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DLLabelsCT.py
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import sys
import os
import csv
import cv2
import pydicom.errors
from pydicom import dcmread
from pathlib import Path
from skimage.morphology import reconstruction
from PyQt6.QtWidgets import QWidget, QTableWidgetItem, QSlider, QLabel, QGridLayout, QHBoxLayout, QFileDialog, QMainWindow, QGraphicsView, QProgressBar, QMessageBox
from PyQt6.QtGui import QImage, QPixmap, QPainter, QActionGroup, QKeySequence, QColor
from gui_utils.custom_widgets import *
from gui_utils.segmentation_utils import segmentation
from gui_utils.image_utils import *
from gui_utils.drawing_utils import *
class DLLabelsCT(QMainWindow):
def __init__(self):
super().__init__()
self.DICOMFolderPath = ""
self.dicoms = []
self.axialDICOMIndex = 0
self.coronalDICOMIndex = 0
self.sagittalDICOMIndex = 0
self.dicomWindowCenter = 50
self.dicomWindowWidth = 400
self.pixelSpacingX = {}
self.pixelSpacingY = {}
self.currentDICOMStack = None
self.currentMaskStack = {}
self.maskColors = {}
self.hiddenLabels = []
self.modelClasses = {}
self.currentStudyID = None
self.currentPatientID = None
self.defaultDirectory = os.path.realpath(__file__)
self.annotableDirectory = None
self.annotableFolders = []
self.annotableIndex = 0
self.saveDirectory = None
self.segmentationModelFolderPath = None
self.segmentationModelPath = None
self.indexesToSegment = []
self.showMasks = True
self.saveImages = True
self.saveFlipped = True
self.removeOutliers = False
self.fillContours = False
self.useFileOrder = False
self.device = "cuda"
self.flip = {"Axial": False, "Coronal": False, "Sagittal": False}
self.axialImageQt = None
self.clickType = {"Selecting": True, "Dragging": False, "Drawing": False, "Erasing": False, "Measuring": False}
self.erasingOrDrawing = 1
self.scaleChanged = False
self.imageScale = 1.0
self.drawnMaskType = None
self.segmentationModelType = None
self.maskOpacity = 128
self.brightness = 0
self.contrast = 1.0
centralWidget = QWidget(self)
self.setCentralWidget(centralWidget)
centralLayout = QHBoxLayout(centralWidget)
self.gridLayout = QGridLayout()
self.gridLayout.setRowStretch(0, 1)
self.gridLayout.setColumnStretch(0, 2)
self.vLayout = QVBoxLayout()
centralLayout.addLayout(self.gridLayout)
centralLayout.addLayout(self.vLayout)
self.initUI()
def initUI(self):
self._createMenu()
self._createLabels()
self._createStatusBar()
self._createButtons()
self._createSliders()
self._createProgressBar()
self.setGeometry(100, 100, 500, 300)
self.setWindowTitle("DLLabelsCT")
def _createMenu(self):
menubar = self.menuBar()
fileMenu = menubar.addMenu('File')
selectDICOMFolderAct = QAction('Select DICOM folder...', self)
selectDICOMFolderAct.triggered.connect(self.getDICOMFolder)
selectSegmentationModelFolderAct = QAction('Select segmentation model folder...', self)
selectSegmentationModelFolderAct.triggered.connect(self.getSegmentationModelFolder)
selectSaveDirectoryAct = QAction('Select save folder...', self)
selectSaveDirectoryAct.triggered.connect(self.getSaveFolder)
selectAnnotableFolderAct = QAction('Select folder to annotate...', self)
selectAnnotableFolderAct.triggered.connect(self.getAnnotableFolder)
saveMasksAct = QAction('Save masks', self)
saveMasksAct.triggered.connect(self.saveMasks)
loadMasksAct = QAction('Load masks...', self)
loadMasksAct.triggered.connect(self.loadMasks)
saveAnnotationsAct = QAction('Save annotations', self)
saveAnnotationsAct.triggered.connect(self.saveAnnotations)
saveLabelsAct = QAction('Save labels...', self)
saveLabelsAct.triggered.connect(self.saveLabels)
