versionDropdown = qt.QComboBox() - buttonLayout.addWidget(self.versionDropdown) - - layout.addLayout(buttonLayout) - - if segmentationInformation_df.shape[0] > 0: - available_versions = segmentationInformation_df['Segmentation version'].to_list() - for v in available_versions: - self.versionDropdown.addItem(v) - - self.versionTableView.setRowCount(len(available_versions)) - self.versionTableView.setColumnCount(4) - self.versionTableView.horizontalHeader().setStretchLastSection(True) - self.versionTableView.horizontalHeader().setSectionResizeMode(qt.QHeaderView.Stretch) - - for index, row in segmentationInformation_df.iterrows(): - cell = qt.QTableWidgetItem(row['Segmentation version']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 0, cell) - self.versionTableView.setHorizontalHeaderItem(0, qt.QTableWidgetItem('Version')) - - cell = qt.QTableWidgetItem(row['Annotator Name']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 1, cell) - self.versionTableView.setHorizontalHeaderItem(1, qt.QTableWidgetItem('Annotator')) - - cell = qt.QTableWidgetItem(row['Annotator degree']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 2, cell) - self.versionTableView.setHorizontalHeaderItem(2, qt.QTableWidgetItem('Degree')) - - cell = qt.QTableWidgetItem(row['Date and time']) - cell.setFlags(QtCore.Qt.NoItemFlags) - cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) - self.versionTableView.setItem(index, 3, cell) - self.versionTableView.setHorizontalHeaderItem(3, qt.QTableWidgetItem('Date and Time')) - - self.loadButton = qt.QPushButton('Load') - self.loadButton.clicked.connect(self.pushLoad) - layout.addWidget(self.loadButton) - - self.cancelButton = qt.QPushButton('Cancel') - self.cancelButton.clicked.connect(self.pushCancel) - layout.addWidget(self.cancelButton) - - self.setLayout(layout) - self.setWindowTitle("Load Segmentations") - self.resize(800, 400) - - def pushLoad(self): - selected_version = self.versionDropdown.currentText - - segmentation_file_extension = "" - if "nii" in INPUT_FILE_EXTENSION: - segmentation_file_extension = ".nii.gz" - elif "nrrd" in INPUT_FILE_EXTENSION: - segmentation_file_extension = ".seg.nrrd" - - absolute_path_to_segmentation = f'{self.segmenter.currentOutputPath}{os.sep}{self.segmenter.currentVolumeFilename}_{selected_version}{segmentation_file_extension}' - self.segmenter.loadSegmentation(absolute_path_to_segmentation) - - self.close() - - def pushCancel(self): - self.close() - -class SemiAutoPheToolThresholdWindow(qt.QWidget): - def __init__(self, segmenter, parent = None): - super(SemiAutoPheToolThresholdWindow, self).__init__(parent) - - self.segmenter = segmenter - self.LB_HU_value = segmenter.LB_HU - self.UB_HU_value = segmenter.UB_HU - - layout = qt.QVBoxLayout() - self.textLabel = qt.QLabel("Threshold bounds: ") - self.textLabel.setStyleSheet("font-weight: bold") - layout.addWidget(self.textLabel) - - self.minimumLabel = qt.QLabel("Minimum") - layout.addWidget(self.minimumLabel) - - self.semiAutoPHE_LB_HU_spinbox = qt.QSpinBox() - self.semiAutoPHE_LB_HU_spinbox.valueChanged.connect(self.LB_HU_valueChanged) - layout.addWidget(self.semiAutoPHE_LB_HU_spinbox) - self.semiAutoPHE_LB_HU_spinbox.setMinimum(-32000) - self.semiAutoPHE_LB_HU_spinbox.setMaximum(29000) - self.semiAutoPHE_LB_HU_spinbox.setValue(self.LB_HU_value) - - self.maximumLabel = qt.QLabel("Maximum") - layout.addWidget(self.maximumLabel) - - self.semiAutoPHE_UB_HU_spinbox = qt.QSpinBox() - self.semiAutoPHE_UB_HU_spinbox.valueChanged.connect(self.UB_HU_valueChanged) - layout.addWidget(self.semiAutoPHE_UB_HU_spinbox) - self.semiAutoPHE_UB_HU_spinbox.setMinimum(-32000) - self.semiAutoPHE_UB_HU_spinbox.setMaximum(29000) - self.semiAutoPHE_UB_HU_spinbox.setValue(self.UB_HU_value) - - self.continueButton = qt.QPushButton('Continue') - self.continueButton.clicked.connect(self.pushContinue) - layout.addWidget(self.continueButton) - - self.cancelButton = qt.QPushButton('Cancel') - self.cancelButton.clicked.connect(self.pushCancel) - layout.addWidget(self.cancelButton) - - self.setLayout(layout) - self.setWindowTitle("Semi-automatic PHE Tool") - self.resize(400, 200) - - def UB_HU_valueChanged(self): - self.UB_HU_value = self.semiAutoPHE_UB_HU_spinbox.value - self.segmenter.ApplyThresholdPHE(self.LB_HU_value, self.UB_HU_value) - - def LB_HU_valueChanged(self): - self.LB_HU_value = self.semiAutoPHE_LB_HU_spinbox.value - self.segmenter.ApplyThresholdPHE(self.LB_HU_value, self.UB_HU_value) - - def pushContinue(self): - self.segmenter.setUpperAndLowerBoundHU(self.LB_HU_value, self.UB_HU_value) - - self.instructionsWindow = SemiAutoPheToolInstructionsWindow(self.segmenter) - self.instructionsWindow.show() - - self.close() - - def pushCancel(self): - self.segmenter.ClearPHESegment() - self.close() - -class SemiAutoPheToolInstructionsWindow(qt.QWidget): - def __init__(self, segmenter, parent = None): - super(SemiAutoPheToolInstructionsWindow, self).__init__(parent) - - self.segmenter = segmenter - - layout = qt.QVBoxLayout() - self.textLabel = qt.QLabel("Instructions:") - self.textLabel.setStyleSheet("font-weight: bold") - layout.addWidget(self.textLabel) - - self.minimumLabel = qt.QLabel("Click Continue and draw a generous boundary of the ICH and PHE complex. Note that the boundary may be drawn in multiple views. When you are finished drawing the boundary, click on Show Result in the main extension menu. " - + "The HU thresholds and manual fine-tuning of included voxels are left to the annotator\'s discretion. " - + "\n(If a popup message about visibility shows up, click No.)") - self.minimumLabel.setWordWrap(True) - layout.addWidget(self.minimumLabel) - - self.continueButton = qt.QPushButton('Continue') - self.continueButton.clicked.connect(self.pushContinue) - layout.addWidget(self.continueButton) - - self.cancelButton = qt.QPushButton('Cancel') - self.cancelButton.clicked.connect(self.pushCancel) - layout.addWidget(self.cancelButton) - - self.setLayout(layout) - self.setWindowTitle("Semi-automatic PHE Tool") - self.resize(400, 200) - - def pushContinue(self): - self.segmenter.ApplySemiAutomaticThresholdAlgorithm() - self.close() - - def pushCancel(self): - self.segmenter.ClearPHESegment() - self.close() - -class SlicerCART(ScriptedLoadableModule): - """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py - """ - - def __init__(self, parent): - ScriptedLoadableModule.__init__(self, parent) - self.parent.title = "SlicerCART" # TODO: make this more human readable by adding spaces - self.parent.categories = ["Examples"] # TODO: set categories (folders where the module shows up in the module selector) - self.parent.dependencies = [] # TODO: add here list of module names that this module requires - self.parent.contributors = ["Delphine Pilon, An Ni Wu, Emmanuel Montagnon, Maxime Bouthillier, Laurent Letourneau-Guillon"] # TODO: replace with "Firstname Lastname (Organization)" - # TODO: update with short description of the module and a link to online module documentation - self.parent.helpText = """ -This is an example of scripted loadable module bundled in an extension. -See more information in module documentation. -""" - # TODO: replace with organization, grant and thanks - self.parent.acknowledgementText = """ -Module supported by funding from : -1. Fonds de Recherche du Québec en Santé and Fondation de l’Association des Radiologistes du Québec -Radiology Research funding (299979) and Clinical Research Scholarship–Junior 1 Salary Award (311203) -2. Foundation of the Radiological Society of North America - Seed Grant (RSD2122) -3. Quebec Bio-Imaging Network, 2022 pilot project grant (Project no 21.24) -4. Support professoral du Département de radiologie, radio-oncologie et médecine nucléaire de l’Université de Montréal, Radiology departement Centre Hospitalier de l’Université de Montréal (CHUM) and CHUM Research Center (CRCHUM) start-up funds - -Thanks to the Slicer community for the support and the development of the software. - -""" - -class Timer(): - def __init__(self, number=None): - with TIMER_MUTEX: - self.number = number - self.total_time = 0 - self.inter_time = 0 - # counting flag to allow to PAUSE the time - self.flag = False # False = not counting, True = counting (for pause button) - - - def start(self): - with TIMER_MUTEX: - if self.flag == False: - # start counting flag (to allow to pause the time if False) - self.flag = True - self.start_time = time.time() - - - def stop(self): - with TIMER_MUTEX: - if self.flag == True: - self.inter_time = time.time() - self.start_time - self.total_time += self.inter_time - self.flag = False - -# MB CODE BELOW: MOUSE CUSTOMIZATION CLASS -class CustomInteractorStyle(vtk.vtkInteractorStyleImage): - def __init__(self, sliceWidget=None): - self.AddObserver("RightButtonPressEvent", - self.onRightButtonPressEvent) - self.AddObserver("MouseMoveEvent", self.onMouseMoveEvent) - self.AddObserver("RightButtonReleaseEvent", - self.onRightButtonReleaseEvent) - self.AddObserver("MouseWheelForwardEvent", - self.onMouseWheelForwardEvent) - self.AddObserver("MouseWheelBackwardEvent", - self.onMouseWheelBackwardEvent) - self.AddObserver("LeftButtonPressEvent", - self.onLeftButtonPressEvent) - self.AddObserver("LeftButtonReleaseEvent", - self.onLeftButtonReleaseEvent) - self.AddObserver("KeyPressEvent", self.onKeyPressEvent) - self.AddObserver("KeyReleaseEvent", self.onKeyReleaseEvent) - self.startPosition = None - self.sliceWidget = sliceWidget - self.sliceNode = self.sliceWidget.mrmlSliceNode() - self.sliceLogic = slicer.app.applicationLogic().GetSliceLogic( - self.sliceNode) - self.panning = False - self.zooming = False - self.adjustingWindowLevel = False - self.z_pressed = False - - def onRightButtonPressEvent(self, obj, event): - self.startPosition = self.GetInteractor().GetEventPosition() - self.panning = True - self.OnRightButtonDown() - return - - def onMouseMoveEvent(self, obj, event): - if self.panning and self.startPosition: - currentPosition = self.GetInteractor().GetEventPosition() - deltaX = self.startPosition[0] - currentPosition[0] - deltaY = self.startPosition[1] - currentPosition[1] - - # Adjust the image position based on mouse movement - pan = self.sliceNode.GetXYZOrigin() - self.sliceNode.SetXYZOrigin(pan[0] + deltaX, pan[1] + deltaY, - pan[2]) - self.sliceNode.Modified() - - self.startPosition = currentPosition - elif self.adjustingWindowLevel and self.startPosition: - currentPosition = self.GetInteractor().GetEventPosition() - deltaX = currentPosition[0] - self.startPosition[0] - deltaY = self.startPosition[1] - currentPosition[1] - - # Adjust the window level and width based on mouse movement - volumeNode = self.sliceLogic.GetBackgroundLayer().GetVolumeNode() - displayNode = volumeNode.GetDisplayNode() - currentWindowLevel = displayNode.GetLevel() - currentWindowWidth = displayNode.GetWindow() - - newWindowLevel = currentWindowLevel + deltaY - newWindowWidth = currentWindowWidth + deltaX - - displayNode.SetLevel(newWindowLevel) - displayNode.SetWindow(newWindowWidth) - - self.startPosition = currentPosition - - elif self.zooming and self.startPosition: - self.zoom() - self.startPosition = self.GetInteractor().GetEventPosition() - - self.OnMouseMove() - return - - def onRightButtonReleaseEvent(self, obj, event): - self.startPosition = None - self.panning = False - self.OnRightButtonUp() - return - - def onLeftButtonPressEvent(self, obj, event): - self.startPosition = self.GetInteractor().GetEventPosition() - self.adjustingWindowLevel = True - self.OnLeftButtonDown() - return - - def onLeftButtonReleaseEvent(self, obj, event): - self.startPosition = None - self.adjustingWindowLevel = False - self.OnLeftButtonUp() - return - - def onKeyPressEvent(self, obj, event): - key = self.GetInteractor().GetKeySym() - if key == "x": - self.z_pressed = True - self.OnKeyPress() - return - - def onKeyReleaseEvent(self, obj, event): - key = self.GetInteractor().GetKeySym() - if key == "x": - self.z_pressed = False - self.OnKeyRelease() - return - - def onMouseWheelForwardEvent(self, obj, event): - if self.z_pressed: - # print("Mouse scroll") - self.zoom_in() - # print("self zoom done") - else: - # Move to the next slice - currentOffset = self.sliceLogic.GetSliceOffset() - newOffset = currentOffset + self.getSliceSpacing() # Move one - # slice forward - self.sliceLogic.SetSliceOffset(newOffset) - self.OnMouseWheelForward() - return - - def onMouseWheelBackwardEvent(self, obj, event): - if self.z_pressed: - # print("Mouse scroll") - self.zoom_out() - else: - # Move to the previous slice - currentOffset = self.sliceLogic.GetSliceOffset() - newOffset = currentOffset - self.getSliceSpacing() # Move one - # slice backward - self.sliceLogic.SetSliceOffset(newOffset) - self.OnMouseWheelBackward() - return - - def zoom_in(self): - fov = self.sliceNode.GetFieldOfView() - self.sliceNode.SetFieldOfView(fov[0] * 0.9, fov[1] * 0.9, fov[2]) - self.sliceNode.Modified() - - def zoom_out(self): - fov = self.sliceNode.GetFieldOfView() - self.sliceNode.SetFieldOfView(fov[0] / 0.9, fov[1] / 0.9, fov[2]) - self.sliceNode.Modified() - - def zoom(self): - if self.startPosition: - fov = self.sliceNode.GetFieldOfView() - currentPos = self.GetInteractor().GetEventPosition() - deltaY = self.startPosition[1] - currentPos[1] - factor = 1.01 if deltaY > 0 else 0.99 - zoomSpeed = 10 - factor = factor ** (abs(deltaY) / zoomSpeed) - self.sliceNode.SetFieldOfView(fov[0] * factor, fov[1] * factor, - fov[2]) - self.sliceNode.Modified() - - def getSliceSpacing(self): - volumeNode = self.sliceLogic.GetBackgroundLayer().GetVolumeNode() - if volumeNode: - spacing = volumeNode.GetSpacing() - return spacing[2] # Return the spacing along the Z-axis - return 1.0 # Default spacing if volumeNode is not available - -class SlicerCARTWidget(ScriptedLoadableModuleWidget, VTKObservationMixin): - """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py - """ - - def __init__(self, parent=None): - """ - Called when the user opens the module the first time and the widget is initialized. - """ - ScriptedLoadableModuleWidget.__init__(self, parent) - VTKObservationMixin.__init__(self) # needed for parameter node observation - self.logic = None - self._parameterNode = None - self._updatingGUIFromParameterNode = False - # LLG CODE BELOW - self.predictions_names= None - self.DefaultDir = DEFAULT_VOLUMES_DIRECTORY - - # ----- ANW Addition ----- : Initialize called var to False so the timer only stops once - self.called = False - self.called_onLoadSegmentation = False - - # MB - self.interactor1 = slicer.app.layoutManager().sliceWidget( - 'Yellow').sliceView().interactor() - self.interactor2 = slicer.app.layoutManager().sliceWidget( - 'Red').sliceView().interactor() - - # Apply the custom interactor style - styleYellow = slicer.app.layoutManager().sliceWidget('Yellow') - self.styleYellow = CustomInteractorStyle(sliceWidget=styleYellow) - self.interactor1.SetInteractorStyle(self.styleYellow) - - styleRed = slicer.app.layoutManager().sliceWidget('Red') - self.styleRed = CustomInteractorStyle(sliceWidget=styleRed) - self.interactor2.SetInteractorStyle(self.styleRed) - - def get_keyboard_shortcuts_config_values(self): - with open(KEYBOARD_SHORTCUTS_CONFIG_FILE_PATH, 'r') as file: - self.keyboard_config_yaml = yaml.safe_load(file) - - def get_classification_config_values(self): - with open(CLASSIFICATION_CONFIG_FILE_PATH, 'r') as file: - self.classification_config_yaml = yaml.safe_load(file) - - def get_label_config_values(self): - with open(LABEL_CONFIG_FILE_PATH, 'r') as file: - self.label_config_yaml = yaml.safe_load(file) - - def get_general_config_values(self): - with open(GENERAL_CONFIG_FILE_PATH, 'r') as file: - self.general_config_yaml = yaml.safe_load(file) - - global INPUT_FILE_EXTENSION - global DEFAULT_VOLUMES_DIRECTORY - global DEFAULT_SEGMENTATION_DIRECTORY - global REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT - global MODALITY - global IS_CLASSIFICATION_REQUESTED - global IS_SEGMENTATION_REQUESTED - global IS_SEMI_AUTOMATIC_PHE_TOOL_REQUESTED - global INTERPOLATE_VALUE - - INPUT_FILE_EXTENSION = self.general_config_yaml["input_filetype"] - DEFAULT_VOLUMES_DIRECTORY = self.general_config_yaml["default_volume_directory"] - self.DefaultDir = DEFAULT_VOLUMES_DIRECTORY - DEFAULT_SEGMENTATION_DIRECTORY = self.general_config_yaml["default_segmentation_directory"] - MODALITY = self.general_config_yaml["modality"] - IS_CLASSIFICATION_REQUESTED = self.general_config_yaml["is_classification_requested"] - IS_SEGMENTATION_REQUESTED = self.general_config_yaml["is_segmentation_requested"] - IS_SEMI_AUTOMATIC_PHE_TOOL_REQUESTED = self.general_config_yaml["is_semi_automatic_phe_tool_requested"] - INTERPOLATE_VALUE = self.general_config_yaml["interpolate_value"] - - if MODALITY == 'CT': - # then BIDS not mandatory because it is not yet supported - # therefore, either .nrrd or .nii.gz accepted - REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT = False - elif MODALITY == 'MRI': - # therefore, .nii.gz required - INPUT_FILE_EXTENSION = '*.nii.gz' - # user can decide whether to impose bids or not - REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT = self.general_config_yaml["impose_bids_format"] - - - def setup(self): - """ - Called when the user opens the module the first time and the widget is initialized. - """ - ### Segment editor widget - self.layout.setContentsMargins(4, 0, 4, 0) - - ScriptedLoadableModuleWidget.setup(self) - - # Load widget from .ui file (created by Qt Designer). - # Additional widgets can be instantiated manually and added to self.layout. - uiWidget = slicer.util.loadUI(self.resourcePath('UI/SlicerCART.ui')) - self.layout.addWidget(uiWidget) - self.ui = slicer.util.childWidgetVariables(uiWidget) - - # Set scene in MRML widgets. Make sure that in Qt designer the top-level qMRMLWidget's - # "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's. - # "setMRMLScene(vtkMRMLScene*)" slot. - uiWidget.setMRMLScene(slicer.mrmlScene) - - # Create logic class. Logic implements all computations that should be possible to run - # in batch mode, without a graphical user interface. - self.logic = SlicerCARTLogic() - self.get_label_config_values() - self.get_keyboard_shortcuts_config_values() - self.get_classification_config_values() - self.get_general_config_values() - - self.outputFolder = None - self.currentCasePath = None - self.CurrentFolder = None - - self.LB_HU = self.label_config_yaml["labels"][0]["lower_bound_HU"] - self.UB_HU = self.label_config_yaml["labels"][0]["upper_bound_HU"] - - - self.ui.PauseTimerButton.setText('Pause') - self.ui.SelectVolumeFolder.connect('clicked(bool)', self.onSelectVolumesFolderButton) - self.ui.SlicerDirectoryListView.clicked.connect(self.getCurrentTableItem) - self.ui.SaveSegmentationButton.connect('clicked(bool)', self.onSaveSegmentationButton) - self.ui.SelectOutputFolder.connect('clicked(bool)', self.onSelectOutputFolder) - self.ui.LoadSegmentation.connect('clicked(bool)', self.onLoadSegmentation) - self.ui.CompareSegmentVersions.connect('clicked(bool)', self.onCompareSegmentVersions) - self.ui.LoadClassification.connect('clicked(bool)', self.onLoadClassification) - self.ui.SaveClassificationButton.connect('clicked(bool)', self.onSaveClassificationButton) - self.ui.pushButton_Interpolate.connect('clicked(bool)', self.onPushButton_Interpolate) - self.ui.Previous.connect('clicked(bool)', self.onPreviousButton) - self.ui.Next.connect('clicked(bool)', self.onNextButton) - self.ui.pushButton_Paint.connect('clicked(bool)', self.onPushButton_Paint) - self.ui.LassoPaintButton.connect('clicked(bool)', self.onPushLassoPaint) - self.ui.pushButton_ToggleVisibility.connect('clicked(bool)', self.onPushButton_ToggleVisibility) - self.ui.PushButton_segmeditor.connect('clicked(bool)', self.onPushButton_segmeditor) - self.ui.pushButton_Erase.connect('clicked(bool)', self.onPushButton_Erase) - self.ui.pushButton_Smooth.connect('clicked(bool)', self.onPushButton_Smooth) - self.ui.pushButton_Small_holes.connect('clicked(bool)', self.onPushButton_Small_holes) - self.ui.pushButton_SemiAutomaticPHE_Launch.connect('clicked(bool)', self.onPushButton_SemiAutomaticPHE_Launch) - self.ui.pushButton_SemiAutomaticPHE_ShowResult.connect('clicked(bool)', self.onPushButton_SemiAutomaticPHE_ShowResult) - self.ui.dropDownButton_label_select.currentIndexChanged.connect(self.onDropDownButton_label_select) - self.ui.PauseTimerButton.connect('clicked(bool)', self.togglePauseTimerButton) - self.ui.StartTimerButton.connect('clicked(bool)', self.toggleStartTimerButton) - self.ui.pushButton_ToggleFill.connect('clicked(bool)', self.toggleFillButton) - self.ui.UB_HU.valueChanged.connect(self.onUB_HU) - self.ui.LB_HU.valueChanged.connect(self.onLB_HU) - self.ui.pushDefaultMin.connect('clicked(bool)', self.onPushDefaultMin) - self.ui.pushDefaultMax.connect('clicked(bool)', self.onPushDefaultMax) - self.ui.pushButton_undo.connect('clicked(bool)', self.onPushButton_undo) - self.ui.ShowSegmentVersionLegendButton.connect('clicked(bool)', self.onPush_ShowSegmentVersionLegendButton) - - self.ui.ShowSegmentVersionLegendButton.setVisible(False) - - # Display the selected color view at module startup - if self.general_config_yaml['slice_view_color'] == "Yellow": - slicer.app.layoutManager().setLayout( - slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpYellowSliceView) - if self.general_config_yaml['slice_view_color'] == "Red": - slicer.app.layoutManager().setLayout( - slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView) - if self.general_config_yaml['slice_view_color'] == "Green": - slicer.app.layoutManager().setLayout( - slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpGreenSliceView) - - for label in self.label_config_yaml["labels"]: - self.ui.dropDownButton_label_select.addItem(label["name"]) - - self.ui.pushButton_SemiAutomaticPHE_ShowResult.setEnabled(False) - self.disablePauseTimerButton() - self.disableSegmentAndPaintButtons() - self.ui.pushButton_Interpolate.setEnabled(False) - self.ui.SaveSegmentationButton.setEnabled(False) - - self.enableStartTimerButton() - - self.ui.LoadClassification.setEnabled(False) - self.ui.SaveClassificationButton.setEnabled(False) - self.ui.LoadSegmentation.setEnabled(False) - - self.ui.ThresholdLabel.setStyleSheet("font-weight: bold") - self.ui.SemiAutomaticPHELabel.setStyleSheet("font-weight: bold") - - self.ui.UB_HU.setMinimum(-32000) - self.ui.LB_HU.setMinimum(-32000) - self.ui.UB_HU.setMaximum(29000) - self.ui.LB_HU.setMaximum(29000) - - self.ui.pushButton_ToggleFill.setStyleSheet("background-color : indianred") - self.ui.pushButton_ToggleVisibility.setStyleSheet("background-color : yellowgreen") - self.ui.lcdNumber.setStyleSheet("background-color : black") - - # Change the value of the upper and lower bound of the HU - self.ui.UB_HU.setValue(self.UB_HU) - self.ui.LB_HU.setValue(self.LB_HU) - - comboboxesStartRow = self.setupCheckboxes(3) - freetextStartRow = self.setupComboboxes(comboboxesStartRow) - self.setupFreeText(freetextStartRow) - - # Initialize timers - self.timers = [] - timer_index = 0 - for label in self.label_config_yaml["labels"]: - self.timers.append(Timer(number=timer_index)) - timer_index = timer_index + 1 - - self.MostRecentPausedCasePath = "" - - if not IS_CLASSIFICATION_REQUESTED: - self.ui.MRMLCollapsibleButton.setVisible(False) - if not IS_SEGMENTATION_REQUESTED: - self.ui.MRMLCollapsibleButton_2.setVisible(False) - if not IS_SEMI_AUTOMATIC_PHE_TOOL_REQUESTED: - self.ui.SemiAutomaticPHELabel.setVisible(False) - self.ui.pushButton_SemiAutomaticPHE_Launch.setVisible(False) - self.ui.pushButton_SemiAutomaticPHE_ShowResult.setVisible(False) - - for i in self.keyboard_config_yaml["KEYBOARD_SHORTCUTS"]: - - shortcutKey = i.get("shortcut") - callback_name = i.get("callback") - button_name = i.get("button") - - button = getattr(self.ui, button_name) - callback = getattr(self, callback_name) - - self.connectShortcut(shortcutKey, button, callback) - - def setupCheckboxes(self, number_of_columns): - self.checkboxWidgets = {} - - for i, (objectName, label) in enumerate(self.classification_config_yaml["checkboxes"].items()): - checkbox = qt.QCheckBox() - checkbox.setText(label) - checkbox.setObjectName(objectName) - - row_index = i / number_of_columns + 1 - column_index = i % number_of_columns - - self.ui.ClassificationGridLayout.addWidget(checkbox, row_index, column_index) - self.checkboxWidgets[objectName] = checkbox - - return row_index + 1 - - def setupComboboxes(self, start_row): - self.comboboxWidgets = {} - - row_index = start_row - for i, (comboBoxName, options) in enumerate(self.classification_config_yaml["comboboxes"].items()): - comboboxLabel = qt.QLabel(comboBoxName.replace("_", " ").capitalize() + " :") - comboboxLabel.setStyleSheet("font-weight: bold") - self.ui.ClassificationGridLayout.addWidget(comboboxLabel, row_index, 0) - - combobox = qt.QComboBox() - combobox.setObjectName(comboBoxName) - for optionKey, optionLabel in options.items(): - combobox.addItem(optionLabel, optionKey) - self.ui.ClassificationGridLayout.addWidget(combobox, row_index, 1) - self.comboboxWidgets[comboBoxName] = combobox - row_index = row_index + 1 - return row_index + 1 - - def setupFreeText(self, start_row): - self.freeTextBoxes = {} - - row_index = start_row - for i, (freeTextObjectName, freeTextLabel) in enumerate(self.classification_config_yaml["freetextboxes"].items()): - freeTextQLabel = qt.QLabel(freeTextLabel.capitalize() + " :") - freeTextQLabel.setStyleSheet("font-weight: bold") - self.ui.ClassificationGridLayout.addWidget(freeTextQLabel, row_index, 0) - lineEdit = qt.QLineEdit() - self.freeTextBoxes[freeTextObjectName] = lineEdit - self.ui.ClassificationGridLayout.addWidget(lineEdit, row_index, 1) - row_index = row_index + 1 - - def connectShortcut(self, shortcutKey, button, callback): - shortcut = qt.QShortcut(slicer.util.mainWindow()) - shortcut.setKey(qt.QKeySequence(shortcutKey)) - shortcut.connect("activated()", lambda: self.toggleKeyboardShortcut(button, callback)) - return shortcut - - def toggleKeyboardShortcut(self, button, callback): - button.toggle() - callback() - - def setUpperAndLowerBoundHU(self, inputLB_HU, inputUB_HU): - self.LB_HU = inputLB_HU - self.UB_HU = inputUB_HU - self.ui.UB_HU.setValue(self.UB_HU) - self.ui.LB_HU.setValue(self.LB_HU) - - def enableSegmentAndPaintButtons(self): - self.ui.pushButton_Paint.setEnabled(True) - self.ui.LassoPaintButton.setEnabled(True) - self.ui.pushButton_Erase.setEnabled(True) - self.ui.pushButton_SemiAutomaticPHE_Launch.setEnabled(True) - - def disableSegmentAndPaintButtons(self): - self.ui.pushButton_Paint.setEnabled(False) - self.ui.LassoPaintButton.setEnabled(False) - self.ui.pushButton_SemiAutomaticPHE_Launch.setEnabled(False) - self.ui.pushButton_SemiAutomaticPHE_ShowResult.setEnabled(False) - self.ui.pushButton_Erase.setEnabled(False) - - def onSelectVolumesFolderButton(self): - self.CurrentFolder= qt.QFileDialog.getExistingDirectory(None,"Open a folder", self.DefaultDir, qt.QFileDialog.ShowDirsOnly) - - file_structure_valid = True - if REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT == True: - file_structure_valid = self.validateBIDS(self.CurrentFolder) - - if file_structure_valid == False: - return # don't load any patient cases - - self.CasesPaths = sorted(glob(f'{self.CurrentFolder}{os.sep}**{os.sep}{INPUT_FILE_EXTENSION}', recursive = True)) - self.Cases = sorted([os.path.split(i)[-1] for i in self.CasesPaths]) - - self.ui.SlicerDirectoryListView.clear() - self.ui.SlicerDirectoryListView.addItems(self.Cases) - - self.ui.pushButton_Interpolate.setEnabled(True) - - self.currentCase_index = 0 # THIS IS THE CENTRAL THING THAT HELPS FOR CASE NAVIGATION - self.updateCaseAll() - self.loadPatient() - - def validateBIDS(self, path): - validator = BIDSValidator() - is_structure_valid = True - class InvalidBIDS(Exception): pass - - try: - for subdir, dirs, files in os.walk(path): - for file in files: - if file.endswith(INPUT_FILE_EXTENSION.split("*")[1]): - try: - path = "/sub" + (subdir + "/" + file).split("/sub", 1)[1] - is_valid = validator.is_bids(path) - except: - raise InvalidBIDS - - if is_valid == False: - raise InvalidBIDS - except InvalidBIDS: - msg_box = qt.QMessageBox() - msg_box.setWindowTitle("BIDS Validation") - msg_box.setText("File hierarchy not in proper BIDS format. \n\nInformation : https://bids.neuroimaging.io \n\nTool : https://bids-standard.github.io/bids-validator") - msg_box.exec() - - is_structure_valid = False - - return is_structure_valid - - def updateCaseAll(self): - # All below is dependent on self.currentCase_index updates, - self.currentCase = self.Cases[self.currentCase_index] - self.currentCasePath = self.CasesPaths[self.currentCase_index] - self.updateCurrentPatient() - # Highlight the current case in the list view (when pressing on next o) - self.ui.SlicerDirectoryListView.setCurrentItem(self.ui.SlicerDirectoryListView.item(self.currentCase_index)) - - def getCurrentTableItem(self): - # ----- ANW Addition ----- : Reset timer when change case and uncheck all checkboxes - self.resetTimer() - self.resetClassificationInformation() - - # When an item in SlicerDirectroyListView is selected the case number is printed - # below we update the case index and we need to pass one parameter to the methods since it takes 2 (1 in addition to self) - self.updateCaseIndex(self.ui.SlicerDirectoryListView.currentRow) # Index starts at 0 - # Update the case index - self.currentCase_index = self.ui.SlicerDirectoryListView.currentRow - # Same code in onBrowseFoldersButton, need to update self.currentCase - # note that updateCaseAll() not implemented here - it is called when a case is selected from the list view or next/previous button is clicked - self.currentCase = self.Cases[self.currentCase_index] - self.currentCasePath = self.CasesPaths[self.currentCase_index] - self.updateCurrentPatient() - self.loadPatient() - - # ----- ANW Addition ----- : Reset timer when change case, also reset button status - self.resetTimer() - - def updateCaseIndex(self, index): - # ----- ANW Modification ----- : Numerator on UI should start at 1 instead of 0 for coherence - self.ui.FileIndex.setText('{} / {}'.format(index+1, len(self.Cases))) - - def updateCurrentPatient(self): - self.updateCaseIndex(self.currentCase_index) - - def updateCurrentPath(self): - self.ui.CurrentPath.setReadOnly(True) - self.ui.CurrentPath.setText(self.currentCasePath) - - def loadPatient(self): - timer_index = 0 - self.timers = [] - for label in self.label_config_yaml["labels"]: - self.timers.append(Timer(number = timer_index)) - timer_index = timer_index + 1 - - # reset dropbox to index 0 - self.ui.dropDownButton_label_select.setCurrentIndex(0) - - # timer reset if we come back to same case - self.called = False - - slicer.mrmlScene.Clear() - slicer.util.loadVolume(self.currentCasePath) - self.VolumeNode = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')[0] - self.updateCaseAll() - # Adjust windowing (no need to use self. since this is used locally) - Vol_displayNode = self.VolumeNode.GetDisplayNode() - Vol_displayNode.AutoWindowLevelOff() - Vol_displayNode.SetWindow(85) - Vol_displayNode.SetLevel(45) - Vol_displayNode.SetInterpolate(INTERPOLATE_VALUE) - self.newSegmentation() - - self.updateCurrentOutputPathAndCurrentVolumeFilename() - - def updateCurrentOutputPathAndCurrentVolumeFilename(self): - if self.currentCasePath == None or self.CurrentFolder == None or self.outputFolder == None: - return - - i = 0 - relativePath = '' - for c in self.currentCasePath: - if i >= len(self.CurrentFolder): - relativePath = relativePath + c - i = i + 1 - - self.currentOutputPath = os.path.split(self.outputFolder + relativePath)[0] - self.currentVolumeFilename = os.path.split(self.outputFolder + relativePath)[1].split(".")[0] - - - # Getter method to get the segmentation node name - Not sure if this is really useful here. - @property - def segmentationNodeName(self): - return f"{os.path.split(self.currentCasePath)[1].split('.')[0]}_segmentation" - - - def newSegments(self): - pass - - def onPushButton_NewMask(self): - self.newSegments() - - def onPushButton_Interpolate(self): - global INTERPOLATE_VALUE - INTERPOLATE_VALUE = 1 - INTERPOLATE_VALUE # toggle - - self.VolumeNode.GetDisplayNode().SetInterpolate(INTERPOLATE_VALUE) - - def onPreviousButton(self): - # ----- ANW Addition ----- : Reset timer when change case and uncheck all checkboxes - self.resetTimer() - self.resetClassificationInformation() - - #Code below avoid getting in negative values. - self.currentCase_index = max(0, self.currentCase_index-1) - self.updateCaseAll() - self.loadPatient() - - - - - def onNextButton(self): - # ----- ANW Addition ----- : Reset timer when change case and uncheck all checkboxes - self.resetTimer() - self.resetClassificationInformation() - - # ----- ANW Modification ----- : Since index starts at 0, we need to do len(cases)-1 (instead of len(cases)+1). - # Ex. if we have 10 cases, then len(case)=10 and index goes from 0-9, - # so we have to take the minimum between len(self.Cases)-1 and the currentCase_index (which is incremented by 1 everytime we click the button) - self.currentCase_index = min(len(self.Cases)-1, self.currentCase_index+1) - self.updateCaseAll() - self.loadPatient() - - - - - def newSegmentation(self): - # Create segment editor widget and node - self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor - self.segmentEditorNode = self.segmentEditorWidget.mrmlSegmentEditorNode() - # Create segmentation node (keep it local since we add a new segmentation node) - # Not for reference in other methods - segmentationNode=slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") - # Set segmentation node name - segmentationNode.SetName(self.segmentationNodeName) - # Set segmentation node to segment editor - self.segmentEditorWidget.setSegmentationNode(segmentationNode) - # Set master volume node to segment editor - self.segmentEditorWidget.setSourceVolumeNode(self.VolumeNode) - # set refenrence geometry to Volume node (important for the segmentation to be in the same space as the volume) - segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(self.VolumeNode) - self.createNewSegments() - - # restart the current timer - self.timers[self.current_label_index] = Timer(number=self.current_label_index) - # reset tool - self.segmentEditorWidget.setActiveEffectByName("No editing") - - # Load all segments at once - def createNewSegments(self): - for label in self.label_config_yaml["labels"]: - self.onNewLabelSegm(label["name"], label["color_r"], label["color_g"], label["color_b"], label["lower_bound_HU"], label["upper_bound_HU"]) - - first_label_name = self.label_config_yaml["labels"][0]["name"] - first_label_segment_name = first_label_name - self.onPushButton_select_label(first_label_segment_name, self.label_config_yaml["labels"][0]["lower_bound_HU"], self.label_config_yaml["labels"][0]["upper_bound_HU"]) - - def newSegment(self, segment_name=None): - - self.segment_name = segment_name - srcNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - self.srcSegmentation = srcNode.GetSegmentation() - - # Below will create a new segment if there are no segments in the segmentation node, avoid overwriting existing segments - if not self.srcSegmentation.GetSegmentIDs(): # if there are no segments in the segmentation node - self.segmentationNode=slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - self.segmentationNode.GetSegmentation().AddEmptySegment(self.segment_name) - - # if there are segments in the segmentation node, check if the segment name is already in the segmentation node - if any([self.segment_name in i for i in self.srcSegmentation.GetSegmentIDs()]): - pass - else: - self.segmentationNode=slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - self.segmentationNode.GetSegmentation().AddEmptySegment(self.segment_name) - - return self.segment_name - - def onNewLabelSegm(self, label_name, label_color_r, label_color_g, label_color_b, label_LB_HU, label_UB_HU): - segment_name = self.newSegment(label_name) - self.segmentationNode=slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - self.segmentationNode.UndoEnabledOn() - Segmentation = self.segmentationNode.GetSegmentation() - self.SegmentID = Segmentation.GetSegmentIdBySegmentName(segment_name) - segment = Segmentation.GetSegment(self.SegmentID) - segment.SetColor(label_color_r/255,label_color_g/255,label_color_b/255) - self.onPushButton_select_label(segment_name, label_LB_HU, label_UB_HU) - - def onPushButton_select_label(self, segment_name, label_LB_HU, label_UB_HU): - self.segmentationNode=slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - Segmentation = self.segmentationNode.GetSegmentation() - self.SegmentID = Segmentation.GetSegmentIdBySegmentName(segment_name) - self.segmentEditorNode.SetSelectedSegmentID(self.SegmentID) - self.updateCurrentPath() - self.LB_HU = label_LB_HU - self.UB_HU = label_UB_HU - self.onPushButton_Paint() - - if (self.MostRecentPausedCasePath != self.currentCasePath and self.MostRecentPausedCasePath != ""): - self.timers[self.current_label_index] = Timer(number=self.current_label_index) # new path, new timer - - self.timer_router() - - def onPushButton_SemiAutomaticPHE_Launch(self): - flag_PHE_label_exists = False - PHE_label = None - PHE_label_index = 0 - for label in self.label_config_yaml["labels"]: - if label["name"] == "PHE": - flag_PHE_label_exists = True - PHE_label = label - break - PHE_label_index = PHE_label_index + 1 - assert flag_PHE_label_exists - - PHE_segment_name = f"{self.currentCase}_PHE" - self.onPushButton_select_label(PHE_segment_name, PHE_label["lower_bound_HU"], PHE_label["upper_bound_HU"]) - self.ui.dropDownButton_label_select.setCurrentIndex(PHE_label_index) - toolWindow = SemiAutoPheToolThresholdWindow(self) - toolWindow.show() - - def onPushButton_SemiAutomaticPHE_ShowResult(self): - self.segmentationNode.GetDisplayNode().SetVisibility(True) - self.onPushButton_Erase() - self.ui.pushButton_SemiAutomaticPHE_ShowResult.setEnabled(False) - - def ApplyThresholdPHE(self, inLB_HU, inUB_HU): - self.segmentEditorWidget.setActiveEffectByName("Threshold") - effect = self.segmentEditorWidget.activeEffect() - effect.setParameter("MinimumThreshold",f"{inLB_HU}") - effect.setParameter("MaximumThreshold",f"{inUB_HU}") - effect.self().onApply() - - def ApplySemiAutomaticThresholdAlgorithm(self): - self.ui.pushButton_SemiAutomaticPHE_ShowResult.setEnabled(True) - - self.segmentationNode.GetDisplayNode().SetVisibility(False) - - self.segmentEditorWidget.setActiveEffectByName("Threshold") - effect = self.segmentEditorWidget.activeEffect() - effect.setParameter("MinimumThreshold",f"{self.LB_HU}") - effect.setParameter("MaximumThreshold",f"{self.UB_HU}") - effect.self().onApply() - - self.segmentEditorWidget.setActiveEffectByName("Scissors") - effect = self.segmentEditorWidget.activeEffect() - effect.setParameter("Operation","EraseOutside") - effect.setParameter("Shape","FreeForm") - - def ClearPHESegment(self): - flag_PHE_label_exists = False - PHE_label = None - PHE_label_index = 0 - for label in self.label_config_yaml["labels"]: - if label["name"] == "PHE": - flag_PHE_label_exists = True - PHE_label = label - break - PHE_label_index = PHE_label_index + 1 - assert flag_PHE_label_exists - - segm_name = f"{self.currentCase}_PHE" - self.srcSegmentation.RemoveSegment(segm_name) - self.onNewLabelSegm(PHE_label["name"], PHE_label["color_r"], PHE_label["color_g"], PHE_label["color_b"], PHE_label["lower_bound_HU"], PHE_label["upper_bound_HU"]) - - def startTimer(self): - with TIMER_MUTEX: - self.counter = 0 - # Add flag to avoid counting time when user clicks on save segm button - self.flag2 = True - - # ----- ANW Addition ----- : Code to keep track of time passed with lcdNumber on UI - # Create a timer - self.timer = qt.QTimer() - self.timer.timeout.connect(self.updatelcdNumber) - - # Start the timer and update every second - self.timer.start(100) # 1000 ms = 1 second - - # Call the updatelcdNumber function - self.updatelcdNumber() - - def updatelcdNumber(self): - # Get the time - with TIMER_MUTEX: - if self.flag2: # add flag to avoid counting time when user clicks on save segm button - # the timer sends a signal every second (1000 ms). - self.counter += 1 # the self.timer.timeout.connect(self.updatelcdNumber) function is called every second and updates the counter - - self.ui.lcdNumber.display(self.counter/10) - - - def stopTimer(self): - with TIMER_MUTEX: - # If already called once (i.e when user pressed save segm button but forgot to annotator name), simply return the time - if self.called: - return self.total_time - else: - try: - self.total_time = self.counter/10 - self.timer.stop() - self.flag2 = False # Flag is for the timer to stop counting - self.called = True - # self.time_allocation() - return self.total_time - except AttributeError as e: - print(f'!!! YOU DID NOT START THE COUNTER !!! :: {e}') - return None - - def resetTimer(self): - with TIMER_MUTEX: - # making flag to false : stops the timer - self.flag2 = False # For case after the first one the timer stops until the user clicks on the - self.counter = 0 - self.ui.lcdNumber.display(0) - - # reset button status - self.enableStartTimerButton() - self.disablePauseTimerButton() - self.ui.PauseTimerButton.setText('Pause') - if (self.ui.PauseTimerButton.isChecked()): - self.ui.PauseTimerButton.toggle() - - self.disableSegmentAndPaintButtons() - - def enableStartTimerButton(self): - self.ui.StartTimerButton.setEnabled(True) - self.ui.StartTimerButton.setStyleSheet("background-color : yellowgreen") - if (self.ui.StartTimerButton.isChecked()): - self.ui.StartTimerButton.toggle() - - def disablePauseTimerButton(self): - self.ui.PauseTimerButton.setStyleSheet("background-color : silver") - self.ui.PauseTimerButton.setEnabled(False) - - def toggleStartTimerButton(self): - if (self.ui.SlicerDirectoryListView.count > 0): - if self.ui.StartTimerButton.isChecked(): - self.startTimer() - self.timer_router() - - self.ui.StartTimerButton.setEnabled(False) - self.ui.StartTimerButton.setStyleSheet("background-color : silver") - - self.ui.PauseTimerButton.setEnabled(True) - self.ui.PauseTimerButton.setStyleSheet("background-color : indianred") - - self.enableSegmentAndPaintButtons() - else: - self.ui.StartTimerButton.toggle() - - def togglePauseTimerButton(self): - # if button is checked - Time paused - if self.ui.PauseTimerButton.isChecked(): - # setting background color to light-blue - self.ui.PauseTimerButton.setStyleSheet("background-color : lightblue") - self.ui.PauseTimerButton.setText('Restart') - self.timer.stop() - for indiv_timer in self.timers: - indiv_timer.stop() - self.flag = False - - self.MostRecentPausedCasePath = self.currentCasePath - - self.disableSegmentAndPaintButtons() - self.onPushButton_Erase() - - # if it is unchecked - else: - # set background color back to light-grey - self.ui.PauseTimerButton.setStyleSheet("background-color : indianred") - self.ui.PauseTimerButton.setText('Pause') - self.timer.start(100) - self.timer_router() - self.flag = True - - self.enableSegmentAndPaintButtons() - - # for the timer Class not the LCD one - def timer_router(self): - self.timers[self.current_label_index].start() - self.flag = True - - timer_index = 0 - for timer in self.timers: - if timer_index != self.current_label_index: - timer.stop() - timer_index = timer_index + 1 - - def createFolders(self): - self.revision_step = self.ui.RevisionStep.currentText - if len(self.revision_step) != 0: - if os.path.exists(self.outputFolder) == False: - msgboxtime = qt.QMessageBox() - msgboxtime.setText("Segmentation not saved : output folder invalid!") - msgboxtime.exec() - else: - self.updateCurrentOutputPathAndCurrentVolumeFilename() - - if os.path.exists(self.currentOutputPath) == False: - os.makedirs(self.currentOutputPath) - - else: - msgboxtime = qt.QMessageBox() - msgboxtime.setText("Segmentation not saved : revision step is not defined! \n Please save again with revision step!") - msgboxtime.exec() - - def resetClassificationInformation(self): - for i, (objectName, label) in enumerate(self.classification_config_yaml["checkboxes"].items()): - self.checkboxWidgets[objectName].setChecked(False) - for i, (comboBoxName, options) in enumerate(self.classification_config_yaml["comboboxes"].items()): - self.comboboxWidgets[comboBoxName].currentText = list(options.items())[0][1] - for i, (freeTextBoxObjectName, label) in enumerate(self.classification_config_yaml["freetextboxes"].items()): - self.freeTextBoxes[freeTextBoxObjectName].setText("") - - - def getClassificationInformation(self): - label_string = "" - data_string = "" - for i, (objectName, label) in enumerate(self.classification_config_yaml["checkboxes"].items()): - if label_string != "": - label_string = label_string + "," - data_string = data_string + "," - - label_string = label_string + label - - data = "No" - if self.checkboxWidgets[objectName].isChecked(): - data = "Yes" - - data_string = data_string + data - - for i, (comboBoxName, options) in enumerate(self.classification_config_yaml["comboboxes"].items()): - label = comboBoxName.replace("_", " ").capitalize() - - if label_string != "": - label_string = label_string + "," - data_string = data_string + "," - - label_string = label_string + label - - data = self.comboboxWidgets[comboBoxName].currentText - data_string = data_string + data - - for i, (freeTextBoxObjectName, label) in enumerate(self.classification_config_yaml["freetextboxes"].items()): - if label_string != "": - label_string = label_string + "," - data_string = data_string + "," - - label_string = label_string + label - - data = self.freeTextBoxes[freeTextBoxObjectName].text.replace("\n", " // ") - data_string = data_string + data - - return label_string, data_string - - def cast_segmentation_to_uint8(self): - for case in self.predictions_paths: - # Load the segmentation - input_path = os.path.basename(case) - if input_path.endswith('.nii') or input_path.endswith('.nii.gz'): - segm = nib.load(case) - segm_data = segm.get_fdata() - print(f'infile: {input_path}, dtype: {segm_data.dtype}') - if segm_data.dtype != np.uint8: - segm_data = segm_data.astype(np.uint8) - segm_nii = nib.Nifti1Image(segm_data, segm.affine) - nib.save(segm_nii, case) - print(f'converted file {input_path} to uint8') - elif input_path.endswith('seg.nrrd'): - segm_data, header = nrrd.read(case) - print(f'infile: {input_path}, dtype: {segm_data.dtype}') - if segm_data.dtype != np.uint8: - segm_data = segm_data.astype(np.uint8) - header['type'] = 'unsigned char' - nrrd.write(case, segm_data, header = header) - print(f'converted file {input_path} to uint8') - else: - raise ValueError('The input segmentation file must be in nii, nii.gz or nrrd format.') - - def onSaveSegmentationButton(self): - # By default creates a new folder in the volume directory - # Stop the timer when the button is pressed - self.time = self.stopTimer() - # Stop timer of the Timer class - for timer in self.timers: - timer.stop() - self.annotator_name = self.ui.Annotator_name.text - self.annotator_degree = self.ui.AnnotatorDegree.currentText - - # Create folders if not exist - self.createFolders() - - # Make sure to select the first segmentation node (i.e. the one that was created when the module was loaded, not the one created when the user clicked on the "Load mask" button) - self.segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - - currentSegmentationVersion = self.getCurrentSegmentationVersion() - - # quality control check - is_valid = self.qualityControlOfLabels() - if is_valid == False: - return - - # Save if annotator_name is not empty and timer started: - if self.annotator_name and self.time is not None: - - self.saveSegmentationInformation(currentSegmentationVersion) - - if 'nrrd' in INPUT_FILE_EXTENSION: - self.saveNrrdSegmentation(currentSegmentationVersion) - - if 'nii' in INPUT_FILE_EXTENSION: - self.saveNiiSegmentation(currentSegmentationVersion) - - msg_box = qt.QMessageBox() - msg_box.setWindowTitle("Success") - msg_box.setIcon(qt.QMessageBox.Information) - msg_box.setText("Segmentation saved successfully!") - msg_box.exec() - - # If annotator_name empty or timer not started. - else: - if not self.annotator_name: - msgboxtime = qt.QMessageBox() - msgboxtime.setText("Segmentation not saved : no annotator name ! \n Please save again with your name!") - msgboxtime.exec() - elif self.time is None: - print("Error: timer is not started for some unknown reason.") - - self.cast_segmentation_to_uint8() - - def qualityControlOfLabels(self): - is_valid = True - - segment_names = self.getAllSegmentNames() - if len(segment_names) != len(self.label_config_yaml["labels"]): - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Critical) - msg.setText("ERROR : Incorrect number of labels") - msg.setInformativeText(f'Expected {len(self.label_config_yaml["labels"])} labels but obtained {len(segment_names)}. ') - msg.setWindowTitle("ERROR : Incorrect number of labels") - msg.exec() - return False - - for i, segment_name in enumerate(segment_names): - if segment_name != self.label_config_yaml["labels"][i]["name"]: - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Critical) - msg.setText("ERROR : Label mismatch") - msg.setInformativeText(f'Expected {self.label_config_yaml["labels"][i]["name"]} but obtained {segment_name}. ') - msg.setWindowTitle("ERROR : Label mismatch") - msg.exec() - return False - return is_valid - - def saveNrrdSegmentation(self, currentSegmentationVersion): - # Save .seg.nrrd file - self.outputSegmFile = os.path.join(self.currentOutputPath, - "{}_{}.seg.nrrd".format(self.currentVolumeFilename, currentSegmentationVersion)) - - if not os.path.isfile(self.outputSegmFile): - slicer.util.saveNode(self.segmentationNode, self.outputSegmFile) - - else: - msg2 = qt.QMessageBox() - msg2.setWindowTitle('Save As') - msg2.setText( - f'The file {self.currentCase}_{self.annotator_name}_{self.revision_step[0]}.seg.nrrd already exists \n Do you want to replace the existing file?') - msg2.setIcon(qt.QMessageBox.Warning) - msg2.setStandardButtons(qt.QMessageBox.Ok | qt.QMessageBox.Cancel) - msg2.buttonClicked.connect(self.msg2_clicked) - msg2.exec() - - def saveNiiSegmentation(self, currentSegmentationVersion): - # Export segmentation to a labelmap volume - # Note to save to nifti you need to convert to labelmapVolumeNode - self.labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode') - slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(self.segmentationNode, - self.labelmapVolumeNode, - self.VolumeNode) - - self.outputSegmFileNifti = os.path.join(self.currentOutputPath, - "{}_{}.nii.gz".format(self.currentVolumeFilename, currentSegmentationVersion)) - - if not os.path.isfile(self.outputSegmFileNifti): - slicer.util.saveNode(self.labelmapVolumeNode, self.outputSegmFileNifti) - else: - msg3 = qt.QMessageBox() - msg3.setWindowTitle('Save As') - msg3.setText( - f'The file {self.currentCase}_{self.annotator_name}_{self.revision_step[0]}.nii.gz already exists \n Do you want to replace the existing file?') - msg3.setIcon(qt.QMessageBox.Warning) - msg3.setStandardButtons(qt.QMessageBox.Ok | qt.QMessageBox.Cancel) - msg3.buttonClicked.connect(self.msg3_clicked) - msg3.exec() - - def saveSegmentationInformation(self, currentSegmentationVersion): - tag_str = "Volume filename,Segmentation version,Annotator Name,Annotator degree,Revision step,Date and time,Duration" - for label in self.label_config_yaml["labels"]: - tag_str = tag_str + "," + label["name"] + " duration" - - data_str = self.currentCase - data_str = data_str + "," + currentSegmentationVersion - data_str = data_str + "," + self.annotator_name - data_str = data_str + "," + self.annotator_degree - data_str = data_str + "," + self.revision_step[0] - data_str = data_str + "," + datetime.today().strftime('%Y-%m-%d %H:%M:%S') - data_str = data_str + "," + str(self.ui.lcdNumber.value) - for timer in self.timers: - data_str = data_str + "," + str(timer.total_time) - - self.outputSegmentationInformationFile = os.path.join(self.currentOutputPath, - '{}_SegmentationInformation.csv'.format(self.currentVolumeFilename)) - if not os.path.isfile(self.outputSegmentationInformationFile): - with open(self.outputSegmentationInformationFile, 'w') as f: - f.write(tag_str) - f.write("\n") - f.write(data_str) - else: - with open(self.outputSegmentationInformationFile, 'a') as f: - f.write("\n") - f.write(data_str) - - def saveClassificationInformation(self, classification_information_labels_string, classification_information_data_string): - currentClassificationInformationVersion = self.getClassificationInformationVersion() - - tag_str = "Volume filename,Classification version,Annotator Name,Annotator degree,Revision step,Date and time" - tag_str = tag_str + "," + classification_information_labels_string - - data_str = self.currentCase - data_str = data_str + "," + currentClassificationInformationVersion - data_str = data_str + "," + self.annotator_name - data_str = data_str + "," + self.annotator_degree - data_str = data_str + "," + self.revision_step[0] - data_str = data_str + "," + datetime.today().strftime('%Y-%m-%d %H:%M:%S') - data_str = data_str + "," + classification_information_data_string - - self.outputClassificationInformationFile = os.path.join(self.currentOutputPath, - '{}_ClassificationInformation.csv'.format(self.currentVolumeFilename)) - if not os.path.isfile(self.outputClassificationInformationFile): - with open(self.outputClassificationInformationFile, 'w') as f: - f.write(tag_str) - f.write("\n") - f.write(data_str) - else: - with open(self.outputClassificationInformationFile, 'a') as f: - f.write("\n") - f.write(data_str) - - def getClassificationInformationVersion(self): - version = "v" - classificationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_ClassificationInformation.csv' - - if os.path.exists(classificationInformationPath) == False: - version = version + "01" - else: - csv_data = pd.read_csv(classificationInformationPath) - existing_version_strings = csv_data['Classification version'].to_list() - existing_version_numbers = [(int)(version_string.split("v")[1]) for version_string in existing_version_strings] - next_version_number = max(existing_version_numbers) + 1 - version = f'{version}{next_version_number:02d}' - - return version - - def getCurrentSegmentationVersion(self): - list_of_segmentation_filenames = glob(f'{self.currentOutputPath}{os.sep}{INPUT_FILE_EXTENSION}') - - version = 'v' - if list_of_segmentation_filenames == []: - version = version + "01" - else: - existing_versions = [(int)(filename.split('_v')[1].split(".")[0]) for filename in list_of_segmentation_filenames] - next_version_number = max(existing_versions) + 1 - next_version_number = min(next_version_number, 99) # max 99 versions - version = f'{version}{next_version_number:02d}' - return version - - - def msg2_clicked(self, msg2_button): - if msg2_button.text == 'OK': - slicer.util.saveNode(self.segmentationNode, self.outputSegmFile) - else: - return - - def msg3_clicked(self, msg3_button): - if msg3_button.text == 'OK': - slicer.util.saveNode(self.labelmapVolumeNode, self.outputSegmFileNifti) - else: - return - - def msg4_clicked(self, msg4_button): - if msg4_button.text == 'OK': - slicer.util.saveNode(self.VolumeNode, self.outputVolfile) - else: - return - - def verifyConfigCompatibilities(self): - if self.outputFolder is not None: - folder_for_config_files = 'conf' - path_to_saved_config_files = f'{self.outputFolder}{os.sep}{folder_for_config_files}' - - if os.path.exists(path_to_saved_config_files) == False: - os.makedirs(path_to_saved_config_files) - - label_config_copy_filename = 'lc_c--do-not-modify.yml' - path_to_label_config_copy = f'{path_to_saved_config_files}{os.sep}{label_config_copy_filename}' - - classification_config_copy_filename = 'cbc_c--do-not-modify.yml' - path_to_classification_config_copy = f'{path_to_saved_config_files}{os.sep}{classification_config_copy_filename}' - - content_of_output_folder = os.listdir(self.outputFolder) - if '.DS_Store' in content_of_output_folder: - content_of_output_folder.remove('.DS_Store') - - if os.path.exists(path_to_label_config_copy): - is_label_config_compatible = filecmp.cmp(path_to_label_config_copy, LABEL_CONFIG_FILE_PATH) - if is_label_config_compatible == False: - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Critical) - msg.setText("ERROR : Incompatible Label Configuration") - msg.setInformativeText('The label_config.yml file has changed since the initial segmentation. ') - msg.setWindowTitle("ERROR : Incompatible Label Configuration") - msg.exec() - - self.outputFolder = None - - if os.path.exists(path_to_classification_config_copy): - is_classification_config_compatible = filecmp.cmp(path_to_classification_config_copy, CLASSIFICATION_CONFIG_FILE_PATH) - if is_classification_config_compatible == False: - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Critical) - msg.setText("ERROR : Incompatible Classification Configuration") - msg.setInformativeText('The classification_config.yml file has changed since the initial classification annotation. ') - msg.setWindowTitle("ERROR : Incompatible Classification Configuration") - msg.exec() - - self.outputFolder = None - - if len(content_of_output_folder) > 1 and os.path.exists(path_to_label_config_copy) == False and os.path.exists(path_to_classification_config_copy) == False: - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Warning) - msg.setText("WARNING : Possible Incompatible Configuration") - msg.setInformativeText('The output folder is not empty. No configuration files have been saved. Possible configuration incompatibility. Proceed with caution. Otherwise, choose an empty output folder. ') - msg.setWindowTitle("WARNING : Possible Incompatible Configuration") - msg.exec() - - shutil.copy(LABEL_CONFIG_FILE_PATH, path_to_label_config_copy) - shutil.copy(CLASSIFICATION_CONFIG_FILE_PATH, path_to_classification_config_copy) - elif len(content_of_output_folder) == 1: - shutil.copy(LABEL_CONFIG_FILE_PATH, path_to_label_config_copy) - shutil.copy(CLASSIFICATION_CONFIG_FILE_PATH, path_to_classification_config_copy) - - def onSelectOutputFolder(self): - self.outputFolder = qt.QFileDialog.getExistingDirectory(None,"Open a folder", self.DefaultDir, qt.QFileDialog.ShowDirsOnly) - - self.verifyConfigCompatibilities() - - if self.outputFolder is not None: - self.ui.LoadClassification.setEnabled(True) - self.ui.LoadSegmentation.setEnabled(True) - - self.ui.SaveSegmentationButton.setEnabled(True) - self.ui.SaveClassificationButton.setEnabled(True) - - self.updateCurrentOutputPathAndCurrentVolumeFilename() - - self.predictions_paths = sorted(glob(os.path.join(self.outputFolder, f'{INPUT_FILE_EXTENSION}'))) - - def msg_warnig_delete_segm_node_clicked(self, msg_warnig_delete_segm_node_button): - if msg_warnig_delete_segm_node_button.text == 'OK': - srcNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - slicer.mrmlScene.RemoveNode(srcNode) - else: - return - - def onLoadClassification(self): - classificationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_ClassificationInformation.csv' - classificationInformation_df = None - if os.path.exists(classificationInformationPath): - classificationInformation_df = pd.read_csv(classificationInformationPath) - else: - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Information) - msg.setText("No saved classifications") - msg.setInformativeText('There are no classifications saved in the ClassificationInformation.csv.') - msg.setWindowTitle("No saved classifications") - msg.exec() - return - - loadClassificationWindow = LoadClassificationWindow(self, classificationInformation_df) - loadClassificationWindow.show() - - def onSaveClassificationButton(self): - self.annotator_name = self.ui.Annotator_name.text - self.annotator_degree = self.ui.AnnotatorDegree.currentText - - classification_information_labels_string, classification_information_data_string = self.getClassificationInformation() - - # Create folders if don't exist - self.createFolders() - - if self.annotator_name is not None: - self.saveClassificationInformation(classification_information_labels_string, classification_information_data_string) - msg_box = qt.QMessageBox() - msg_box.setWindowTitle("Success") - msg_box.setIcon(qt.QMessageBox.Information) - msg_box.setText("Classification saved successfully!") - msg_box.exec() - - else: - msgboxtime = qt.QMessageBox() - msgboxtime.setText("Classification not saved : no annotator name ! \n Please save again with your name!") - msgboxtime.exec() - - - def onCompareSegmentVersions(self): - if 'Clear' in self.ui.CompareSegmentVersions.text: - self.onClearCompareSegmentVersions() - else: - msg_warnig_delete_segm_node = self.warnAgainstDeletingCurrentSegmentation() - msg_warnig_delete_segm_node.buttonClicked.connect(self.onCompareSegmentVersionsWillEraseCurrentSegmentsWarningClicked) - msg_warnig_delete_segm_node.exec() - - def onCompareSegmentVersionsWillEraseCurrentSegmentsWarningClicked(self, msg_warnig_delete_segm_node_button): - if msg_warnig_delete_segm_node_button.text == 'OK': - srcNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - slicer.mrmlScene.RemoveNode(srcNode) - - self.openCompareSegmentVersionsWindow() - else: - return - - def warnAgainstDeletingCurrentSegmentation(self): - msg_warnig_delete_segm_node = qt.QMessageBox() - msg_warnig_delete_segm_node.setText('This will delete the current segmentation. Do you want to continue?') - msg_warnig_delete_segm_node.setIcon(qt.QMessageBox.Warning) - msg_warnig_delete_segm_node.setStandardButtons(qt.QMessageBox.Ok | qt.QMessageBox.Cancel) - - return msg_warnig_delete_segm_node - - def onLoadSegmentation(self): - msg_warnig_delete_segm_node = self.warnAgainstDeletingCurrentSegmentation() - msg_warnig_delete_segm_node.buttonClicked.connect(self.onLoadSegmentationWillEraseCurrentSegmentsWarningClicked) - msg_warnig_delete_segm_node.exec() - - def onLoadSegmentationWillEraseCurrentSegmentsWarningClicked(self, msg_warnig_delete_segm_node_button): - if msg_warnig_delete_segm_node_button.text == 'OK': - srcNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - slicer.mrmlScene.RemoveNode(srcNode) - self.openLoadSegmentationWindow() - else: - return - - def openLoadSegmentationWindow(self): - segmentationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_SegmentationInformation.csv' - segmentationInformation_df = None - if os.path.exists(segmentationInformationPath): - segmentationInformation_df = pd.read_csv(segmentationInformationPath) - else: - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Information) - msg.setText("No saved segmentations") - msg.setInformativeText('There are no segmentations saved in the SegmentationInformation.csv.') - msg.setWindowTitle("No saved segmentations") - msg.exec() - return - - loadSegmentationWindow = LoadSegmentationsWindow(self, segmentationInformation_df) - loadSegmentationWindow.show() - - def openCompareSegmentVersionsWindow(self): - segmentationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_SegmentationInformation.csv' - segmentationInformation_df = None - if os.path.exists(segmentationInformationPath): - segmentationInformation_df = pd.read_csv(segmentationInformationPath) - else: - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Information) - msg.setText("No saved segmentations") - msg.setInformativeText('There are no segmentations saved in the SegmentationInformation.csv.') - msg.setWindowTitle("No saved segmentations") - msg.exec() - return - - compareSegmentVersionsWindow = CompareSegmentVersionsWindow(self, segmentationInformation_df) - compareSegmentVersionsWindow.show() - - def compareSegmentVersions(self, selected_label, selected_version_file_paths): - self.labelOfCompareSegmentVersions = selected_label - self.colorsSelectedVersionFilePathsForCompareSegmentVersions = {} - - selected_label_value = 0 - for label in self.label_config_yaml['labels']: - if selected_label == label['name']: - selected_label_value = label['value'] - - slicer.mrmlScene.Clear() - slicer.util.loadVolume(self.currentCasePath) - self.VolumeNode = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')[0] - - Vol_displayNode = self.VolumeNode.GetDisplayNode() - Vol_displayNode.AutoWindowLevelOff() - Vol_displayNode.SetWindow(85) - Vol_displayNode.SetLevel(45) - Vol_displayNode.SetInterpolate(INTERPOLATE_VALUE) - - self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor - self.segmentEditorWidget.setActiveEffectByName("No editing") - - self.resetTimer() - - for (segment_name, version_file_path) in selected_version_file_paths.items(): - if 'nrrd' in INPUT_FILE_EXTENSION: - slicer.util.loadSegmentation(version_file_path) - currentSegmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - elif 'nii' in INPUT_FILE_EXTENSION: - labelmapVolumeNode = slicer.util.loadLabelVolume(version_file_path) - currentSegmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") - slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, currentSegmentationNode) - - self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor - self.segmentEditorNode = self.segmentEditorWidget.mrmlSegmentEditorNode() - self.segmentEditorWidget.setSegmentationNode(currentSegmentationNode) - self.segmentEditorWidget.setSourceVolumeNode(self.VolumeNode) - currentSegmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(self.VolumeNode) - segmentationDisplayNode = currentSegmentationNode.GetDisplayNode() - segmentationDisplayNode.SetAllSegmentsVisibility(False) - - currentSegmentationNode.SetName(os.path.split(version_file_path)[1].split('.')[0]) - - segment = currentSegmentationNode.GetSegmentation().GetSegment(str(selected_label_value)) - - if segment is not None : - segment.SetName(segment_name) - - # OBTAIN RANDOM BRIGHT COLOR : https://stackoverflow.com/questions/43437309/get-a-bright-random-colour-python - h,s,l = random.random(), 0.5 + random.random()/2.0, 0.4 + random.random()/5.0 - r,g,b = [int(256*i) for i in colorsys.hls_to_rgb(h,l,s)] - self.colorsSelectedVersionFilePathsForCompareSegmentVersions[segment_name] = [r, g, b] - segment.SetColor(r / 255, g / 255, b / 255) - - segmentationDisplayNode.SetSegmentVisibility(str(selected_label_value), True) - - self.disableSegmentAndPaintButtons() - self.disablePauseTimerButton() - self.ui.StartTimerButton.setEnabled(False) - self.ui.StartTimerButton.setStyleSheet("background-color : light gray") - self.ui.CompareSegmentVersions.setText('Clear Read Only Segment Versions') - self.ui.CompareSegmentVersions.setStyleSheet("background-color : yellowgreen") - self.ui.SaveSegmentationButton.setEnabled(False) - - self.ui.ShowSegmentVersionLegendButton.setVisible(True) - - def onClearCompareSegmentVersions(self): - self.loadPatient() - - self.enableStartTimerButton() - - self.ui.CompareSegmentVersions.setText('Compare segment versions') - self.ui.CompareSegmentVersions.setStyleSheet("background-color : light gray") - - self.ui.SaveSegmentationButton.setEnabled(True) - - self.ui.ShowSegmentVersionLegendButton.setVisible(False) - - def loadSegmentation(self, absolute_path_to_segmentation_file): - if 'nrrd' in INPUT_FILE_EXTENSION: - slicer.util.loadSegmentation(absolute_path_to_segmentation_file) - self.segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] - elif 'nii' in INPUT_FILE_EXTENSION: - labelmapVolumeNode = slicer.util.loadLabelVolume(absolute_path_to_segmentation_file) - self.segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") - slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, self.segmentationNode) - - self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor - self.segmentEditorNode = self.segmentEditorWidget.mrmlSegmentEditorNode() - self.segmentEditorWidget.setSegmentationNode(self.segmentationNode) - self.segmentEditorWidget.setSourceVolumeNode(self.VolumeNode) - # set refenrence geometry to Volume node - self.segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(self.VolumeNode) - nn = self.segmentationNode.GetDisplayNode() - # set Segmentation visible: - nn.SetAllSegmentsVisibility(True) - - loaded_segment_ids = self.segmentationNode.GetSegmentation().GetSegmentIDs() - for i, segment_id in enumerate(loaded_segment_ids): - for label in self.label_config_yaml["labels"]: - if str(label['value']) == str(segment_id): - segment = self.segmentationNode.GetSegmentation().GetSegment(segment_id) - segment.SetName(label["name"]) - segment.SetColor(label["color_r"]/255, label["color_g"]/255, label["color_b"]/255) - - list_of_segment_names = self.getAllSegmentNames() - for label in self.label_config_yaml["labels"]: - if label['name'] not in list_of_segment_names: - self.onNewLabelSegm(label["name"], label["color_r"], label["color_g"], label["color_b"], label["lower_bound_HU"], label["upper_bound_HU"]) - - for segment_id in loaded_segment_ids: - for label in self.label_config_yaml["labels"]: - if str(segment_id) == str(label['value']) or str(segment_id) == str(label['name']): - self.segmentationNode.GetSegmentation().SetSegmentIndex(str(segment_id), label['value']-1) - - def getAllSegmentNames(self): - list_of_segment_ids = self.segmentationNode.GetSegmentation().GetSegmentIDs() - list_of_segment_names = [] - for segment_id in list_of_segment_ids: - segment = self.segmentationNode.GetSegmentation().GetSegment(segment_id) - list_of_segment_names.append(segment.GetName()) - return list_of_segment_names - - def onPushDefaultMin(self): - with open(LABEL_CONFIG_FILE_PATH, 'r') as file: - fresh_config = yaml.safe_load(file) - self.label_config_yaml["labels"][self.current_label_index]["lower_bound_HU"] = fresh_config["labels"][self.current_label_index]["lower_bound_HU"] - self.setUpperAndLowerBoundHU(self.label_config_yaml["labels"][self.current_label_index]["lower_bound_HU"], self.label_config_yaml["labels"][self.current_label_index]["upper_bound_HU"]) - - def onPushDefaultMax(self): - with open(LABEL_CONFIG_FILE_PATH, 'r') as file: - fresh_config = yaml.safe_load(file) - self.label_config_yaml["labels"][self.current_label_index]["upper_bound_HU"] = fresh_config["labels"][self.current_label_index]["upper_bound_HU"] - self.setUpperAndLowerBoundHU(self.label_config_yaml["labels"][self.current_label_index]["lower_bound_HU"], self.label_config_yaml["labels"][self.current_label_index]["upper_bound_HU"]) - - def onPush_ShowSegmentVersionLegendButton(self): - segmentationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_SegmentationInformation.csv' - segmentationInformation_df = None - if os.path.exists(segmentationInformationPath): - segmentationInformation_df = pd.read_csv(segmentationInformationPath) - else: - msg = qt.QMessageBox() - msg.setIcon(qt.QMessageBox.Information) - msg.setText("No saved segmentations") - msg.setInformativeText('There are no segmentations saved in the SegmentationInformation.csv.') - msg.setWindowTitle("No saved segmentations") - msg.exec() - return - - showSegmentVersionLegendWindow = ShowSegmentVersionLegendWindow(self, segmentationInformation_df) - showSegmentVersionLegendWindow.show() - - def onPushButton_undo(self): - self.segmentEditorWidget.undo() - - def onDropDownButton_label_select(self, value): - self.current_label_index = value - label = self.label_config_yaml["labels"][value] - self.setUpperAndLowerBoundHU(label["lower_bound_HU"], label["upper_bound_HU"]) - - label_name = label["name"] - try: - segment_name = label_name - self.onPushButton_select_label(segment_name, label["lower_bound_HU"], label["upper_bound_HU"]) - except: - pass - - def onPushLassoPaint(self): - self.segmentEditorWidget.setActiveEffectByName("Scissors") - self.segmentEditorNode.SetMasterVolumeIntensityMask(False) - effect = self.segmentEditorWidget.activeEffect() - effect.setParameter("Operation","FillInside") - effect.setParameter("Shape","FreeForm") - effect.setSliceCutMode(3) - - def onPushButton_Paint(self): - selected_segment_id = self.segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(self.label_config_yaml["labels"][self.current_label_index]['name']) - self.segmentEditorNode.SetSelectedSegmentID(selected_segment_id) - self.segmentEditorWidget.setActiveEffectByName("Paint") - # Note it seems that sometimes you need to activate the effect first with : - # Assign effect to the segmentEditorWidget using the active effect - self.effect = self.segmentEditorWidget.activeEffect() - self.effect.activate() - self.effect.setParameter('BrushSphere',1) - # Seems that you need to activate the effect to see it in Slicer - # Set up the mask parameters (note that PaintAllowed...was changed to EditAllowed) - self.segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentationNode.EditAllowedEverywhere) - #Set if using Editable intensity range (the range is defined below using object.setParameter) - self.segmentEditorNode.SetMasterVolumeIntensityMask(True) - self.segmentEditorNode.SetSourceVolumeIntensityMaskRange(self.LB_HU, self.UB_HU) - self.segmentEditorNode.SetOverwriteMode(slicer.vtkMRMLSegmentEditorNode.OverwriteAllSegments) - - def toggleFillButton(self): - if self.ui.pushButton_ToggleFill.isChecked(): - self.ui.pushButton_ToggleFill.setStyleSheet("background-color : yellowgreen") - self.ui.pushButton_ToggleFill.setText('Fill: ON') - self.segmentationNode.GetDisplayNode().SetOpacity2DFill(0) - else: - self.ui.pushButton_ToggleFill.setStyleSheet("background-color : indianred") - self.ui.pushButton_ToggleFill.setText('Fill: OFF') - self.segmentationNode.GetDisplayNode().SetOpacity2DFill(100) - - def onPushButton_ToggleVisibility(self): - if self.ui.pushButton_ToggleVisibility.isChecked(): - self.ui.pushButton_ToggleVisibility.setStyleSheet("background-color : indianred") - self.ui.pushButton_ToggleVisibility.setText('Visibility: OFF') - self.segmentationNode.GetDisplayNode().SetAllSegmentsVisibility(False) - else: - self.ui.pushButton_ToggleVisibility.setStyleSheet("background-color : yellowgreen") - self.ui.pushButton_ToggleVisibility.setText('Visibility: ON') - self.segmentationNode.GetDisplayNode().SetAllSegmentsVisibility(True) - - def togglePaintMask(self): - if self.ui.pushButton_TogglePaintMask.isChecked(): - self.ui.pushButton_TogglePaintMask.setStyleSheet("background-color : yellowgreen") - self.ui.pushButton_TogglePaintMask.setText('Paint Mask ON') - self.segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentationNode.EditAllowedEverywhere) - - - def onPushButton_segmeditor(self): - slicer.util.selectModule("SegmentEditor") - - def onPushButton_Erase(self): - self.segmentEditorWidget.setActiveEffectByName("Erase") - # Note it seems that sometimes you need to activate the effect first with : - # Assign effect to the segmentEditorWidget using the active effect - self.effect = self.segmentEditorWidget.activeEffect() - # Seems that you need to activate the effect to see it in Slicer - self.effect.activate() - self.segmentEditorNode.SetMasterVolumeIntensityMask(False) - - def onPushButton_Smooth(self): - # pass - # Smoothing - self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor - self.segmentEditorWidget.setActiveEffectByName("Smoothing") - effect = self.segmentEditorWidget.activeEffect() - effect.setParameter("SmoothingMethod", "MEDIAN") - effect.setParameter("KernelSizeMm", 3) - effect.self().onApply() - - - - def onPushButton_Small_holes(self): - # pass - # Fill holes smoothing - self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor - self.segmentEditorWidget.setActiveEffectByName("Smoothing") - effect = self.segmentEditorWidget.activeEffect() - effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_CLOSING") - effect.setParameter("KernelSizeMm", 3) - effect.self().onApply() - - def onLB_HU(self): - try: - self.LB_HU=self.ui.LB_HU.value - self.segmentEditorNode.SetMasterVolumeIntensityMask(True) - self.segmentEditorNode.SetSourceVolumeIntensityMaskRange(self.LB_HU, self.UB_HU) - self.label_config_yaml["labels"][self.current_label_index]["lower_bound_HU"] = self.LB_HU - except: - pass - - def onUB_HU(self): - try: - self.UB_HU=self.ui.UB_HU.value - self.segmentEditorNode.SetMasterVolumeIntensityMask(True) - self.segmentEditorNode.SetSourceVolumeIntensityMaskRange(self.LB_HU, self.UB_HU) - self.label_config_yaml["labels"][self.current_label_index]["upper_bound_HU"] = self.UB_HU - except: - pass - -class SlicerCARTLogic(ScriptedLoadableModuleLogic): - """This class should implement all the actual - computation done by your module. The interface - should be such that other python code can import - this class and make use of the functionality without - requiring an instance of the Widget. - Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py - """ - - def __init__(self): - """ - Called when the logic class is instantiated. Can be used for initializing member variables. - """ - ScriptedLoadableModuleLogic.