loadLabelsAct = QAction('Load labels...', self)
loadLabelsAct.triggered.connect(self.loadLabels)
fileMenu.addAction(selectDICOMFolderAct)
fileMenu.addAction(selectSegmentationModelFolderAct)
fileMenu.addAction(selectAnnotableFolderAct)
fileMenu.addAction(selectSaveDirectoryAct)
fileMenu.addSeparator()
fileMenu.addAction(saveMasksAct)
fileMenu.addAction(loadMasksAct)
fileMenu.addSeparator()
fileMenu.addAction(saveAnnotationsAct)
fileMenu.addSeparator()
fileMenu.addAction(saveLabelsAct)
fileMenu.addAction(loadLabelsAct)
self.showMenu = menubar.addMenu('Show')
showAxialAct = QAction('Axial', self, checkable=True)
showAxialAct.setShortcut(QKeySequence("Z"))
showCoronalAct = QAction('Coronal', self, checkable=True)
showCoronalAct.setShortcut(QKeySequence("X"))
showSagittalAct = QAction('Sagittal', self, checkable=True)
showSagittalAct.setShortcut(QKeySequence("C"))
showMasksAct = QAction('Masks', self, checkable=True)
showMasksAct.setShortcut(QKeySequence("V"))
self.showMenu.triggered.connect(self.showOrHide)
showAxialAct.setChecked(True)
showCoronalAct.setChecked(True)
showSagittalAct.setChecked(True)
showMasksAct.setChecked(True)
self.showMenu.addAction(showAxialAct)
self.showMenu.addAction(showCoronalAct)
self.showMenu.addAction(showSagittalAct)
self.showMenu.addAction(showMasksAct)
self.showMenu.hide()
windowingMenu = menubar.addMenu('Windowing')
selectDefaultAct = QAction('Tissue 1', self, checkable=True)
selectTissue2Act = QAction('Tissue 2', self, checkable=True)
selectTissue3Act = QAction('Tissue 3', self, checkable=True)
selectLungsAct = QAction('Lungs', self, checkable=True)
selectBoneAct = QAction('Bone', self, checkable=True)
selectCustomWindowAct = QAction("Custom...", self, checkable=True)
self.agWindowing = QActionGroup(self)
d = self.agWindowing.addAction(selectDefaultAct)
t2 = self.agWindowing.addAction(selectTissue2Act)
t3 = self.agWindowing.addAction(selectTissue3Act)
l = self.agWindowing.addAction(selectLungsAct)
b = self.agWindowing.addAction(selectBoneAct)
cw = self.agWindowing.addAction(selectCustomWindowAct)
self.agWindowing.setExclusive(True)
d.setChecked(True)
windowingMenu.addAction(d)
windowingMenu.addAction(t2)
windowingMenu.addAction(t3)
windowingMenu.addAction(l)
windowingMenu.addAction(b)
windowingMenu.addAction(cw)
self.agWindowing.triggered.connect(self.changeWindowing)
deviceMenu = menubar.addMenu('Device')
selectGPUAct = QAction('GPU', self, checkable=True)
selectCPUAct = QAction('CPU', self, checkable=True)
agDevice = QActionGroup(self)
gpu = agDevice.addAction(selectGPUAct)
cpu = agDevice.addAction(selectCPUAct)
agDevice.setExclusive(True)
gpu.setChecked(True)
deviceMenu.addAction(gpu)
deviceMenu.addAction(cpu)
agDevice.triggered.connect(self.changeDevice)
optionsMenu = menubar.addMenu('Options')
selectDICOMPathShowingAct = QAction('Show DICOM path', self, checkable=True)
selectSegmentationPathShowingAct = QAction('Show segmentation model path', self, checkable=True)
selectSaveFolderShowingAct = QAction('Show save folder path', self, checkable=True)
selectPatientIDShowingAct = QAction('Show patient ID', self, checkable=True)
selectRemovingAct = QAction('Remove outliers after segmentation/when saving', self, checkable=True)
selectFillingAct = QAction('Automatically fill holes in masks', self, checkable=True)
selectImageSavingAct = QAction('Save images when annotating', self, checkable=True)
selectImageFlippingAct = QAction('Save flipped images when annotating', self, checkable=True)
useFileOrderAct = QAction('Show DICOMs by filename order', self, checkable=True)
self.agOptions = QActionGroup(self)
showingDICOMPath = self.agOptions.addAction(selectDICOMPathShowingAct)