__init__(self) - - def setDefaultParameters(self, parameterNode): - """ - Initialize parameter node with default settings. - """ - if not parameterNode.GetParameter("Threshold"): - parameterNode.SetParameter("Threshold", "100.0") - if not parameterNode.GetParameter("Invert"): - parameterNode.SetParameter("Invert", "false") - - def process(self, inputVolume, outputVolume, imageThreshold, invert=False, showResult=True): - """ - Run the processing algorithm. - Can be used without GUI widget. - :param inputVolume: volume to be thresholded - :param outputVolume: thresholding result - :param imageThreshold: values above/below this threshold will be set to 0 - :param invert: if True then values above the threshold will be set to 0, otherwise values below are set to 0 - :param showResult: show output volume in slice viewers - """ - - if not inputVolume or not outputVolume: - raise ValueError("Input or output volume is invalid") - - import time - startTime = time.time() - logging.info('Processing started') - - # Compute the thresholded output volume using the "Threshold Scalar Volume" CLI module - cliParams = { - 'InputVolume': inputVolume.GetID(), - 'OutputVolume': outputVolume.GetID(), - 'ThresholdValue' : imageThreshold, - 'ThresholdType' : 'Above' if invert else 'Below' - } - cliNode = slicer.cli.run(slicer.modules.thresholdscalarvolume, None, cliParams, wait_for_completion=True, update_display=showResult) - # We don't need the CLI module node anymore, remove it to not clutter the scene with it - slicer.mrmlScene.RemoveNode(cliNode) - - stopTime = time.time() - logging.info(f'Processing completed in {stopTime-startTime:.2f} seconds') - -class SlicerCARTTest(ScriptedLoadableModuleTest): - """ - This is the test case for your scripted module. - Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py - """ - - def setUp(self): - """ Do whatever is needed to reset the state - typically a scene clear will be enough. - """ - slicer.mrmlScene.Clear() - - def runTest(self): - """Run as few or as many tests as needed here. - """ - self.setUp() - self.test_SlicerCART1() - - def test_SlicerCART1(self): - """ Ideally you should have several levels of tests. At the lowest level - tests should exercise the functionality of the logic with different inputs - (both valid and invalid). At higher levels your tests should emulate the - way the user would interact with your code and confirm that it still works - the way you intended. - One of the most important features of the tests is that it should alert other - developers when their changes will have an impact on the behavior of your - module. For example, if a developer removes a feature that you depend on, - your test should break so they know that the feature is needed. - """ - - self.delayDisplay("Starting the test") - - # Get/create input data - - import SampleData - registerSampleData() - inputVolume = SampleData.downloadSample('SlicerCART1') - self.delayDisplay('Loaded test data set') - - inputScalarRange = inputVolume.GetImageData().GetScalarRange() - self.assertEqual(inputScalarRange[0], 0) - self.assertEqual(inputScalarRange[1], 695) - - outputVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode") - threshold = 100 - - # Test the module logic - - logic = SlicerCARTLogic() - - # Test algorithm with non-inverted threshold - logic.process(inputVolume, outputVolume, threshold, True) - outputScalarRange = outputVolume.GetImageData().GetScalarRange() - self.assertEqual(outputScalarRange[0], inputScalarRange[0]) - self.assertEqual(outputScalarRange[1], threshold) - - # Test algorithm with inverted threshold - logic.process(inputVolume, outputVolume, threshold, False) - outputScalarRange = outputVolume.GetImageData().GetScalarRange() - self.assertEqual(outputScalarRange[0], inputScalarRange[0]) - self.assertEqual(outputScalarRange[1], inputScalarRange[1]) - - self.delayDisplay('Test passed') diff --git a/SlicerCART/src/resources/UI/SlicerCART.ui b/SlicerCART/src/resources/UI/SlicerCART.ui deleted file mode 100644 index d14f880..0000000 --- a/SlicerCART/src/resources/UI/SlicerCART.ui +++ /dev/null @@ -1,485 +0,0 @@ - - - Form - - - - 0 - 0 - 883 - 1278 - - - - Form - - - - - - Configuration - - - - - - - - Segmentation - - - true - - - - - - Segment Editor - - - - - - - - - Lasso Paint - - - - - - - Visibility: ON - - - true - - - - - - - Undo - - - - - - - Smooth margins - - - - - - - Remove small holes - - - - - - - Fill: OFF - - - true - - - - - - - - - - - Paint - - - - - - - Start - - - true - - - - - - - - - - Pause - - - true - - - - - - - Erase mode - - - - - - - - - - - Saving segmentation - - - Save segmentation - - - Ctrl+S - - - - - - - Load segmentation... - - - - - - - Compare segment versions - - - - - - - Show segment version legend - - - - - - - - - - - Thresholds - - - - - - - Minimum - - - - - - - Maximum - - - - - - - - - - - - - - - Default Min. HU - - - - - - - Default Max. HU - - - - - - - - - Semi-automatic PHE Tool - - - - - - - Launch - - - - - - - Show Result - - - - - - - - - - - - - - Select volumes folder - - - - - - - - - - - Annotator's name - - - - - - - - - - - - - - Degree - - - - - - - - - - - - - Medical Student - - - - - Resident - - - - - Radiologist - - - - - Supervisor - - - - - Research Team - - - - - - - - - - - - Revision step - - - - - - - - - - - - - 0 - First - - - - - 1 - Revision - - - - - 2 - Final - - - - - - - - - - - - - - Interpolate - - - - - - - << Previous - - - - - - - Next >> - - - - - - - - - - - - - - - - Path... - - - - - - - Select output folder - - - - - - - - - Case list - - - - - - - - - - - - - - - - - 16777215 - 350 - - - - Classification - - - true - - - - - - - - Load classification... - - - - - - - Save classification - - - - - - - - - - - - - - - - ctkCollapsibleButton - QWidget -
ctkCollapsibleButton.h
- 1 - - - ctkCollapsibleGroupBox - QGroupBox -
ctkCollapsibleGroupBox.h
- 1 - - - qMRMLCollapsibleButton - ctkCollapsibleButton -
qMRMLCollapsibleButton.h
- 1 - - - qMRMLWidget - QWidget -
qMRMLWidget.h
- 1 - - - - - \ No newline at end of file From 6a5de7c6563ce17daee531d78984b8fbefdf592a Mon Sep 17 00:00:00 2001 From: laurentletg <48111184+laurentletg@users.noreply.github.com> Date: Fri, 12 Jul 2024 08:42:11 -0400 Subject: [PATCH 02/10] added config for window width and level if CT and warning message in onSelectVolumesFolderButton() method --- SlicerCART/src/SlicerCART.py | 2433 +++++++++++++++++++++ SlicerCART/src/general_config.yml | 9 +- SlicerCART/src/resources/UI/SlicerCART.ui | 489 +++++ 3 files changed, 2928 insertions(+), 3 deletions(-) create mode 100644 SlicerCART/src/SlicerCART.py create mode 100644 SlicerCART/src/resources/UI/SlicerCART.ui diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py new file mode 100644 index 0000000..10718ad --- /dev/null +++ b/SlicerCART/src/SlicerCART.py @@ -0,0 +1,2433 @@ +# To install a package in slicer python environment, use the following command: +# pip install --user package_name +import os +import importlib +import logging +import qt, slicer +from slicer.ScriptedLoadableModule import * +from slicer.util import VTKObservationMixin +from glob import glob +import re +import pandas as pd +import time +import slicerio # cannot install in slicer +import nrrd +import yaml +from pathlib import Path +from threading import RLock +from datetime import datetime +from bids_validator import BIDSValidator +import filecmp +import shutil +import nibabel as nib +import numpy as np +import vtk +import random +import colorsys + + +import sys +import os + +import sys +import os + + +# TODO: There is probably a more elegant way to install pacakages through the extension manager when the user installs the extension. +REQUIRED_PYTHON_PACKAGES = { + "nibabel": "nibabel", + "bids_validator": "bids_validator" +} + + +def check_and_install_python_packages(): + for pip_name, import_name in REQUIRED_PYTHON_PACKAGES.items(): + try: + __import__(import_name) + except ImportError: + msg = "SlicerCART module: The following required python package is missing:" + msg += f"\n{pip_name}" + msg += "\nWould you like to install them now?" + response = qt.QMessageBox.question(slicer.util.mainWindow(), 'Install Extensions', msg, + qt.QMessageBox.Yes | qt.QMessageBox.No) + + if response == qt.QMessageBox.Yes: + slicer.util.pip_install(pip_name) + # Wait for the installation to complete and restart Slicer + slicer.app.processEvents() + qt.QMessageBox.information(slicer.util.mainWindow(), 'Restart Slicer', + 'Slicer will now restart to complete the installation.') + slicer.app.restart() + else: + qt.QMessageBox.warning(slicer.util.mainWindow(), 'Missing Extensions', + 'The SlicerCART module cannot be loaded without the required extensions.') + + +check_and_install_python_packages() + + +INPUT_FILE_EXTENSION = '*.nii.gz' +INTERPOLATE_VALUE = 0 + +DEFAULT_VOLUMES_DIRECTORY = '' +DEFAULT_SEGMENTATION_DIRECTORY = '' + +REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT = False + +IS_CLASSIFICATION_REQUESTED = True +IS_SEGMENTATION_REQUESTED = True +IS_SEMI_AUTOMATIC_PHE_TOOL_REQUESTED = True + +MODALITY = 'CT' + +LABEL_CONFIG_FILE_PATH = os.path.join(Path(__file__).parent.resolve(), "label_config.yml") +KEYBOARD_SHORTCUTS_CONFIG_FILE_PATH = os.path.join(Path(__file__).parent.resolve(), "keyboard_shortcuts_config.yml") +CLASSIFICATION_CONFIG_FILE_PATH = os.path.join(Path(__file__).parent.resolve(), "classification_config.yml") +GENERAL_CONFIG_FILE_PATH = os.path.join(Path(__file__).parent.resolve(), "general_config.yml") + +CT_WINDOW_WIDTH = 90 +CT_WINDOW_LEVEL = 45 + + + +TIMER_MUTEX = RLock() + +class LoadClassificationWindow(qt.QWidget): + def __init__(self, segmenter, classificationInformation_df, parent = None): + super(LoadClassificationWindow, self).__init__(parent) + + self.classificationInformation_df = classificationInformation_df + + self.segmenter = segmenter + + layout = qt.QVBoxLayout() + + self.versionTableView = qt.QTableWidget() + layout.addWidget(self.versionTableView) + + buttonLayout = qt.QHBoxLayout() + + versionLabel = qt.QLabel() + versionLabel.setText('Classification version to load: ') + versionLabel.setStyleSheet("font-weight: bold") + buttonLayout.addWidget(versionLabel) + + self.versionDropdown = qt.QComboBox() + buttonLayout.addWidget(self.versionDropdown) + + layout.addLayout(buttonLayout) + + if classificationInformation_df.shape[0] > 0: + available_versions = classificationInformation_df['Classification version'].to_list() + for v in available_versions: + self.versionDropdown.addItem(v) + + self.versionTableView.setRowCount(len(available_versions)) + self.versionTableView.setColumnCount(4) + self.versionTableView.horizontalHeader().setStretchLastSection(True) + self.versionTableView.horizontalHeader().setSectionResizeMode(qt.QHeaderView.Stretch) + + for index, row in classificationInformation_df.iterrows(): + cell = qt.QTableWidgetItem(row['Classification version']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 0, cell) + self.versionTableView.setHorizontalHeaderItem(0, qt.QTableWidgetItem('Version')) + + cell = qt.QTableWidgetItem(row['Annotator Name']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 1, cell) + self.versionTableView.setHorizontalHeaderItem(1, qt.QTableWidgetItem('Annotator')) + + cell = qt.QTableWidgetItem(row['Annotator degree']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 2, cell) + self.versionTableView.setHorizontalHeaderItem(2, qt.QTableWidgetItem('Degree')) + + cell = qt.QTableWidgetItem(row['Date and time']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 3, cell) + self.versionTableView.setHorizontalHeaderItem(3, qt.QTableWidgetItem('Date and Time')) + + self.loadButton = qt.QPushButton('Load') + self.loadButton.clicked.connect(self.pushLoad) + layout.addWidget(self.loadButton) + + self.cancelButton = qt.QPushButton('Cancel') + self.cancelButton.clicked.connect(self.pushCancel) + layout.addWidget(self.cancelButton) + + self.setLayout(layout) + self.setWindowTitle("Load Classification") + self.resize(800, 400) + + def pushLoad(self): + selected_version = self.versionDropdown.currentText + + selected_version_df = self.classificationInformation_df[self.classificationInformation_df['Classification version']==selected_version].reset_index(drop = True) + + for i, (objectName, label) in enumerate(self.segmenter.classification_config_yaml["checkboxes"].items()): + if selected_version_df.at[0, label] == 'Yes': + self.segmenter.checkboxWidgets[objectName].setChecked(True) + elif selected_version_df.at[0, label] == 'No': + self.segmenter.checkboxWidgets[objectName].setChecked(False) + + for i, (comboBoxName, options) in enumerate(self.segmenter.classification_config_yaml["comboboxes"].items()): + self.segmenter.comboboxWidgets[comboBoxName].setCurrentText(selected_version_df.at[0, comboBoxName.replace("_", " ").capitalize()]) + + for i, (freeTextBoxObjectName, label) in enumerate(self.segmenter.classification_config_yaml["freetextboxes"].items()): + saved_text = selected_version_df.at[0, label.capitalize()] + if str(saved_text) != 'nan': + self.segmenter.freeTextBoxes[freeTextBoxObjectName].setText(saved_text) + else: + self.segmenter.freeTextBoxes[freeTextBoxObjectName].setText("") + + self.close() + + def pushCancel(self): + self.close() + +class ShowSegmentVersionLegendWindow(qt.QWidget): + def __init__(self, segmenter, segmentationInformation_df, parent = None): + super(ShowSegmentVersionLegendWindow, self).__init__(parent) + + self.segmentationInformation_df = segmentationInformation_df + + self.segmenter = segmenter + + layout = qt.QVBoxLayout() + + informativeLabel = qt.QLabel() + informativeLabel.setText(f'Legend of [{self.segmenter.labelOfCompareSegmentVersions}] segment versions') + layout.addWidget(informativeLabel) + + self.versionTableView = qt.QTableWidget() + layout.addWidget(self.versionTableView) + + if segmentationInformation_df.shape[0] > 0: + + self.versionTableView.setRowCount(len(self.segmenter.colorsSelectedVersionFilePathsForCompareSegmentVersions)) + self.versionTableView.setColumnCount(5) + self.versionTableView.horizontalHeader().setStretchLastSection(True) + self.versionTableView.horizontalHeader().setSectionResizeMode(qt.QHeaderView.Stretch) + + for index, row in segmentationInformation_df.iterrows(): + currentColor = None + for (segment_name, color) in self.segmenter.colorsSelectedVersionFilePathsForCompareSegmentVersions.items(): + if row['Segmentation version'] in segment_name: + currentColor = color + + colorItem = qt.QTableWidgetItem() + colorItem.setBackground(qt.QBrush(qt.QColor(currentColor[0], currentColor[1], currentColor[2]))) + self.versionTableView.setItem(index, 0, colorItem) + self.versionTableView.setHorizontalHeaderItem(0, qt.QTableWidgetItem('Color')) + + cell = qt.QTableWidgetItem(row['Segmentation version']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 1, cell) + self.versionTableView.setHorizontalHeaderItem(1, qt.QTableWidgetItem('Version')) + + cell = qt.QTableWidgetItem(row['Annotator Name']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 2, cell) + self.versionTableView.setHorizontalHeaderItem(2, qt.QTableWidgetItem('Annotator')) + + cell = qt.QTableWidgetItem(row['Annotator degree']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 3, cell) + self.versionTableView.setHorizontalHeaderItem(3, qt.QTableWidgetItem('Degree')) + + cell = qt.QTableWidgetItem(row['Date and time']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 4, cell) + self.versionTableView.setHorizontalHeaderItem(4, qt.QTableWidgetItem('Date and Time')) + + self.cancelButton = qt.QPushButton('Done') + self.cancelButton.clicked.connect(self.pushCancel) + layout.addWidget(self.cancelButton) + + self.setLayout(layout) + self.setWindowTitle("Legend of Segment Versions") + self.resize(800, 200) + + def pushCancel(self): + self.close() + +class CompareSegmentVersionsWindow(qt.QWidget): + def __init__(self, segmenter, segmentationInformation_df, parent = None): + super(CompareSegmentVersionsWindow, self).__init__(parent) + + self.segmentationInformation_df = segmentationInformation_df + + self.segmenter = segmenter + + layout = qt.QVBoxLayout() + + informativeLabel = qt.QLabel() + informativeLabel.setText('READ ONLY feature. Please use the Load Segmentation button to modify an existing segmentation.') + layout.addWidget(informativeLabel) + + self.versionTableView = qt.QTableWidget() + layout.addWidget(self.versionTableView) + + buttonLayout = qt.QHBoxLayout() + + labelLabel = qt.QLabel() + labelLabel.setText('Label of interest for comparison ') + labelLabel.setStyleSheet("font-weight: bold") + buttonLayout.addWidget(labelLabel) + + self.labelDropdown = qt.QComboBox() + for label in self.segmenter.label_config_yaml['labels']: + self.labelDropdown.addItem(label['name']) + buttonLayout.addWidget(self.labelDropdown) + + layout.addLayout(buttonLayout) + + self.versionCheckboxWidgets = {} + + if segmentationInformation_df.shape[0] > 0: + available_versions = segmentationInformation_df['Segmentation version'].to_list() + + self.versionTableView.setRowCount(len(available_versions)) + self.versionTableView.setColumnCount(5) + self.versionTableView.horizontalHeader().setStretchLastSection(True) + self.versionTableView.horizontalHeader().setSectionResizeMode(qt.QHeaderView.Stretch) + + for index, row in segmentationInformation_df.iterrows(): + checkboxItem = qt.QTableWidgetItem() + checkboxItem.setFlags(qt.Qt.ItemIsUserCheckable | qt.Qt.ItemIsEnabled) + checkboxItem.setCheckState(qt.Qt.Unchecked) + checkboxItem.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 0, checkboxItem) + self.versionTableView.setHorizontalHeaderItem(0, qt.QTableWidgetItem('Select')) + self.versionCheckboxWidgets[index] = checkboxItem + + cell = qt.QTableWidgetItem(row['Segmentation version']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 1, cell) + self.versionTableView.setHorizontalHeaderItem(1, qt.QTableWidgetItem('Version')) + + cell = qt.QTableWidgetItem(row['Annotator Name']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 2, cell) + self.versionTableView.setHorizontalHeaderItem(2, qt.QTableWidgetItem('Annotator')) + + cell = qt.QTableWidgetItem(row['Annotator degree']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 3, cell) + self.versionTableView.setHorizontalHeaderItem(3, qt.QTableWidgetItem('Degree')) + + cell = qt.QTableWidgetItem(row['Date and time']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 4, cell) + self.versionTableView.setHorizontalHeaderItem(4, qt.QTableWidgetItem('Date and Time')) + + self.viewSegmentsButton = qt.QPushButton('Compare') + self.viewSegmentsButton.clicked.connect(self.pushViewSegmentsButton) + layout.addWidget(self.viewSegmentsButton) + + self.cancelButton = qt.QPushButton('Cancel') + self.cancelButton.clicked.connect(self.pushCancel) + layout.addWidget(self.cancelButton) + + self.setLayout(layout) + self.setWindowTitle("[READ ONLY] Compare Segment Versions") + self.resize(800, 400) + + def pushViewSegmentsButton(self): + selected_label = self.labelDropdown.currentText + selected_version_file_paths = {} + + segmentation_file_extension = "" + if "nii" in INPUT_FILE_EXTENSION: + segmentation_file_extension = ".nii.gz" + elif "nrrd" in INPUT_FILE_EXTENSION: + segmentation_file_extension = ".seg.nrrd" + + for index, row in self.segmentationInformation_df.iterrows(): + if self.versionCheckboxWidgets[index].checkState() > 0: + selected_version = row['Segmentation version'] + absolute_path_to_segmentation = f'{self.segmenter.currentOutputPath}{os.sep}{self.segmenter.currentVolumeFilename}_{selected_version}{segmentation_file_extension}' + selected_version_file_paths[f"{selected_label}_{selected_version}_{row['Annotator Name']}"] = absolute_path_to_segmentation + + self.segmenter.compareSegmentVersions(selected_label, selected_version_file_paths) + + self.close() + + def pushCancel(self): + self.close() + +class LoadSegmentationsWindow(qt.QWidget): + def __init__(self, segmenter, segmentationInformation_df, parent = None): + super(LoadSegmentationsWindow, self).__init__(parent) + + self.segmentationInformation_df = segmentationInformation_df + + self.segmenter = segmenter + + layout = qt.QVBoxLayout() + + self.versionTableView = qt.QTableWidget() + layout.addWidget(self.versionTableView) + + buttonLayout = qt.QHBoxLayout() + + versionLabel = qt.QLabel() + versionLabel.setText('Segmentation version to load: ') + versionLabel.setStyleSheet("font-weight: bold") + buttonLayout.addWidget(versionLabel) + + self.versionDropdown = qt.QComboBox() + buttonLayout.addWidget(self.versionDropdown) + + layout.addLayout(buttonLayout) + + if segmentationInformation_df.shape[0] > 0: + available_versions = segmentationInformation_df['Segmentation version'].to_list() + for v in available_versions: + self.versionDropdown.addItem(v) + + self.versionTableView.setRowCount(len(available_versions)) + self.versionTableView.setColumnCount(4) + self.versionTableView.horizontalHeader().setStretchLastSection(True) + self.versionTableView.horizontalHeader().setSectionResizeMode(qt.QHeaderView.Stretch) + + for index, row in segmentationInformation_df.iterrows(): + cell = qt.QTableWidgetItem(row['Segmentation version']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 0, cell) + self.versionTableView.setHorizontalHeaderItem(0, qt.QTableWidgetItem('Version')) + + cell = qt.QTableWidgetItem(row['Annotator Name']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 1, cell) + self.versionTableView.setHorizontalHeaderItem(1, qt.QTableWidgetItem('Annotator')) + + cell = qt.QTableWidgetItem(row['Annotator degree']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 2, cell) + self.versionTableView.setHorizontalHeaderItem(2, qt.QTableWidgetItem('Degree')) + + cell = qt.QTableWidgetItem(row['Date and time']) + cell.setFlags(qt.Qt.NoItemFlags) + cell.setForeground(qt.QBrush(qt.QColor(0, 0, 0))) + self.versionTableView.setItem(index, 3, cell) + self.versionTableView.setHorizontalHeaderItem(3, qt.QTableWidgetItem('Date and Time')) + + self.loadButton = qt.QPushButton('Load') + self.loadButton.clicked.connect(self.pushLoad) + layout.addWidget(self.loadButton) + + self.cancelButton = qt.QPushButton('Cancel') + self.cancelButton.clicked.connect(self.pushCancel) + layout.addWidget(self.cancelButton) + + self.setLayout(layout) + self.setWindowTitle("Load Segmentations") + self.resize(800, 400) + + def pushLoad(self): + selected_version = self.versionDropdown.currentText + + segmentation_file_extension = "" + if "nii" in INPUT_FILE_EXTENSION: + segmentation_file_extension = ".nii.gz" + elif "nrrd" in INPUT_FILE_EXTENSION: + segmentation_file_extension = ".seg.nrrd" + + absolute_path_to_segmentation = f'{self.segmenter.currentOutputPath}{os.sep}{self.segmenter.currentVolumeFilename}_{selected_version}{segmentation_file_extension}' + self.segmenter.loadSegmentation(absolute_path_to_segmentation) + + self.close() + + def pushCancel(self): + self.close() + +class SemiAutoPheToolThresholdWindow(qt.QWidget): + def __init__(self, segmenter, parent = None): + super(SemiAutoPheToolThresholdWindow, self).__init__(parent) + + self.segmenter = segmenter + self.LB_HU_value = segmenter.LB_HU + self.UB_HU_value = segmenter.UB_HU + + layout = qt.QVBoxLayout() + self.textLabel = qt.QLabel("Threshold bounds: ") + self.textLabel.setStyleSheet("font-weight: bold") + layout.addWidget(self.textLabel) + + self.minimumLabel = qt.QLabel("Minimum") + layout.addWidget(self.minimumLabel) + + self.semiAutoPHE_LB_HU_spinbox = qt.QSpinBox() + self.semiAutoPHE_LB_HU_spinbox.valueChanged.connect(self.LB_HU_valueChanged) + layout.addWidget(self.semiAutoPHE_LB_HU_spinbox) + self.semiAutoPHE_LB_HU_spinbox.setMinimum(-32000) + self.semiAutoPHE_LB_HU_spinbox.setMaximum(29000) + self.semiAutoPHE_LB_HU_spinbox.setValue(self.LB_HU_value) + + self.maximumLabel = qt.QLabel("Maximum") + layout.addWidget(self.maximumLabel) + + self.semiAutoPHE_UB_HU_spinbox = qt.QSpinBox() + self.semiAutoPHE_UB_HU_spinbox.valueChanged.connect(self.UB_HU_valueChanged) + layout.addWidget(self.semiAutoPHE_UB_HU_spinbox) + self.semiAutoPHE_UB_HU_spinbox.setMinimum(-32000) + self.semiAutoPHE_UB_HU_spinbox.setMaximum(29000) + self.semiAutoPHE_UB_HU_spinbox.setValue(self.UB_HU_value) + + self.continueButton = qt.QPushButton('Continue') + self.continueButton.clicked.connect(self.pushContinue) + layout.addWidget(self.continueButton) + + self.cancelButton = qt.QPushButton('Cancel') + self.cancelButton.clicked.connect(self.pushCancel) + layout.addWidget(self.cancelButton) + + self.setLayout(layout) + self.setWindowTitle("Semi-automatic PHE Tool") + self.resize(400, 200) + + def UB_HU_valueChanged(self): + self.UB_HU_value = self.semiAutoPHE_UB_HU_spinbox.value + self.segmenter.ApplyThresholdPHE(self.LB_HU_value, self.UB_HU_value) + + def LB_HU_valueChanged(self): + self.LB_HU_value = self.semiAutoPHE_LB_HU_spinbox.value + self.segmenter.ApplyThresholdPHE(self.LB_HU_value, self.UB_HU_value) + + def pushContinue(self): + self.segmenter.setUpperAndLowerBoundHU(self.LB_HU_value, self.UB_HU_value) + + self.instructionsWindow = SemiAutoPheToolInstructionsWindow(self.segmenter) + self.instructionsWindow.show() + + self.close() + + def pushCancel(self): + self.segmenter.ClearPHESegment() + self.close() + +class SemiAutoPheToolInstructionsWindow(qt.QWidget): + def __init__(self, segmenter, parent = None): + super(SemiAutoPheToolInstructionsWindow, self).__init__(parent) + + self.segmenter = segmenter + + layout = qt.QVBoxLayout() + self.textLabel = qt.QLabel("Instructions:") + self.textLabel.setStyleSheet("font-weight: bold") + layout.addWidget(self.textLabel) + + self.minimumLabel = qt.QLabel("Click Continue and draw a generous boundary of the ICH and PHE complex. Note that the boundary may be drawn in multiple views. When you are finished drawing the boundary, click on Show Result in the main extension menu. " + + "The HU thresholds and manual fine-tuning of included voxels are left to the annotator\'s discretion. " + + "\n(If a popup message about visibility shows up, click No.)") + self.minimumLabel.setWordWrap(True) + layout.addWidget(self.minimumLabel) + + self.continueButton = qt.QPushButton('Continue') + self.continueButton.clicked.connect(self.pushContinue) + layout.addWidget(self.continueButton) + + self.cancelButton = qt.QPushButton('Cancel') + self.cancelButton.clicked.connect(self.pushCancel) + layout.addWidget(self.cancelButton) + + self.setLayout(layout) + self.setWindowTitle("Semi-automatic PHE Tool") + self.resize(400, 200) + + def pushContinue(self): + self.segmenter.ApplySemiAutomaticThresholdAlgorithm() + self.close() + + def pushCancel(self): + self.segmenter.ClearPHESegment() + self.close() + + + +class OptionalMethods(): + + + +class SlicerCART(ScriptedLoadableModule): + """Uses ScriptedLoadableModule base class, available at: + https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + """ + + def __init__(self, parent): + ScriptedLoadableModule.__init__(self, parent) + self.parent.title = "SlicerCART" # TODO: make this more human readable by adding spaces + self.parent.categories = ["Examples"] # TODO: set categories (folders where the module shows up in the module selector) + self.parent.dependencies = [] # TODO: add here list of module names that this module requires + self.parent.contributors = ["Delphine Pilon, An Ni Wu, Emmanuel Montagnon, Maxime Bouthillier, Laurent Letourneau-Guillon"] # TODO: replace with "Firstname Lastname (Organization)" + # TODO: update with short description of the module and a link to online module documentation + self.parent.helpText = """ +This is an example of scripted loadable module bundled in an extension. +See more information in module documentation. +""" + # TODO: replace with organization, grant and thanks + self.parent.acknowledgementText = """ +Module supported by funding from : +1. Fonds de Recherche du Québec en Santé and Fondation de l’Association des Radiologistes du Québec +Radiology Research funding (299979) and Clinical Research Scholarship–Junior 1 Salary Award (311203) +2. Foundation of the Radiological Society of North America - Seed Grant (RSD2122) +3. Quebec Bio-Imaging Network, 2022 pilot project grant (Project no 21.24) +4. Support professoral du Département de radiologie, radio-oncologie et médecine nucléaire de l’Université de Montréal, Radiology departement Centre Hospitalier de l’Université de Montréal (CHUM) and CHUM Research Center (CRCHUM) start-up funds + +Thanks to the Slicer community for the support and the development of the software. + +""" + +class Timer(): + def __init__(self, number=None): + with TIMER_MUTEX: + self.number = number + self.total_time = 0 + self.inter_time = 0 + # counting flag to allow to PAUSE the time + self.flag = False # False = not counting, True = counting (for pause button) + + + def start(self): + with TIMER_MUTEX: + if self.flag == False: + # start counting flag (to allow to pause the time if False) + self.flag = True + self.start_time = time.time() + + + def stop(self): + with TIMER_MUTEX: + if self.flag == True: + self.inter_time = time.time() - self.start_time + self.total_time += self.inter_time + self.flag = False + +# MB CODE BELOW: MOUSE CUSTOMIZATION CLASS +class CustomInteractorStyle(vtk.vtkInteractorStyleImage): + def __init__(self, sliceWidget=None): + self.AddObserver("RightButtonPressEvent", + self.onRightButtonPressEvent) + self.AddObserver("MouseMoveEvent", self.onMouseMoveEvent) + self.AddObserver("RightButtonReleaseEvent", + self.onRightButtonReleaseEvent) + self.AddObserver("MouseWheelForwardEvent", + self.onMouseWheelForwardEvent) + self.AddObserver("MouseWheelBackwardEvent", + self.onMouseWheelBackwardEvent) + self.AddObserver("LeftButtonPressEvent", + self.onLeftButtonPressEvent) + self.AddObserver("LeftButtonReleaseEvent", + self.onLeftButtonReleaseEvent) + self.AddObserver("KeyPressEvent", self.onKeyPressEvent) + self.AddObserver("KeyReleaseEvent", self.onKeyReleaseEvent) + self.startPosition = None + self.sliceWidget = sliceWidget + self.sliceNode = self.sliceWidget.mrmlSliceNode() + self.sliceLogic = slicer.app.applicationLogic().GetSliceLogic( + self.sliceNode) + self.panning = False + self.zooming = False + self.adjustingWindowLevel = False + self.z_pressed = False + + def onRightButtonPressEvent(self, obj, event): + self.startPosition = self.GetInteractor().GetEventPosition() + self.panning = True + self.OnRightButtonDown() + return + + def onMouseMoveEvent(self, obj, event): + if self.panning and self.startPosition: + currentPosition = self.GetInteractor().GetEventPosition() + deltaX = self.startPosition[0] - currentPosition[0] + deltaY = self.startPosition[1] - currentPosition[1] + + # Adjust the image position based on mouse movement + pan = self.sliceNode.GetXYZOrigin() + self.sliceNode.SetXYZOrigin(pan[0] + deltaX, pan[1] + deltaY, + pan[2]) + self.sliceNode.Modified() + + self.startPosition = currentPosition + elif self.adjustingWindowLevel and self.startPosition: + currentPosition = self.GetInteractor().GetEventPosition() + deltaX = currentPosition[0] - self.startPosition[0] + deltaY = self.startPosition[1] - currentPosition[1] + + # Adjust the window level and width based on mouse movement + volumeNode = self.sliceLogic.GetBackgroundLayer().GetVolumeNode() + displayNode = volumeNode.GetDisplayNode() + currentWindowLevel = displayNode.GetLevel() + currentWindowWidth = displayNode.GetWindow() + + newWindowLevel = currentWindowLevel + deltaY + newWindowWidth = currentWindowWidth + deltaX + + displayNode.SetLevel(newWindowLevel) + displayNode.SetWindow(newWindowWidth) + + self.startPosition = currentPosition + + elif self.zooming and self.startPosition: + self.zoom() + self.startPosition = self.GetInteractor().GetEventPosition() + + self.OnMouseMove() + return + + def onRightButtonReleaseEvent(self, obj, event): + self.startPosition = None + self.panning = False + self.OnRightButtonUp() + return + + def onLeftButtonPressEvent(self, obj, event): + self.startPosition = self.GetInteractor().GetEventPosition() + self.adjustingWindowLevel = True + self.OnLeftButtonDown() + return + + def onLeftButtonReleaseEvent(self, obj, event): + self.startPosition = None + self.adjustingWindowLevel = False + self.OnLeftButtonUp() + return + + def onKeyPressEvent(self, obj, event): + key = self.GetInteractor().GetKeySym() + if key == "x": + self.z_pressed = True + self.OnKeyPress() + return + + def onKeyReleaseEvent(self, obj, event): + key = self.GetInteractor().GetKeySym() + if key == "x": + self.z_pressed = False + self.OnKeyRelease() + return + + def onMouseWheelForwardEvent(self, obj, event): + if self.z_pressed: + # print("Mouse scroll") + self.zoom_in() + # print("self zoom done") + else: + # Move to the next slice + currentOffset = self.sliceLogic.GetSliceOffset() + newOffset = currentOffset + self.getSliceSpacing() # Move one + # slice forward + self.sliceLogic.SetSliceOffset(newOffset) + self.OnMouseWheelForward() + return + + def onMouseWheelBackwardEvent(self, obj, event): + if self.z_pressed: + # print("Mouse scroll") + self.zoom_out() + else: + # Move to the previous slice + currentOffset = self.sliceLogic.GetSliceOffset() + newOffset = currentOffset - self.getSliceSpacing() # Move one + # slice backward + self.sliceLogic.SetSliceOffset(newOffset) + self.OnMouseWheelBackward() + return + + def zoom_in(self): + fov = self.sliceNode.GetFieldOfView() + self.sliceNode.SetFieldOfView(fov[0] * 0.9, fov[1] * 0.9, fov[2]) + self.sliceNode.Modified() + + def zoom_out(self): + fov = self.sliceNode.GetFieldOfView() + self.sliceNode.SetFieldOfView(fov[0] / 0.9, fov[1] / 0.9, fov[2]) + self.sliceNode.Modified() + + def zoom(self): + if self.startPosition: + fov = self.sliceNode.GetFieldOfView() + currentPos = self.GetInteractor().GetEventPosition() + deltaY = self.startPosition[1] - currentPos[1] + factor = 1.01 if deltaY > 0 else 0.99 + zoomSpeed = 10 + factor = factor ** (abs(deltaY) / zoomSpeed) + self.sliceNode.SetFieldOfView(fov[0] * factor, fov[1] * factor, + fov[2]) + self.sliceNode.Modified() + + def getSliceSpacing(self): + volumeNode = self.sliceLogic.GetBackgroundLayer().GetVolumeNode() + if volumeNode: + spacing = volumeNode.GetSpacing() + return spacing[2] # Return the spacing along the Z-axis + return 1.0 # Default spacing if volumeNode is not available + +class SlicerCARTWidget(ScriptedLoadableModuleWidget, VTKObservationMixin): + """Uses ScriptedLoadableModuleWidget base class, available at: + https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + """ + + def __init__(self, parent=None): + """ + Called when the user opens the module the first time and the widget is initialized. + """ + ScriptedLoadableModuleWidget.__init__(self, parent) + VTKObservationMixin.__init__(self) # needed for parameter node observation + self.logic = None + self._parameterNode = None + self._updatingGUIFromParameterNode = False + # LLG CODE BELOW + self.predictions_names= None + self.DefaultDir = DEFAULT_VOLUMES_DIRECTORY + + # ----- ANW Addition ----- : Initialize called var to False so the timer only stops once + self.called = False + self.called_onLoadSegmentation = False + + # MB + self.interactor1 = slicer.app.layoutManager().sliceWidget( + 'Yellow').sliceView().interactor() + self.interactor2 = slicer.app.layoutManager().sliceWidget( + 'Red').sliceView().interactor() + + # Apply the custom interactor style + styleYellow = slicer.app.layoutManager().sliceWidget('Yellow') + self.styleYellow = CustomInteractorStyle(sliceWidget=styleYellow) + self.interactor1.SetInteractorStyle(self.styleYellow) + + styleRed = slicer.app.layoutManager().sliceWidget('Red') + self.styleRed = CustomInteractorStyle(sliceWidget=styleRed) + self.interactor2.SetInteractorStyle(self.styleRed) + + def get_keyboard_shortcuts_config_values(self): + with open(KEYBOARD_SHORTCUTS_CONFIG_FILE_PATH, 'r') as file: + self.keyboard_config_yaml = yaml.safe_load(file) + + def get_classification_config_values(self): + with open(CLASSIFICATION_CONFIG_FILE_PATH, 'r') as file: + self.classification_config_yaml = yaml.safe_load(file) + + def get_label_config_values(self): + with open(LABEL_CONFIG_FILE_PATH, 'r') as file: + self.label_config_yaml = yaml.safe_load(file) + + def get_general_config_values(self): + with open(GENERAL_CONFIG_FILE_PATH, 'r') as file: + self.general_config_yaml = yaml.safe_load(file) + + global INPUT_FILE_EXTENSION + global DEFAULT_VOLUMES_DIRECTORY + global DEFAULT_SEGMENTATION_DIRECTORY + global REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT + global MODALITY + global IS_CLASSIFICATION_REQUESTED + global IS_SEGMENTATION_REQUESTED + global IS_SEMI_AUTOMATIC_PHE_TOOL_REQUESTED + global INTERPOLATE_VALUE + global CT_WINDOW_WIDTH + global CT_WINDOW_LEVEL + + INPUT_FILE_EXTENSION = self.general_config_yaml["input_filetype"] + DEFAULT_VOLUMES_DIRECTORY = self.general_config_yaml["default_volume_directory"] + self.DefaultDir = DEFAULT_VOLUMES_DIRECTORY + DEFAULT_SEGMENTATION_DIRECTORY = self.general_config_yaml["default_segmentation_directory"] + MODALITY = self.general_config_yaml["modality"] + IS_CLASSIFICATION_REQUESTED = self.general_config_yaml["is_classification_requested"] + IS_SEGMENTATION_REQUESTED = self.general_config_yaml["is_segmentation_requested"] + IS_SEMI_AUTOMATIC_PHE_TOOL_REQUESTED = self.general_config_yaml["is_semi_automatic_phe_tool_requested"] + INTERPOLATE_VALUE = self.general_config_yaml["interpolate_value"] + + if MODALITY == 'CT': + # then BIDS not mandatory because it is not yet supported + # therefore, either .nrrd or .nii.gz accepted + REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT = False + CT_WINDOW_WIDTH = self.general_config_yaml["ct_window_width"] + CT_WINDOW_LEVEL = self.general_config_yaml["ct_window_level"] + + elif MODALITY == 'MRI': + # therefore, .nii.gz required + INPUT_FILE_EXTENSION = '*.nii.gz' + # user can decide whether to impose bids or not + REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT = self.general_config_yaml["impose_bids_format"] + + + def setup(self): + """ + Called when the user opens the module the first time and the widget is initialized. + """ + ### Segment editor widget + self.layout.setContentsMargins(4, 0, 4, 0) + + ScriptedLoadableModuleWidget.setup(self) + + # Load widget from .ui file (created by Qt Designer). + # Additional widgets can be instantiated manually and added to self.layout. + uiWidget = slicer.util.loadUI(self.resourcePath('UI/SlicerCART.ui')) + self.layout.addWidget(uiWidget) + self.ui = slicer.util.childWidgetVariables(uiWidget) + + # Set scene in MRML widgets. Make sure that in Qt designer the top-level qMRMLWidget's + # "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's. + # "setMRMLScene(vtkMRMLScene*)" slot. + uiWidget.setMRMLScene(slicer.mrmlScene) + + # Create logic class. Logic implements all computations that should be possible to run + # in batch mode, without a graphical user interface. + self.logic = SlicerCARTLogic() + self.get_label_config_values() + self.get_keyboard_shortcuts_config_values() + self.get_classification_config_values() + self.get_general_config_values() + + self.outputFolder = None + self.currentCasePath = None + self.CurrentFolder = None + + self.LB_HU = self.label_config_yaml["labels"][0]["lower_bound_HU"] + self.UB_HU = self.label_config_yaml["labels"][0]["upper_bound_HU"] + + + self.ui.PauseTimerButton.setText('Pause') + self.ui.SelectVolumeFolder.connect('clicked(bool)', self.onSelectVolumesFolderButton) + self.ui.SlicerDirectoryListView.clicked.connect(self.getCurrentTableItem) + self.ui.SaveSegmentationButton.connect('clicked(bool)', self.onSaveSegmentationButton) + self.ui.SelectOutputFolder.connect('clicked(bool)', self.onSelectOutputFolder) + self.ui.LoadSegmentation.connect('clicked(bool)', self.onLoadSegmentation) + self.ui.CompareSegmentVersions.connect('clicked(bool)', self.onCompareSegmentVersions) + self.ui.LoadClassification.connect('clicked(bool)', self.onLoadClassification) + self.ui.SaveClassificationButton.connect('clicked(bool)', self.onSaveClassificationButton) + self.ui.pushButton_Interpolate.connect('clicked(bool)', self.onPushButton_Interpolate) + self.ui.Previous.connect('clicked(bool)', self.onPreviousButton) + self.ui.Next.connect('clicked(bool)', self.onNextButton) + self.ui.pushButton_Paint.connect('clicked(bool)', self.onPushButton_Paint) + self.ui.LassoPaintButton.connect('clicked(bool)', self.onPushLassoPaint) + self.ui.pushButton_ToggleVisibility.connect('clicked(bool)', self.onPushButton_ToggleVisibility) + self.ui.PushButton_segmeditor.connect('clicked(bool)', self.onPushButton_segmeditor) + self.ui.pushButton_Erase.connect('clicked(bool)', self.onPushButton_Erase) + self.ui.pushButton_Smooth.connect('clicked(bool)', self.onPushButton_Smooth) + self.ui.pushButton_Small_holes.connect('clicked(bool)', self.onPushButton_Small_holes) + self.ui.pushButton_SemiAutomaticPHE_Launch.connect('clicked(bool)', self.onPushButton_SemiAutomaticPHE_Launch) + self.ui.pushButton_SemiAutomaticPHE_ShowResult.connect('clicked(bool)', self.onPushButton_SemiAutomaticPHE_ShowResult) + self.ui.dropDownButton_label_select.currentIndexChanged.connect(self.onDropDownButton_label_select) + self.ui.PauseTimerButton.connect('clicked(bool)', self.togglePauseTimerButton) + self.ui.StartTimerButton.connect('clicked(bool)', self.toggleStartTimerButton) + self.ui.pushButton_ToggleFill.connect('clicked(bool)', self.toggleFillButton) + self.ui.UB_HU.valueChanged.connect(self.onUB_HU) + self.ui.LB_HU.valueChanged.connect(self.onLB_HU) + self.ui.pushDefaultMin.connect('clicked(bool)', self.onPushDefaultMin) + self.ui.pushDefaultMax.connect('clicked(bool)', self.onPushDefaultMax) + self.ui.pushButton_undo.connect('clicked(bool)', self.onPushButton_undo) + self.ui.ShowSegmentVersionLegendButton.connect('clicked(bool)', self.onPush_ShowSegmentVersionLegendButton) + + self.ui.ShowSegmentVersionLegendButton.setVisible(False) + + # Display the selected color view at module startup + if self.general_config_yaml['slice_view_color'] == "Yellow": + slicer.app.layoutManager().setLayout( + slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpYellowSliceView) + if self.general_config_yaml['slice_view_color'] == "Red": + slicer.app.layoutManager().setLayout( + slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView) + if self.general_config_yaml['slice_view_color'] == "Green": + slicer.app.layoutManager().setLayout( + slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpGreenSliceView) + + for label in self.label_config_yaml["labels"]: + self.ui.dropDownButton_label_select.addItem(label["name"]) + + self.ui.pushButton_SemiAutomaticPHE_ShowResult.setEnabled(False) + self.disablePauseTimerButton() + self.disableSegmentAndPaintButtons() + self.ui.pushButton_Interpolate.setEnabled(False) + self.ui.SaveSegmentationButton.setEnabled(False) + + self.enableStartTimerButton() + + self.ui.LoadClassification.setEnabled(False) + self.ui.SaveClassificationButton.setEnabled(False) + self.ui.LoadSegmentation.setEnabled(False) + + self.ui.ThresholdLabel.setStyleSheet("font-weight: bold") + self.ui.SemiAutomaticPHELabel.setStyleSheet("font-weight: bold") + + self.ui.UB_HU.setMinimum(-32000) + self.ui.LB_HU.setMinimum(-32000) + self.ui.UB_HU.setMaximum(29000) + self.ui.LB_HU.setMaximum(29000) + + self.ui.pushButton_ToggleFill.setStyleSheet("background-color : indianred") + self.ui.pushButton_ToggleVisibility.setStyleSheet("background-color : yellowgreen") + self.ui.lcdNumber.setStyleSheet("background-color : black") + + # Change the value of the upper and lower bound of the HU + self.ui.UB_HU.setValue(self.UB_HU) + self.ui.LB_HU.setValue(self.LB_HU) + + comboboxesStartRow = self.setupCheckboxes(3) + freetextStartRow = self.setupComboboxes(comboboxesStartRow) + self.setupFreeText(freetextStartRow) + + # Initialize timers + self.timers = [] + timer_index = 0 + for label in self.label_config_yaml["labels"]: + self.timers.append(Timer(number=timer_index)) + timer_index = timer_index + 1 + + self.MostRecentPausedCasePath = "" + + if not IS_CLASSIFICATION_REQUESTED: + self.ui.MRMLCollapsibleButton.setVisible(False) + if not IS_SEGMENTATION_REQUESTED: + self.ui.MRMLCollapsibleButton_2.setVisible(False) + if not IS_SEMI_AUTOMATIC_PHE_TOOL_REQUESTED: + self.ui.SemiAutomaticPHELabel.setVisible(False) + self.ui.pushButton_SemiAutomaticPHE_Launch.setVisible(False) + self.ui.pushButton_SemiAutomaticPHE_ShowResult.setVisible(False) + + for i in self.keyboard_config_yaml["KEYBOARD_SHORTCUTS"]: + + shortcutKey = i.get("shortcut") + callback_name = i.get("callback") + button_name = i.get("button") + + button = getattr(self.ui, button_name) + callback = getattr(self, callback_name) + + self.connectShortcut(shortcutKey, button, callback) + + def setupCheckboxes(self, number_of_columns): + self.checkboxWidgets = {} + + for i, (objectName, label) in enumerate(self.classification_config_yaml["checkboxes"].items()): + checkbox = qt.QCheckBox() + checkbox.setText(label) + checkbox.setObjectName(objectName) + + row_index = i / number_of_columns + 1 + column_index = i % number_of_columns + + self.ui.ClassificationGridLayout.addWidget(checkbox, row_index, column_index) + self.checkboxWidgets[objectName] = checkbox + + return row_index + 1 + + def setupComboboxes(self, start_row): + self.comboboxWidgets = {} + + row_index = start_row + for i, (comboBoxName, options) in enumerate(self.classification_config_yaml["comboboxes"].items()): + comboboxLabel = qt.QLabel(comboBoxName.replace("_", " ").capitalize() + " :") + comboboxLabel.setStyleSheet("font-weight: bold") + self.ui.ClassificationGridLayout.addWidget(comboboxLabel, row_index, 0) + + combobox = qt.QComboBox() + combobox.setObjectName(comboBoxName) + for optionKey, optionLabel in options.items(): + combobox.addItem(optionLabel, optionKey) + self.ui.ClassificationGridLayout.addWidget(combobox, row_index, 1) + self.comboboxWidgets[comboBoxName] = combobox + row_index = row_index + 1 + return row_index + 1 + + def setupFreeText(self, start_row): + self.freeTextBoxes = {} + + row_index = start_row + for i, (freeTextObjectName, freeTextLabel) in enumerate(self.classification_config_yaml["freetextboxes"].items()): + freeTextQLabel = qt.QLabel(freeTextLabel.capitalize() + " :") + freeTextQLabel.setStyleSheet("font-weight: bold") + self.ui.ClassificationGridLayout.addWidget(freeTextQLabel, row_index, 0) + lineEdit = qt.QLineEdit() + self.freeTextBoxes[freeTextObjectName] = lineEdit + self.ui.ClassificationGridLayout.addWidget(lineEdit, row_index, 1) + row_index = row_index + 1 + + def connectShortcut(self, shortcutKey, button, callback): + shortcut = qt.QShortcut(slicer.util.mainWindow()) + shortcut.setKey(qt.QKeySequence(shortcutKey)) + shortcut.connect("activated()", lambda: self.toggleKeyboardShortcut(button, callback)) + return shortcut + + def toggleKeyboardShortcut(self, button, callback): + button.toggle() + callback() + + def setUpperAndLowerBoundHU(self, inputLB_HU, inputUB_HU): + self.LB_HU = inputLB_HU + self.UB_HU = inputUB_HU + self.ui.UB_HU.setValue(self.UB_HU) + self.ui.LB_HU.setValue(self.LB_HU) + + def enableSegmentAndPaintButtons(self): + self.ui.pushButton_Paint.setEnabled(True) + self.ui.LassoPaintButton.setEnabled(True) + self.ui.pushButton_Erase.setEnabled(True) + self.ui.pushButton_SemiAutomaticPHE_Launch.setEnabled(True) + + def disableSegmentAndPaintButtons(self): + self.ui.pushButton_Paint.setEnabled(False) + self.ui.LassoPaintButton.setEnabled(False) + self.ui.pushButton_SemiAutomaticPHE_Launch.setEnabled(False) + self.ui.pushButton_SemiAutomaticPHE_ShowResult.setEnabled(False) + self.ui.pushButton_Erase.setEnabled(False) + + def onSelectVolumesFolderButton(self): + self.CurrentFolder= qt.QFileDialog.getExistingDirectory(None,"Open a folder", self.DefaultDir, qt.QFileDialog.ShowDirsOnly) + + file_structure_valid = True + if REQUIRE_VOLUME_DATA_HIERARCHY_BIDS_FORMAT == True: + file_structure_valid = self.validateBIDS(self.CurrentFolder) + + if file_structure_valid == False: + return # don't load any patient cases + + self.CasesPaths = sorted(glob(f'{self.CurrentFolder}{os.sep}**{os.sep}{INPUT_FILE_EXTENSION}', recursive = True)) + + if not self.CasesPaths: + msg_box = qt.QMessageBox() + msg_box.setWindowTitle("No files found") + msg_box.setIcon(qt.QMessageBox.Warning) + text = "No files found in the selected directory!" + text += "\n\nMake sure the configured extension is in the right format." + text += "\n\nThen restart the module" + msg_box.setText(text) + msg_box.exec() + return + + self.Cases = sorted([os.path.split(i)[-1] for i in self.CasesPaths]) + + self.ui.SlicerDirectoryListView.clear() + self.ui.SlicerDirectoryListView.addItems(self.Cases) + + self.ui.pushButton_Interpolate.setEnabled(True) + + self.currentCase_index = 0 # THIS IS THE CENTRAL THING THAT HELPS FOR CASE NAVIGATION + self.updateCaseAll() + self.loadPatient() + + def validateBIDS(self, path): + validator = BIDSValidator() + is_structure_valid = True + class InvalidBIDS(Exception): pass + + try: + for subdir, dirs, files in os.walk(path): + for file in files: + if file.endswith(INPUT_FILE_EXTENSION.split("*")[1]): + try: + path = "/sub" + (subdir + "/" + file).split("/sub", 1)[1] + is_valid = validator.is_bids(path) + except: + raise InvalidBIDS + + if is_valid == False: + raise InvalidBIDS + except InvalidBIDS: + msg_box = qt.QMessageBox() + msg_box.setWindowTitle("BIDS Validation") + msg_box.setText("File hierarchy not in proper BIDS format. \n\nInformation : https://bids.neuroimaging.io \n\nTool : https://bids-standard.github.io/bids-validator") + msg_box.exec() + + is_structure_valid = False + + return is_structure_valid + + def updateCaseAll(self): + # All below is dependent on self.currentCase_index updates, + self.currentCase = self.Cases[self.currentCase_index] + self.currentCasePath = self.CasesPaths[self.currentCase_index] + self.updateCurrentPatient() + # Highlight the current case in the list view (when pressing on next o) + self.ui.SlicerDirectoryListView.setCurrentItem(self.ui.SlicerDirectoryListView.item(self.currentCase_index)) + + def getCurrentTableItem(self): + # ----- ANW Addition ----- : Reset timer when change case and uncheck all checkboxes + self.resetTimer() + self.resetClassificationInformation() + + # When an item in SlicerDirectroyListView is selected the case number is printed + # below we update the case index and we need to pass one parameter to the methods since it takes 2 (1 in addition to self) + self.updateCaseIndex(self.ui.SlicerDirectoryListView.currentRow) # Index starts at 0 + # Update the case index + self.currentCase_index = self.ui.SlicerDirectoryListView.currentRow + # Same code in onBrowseFoldersButton, need to update self.currentCase + # note that updateCaseAll() not implemented here - it is called when a case is selected from the list view or next/previous button is clicked + self.currentCase = self.Cases[self.currentCase_index] + self.currentCasePath = self.CasesPaths[self.currentCase_index] + self.updateCurrentPatient() + self.loadPatient() + + # ----- ANW Addition ----- : Reset timer when change case, also reset button status + self.resetTimer() + + def updateCaseIndex(self, index): + # ----- ANW Modification ----- : Numerator on UI should start at 1 instead of 0 for coherence + self.ui.FileIndex.setText('{} / {}'.format(index+1, len(self.Cases))) + + def updateCurrentPatient(self): + self.updateCaseIndex(self.currentCase_index) + + def updateCurrentPath(self): + self.ui.CurrentPath.setReadOnly(True) + self.ui.CurrentPath.setText(self.currentCasePath) + + def loadPatient(self): + timer_index = 0 + self.timers = [] + for label in self.label_config_yaml["labels"]: + self.timers.append(Timer(number = timer_index)) + timer_index = timer_index + 1 + + # reset dropbox to index 0 + self.ui.dropDownButton_label_select.setCurrentIndex(0) + + # timer reset if we come back to same case + self.called = False + + slicer.mrmlScene.Clear() + slicer.util.loadVolume(self.currentCasePath) + self.VolumeNode = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')[0] + self.updateCaseAll() + # Adjust windowing (no need to use self. since this is used locally) + Vol_displayNode = self.VolumeNode.GetDisplayNode() + Vol_displayNode.AutoWindowLevelOff() + Vol_displayNode.SetWindow(85) + Vol_displayNode.SetLevel(45) + Vol_displayNode.SetInterpolate(INTERPOLATE_VALUE) + self.newSegmentation() + + self.updateCurrentOutputPathAndCurrentVolumeFilename() + + def updateCurrentOutputPathAndCurrentVolumeFilename(self): + if self.currentCasePath == None or self.CurrentFolder == None or self.outputFolder == None: + return + + i = 0 + relativePath = '' + for c in self.currentCasePath: + if i >= len(self.CurrentFolder): + relativePath = relativePath + c + i = i + 1 + + self.currentOutputPath = os.path.split(self.outputFolder + relativePath)[0] + self.currentVolumeFilename = os.path.split(self.outputFolder + relativePath)[1].split(".")[0] + + + # Getter method to get the segmentation node name - Not sure if this is really useful here. + @property + def segmentationNodeName(self): + return f"{os.path.split(self.currentCasePath)[1].split('.')[0]}_segmentation" + + + def newSegments(self): + pass + + def onPushButton_NewMask(self): + self.newSegments() + + def onPushButton_Interpolate(self): + global INTERPOLATE_VALUE + INTERPOLATE_VALUE = 1 - INTERPOLATE_VALUE # toggle + + self.VolumeNode.GetDisplayNode().SetInterpolate(INTERPOLATE_VALUE) + + def onPreviousButton(self): + # ----- ANW Addition ----- : Reset timer when change case and uncheck all checkboxes + self.resetTimer() + self.resetClassificationInformation() + + #Code below avoid getting in negative values. + self.currentCase_index = max(0, self.currentCase_index-1) + self.updateCaseAll() + self.loadPatient() + + + + + def onNextButton(self): + # ----- ANW Addition ----- : Reset timer when change case and uncheck all checkboxes + self.resetTimer() + self.resetClassificationInformation() + + # ----- ANW Modification ----- : Since index starts at 0, we need to do len(cases)-1 (instead of len(cases)+1). + # Ex. if we have 10 cases, then len(case)=10 and index goes from 0-9, + # so we have to take the minimum between len(self.Cases)-1 and the currentCase_index (which is incremented by 1 everytime we click the button) + self.currentCase_index = min(len(self.Cases)-1, self.currentCase_index+1) + self.updateCaseAll() + self.loadPatient() + + + + + def newSegmentation(self): + # Create segment editor widget and node + self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor + self.segmentEditorNode = self.segmentEditorWidget.mrmlSegmentEditorNode() + # Create segmentation node (keep it local since we add a new segmentation node) + # Not for reference in other methods + segmentationNode=slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") + # Set segmentation node name + segmentationNode.SetName(self.segmentationNodeName) + # Set segmentation node to segment editor + self.segmentEditorWidget.setSegmentationNode(segmentationNode) + # Set master volume node to segment editor + self.segmentEditorWidget.setSourceVolumeNode(self.VolumeNode) + # set refenrence geometry to Volume node (important for the segmentation to be in the same space as the volume) + segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(self.VolumeNode) + self.createNewSegments() + + # restart the current timer + self.timers[self.current_label_index] = Timer(number=self.current_label_index) + # reset tool + self.segmentEditorWidget.setActiveEffectByName("No editing") + + # Load all segments at once + def createNewSegments(self): + for label in self.label_config_yaml["labels"]: + self.onNewLabelSegm(label["name"], label["color_r"], label["color_g"], label["color_b"], label["lower_bound_HU"], label["upper_bound_HU"]) + + first_label_name = self.label_config_yaml["labels"][0]["name"] + first_label_segment_name = first_label_name + self.onPushButton_select_label(first_label_segment_name, self.label_config_yaml["labels"][0]["lower_bound_HU"], self.label_config_yaml["labels"][0]["upper_bound_HU"]) + + def newSegment(self, segment_name=None): + + self.segment_name = segment_name + srcNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + self.srcSegmentation = srcNode.GetSegmentation() + + # Below will create a new segment if there are no segments in the segmentation node, avoid overwriting existing segments + if not self.srcSegmentation.GetSegmentIDs(): # if there are no segments in the segmentation node + self.segmentationNode=slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + self.segmentationNode.GetSegmentation().AddEmptySegment(self.segment_name) + + # if there are segments in the segmentation node, check if the segment name is already in the segmentation node + if any([self.segment_name in i for i in self.srcSegmentation.GetSegmentIDs()]): + pass + else: + self.segmentationNode=slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + self.segmentationNode.GetSegmentation().AddEmptySegment(self.segment_name) + + return self.segment_name + + def onNewLabelSegm(self, label_name, label_color_r, label_color_g, label_color_b, label_LB_HU, label_UB_HU): + segment_name = self.newSegment(label_name) + self.segmentationNode=slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + self.segmentationNode.UndoEnabledOn() + Segmentation = self.segmentationNode.GetSegmentation() + self.SegmentID = Segmentation.GetSegmentIdBySegmentName(segment_name) + segment = Segmentation.GetSegment(self.SegmentID) + segment.SetColor(label_color_r/255,label_color_g/255,label_color_b/255) + self.onPushButton_select_label(segment_name, label_LB_HU, label_UB_HU) + + def onPushButton_select_label(self, segment_name, label_LB_HU, label_UB_HU): + self.segmentationNode=slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + Segmentation = self.segmentationNode.GetSegmentation() + self.SegmentID = Segmentation.GetSegmentIdBySegmentName(segment_name) + self.segmentEditorNode.SetSelectedSegmentID(self.SegmentID) + self.updateCurrentPath() + self.LB_HU = label_LB_HU + self.UB_HU = label_UB_HU + self.onPushButton_Paint() + + if (self.MostRecentPausedCasePath != self.currentCasePath and self.MostRecentPausedCasePath != ""): + self.timers[self.current_label_index] = Timer(number=self.current_label_index) # new path, new timer + + self.timer_router() + + def onPushButton_SemiAutomaticPHE_Launch(self): + flag_PHE_label_exists = False + PHE_label = None + PHE_label_index = 0 + for label in self.label_config_yaml["labels"]: + if label["name"] == "PHE": + flag_PHE_label_exists = True + PHE_label = label + break + PHE_label_index = PHE_label_index + 1 + assert flag_PHE_label_exists + + PHE_segment_name = f"{self.currentCase}_PHE" + self.onPushButton_select_label(PHE_segment_name, PHE_label["lower_bound_HU"], PHE_label["upper_bound_HU"]) + self.ui.dropDownButton_label_select.setCurrentIndex(PHE_label_index) + toolWindow = SemiAutoPheToolThresholdWindow(self) + toolWindow.show() + + def onPushButton_SemiAutomaticPHE_ShowResult(self): + self.segmentationNode.GetDisplayNode().SetVisibility(True) + self.onPushButton_Erase() + self.ui.pushButton_SemiAutomaticPHE_ShowResult.setEnabled(False) + + def ApplyThresholdPHE(self, inLB_HU, inUB_HU): + self.segmentEditorWidget.setActiveEffectByName("Threshold") + effect = self.segmentEditorWidget.activeEffect() + effect.setParameter("MinimumThreshold",f"{inLB_HU}") + effect.setParameter("MaximumThreshold",f"{inUB_HU}") + effect.self().onApply() + + def ApplySemiAutomaticThresholdAlgorithm(self): + self.ui.pushButton_SemiAutomaticPHE_ShowResult.setEnabled(True) + + self.segmentationNode.GetDisplayNode().SetVisibility(False) + + self.segmentEditorWidget.setActiveEffectByName("Threshold") + effect = self.segmentEditorWidget.activeEffect() + effect.setParameter("MinimumThreshold",f"{self.LB_HU}") + effect.setParameter("MaximumThreshold",f"{self.UB_HU}") + effect.self().onApply() + + self.segmentEditorWidget.setActiveEffectByName("Scissors") + effect = self.segmentEditorWidget.activeEffect() + effect.setParameter("Operation","EraseOutside") + effect.setParameter("Shape","FreeForm") + + def ClearPHESegment(self): + flag_PHE_label_exists = False + PHE_label = None + PHE_label_index = 0 + for label in self.label_config_yaml["labels"]: + if label["name"] == "PHE": + flag_PHE_label_exists = True + PHE_label = label + break + PHE_label_index = PHE_label_index + 1 + assert flag_PHE_label_exists + + segm_name = f"{self.currentCase}_PHE" + self.srcSegmentation.RemoveSegment(segm_name) + self.onNewLabelSegm(PHE_label["name"], PHE_label["color_r"], PHE_label["color_g"], PHE_label["color_b"], PHE_label["lower_bound_HU"], PHE_label["upper_bound_HU"]) + + def startTimer(self): + with TIMER_MUTEX: + self.counter = 0 + # Add flag to avoid counting time when user clicks on save segm button + self.flag2 = True + + # ----- ANW Addition ----- : Code to keep track of time passed with lcdNumber on UI + # Create a timer + self.timer = qt.QTimer() + self.timer.timeout.connect(self.updatelcdNumber) + + # Start the timer and update every second + self.timer.start(100) # 1000 ms = 1 second + + # Call the updatelcdNumber function + self.updatelcdNumber() + + def updatelcdNumber(self): + # Get the time + with TIMER_MUTEX: + if self.flag2: # add flag to avoid counting time when user clicks on save segm button + # the timer sends a signal every second (1000 ms). + self.counter += 1 # the self.timer.timeout.connect(self.updatelcdNumber) function is called every second and updates the counter + + self.ui.lcdNumber.display(self.counter/10) + + + def stopTimer(self): + with TIMER_MUTEX: + # If already called once (i.e when user pressed save segm button but forgot to annotator name), simply return the time + if self.called: + return self.total_time + else: + try: + self.total_time = self.counter/10 + self.timer.stop() + self.flag2 = False # Flag is for the timer to stop counting + self.called = True + # self.time_allocation() + return self.total_time + except AttributeError as e: + print(f'!!! YOU DID NOT START THE COUNTER !!! :: {e}') + return None + + def resetTimer(self): + with TIMER_MUTEX: + # making flag to false : stops the timer + self.flag2 = False # For case after the first one the timer stops until the user clicks on the + self.counter = 0 + self.ui.lcdNumber.display(0) + + # reset button status + self.enableStartTimerButton() + self.disablePauseTimerButton() + self.ui.PauseTimerButton.setText('Pause') + if (self.ui.PauseTimerButton.isChecked()): + self.ui.PauseTimerButton.toggle() + + self.disableSegmentAndPaintButtons() + + def enableStartTimerButton(self): + self.ui.StartTimerButton.setEnabled(True) + self.ui.StartTimerButton.setStyleSheet("background-color : yellowgreen") + if (self.ui.StartTimerButton.isChecked()): + self.ui.StartTimerButton.toggle() + + def disablePauseTimerButton(self): + self.ui.PauseTimerButton.setStyleSheet("background-color : silver") + self.ui.PauseTimerButton.setEnabled(False) + + def toggleStartTimerButton(self): + if (self.ui.SlicerDirectoryListView.count > 0): + if self.ui.StartTimerButton.isChecked(): + self.startTimer() + self.timer_router() + + self.ui.StartTimerButton.setEnabled(False) + self.ui.StartTimerButton.setStyleSheet("background-color : silver") + + self.ui.PauseTimerButton.setEnabled(True) + self.ui.PauseTimerButton.setStyleSheet("background-color : indianred") + + self.enableSegmentAndPaintButtons() + else: + self.ui.StartTimerButton.toggle() + + def togglePauseTimerButton(self): + # if button is checked - Time paused + if self.ui.PauseTimerButton.isChecked(): + # setting background color to light-blue + self.ui.PauseTimerButton.setStyleSheet("background-color : lightblue") + self.ui.PauseTimerButton.setText('Restart') + self.timer.stop() + for indiv_timer in self.timers: + indiv_timer.stop() + self.flag = False + + self.MostRecentPausedCasePath = self.currentCasePath + + self.disableSegmentAndPaintButtons() + self.onPushButton_Erase() + + # if it is unchecked + else: + # set background color back to light-grey + self.ui.PauseTimerButton.setStyleSheet("background-color : indianred") + self.ui.PauseTimerButton.setText('Pause') + self.timer.start(100) + self.timer_router() + self.flag = True + + self.enableSegmentAndPaintButtons() + + # for the timer Class not the LCD one + def timer_router(self): + self.timers[self.current_label_index].start() + self.flag = True + + timer_index = 0 + for timer in self.timers: + if timer_index != self.current_label_index: + timer.stop() + timer_index = timer_index + 1 + + def createFolders(self): + self.revision_step = self.ui.RevisionStep.currentText + if len(self.revision_step) != 0: + if os.path.exists(self.outputFolder) == False: + msgboxtime = qt.QMessageBox() + msgboxtime.setText("Segmentation not saved : output folder invalid!") + msgboxtime.exec() + else: + self.updateCurrentOutputPathAndCurrentVolumeFilename() + + if os.path.exists(self.currentOutputPath) == False: + os.makedirs(self.currentOutputPath) + + else: + msgboxtime = qt.QMessageBox() + msgboxtime.setText("Segmentation not saved : revision step is not defined! \n Please save again with revision step!") + msgboxtime.exec() + + def resetClassificationInformation(self): + for i, (objectName, label) in enumerate(self.classification_config_yaml["checkboxes"].items()): + self.checkboxWidgets[objectName].setChecked(False) + for i, (comboBoxName, options) in enumerate(self.classification_config_yaml["comboboxes"].items()): + self.comboboxWidgets[comboBoxName].currentText = list(options.items())[0][1] + for i, (freeTextBoxObjectName, label) in enumerate(self.classification_config_yaml["freetextboxes"].items()): + self.freeTextBoxes[freeTextBoxObjectName].setText("") + + + def getClassificationInformation(self): + label_string = "" + data_string = "" + for i, (objectName, label) in enumerate(self.classification_config_yaml["checkboxes"].items()): + if label_string != "": + label_string = label_string + "," + data_string = data_string + "," + + label_string = label_string + label + + data = "No" + if self.checkboxWidgets[objectName].isChecked(): + data = "Yes" + + data_string = data_string + data + + for i, (comboBoxName, options) in enumerate(self.classification_config_yaml["comboboxes"].items()): + label = comboBoxName.replace("_", " ").capitalize() + + if label_string != "": + label_string = label_string + "," + data_string = data_string + "," + + label_string = label_string + label + + data = self.comboboxWidgets[comboBoxName].currentText + data_string = data_string + data + + for i, (freeTextBoxObjectName, label) in enumerate(self.classification_config_yaml["freetextboxes"].items()): + if label_string != "": + label_string = label_string + "," + data_string = data_string + "," + + label_string = label_string + label + + data = self.freeTextBoxes[freeTextBoxObjectName].text.replace("\n", " // ") + data_string = data_string + data + + return label_string, data_string + + def cast_segmentation_to_uint8(self): + for case in self.predictions_paths: + # Load the segmentation + input_path = os.path.basename(case) + if input_path.endswith('.nii') or input_path.endswith('.nii.gz'): + segm = nib.load(case) + segm_data_dtype = segm.dataobj.dtype + print(f'infile: {input_path}, dtype: {segm_data.dtype}') + if segm_data_dtype != np.uint8: + segm_data = segm_data.astype(np.uint8) + segm.header.set_data_dtype(np.uint8) + segm_nii = nib.Nifti1Image(segm_data, segm.affine, segm.header) + nib.save(segm_nii, case) + print(f'converted file {input_path} to uint8') + elif input_path.endswith('seg.nrrd'): + segm_data, header = nrrd.read(case) + print(f'infile: {input_path}, dtype: {segm_data.dtype}') + if segm_data.dtype != np.uint8: + segm_data = segm_data.astype(np.uint8) + header['type'] = 'unsigned char' + nrrd.write(case, segm_data, header = header) + print(f'converted file {input_path} to uint8') + else: + raise ValueError('The input segmentation file must be in nii, nii.gz or nrrd format.') + + def onSaveSegmentationButton(self): + # By default creates a new folder in the volume directory + # Stop the timer when the button is pressed + self.time = self.stopTimer() + # Stop timer of the Timer class + for timer in self.timers: + timer.stop() + self.annotator_name = self.ui.Annotator_name.text + self.annotator_degree = self.ui.AnnotatorDegree.currentText + + # Create folders if not exist + self.createFolders() + + # Make sure to select the first segmentation node (i.e. the one that was created when the module was loaded, not the one created when the user clicked on the "Load mask" button) + self.segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + + currentSegmentationVersion = self.getCurrentSegmentationVersion() + + # quality control check + is_valid = self.qualityControlOfLabels() + if is_valid == False: + return + + # Save if annotator_name is not empty and timer started: + if self.annotator_name and self.time is not None: + + self.saveSegmentationInformation(currentSegmentationVersion) + + if 'nrrd' in INPUT_FILE_EXTENSION: + self.saveNrrdSegmentation(currentSegmentationVersion) + + if 'nii' in INPUT_FILE_EXTENSION: + self.saveNiiSegmentation(currentSegmentationVersion) + + msg_box = qt.QMessageBox() + msg_box.setWindowTitle("Success") + msg_box.setIcon(qt.QMessageBox.Information) + msg_box.setText("Segmentation saved successfully!") + msg_box.exec() + + # If annotator_name empty or timer not started. + else: + if not self.annotator_name: + msgboxtime = qt.QMessageBox() + msgboxtime.setText("Segmentation not saved : no annotator name ! \n Please save again with your name!") + msgboxtime.exec() + elif self.time is None: + print("Error: timer is not started for some unknown reason.") + + self.cast_segmentation_to_uint8() + + def qualityControlOfLabels(self): + is_valid = True + + segment_names = self.getAllSegmentNames() + if len(segment_names) != len(self.label_config_yaml["labels"]): + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Critical) + msg.setText("ERROR : Incorrect number of labels") + msg.setInformativeText(f'Expected {len(self.label_config_yaml["labels"])} labels but obtained {len(segment_names)}. ') + msg.setWindowTitle("ERROR : Incorrect number of labels") + msg.exec() + return False + + for i, segment_name in enumerate(segment_names): + if segment_name != self.label_config_yaml["labels"][i]["name"]: + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Critical) + msg.setText("ERROR : Label mismatch") + msg.setInformativeText(f'Expected {self.label_config_yaml["labels"][i]["name"]} but obtained {segment_name}. ') + msg.setWindowTitle("ERROR : Label mismatch") + msg.exec() + return False + return is_valid + + def saveNrrdSegmentation(self, currentSegmentationVersion): + # Save .seg.nrrd file + self.outputSegmFile = os.path.join(self.currentOutputPath, + "{}_{}.seg.nrrd".format(self.currentVolumeFilename, currentSegmentationVersion)) + + if not os.path.isfile(self.outputSegmFile): + slicer.util.saveNode(self.segmentationNode, self.outputSegmFile) + + else: + msg2 = qt.QMessageBox() + msg2.setWindowTitle('Save As') + msg2.setText( + f'The file {self.currentCase}_{self.annotator_name}_{self.revision_step[0]}.seg.nrrd already exists \n Do you want to replace the existing file?') + msg2.setIcon(qt.QMessageBox.Warning) + msg2.setStandardButtons(qt.QMessageBox.Ok | qt.QMessageBox.Cancel) + msg2.buttonClicked.connect(self.msg2_clicked) + msg2.exec() + + def saveNiiSegmentation(self, currentSegmentationVersion): + # Export segmentation to a labelmap volume + # Note to save to nifti you need to convert to labelmapVolumeNode + self.labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode') + slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(self.segmentationNode, + self.labelmapVolumeNode, + self.VolumeNode) + + self.outputSegmFileNifti = os.path.join(self.currentOutputPath, + "{}_{}.nii.gz".format(self.currentVolumeFilename, currentSegmentationVersion)) + + if not os.path.isfile(self.outputSegmFileNifti): + slicer.util.saveNode(self.labelmapVolumeNode, self.outputSegmFileNifti) + else: + msg3 = qt.QMessageBox() + msg3.setWindowTitle('Save As') + msg3.setText( + f'The file {self.currentCase}_{self.annotator_name}_{self.revision_step[0]}.nii.gz already exists \n Do you want to replace the existing file?') + msg3.setIcon(qt.QMessageBox.Warning) + msg3.setStandardButtons(qt.QMessageBox.Ok | qt.QMessageBox.Cancel) + msg3.buttonClicked.connect(self.msg3_clicked) + msg3.exec() + + def saveSegmentationInformation(self, currentSegmentationVersion): + tag_str = "Volume filename,Segmentation version,Annotator Name,Annotator degree,Revision step,Date and time,Duration" + for label in self.label_config_yaml["labels"]: + tag_str = tag_str + "," + label["name"] + " duration" + + data_str = self.currentCase + data_str = data_str + "," + currentSegmentationVersion + data_str = data_str + "," + self.annotator_name + data_str = data_str + "," + self.annotator_degree + data_str = data_str + "," + self.revision_step[0] + data_str = data_str + "," + datetime.today().strftime('%Y-%m-%d %H:%M:%S') + data_str = data_str + "," + str(self.ui.lcdNumber.value) + for timer in self.timers: + data_str = data_str + "," + str(timer.total_time) + + self.outputSegmentationInformationFile = os.path.join(self.currentOutputPath, + '{}_SegmentationInformation.csv'.format(self.currentVolumeFilename)) + if not os.path.isfile(self.outputSegmentationInformationFile): + with open(self.outputSegmentationInformationFile, 'w') as f: + f.write(tag_str) + f.write("\n") + f.write(data_str) + else: + with open(self.outputSegmentationInformationFile, 'a') as f: + f.write("\n") + f.write(data_str) + + def saveClassificationInformation(self, classification_information_labels_string, classification_information_data_string): + currentClassificationInformationVersion = self.getClassificationInformationVersion() + + tag_str = "Volume filename,Classification version,Annotator Name,Annotator degree,Revision step,Date and time" + tag_str = tag_str + "," + classification_information_labels_string + + data_str = self.currentCase + data_str = data_str + "," + currentClassificationInformationVersion + data_str = data_str + "," + self.annotator_name + data_str = data_str + "," + self.annotator_degree + data_str = data_str + "," + self.revision_step[0] + data_str = data_str + "," + datetime.today().strftime('%Y-%m-%d %H:%M:%S') + data_str = data_str + "," + classification_information_data_string + + self.outputClassificationInformationFile = os.path.join(self.currentOutputPath, + '{}_ClassificationInformation.csv'.format(self.currentVolumeFilename)) + if not os.path.isfile(self.outputClassificationInformationFile): + with open(self.outputClassificationInformationFile, 'w') as f: + f.write(tag_str) + f.write("\n") + f.write(data_str) + else: + with open(self.outputClassificationInformationFile, 'a') as f: + f.write("\n") + f.write(data_str) + + def getClassificationInformationVersion(self): + version = "v" + classificationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_ClassificationInformation.csv' + + if os.path.exists(classificationInformationPath) == False: + version = version + "01" + else: + csv_data = pd.read_csv(classificationInformationPath) + existing_version_strings = csv_data['Classification version'].to_list() + existing_version_numbers = [(int)(version_string.split("v")[1]) for version_string in existing_version_strings] + next_version_number = max(existing_version_numbers) + 1 + version = f'{version}{next_version_number:02d}' + + return version + + def getCurrentSegmentationVersion(self): + list_of_segmentation_filenames = glob(f'{self.currentOutputPath}{os.sep}{INPUT_FILE_EXTENSION}') + + version = 'v' + if list_of_segmentation_filenames == []: + version = version + "01" + else: + existing_versions = [(int)(filename.split('_v')[1].split(".")[0]) for filename in list_of_segmentation_filenames] + next_version_number = max(existing_versions) + 1 + next_version_number = min(next_version_number, 99) # max 99 versions + version = f'{version}{next_version_number:02d}' + return version + + + def msg2_clicked(self, msg2_button): + if msg2_button.text == 'OK': + slicer.util.saveNode(self.segmentationNode, self.outputSegmFile) + else: + return + + def msg3_clicked(self, msg3_button): + if msg3_button.text == 'OK': + slicer.util.saveNode(self.labelmapVolumeNode, self.outputSegmFileNifti) + else: + return + + def msg4_clicked(self, msg4_button): + if msg4_button.text == 'OK': + slicer.util.saveNode(self.VolumeNode, self.outputVolfile) + else: + return + + def verifyConfigCompatibilities(self): + if self.outputFolder is not None: + folder_for_config_files = 'conf' + path_to_saved_config_files = f'{self.outputFolder}{os.sep}{folder_for_config_files}' + + if os.path.exists(path_to_saved_config_files) == False: + os.makedirs(path_to_saved_config_files) + + label_config_copy_filename = 'lc_c--do-not-modify.yml' + path_to_label_config_copy = f'{path_to_saved_config_files}{os.sep}{label_config_copy_filename}' + + classification_config_copy_filename = 'cbc_c--do-not-modify.yml' + path_to_classification_config_copy = f'{path_to_saved_config_files}{os.sep}{classification_config_copy_filename}' + + content_of_output_folder = os.listdir(self.outputFolder) + if '.DS_Store' in content_of_output_folder: + content_of_output_folder.remove('.DS_Store') + + if os.path.exists(path_to_label_config_copy): + is_label_config_compatible = filecmp.cmp(path_to_label_config_copy, LABEL_CONFIG_FILE_PATH) + if is_label_config_compatible == False: + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Critical) + msg.setText("ERROR : Incompatible Label Configuration") + msg.setInformativeText('The label_config.yml file has changed since the initial segmentation. ') + msg.setWindowTitle("ERROR : Incompatible Label Configuration") + msg.exec() + + self.outputFolder = None + + if os.path.exists(path_to_classification_config_copy): + is_classification_config_compatible = filecmp.cmp(path_to_classification_config_copy, CLASSIFICATION_CONFIG_FILE_PATH) + if is_classification_config_compatible == False: + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Critical) + msg.setText("ERROR : Incompatible Classification Configuration") + msg.setInformativeText('The classification_config.yml file has changed since the initial classification annotation. ') + msg.setWindowTitle("ERROR : Incompatible Classification Configuration") + msg.exec() + + self.outputFolder = None + + if len(content_of_output_folder) > 1 and os.path.exists(path_to_label_config_copy) == False and os.path.exists(path_to_classification_config_copy) == False: + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Warning) + msg.setText("WARNING : Possible Incompatible Configuration") + msg.setInformativeText('The output folder is not empty. No configuration files have been saved. Possible configuration incompatibility. Proceed with caution. Otherwise, choose an empty output folder. ') + msg.setWindowTitle("WARNING : Possible Incompatible Configuration") + msg.exec() + + shutil.copy(LABEL_CONFIG_FILE_PATH, path_to_label_config_copy) + shutil.copy(CLASSIFICATION_CONFIG_FILE_PATH, path_to_classification_config_copy) + elif len(content_of_output_folder) == 1: + shutil.copy(LABEL_CONFIG_FILE_PATH, path_to_label_config_copy) + shutil.copy(CLASSIFICATION_CONFIG_FILE_PATH, path_to_classification_config_copy) + + def onSelectOutputFolder(self): + self.outputFolder = qt.QFileDialog.getExistingDirectory(None,"Open a folder", self.DefaultDir, qt.QFileDialog.ShowDirsOnly) + + self.verifyConfigCompatibilities() + + if self.outputFolder is not None: + self.ui.LoadClassification.setEnabled(True) + self.ui.LoadSegmentation.setEnabled(True) + + self.ui.SaveSegmentationButton.setEnabled(True) + self.ui.SaveClassificationButton.setEnabled(True) + + self.updateCurrentOutputPathAndCurrentVolumeFilename() + + self.predictions_paths = sorted(glob(os.path.join(self.outputFolder, f'{INPUT_FILE_EXTENSION}'))) + + def msg_warnig_delete_segm_node_clicked(self, msg_warnig_delete_segm_node_button): + if msg_warnig_delete_segm_node_button.text == 'OK': + srcNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + slicer.mrmlScene.RemoveNode(srcNode) + else: + return + + def onLoadClassification(self): + classificationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_ClassificationInformation.csv' + classificationInformation_df = None + if os.path.exists(classificationInformationPath): + classificationInformation_df = pd.read_csv(classificationInformationPath) + else: + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Information) + msg.setText("No saved classifications") + msg.setInformativeText('There are no classifications saved in the ClassificationInformation.csv.') + msg.setWindowTitle("No saved classifications") + msg.exec() + return + + loadClassificationWindow = LoadClassificationWindow(self, classificationInformation_df) + loadClassificationWindow.show() + + def onSaveClassificationButton(self): + self.annotator_name = self.ui.Annotator_name.text + self.annotator_degree = self.ui.AnnotatorDegree.currentText + + classification_information_labels_string, classification_information_data_string = self.getClassificationInformation() + + # Create folders if don't exist + self.createFolders() + + if self.annotator_name is not None: + self.saveClassificationInformation(classification_information_labels_string, classification_information_data_string) + msg_box = qt.QMessageBox() + msg_box.setWindowTitle("Success") + msg_box.setIcon(qt.QMessageBox.Information) + msg_box.setText("Classification saved successfully!") + msg_box.exec() + + else: + msgboxtime = qt.QMessageBox() + msgboxtime.setText("Classification not saved : no annotator name ! \n Please save again with your name!") + msgboxtime.exec() + + + def onCompareSegmentVersions(self): + if 'Clear' in self.ui.CompareSegmentVersions.text: + self.onClearCompareSegmentVersions() + else: + msg_warnig_delete_segm_node = self.warnAgainstDeletingCurrentSegmentation() + msg_warnig_delete_segm_node.buttonClicked.connect(self.onCompareSegmentVersionsWillEraseCurrentSegmentsWarningClicked) + msg_warnig_delete_segm_node.exec() + + def onCompareSegmentVersionsWillEraseCurrentSegmentsWarningClicked(self, msg_warnig_delete_segm_node_button): + if msg_warnig_delete_segm_node_button.text == 'OK': + srcNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + slicer.mrmlScene.RemoveNode(srcNode) + + self.openCompareSegmentVersionsWindow() + else: + return + + def warnAgainstDeletingCurrentSegmentation(self): + msg_warnig_delete_segm_node = qt.QMessageBox() + msg_warnig_delete_segm_node.setText('This will delete the current segmentation. Do you want to continue?') + msg_warnig_delete_segm_node.setIcon(qt.QMessageBox.Warning) + msg_warnig_delete_segm_node.setStandardButtons(qt.QMessageBox.Ok | qt.QMessageBox.Cancel) + + return msg_warnig_delete_segm_node + + def onLoadSegmentation(self): + msg_warnig_delete_segm_node = self.warnAgainstDeletingCurrentSegmentation() + msg_warnig_delete_segm_node.buttonClicked.connect(self.onLoadSegmentationWillEraseCurrentSegmentsWarningClicked) + msg_warnig_delete_segm_node.exec() + + def onLoadSegmentationWillEraseCurrentSegmentsWarningClicked(self, msg_warnig_delete_segm_node_button): + if msg_warnig_delete_segm_node_button.text == 'OK': + srcNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + slicer.mrmlScene.RemoveNode(srcNode) + self.openLoadSegmentationWindow() + else: + return + + def openLoadSegmentationWindow(self): + segmentationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_SegmentationInformation.csv' + segmentationInformation_df = None + if os.path.exists(segmentationInformationPath): + segmentationInformation_df = pd.read_csv(segmentationInformationPath) + else: + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Information) + msg.setText("No saved segmentations") + msg.setInformativeText('There are no segmentations saved in the SegmentationInformation.csv.') + msg.setWindowTitle("No saved segmentations") + msg.exec() + return + + loadSegmentationWindow = LoadSegmentationsWindow(self, segmentationInformation_df) + loadSegmentationWindow.show() + + def openCompareSegmentVersionsWindow(self): + segmentationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_SegmentationInformation.csv' + segmentationInformation_df = None + if os.path.exists(segmentationInformationPath): + segmentationInformation_df = pd.read_csv(segmentationInformationPath) + else: + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Information) + msg.setText("No saved segmentations") + msg.setInformativeText('There are no segmentations saved in the SegmentationInformation.csv.') + msg.setWindowTitle("No saved segmentations") + msg.exec() + return + + compareSegmentVersionsWindow = CompareSegmentVersionsWindow(self, segmentationInformation_df) + compareSegmentVersionsWindow.show() + + def compareSegmentVersions(self, selected_label, selected_version_file_paths): + self.labelOfCompareSegmentVersions = selected_label + self.colorsSelectedVersionFilePathsForCompareSegmentVersions = {} + + selected_label_value = 0 + for label in self.label_config_yaml['labels']: + if selected_label == label['name']: + selected_label_value = label['value'] + + slicer.mrmlScene.Clear() + slicer.util.loadVolume(self.currentCasePath) + self.VolumeNode = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')[0] + + Vol_displayNode = self.VolumeNode.GetDisplayNode() + Vol_displayNode.AutoWindowLevelOff() + Vol_displayNode.SetWindow(85) + Vol_displayNode.SetLevel(45) + Vol_displayNode.SetInterpolate(INTERPOLATE_VALUE) + + self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor + self.segmentEditorWidget.setActiveEffectByName("No editing") + + self.resetTimer() + + for (segment_name, version_file_path) in selected_version_file_paths.items(): + if 'nrrd' in INPUT_FILE_EXTENSION: + slicer.util.loadSegmentation(version_file_path) + currentSegmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + elif 'nii' in INPUT_FILE_EXTENSION: + labelmapVolumeNode = slicer.util.loadLabelVolume(version_file_path) + currentSegmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") + slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, currentSegmentationNode) + + self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor + self.segmentEditorNode = self.segmentEditorWidget.mrmlSegmentEditorNode() + self.segmentEditorWidget.setSegmentationNode(currentSegmentationNode) + self.segmentEditorWidget.setSourceVolumeNode(self.VolumeNode) + currentSegmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(self.VolumeNode) + segmentationDisplayNode = currentSegmentationNode.GetDisplayNode() + segmentationDisplayNode.SetAllSegmentsVisibility(False) + + currentSegmentationNode.SetName(os.path.split(version_file_path)[1].split('.')[0]) + + segment = currentSegmentationNode.GetSegmentation().GetSegment(str(selected_label_value)) + + if segment is not None : + segment.SetName(segment_name) + + # OBTAIN RANDOM BRIGHT COLOR : https://stackoverflow.com/questions/43437309/get-a-bright-random-colour-python + h,s,l = random.random(), 0.5 + random.random()/2.0, 0.4 + random.random()/5.0 + r,g,b = [int(256*i) for i in colorsys.hls_to_rgb(h,l,s)] + self.colorsSelectedVersionFilePathsForCompareSegmentVersions[segment_name] = [r, g, b] + segment.SetColor(r / 255, g / 255, b / 255) + + segmentationDisplayNode.SetSegmentVisibility(str(selected_label_value), True) + + self.disableSegmentAndPaintButtons() + self.disablePauseTimerButton() + self.ui.StartTimerButton.setEnabled(False) + self.ui.StartTimerButton.setStyleSheet("background-color : light gray") + self.ui.CompareSegmentVersions.setText('Clear Read Only Segment Versions') + self.ui.CompareSegmentVersions.setStyleSheet("background-color : yellowgreen") + self.ui.SaveSegmentationButton.setEnabled(False) + + self.ui.ShowSegmentVersionLegendButton.setVisible(True) + + def onClearCompareSegmentVersions(self): + self.loadPatient() + + self.enableStartTimerButton() + + self.ui.CompareSegmentVersions.setText('Compare segment versions') + self.ui.CompareSegmentVersions.setStyleSheet("background-color : light gray") + + self.ui.SaveSegmentationButton.setEnabled(True) + + self.ui.ShowSegmentVersionLegendButton.setVisible(False) + + def loadSegmentation(self, absolute_path_to_segmentation_file): + if 'nrrd' in INPUT_FILE_EXTENSION: + slicer.util.loadSegmentation(absolute_path_to_segmentation_file) + self.segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[0] + elif 'nii' in INPUT_FILE_EXTENSION: + labelmapVolumeNode = slicer.util.loadLabelVolume(absolute_path_to_segmentation_file) + self.segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") + slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, self.segmentationNode) + + self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor + self.segmentEditorNode = self.segmentEditorWidget.mrmlSegmentEditorNode() + self.segmentEditorWidget.setSegmentationNode(self.segmentationNode) + self.segmentEditorWidget.setSourceVolumeNode(self.VolumeNode) + # set refenrence geometry to Volume node + self.segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(self.VolumeNode) + nn = self.segmentationNode.GetDisplayNode() + # set Segmentation visible: + nn.SetAllSegmentsVisibility(True) + + loaded_segment_ids = self.segmentationNode.GetSegmentation().GetSegmentIDs() + for i, segment_id in enumerate(loaded_segment_ids): + for label in self.label_config_yaml["labels"]: + if str(label['value']) == str(segment_id): + segment = self.segmentationNode.GetSegmentation().GetSegment(segment_id) + segment.SetName(label["name"]) + segment.SetColor(label["color_r"]/255, label["color_g"]/255, label["color_b"]/255) + + list_of_segment_names = self.getAllSegmentNames() + for label in self.label_config_yaml["labels"]: + if label['name'] not in list_of_segment_names: + self.onNewLabelSegm(label["name"], label["color_r"], label["color_g"], label["color_b"], label["lower_bound_HU"], label["upper_bound_HU"]) + + for segment_id in loaded_segment_ids: + for label in self.label_config_yaml["labels"]: + if str(segment_id) == str(label['value']) or str(segment_id) == str(label['name']): + self.segmentationNode.GetSegmentation().SetSegmentIndex(str(segment_id), label['value']-1) + + def getAllSegmentNames(self): + list_of_segment_ids = self.segmentationNode.GetSegmentation().GetSegmentIDs() + list_of_segment_names = [] + for segment_id in list_of_segment_ids: + segment = self.segmentationNode.GetSegmentation().GetSegment(segment_id) + list_of_segment_names.append(segment.GetName()) + return list_of_segment_names + + def onPushDefaultMin(self): + with open(LABEL_CONFIG_FILE_PATH, 'r') as file: + fresh_config = yaml.safe_load(file) + self.label_config_yaml["labels"][self.current_label_index]["lower_bound_HU"] = fresh_config["labels"][self.current_label_index]["lower_bound_HU"] + self.setUpperAndLowerBoundHU(self.label_config_yaml["labels"][self.current_label_index]["lower_bound_HU"], self.label_config_yaml["labels"][self.current_label_index]["upper_bound_HU"]) + + def onPushDefaultMax(self): + with open(LABEL_CONFIG_FILE_PATH, 'r') as file: + fresh_config = yaml.safe_load(file) + self.label_config_yaml["labels"][self.current_label_index]["upper_bound_HU"] = fresh_config["labels"][self.current_label_index]["upper_bound_HU"] + self.setUpperAndLowerBoundHU(self.label_config_yaml["labels"][self.current_label_index]["lower_bound_HU"], self.label_config_yaml["labels"][self.current_label_index]["upper_bound_HU"]) + + def onPush_ShowSegmentVersionLegendButton(self): + segmentationInformationPath = f'{self.currentOutputPath}{os.sep}{self.currentVolumeFilename}_SegmentationInformation.csv' + segmentationInformation_df = None + if os.path.exists(segmentationInformationPath): + segmentationInformation_df = pd.read_csv(segmentationInformationPath) + else: + msg = qt.QMessageBox() + msg.setIcon(qt.QMessageBox.Information) + msg.setText("No saved segmentations") + msg.setInformativeText('There are no segmentations saved in the SegmentationInformation.csv.') + msg.setWindowTitle("No saved segmentations") + msg.exec() + return + + showSegmentVersionLegendWindow = ShowSegmentVersionLegendWindow(self, segmentationInformation_df) + showSegmentVersionLegendWindow.show() + + def onPushButton_undo(self): + self.segmentEditorWidget.undo() + + def onDropDownButton_label_select(self, value): + self.current_label_index = value + label = self.label_config_yaml["labels"][value] + self.setUpperAndLowerBoundHU(label["lower_bound_HU"], label["upper_bound_HU"]) + + label_name = label["name"] + try: + segment_name = label_name + self.onPushButton_select_label(segment_name, label["lower_bound_HU"], label["upper_bound_HU"]) + except: + pass + + def onPushLassoPaint(self): + self.segmentEditorWidget.setActiveEffectByName("Scissors") + self.segmentEditorNode.SetMasterVolumeIntensityMask(False) + effect = self.segmentEditorWidget.activeEffect() + effect.setParameter("Operation","FillInside") + effect.setParameter("Shape","FreeForm") + effect.setSliceCutMode(3) + + def onPushButton_Paint(self): + selected_segment_id = self.segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(self.label_config_yaml["labels"][self.current_label_index]['name']) + self.segmentEditorNode.SetSelectedSegmentID(selected_segment_id) + self.segmentEditorWidget.setActiveEffectByName("Paint") + # Note it seems that sometimes you need to activate the effect first with : + # Assign effect to the segmentEditorWidget using the active effect + self.effect = self.segmentEditorWidget.activeEffect() + self.effect.activate() + self.effect.setParameter('BrushSphere',1) + # Seems that you need to activate the effect to see it in Slicer + # Set up the mask parameters (note that PaintAllowed...was changed to EditAllowed) + self.segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentationNode.EditAllowedEverywhere) + #Set if using Editable intensity range (the range is defined below using object.setParameter) + self.segmentEditorNode.SetMasterVolumeIntensityMask(True) + self.segmentEditorNode.SetSourceVolumeIntensityMaskRange(self.LB_HU, self.UB_HU) + self.segmentEditorNode.SetOverwriteMode(slicer.vtkMRMLSegmentEditorNode.OverwriteAllSegments) + + def toggleFillButton(self): + if self.ui.pushButton_ToggleFill.isChecked(): + self.ui.pushButton_ToggleFill.setStyleSheet("background-color : yellowgreen") + self.ui.pushButton_ToggleFill.setText('Fill: ON') + self.segmentationNode.GetDisplayNode().SetOpacity2DFill(0) + else: + self.ui.pushButton_ToggleFill.setStyleSheet("background-color : indianred") + self.ui.pushButton_ToggleFill.setText('Fill: OFF') + self.segmentationNode.GetDisplayNode().SetOpacity2DFill(100) + + def onPushButton_ToggleVisibility(self): + if self.ui.pushButton_ToggleVisibility.isChecked(): + self.ui.pushButton_ToggleVisibility.setStyleSheet("background-color : indianred") + self.ui.pushButton_ToggleVisibility.setText('Visibility: OFF') + self.segmentationNode.GetDisplayNode().SetAllSegmentsVisibility(False) + else: + self.ui.pushButton_ToggleVisibility.setStyleSheet("background-color : yellowgreen") + self.ui.pushButton_ToggleVisibility.setText('Visibility: ON') + self.segmentationNode.GetDisplayNode().SetAllSegmentsVisibility(True) + + def togglePaintMask(self): + if self.ui.pushButton_TogglePaintMask.isChecked(): + self.ui.pushButton_TogglePaintMask.setStyleSheet("background-color : yellowgreen") + self.ui.pushButton_TogglePaintMask.setText('Paint Mask ON') + self.segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentationNode.EditAllowedEverywhere) + + + def onPushButton_segmeditor(self): + slicer.util.selectModule("SegmentEditor") + + def onPushButton_Erase(self): + self.segmentEditorWidget.setActiveEffectByName("Erase") + # Note it seems that sometimes you need to activate the effect first with : + # Assign effect to the segmentEditorWidget using the active effect + self.effect = self.segmentEditorWidget.activeEffect() + # Seems that you need to activate the effect to see it in Slicer + self.effect.activate() + self.segmentEditorNode.SetMasterVolumeIntensityMask(False) + + def onPushButton_Smooth(self): + # pass + # Smoothing + self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor + self.segmentEditorWidget.setActiveEffectByName("Smoothing") + effect = self.segmentEditorWidget.activeEffect() + effect.setParameter("SmoothingMethod", "MEDIAN") + effect.setParameter("KernelSizeMm", 3) + effect.self().onApply() + + + + def onPushButton_Small_holes(self): + # pass + # Fill holes smoothing + self.segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor + self.segmentEditorWidget.setActiveEffectByName("Smoothing") + effect = self.segmentEditorWidget.activeEffect() + effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_CLOSING") + effect.setParameter("KernelSizeMm", 3) + effect.self().onApply() + + def onLB_HU(self): + try: + self.LB_HU=self.ui.LB_HU.value + self.segmentEditorNode.SetMasterVolumeIntensityMask(True) + self.segmentEditorNode.SetSourceVolumeIntensityMaskRange(self.LB_HU, self.UB_HU) + self.label_config_yaml["labels"][self.current_label_index]["lower_bound_HU"] = self.LB_HU + except: + pass + + def onUB_HU(self): + try: + self.UB_HU=self.ui.UB_HU.value + self.segmentEditorNode.SetMasterVolumeIntensityMask(True) + self.segmentEditorNode.SetSourceVolumeIntensityMaskRange(self.LB_HU, self.UB_HU) + self.label_config_yaml["labels"][self.current_label_index]["upper_bound_HU"] = self.UB_HU + except: + pass + +class SlicerCARTLogic(ScriptedLoadableModuleLogic): + """This class should implement all the actual + computation done by your module. The interface + should be such that other python code can import + this class and make use of the functionality without + requiring an instance of the Widget. + Uses ScriptedLoadableModuleLogic base class, available at: + https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + """ + + def __init__(self): + """ + Called when the logic class is instantiated. Can be used for initializing member variables. + """ + ScriptedLoadableModuleLogic.__init__(self) + + def setDefaultParameters(self, parameterNode): + """ + Initialize parameter node with default settings. + """ + if not parameterNode.GetParameter("Threshold"): + parameterNode.SetParameter("Threshold", "100.0") + if not parameterNode.GetParameter("Invert"): + parameterNode.SetParameter("Invert", "false") + + def process(self, inputVolume, outputVolume, imageThreshold, invert=False, showResult=True): + """ + Run the processing algorithm. + Can be used without GUI widget. + :param inputVolume: volume to be thresholded + :param outputVolume: thresholding result + :param imageThreshold: values above/below this threshold will be set to 0 + :param invert: if True then values above the threshold will be set to 0, otherwise values below are set to 0 + :param showResult: show output volume in slice viewers + """ + + if not inputVolume or not outputVolume: + raise ValueError("Input or output volume is invalid") + + import time + startTime = time.time() + logging.info('Processing started') + + # Compute the thresholded output volume using the "Threshold Scalar Volume" CLI module + cliParams = { + 'InputVolume': inputVolume.GetID(), + 'OutputVolume': outputVolume.GetID(), + 'ThresholdValue' : imageThreshold, + 'ThresholdType' : 'Above' if invert else 'Below' + } + cliNode = slicer.cli.run(slicer.modules.thresholdscalarvolume, None, cliParams, wait_for_completion=True, update_display=showResult) + # We don't need the CLI module node anymore, remove it to not clutter the scene with it + slicer.mrmlScene.RemoveNode(cliNode) + + stopTime = time.time() + logging.info(f'Processing completed in {stopTime-startTime:.2f} seconds') + +class SlicerCARTTest(ScriptedLoadableModuleTest): + """ + This is the test case for your scripted module. + Uses ScriptedLoadableModuleTest base class, available at: + https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + """ + + def setUp(self): + """ Do whatever is needed to reset the state - typically a scene clear will be enough. + """ + slicer.mrmlScene.Clear() + + def runTest(self): + """Run as few or as many tests as needed here. + """ + self.setUp() + self.test_SlicerCART1() + + def test_SlicerCART1(self): + """ Ideally you should have several levels of tests. At the lowest level + tests should exercise the functionality of the logic with different inputs + (both valid and invalid). At higher levels your tests should emulate the + way the user would interact with your code and confirm that it still works + the way you intended. + One of the most important features of the tests is that it should alert other + developers when their changes will have an impact on the behavior of your + module. For example, if a developer removes a feature that you depend on, + your test should break so they know that the feature is needed. + """ + + self.delayDisplay("Starting the test") + + # Get/create input data + + import SampleData + registerSampleData() + inputVolume = SampleData.downloadSample('SlicerCART1') + self.delayDisplay('Loaded test data set') + + inputScalarRange = inputVolume.GetImageData().GetScalarRange() + self.assertEqual(inputScalarRange[0], 0) + self.assertEqual(inputScalarRange[1], 695) + + outputVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode") + threshold = 100 + + # Test the module logic + + logic = SlicerCARTLogic() + + # Test algorithm with non-inverted threshold + logic.process(inputVolume, outputVolume, threshold, True) + outputScalarRange = outputVolume.GetImageData().GetScalarRange() + self.assertEqual(outputScalarRange[0], inputScalarRange[0]) + self.assertEqual(outputScalarRange[1], threshold) + + # Test algorithm with inverted threshold + logic.process(inputVolume, outputVolume, threshold, False) + outputScalarRange = outputVolume.GetImageData().GetScalarRange() + self.assertEqual(outputScalarRange[0], inputScalarRange[0]) + self.assertEqual(outputScalarRange[1], inputScalarRange[1]) + + self.delayDisplay('Test passed') diff --git a/SlicerCART/src/general_config.yml b/SlicerCART/src/general_config.yml index fdae993..074db36 100644 --- a/SlicerCART/src/general_config.yml +++ b/SlicerCART/src/general_config.yml @@ -3,13 +3,16 @@ input_filetype: '*.nii.gz' # '*.nrrd' or '*.nii.gz' default_volume_directory: '' default_segmentation_directory: '' -modality: 'MRI' # 'CT' or 'MRI' +modality: 'CT' # 'CT' or 'MRI' slice_view_color: 'Red' # 'Red' or 'Yellow' or 'Green' -interpolate_value: 0 +interpolate_value: 1 -impose_bids_format: True +impose_bids_format: False is_classification_requested: True is_segmentation_requested: True is_semi_automatic_phe_tool_requested: True + +ct_window_width: 85 +ct_window_level: 45 \ No newline at end of file diff --git a/SlicerCART/src/resources/UI/SlicerCART.ui b/SlicerCART/src/resources/UI/SlicerCART.ui new file mode 100644 index 0000000..d7c56be --- /dev/null +++ b/SlicerCART/src/resources/UI/SlicerCART.ui @@ -0,0 +1,489 @@ + + + Form + + + + 0 + 0 + 883 + 1067 + + + + Form + + + + + + Configuration + + + + + + + + Segmentation + + + true + + + + + + Segment Editor + + + + + + + + + Lasso Paint + + + + + + + Visibility: ON + + + true + + + + + + + Undo + + + + + + + Smooth margins + + + + + + + Remove small holes + + + + + + + Fill: OFF + + + true + + + + + + + + + + Paint + + + + + + + Start + + + true + + + + + + + + + + Pause + + + true + + + + + + + Erase mode + + + + + + + + + + + Saving segmentation + + + Save segmentation + + + Ctrl+S + + + + + + + Load segmentation... + + + + + + + Compare segment versions + + + + + + + Show segment version legend + + + + + + + + + + + Thresholds + + + + + + + Minimum + + + + + + + Maximum + + + + + + + + + + + + + Default Min. HU + + + + + + + Default Max. HU + + + + + + + + + Semi-automatic PHE Tool + + + + + + + Launch + + + + + + + Show Result + + + + + + + + + + + + + 16777215 + 38 + + + + Classification + + + true + + + + + + + + Load classification... + + + + + + + Save classification + + + + + + + + + PushButton + + + + + + + + + + Case list + + + + + + + + + + + + + + + + + + Select volumes folder + + + + + + + + + + + Annotator's name + + + + + + + + + + + + + + Degree + + + + + + + + + + + + + Medical Student + + + + + Resident + + + + + Radiologist + + + + + Supervisor + + + + + Research Team + + + + + + + + + + + + Revision step + + + + + + + + + + + + + 0 - First + + + + + 1 - Revision + + + + + 2 - Final + + + + + + + + + + + + + + Interpolate + + + + + + + << Previous + + + + + + + Next >> + + + + + + + + + + + + + + + + Path... + + + + + + + Select output folder + + + + + + + + + + + + + ctkCollapsibleButton + QWidget +
ctkCollapsibleButton.h
+ 1 + + + ctkCollapsibleGroupBox + QGroupBox +
ctkCollapsibleGroupBox.h
+ 1 + + + qMRMLCollapsibleButton + ctkCollapsibleButton +
qMRMLCollapsibleButton.h
+ 1 + + + qMRMLWidget + QWidget +
qMRMLWidget.h
+ 1 + + + + + From 2d150e548be8f533c8a1262ca788e8ef7eba6522 Mon Sep 17 00:00:00 2001 From: laurentletg <48111184+laurentletg@users.noreply.github.com> Date: Fri, 12 Jul 2024 09:20:25 -0400 Subject: [PATCH 03/10] Fixed .ui error introduced on my laurent branch. Cleaned some code. --- SlicerCART/src/SlicerCART.py | 12 +- SlicerCART/src/resources/UI/SlicerCART.ui | 292 +++++++++++----------- 2 files changed, 150 insertions(+), 154 deletions(-) diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py index 10718ad..2f9c3ee 100644 --- a/SlicerCART/src/SlicerCART.py +++ b/SlicerCART/src/SlicerCART.py @@ -1,7 +1,6 @@ # To install a package in slicer python environment, use the following command: # pip install --user package_name import os -import importlib import logging import qt, slicer from slicer.ScriptedLoadableModule import * @@ -24,6 +23,7 @@ import vtk import random import colorsys +from PyQt5 import QtCore import sys @@ -97,11 +97,9 @@ def __init__(self, segmenter, classificationInformation_df, parent = None): super(LoadClassificationWindow, self).__init__(parent) self.classificationInformation_df = classificationInformation_df - self.segmenter = segmenter layout = qt.QVBoxLayout() - self.versionTableView = qt.QTableWidget() layout.addWidget(self.versionTableView) @@ -166,7 +164,6 @@ def __init__(self, segmenter, classificationInformation_df, parent = None): def pushLoad(self): selected_version = self.versionDropdown.currentText - selected_version_df = self.classificationInformation_df[self.classificationInformation_df['Classification version']==selected_version].reset_index(drop = True) for i, (objectName, label) in enumerate(self.segmenter.classification_config_yaml["checkboxes"].items()): @@ -195,7 +192,6 @@ def __init__(self, segmenter, segmentationInformation_df, parent = None): super(ShowSegmentVersionLegendWindow, self).__init__(parent) self.segmentationInformation_df = segmentationInformation_df - self.segmenter = segmenter layout = qt.QVBoxLayout() @@ -563,6 +559,8 @@ def pushCancel(self): class OptionalMethods(): + pass + @@ -580,7 +578,7 @@ def __init__(self, parent): # TODO: update with short description of the module and a link to online module documentation self.parent.helpText = """ This is an example of scripted loadable module bundled in an extension. -See more information in module documentation. +See more information in module documentation. """ # TODO: replace with organization, grant and thanks self.parent.acknowledgementText = """ @@ -1019,6 +1017,7 @@ def setupCheckboxes(self, number_of_columns): self.checkboxWidgets = {} for i, (objectName, label) in enumerate(self.classification_config_yaml["checkboxes"].items()): + print(objectName, label) checkbox = qt.QCheckBox() checkbox.setText(label) checkbox.setObjectName(objectName) @@ -1029,6 +1028,7 @@ def setupCheckboxes(self, number_of_columns): self.ui.ClassificationGridLayout.addWidget(checkbox, row_index, column_index) self.checkboxWidgets[objectName] = checkbox + return row_index + 1 def setupComboboxes(self, start_row): diff --git a/SlicerCART/src/resources/UI/SlicerCART.ui b/SlicerCART/src/resources/UI/SlicerCART.ui index d7c56be..d14f880 100644 --- a/SlicerCART/src/resources/UI/SlicerCART.ui +++ b/SlicerCART/src/resources/UI/SlicerCART.ui @@ -7,7 +7,7 @@ 0 0 883 - 1067 + 1278 @@ -89,7 +89,8 @@ - + + @@ -99,28 +100,28 @@ - - - Start - - - true - - - - - - - - - - Pause - - - true - - - + + + Start + + + true + + + + + + + + + + Pause + + + true + + + @@ -131,82 +132,84 @@ - - - - - Saving segmentation - - - Save segmentation - - - Ctrl+S - - - - - - - Load segmentation... - - - - - - - Compare segment versions - - - - - - - Show segment version legend - - - - + + + + + Saving segmentation + + + Save segmentation + + + Ctrl+S + + + + + + + Load segmentation... + + + + + + + Compare segment versions + + + + + + + Show segment version legend + + + + - - + + Thresholds - + - - + + Minimum - + - - + + Maximum - + - + + - + + - + Default Min. HU - + Default Max. HU @@ -214,90 +217,31 @@ - + - Semi-automatic PHE Tool - - + Semi-automatic PHE Tool + + - - - Launch - - + + + Launch + + - - - Show Result - - + + + Show Result + + - - - - - 16777215 - 38 - - - - Classification - - - true - - - - - - - - Load classification... - - - - - - - Save classification - - - - - - - - - PushButton - - - - - - - - - - Case list - - - - - - - - - - - - @@ -407,7 +351,7 @@ - + Interpolate @@ -453,6 +397,58 @@ + + + + Case list + + + + + + + + + + + + + + + + + 16777215 + 350 + + + + Classification + + + true + + + + + + + + Load classification... + + + + + + + Save classification + + + + + + + + @@ -486,4 +482,4 @@ - + \ No newline at end of file From e7e310fcb1d6505fb8e38a286c3c775ca9e0dbae Mon Sep 17 00:00:00 2001 From: jcohenadad Date: Fri, 12 Jul 2024 12:30:56 -0400 Subject: [PATCH 04/10] Moved imports after check_and_install_python_packages() --- SlicerCART/src/SlicerCART.py | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py index 2f9c3ee..1a334ae 100644 --- a/SlicerCART/src/SlicerCART.py +++ b/SlicerCART/src/SlicerCART.py @@ -7,35 +7,26 @@ from slicer.util import VTKObservationMixin from glob import glob import re -import pandas as pd import time import slicerio # cannot install in slicer import nrrd -import yaml from pathlib import Path from threading import RLock from datetime import datetime from bids_validator import BIDSValidator import filecmp import shutil -import nibabel as nib import numpy as np import vtk import random import colorsys -from PyQt5 import QtCore - - -import sys -import os - import sys -import os # TODO: There is probably a more elegant way to install pacakages through the extension manager when the user installs the extension. REQUIRED_PYTHON_PACKAGES = { "nibabel": "nibabel", + "yaml": "yaml", "bids_validator": "bids_validator" } @@ -65,6 +56,10 @@ def check_and_install_python_packages(): check_and_install_python_packages() +import yaml +import nibabel as nib +import pandas as pd +from PyQt5 import QtCore INPUT_FILE_EXTENSION = '*.nii.gz' INTERPOLATE_VALUE = 0 From 2c1426105ab78817326cd580790f92a5a3b6c8ec Mon Sep 17 00:00:00 2001 From: jcohenadad Date: Fri, 12 Jul 2024 12:42:44 -0400 Subject: [PATCH 05/10] Loop through all packages and install them at once --- SlicerCART/src/SlicerCART.py | 42 ++++++++++++++++++++++-------------- 1 file changed, 26 insertions(+), 16 deletions(-) diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py index 1a334ae..fe1f589 100644 --- a/SlicerCART/src/SlicerCART.py +++ b/SlicerCART/src/SlicerCART.py @@ -24,34 +24,44 @@ # TODO: There is probably a more elegant way to install pacakages through the extension manager when the user installs the extension. +# TODO: add a check for the version of the package +# TODO: use requirements.txt instead +# TODO: check if the package installed with error + +# Dictionary of required python packages and their import names REQUIRED_PYTHON_PACKAGES = { "nibabel": "nibabel", - "yaml": "yaml", + "pandas": "pandas", + "PyYAML": "yaml", "bids_validator": "bids_validator" } - def check_and_install_python_packages(): + missing_packages = [] + for pip_name, import_name in REQUIRED_PYTHON_PACKAGES.items(): try: __import__(import_name) except ImportError: - msg = "SlicerCART module: The following required python package is missing:" - msg += f"\n{pip_name}" - msg += "\nWould you like to install them now?" - response = qt.QMessageBox.question(slicer.util.mainWindow(), 'Install Extensions', msg, - qt.QMessageBox.Yes | qt.QMessageBox.No) - - if response == qt.QMessageBox.Yes: + missing_packages.append(pip_name) + + if missing_packages: + msg = "SlicerCART module: The following required python packages are missing:" + msg += "\n" + "\n".join(missing_packages) + msg += "\nWould you like to install them now?" + response = qt.QMessageBox.question(slicer.util.mainWindow(), 'Install Extensions', msg, + qt.QMessageBox.Yes | qt.QMessageBox.No) + if response == qt.QMessageBox.Yes: + for pip_name in missing_packages: slicer.util.pip_install(pip_name) - # Wait for the installation to complete and restart Slicer + # Wait for the installation to complete slicer.app.processEvents() - qt.QMessageBox.information(slicer.util.mainWindow(), 'Restart Slicer', - 'Slicer will now restart to complete the installation.') - slicer.app.restart() - else: - qt.QMessageBox.warning(slicer.util.mainWindow(), 'Missing Extensions', - 'The SlicerCART module cannot be loaded without the required extensions.') + qt.QMessageBox.information(slicer.util.mainWindow(), 'Restart Slicer', + 'Slicer will now restart to complete the installation.') + slicer.app.restart() + else: + qt.QMessageBox.warning(slicer.util.mainWindow(), 'Missing Extensions', + 'The SlicerCART module cannot be loaded without the required extensions.') check_and_install_python_packages() From af0fdabd2cf0b2606b3f55ac291d7e79b7fa52d5 Mon Sep 17 00:00:00 2001 From: jcohenadad Date: Fri, 12 Jul 2024 13:06:46 -0400 Subject: [PATCH 06/10] Added other packages --- SlicerCART/src/SlicerCART.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py index fe1f589..c0db8bb 100644 --- a/SlicerCART/src/SlicerCART.py +++ b/SlicerCART/src/SlicerCART.py @@ -2,18 +2,15 @@ # pip install --user package_name import os import logging -import qt, slicer +import slicer from slicer.ScriptedLoadableModule import * from slicer.util import VTKObservationMixin from glob import glob import re import time -import slicerio # cannot install in slicer -import nrrd from pathlib import Path from threading import RLock from datetime import datetime -from bids_validator import BIDSValidator import filecmp import shutil import numpy as np @@ -33,7 +30,10 @@ "nibabel": "nibabel", "pandas": "pandas", "PyYAML": "yaml", - "bids_validator": "bids_validator" + "pynrrd": "nrrd", + "slicerio": "slicerio", + "bids_validator": "bids_validator", + "PyQt5": "PyQt5" } def check_and_install_python_packages(): @@ -66,10 +66,14 @@ def check_and_install_python_packages(): check_and_install_python_packages() -import yaml +from bids_validator import BIDSValidator import nibabel as nib +import nrrd import pandas as pd +import slicerio +import qt from PyQt5 import QtCore +import yaml INPUT_FILE_EXTENSION = '*.nii.gz' INTERPOLATE_VALUE = 0 From dbed0c8869210fcda5da947dae94399e91c462c7 Mon Sep 17 00:00:00 2001 From: jcohenadad Date: Fri, 12 Jul 2024 13:26:28 -0400 Subject: [PATCH 07/10] Import qt before package install Addresses https://github.com/neuropoly/slicer-manual-annotation/pull/43#issuecomment-2226006676 --- SlicerCART/src/SlicerCART.py | 1 + 1 file changed, 1 insertion(+) diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py index c0db8bb..940912e 100644 --- a/SlicerCART/src/SlicerCART.py +++ b/SlicerCART/src/SlicerCART.py @@ -3,6 +3,7 @@ import os import logging import slicer +import qt from slicer.ScriptedLoadableModule import * from slicer.util import VTKObservationMixin from glob import glob From ce20a32e4ce69ea3fc9dfefbdadd412c149e9188 Mon Sep 17 00:00:00 2001 From: jcohenadad Date: Fri, 12 Jul 2024 13:27:19 -0400 Subject: [PATCH 08/10] Removed package installation from README troubleshooting Not needed anymore --- README.md | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/README.md b/README.md index ce97eb7..13538a8 100644 --- a/README.md +++ b/README.md @@ -67,22 +67,8 @@ Although it may work on other versions and/or operating system, please note that 8. (Optional) Set the SlicerCART module to launch at 3DSlicer startup. To do so, go to `Edit -> Application Settings -> Modules -> Default startup module` ### Trouble shooting + * Qt might need to be installed. The first five steps of the following procedure might be useful for this: [procedure](https://web.stanford.edu/dept/cs_edu/resources/qt/install-mac). -* If some modules are missing (`ModuleNotFoundError`), they must be added to the 3D Slicer environment by using the following commands in the Python Console: - `from slicer.util import pip_install` - `pip_install("XYZ")` where `XYZ` is replaced by the proper library - -> Minimally the following packages are not already available (copy and paste in the 3D Slicer python interactor): -> - - ```py - slicer.util.pip_install('pandas') - slicer.util.pip_install('nibabel') - slicer.util.pip_install('pynrrd') - slicer.util.pip_install('pyyaml') - slicer.util.pip_install('slicerio') - slicer.util.pip_install('PyQt5') - ``` ### Other extensions that could be useful * `SlicerJupyter` to be able to use Jupyter Notebooks connected to 3D Slicer. From 37320695db81f7f026b49b9aa6e70971329f7954 Mon Sep 17 00:00:00 2001 From: jcohenadad Date: Fri, 12 Jul 2024 13:30:37 -0400 Subject: [PATCH 09/10] Removed mention of requirements.txt --- SlicerCART/src/SlicerCART.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py index 940912e..11f6d53 100644 --- a/SlicerCART/src/SlicerCART.py +++ b/SlicerCART/src/SlicerCART.py @@ -22,8 +22,6 @@ # TODO: There is probably a more elegant way to install pacakages through the extension manager when the user installs the extension. -# TODO: add a check for the version of the package -# TODO: use requirements.txt instead # TODO: check if the package installed with error # Dictionary of required python packages and their import names From 75d6b83265b7b4e4c40d5d79d4bb70accb78d3fa Mon Sep 17 00:00:00 2001 From: jcohenadad Date: Tue, 16 Jul 2024 18:13:24 -0400 Subject: [PATCH 10/10] No need to import qt twice --- SlicerCART/src/SlicerCART.py | 1 - 1 file changed, 1 deletion(-) diff --git a/SlicerCART/src/SlicerCART.py b/SlicerCART/src/SlicerCART.py index 11f6d53..f8c6f49 100644 --- a/SlicerCART/src/SlicerCART.py +++ b/SlicerCART/src/SlicerCART.py @@ -70,7 +70,6 @@ def check_and_install_python_packages(): import nrrd import pandas as pd import slicerio -import qt from PyQt5 import QtCore import yaml