showingSegmentationPath = self.agOptions.addAction(selectSegmentationPathShowingAct)
showingSaveFolderPath = self.agOptions.addAction(selectSaveFolderShowingAct)
showingPatientID = self.agOptions.addAction(selectPatientIDShowingAct)
removing = self.agOptions.addAction(selectRemovingAct)
filling = self.agOptions.addAction(selectFillingAct)
savingImages = self.agOptions.addAction(selectImageSavingAct)
savingFlipped = self.agOptions.addAction(selectImageFlippingAct)
fileOrder = self.agOptions.addAction(useFileOrderAct)
self.agOptions.setExclusive(False)
savingImages.setChecked(True)
savingFlipped.setChecked(True)
showingDICOMPath.setChecked(True)
showingSegmentationPath.setChecked(True)
showingSaveFolderPath.setChecked(True)
optionsMenu.addAction(showingDICOMPath)
optionsMenu.addAction(showingSegmentationPath)
optionsMenu.addAction(showingSaveFolderPath)
optionsMenu.addAction(showingPatientID)
optionsMenu.addSeparator()
optionsMenu.addAction(removing)
optionsMenu.addAction(filling)
optionsMenu.addSeparator()
optionsMenu.addAction(savingImages)
optionsMenu.addAction(savingFlipped)
optionsMenu.addSeparator()
optionsMenu.addAction(fileOrder)
self.agOptions.triggered.connect(self.changeOptions)
drawingMenu = menubar.addMenu('Drawing options')
selectSelectingAct = QAction('Selecting', self, checkable=True)
selectSelectingAct.setShortcut(QKeySequence("S"))
selectDrawingAct = QAction('Drawing', self, checkable=True)
selectDrawingAct.setShortcut(QKeySequence("D"))
selectErasingAct = QAction('Erasing', self, checkable=True)
selectErasingAct.setShortcut(QKeySequence("E"))
selectDraggingAct = QAction('Dragging', self, checkable=True)
selectDraggingAct.setShortcut(QKeySequence("F"))
selectMeasuringAct = QAction('Measuring', self, checkable=True)
selectMeasuringAct.setShortcut(QKeySequence("G"))
agDrawErase = QActionGroup(self)
selecting = agDrawErase.addAction(selectSelectingAct)
drawing = agDrawErase.addAction(selectDrawingAct)
erasing = agDrawErase.addAction(selectErasingAct)
dragging = agDrawErase.addAction(selectDraggingAct)
measuring = agDrawErase.addAction(selectMeasuringAct)
agDrawErase.setExclusive(True)
selecting.setChecked(True)
drawingMenu.addAction(selecting)
drawingMenu.addAction(drawing)
drawingMenu.addAction(erasing)
drawingMenu.addAction(dragging)
drawingMenu.addAction(measuring)
drawingMenu.addSeparator()
agDrawErase.triggered.connect(self.changeDrawingErasing)
select1x1Act = QAction('1x1', self, checkable=True)
select1x1Act.setShortcut(QKeySequence("1"))
select3x3Act = QAction('3x3', self, checkable=True)
select3x3Act.setShortcut(QKeySequence("2"))
select5x5Act = QAction('5x5', self, checkable=True)
select5x5Act.setShortcut(QKeySequence("3"))
select7x7Act = QAction('7x7', self, checkable=True)
select7x7Act.setShortcut(QKeySequence("4"))
agDrawSize = QActionGroup(self)
onexone = agDrawSize.addAction(select1x1Act)
threexthree = agDrawSize.addAction(select3x3Act)
fivexfive = agDrawSize.addAction(select5x5Act)
sevenxseven = agDrawSize.addAction(select7x7Act)
agDrawSize.setExclusive(True)
sevenxseven.setChecked(True)
drawingMenu.addAction(onexone)
drawingMenu.addAction(threexthree)
drawingMenu.addAction(fivexfive)
drawingMenu.addAction(sevenxseven)
drawingMenu.addSeparator()
agDrawSize.triggered.connect(self.changeDrawingSize)
selectCircleAct = QAction('Circle', self, checkable=True)
selectSquareAct = QAction('Square', self, checkable=True)
self.agDrawShape = QActionGroup(self)
circle = self.agDrawShape.addAction(selectCircleAct)
square = self.agDrawShape.addAction(selectSquareAct)
self.agDrawShape.setExclusive(True)
circle.setChecked(True)
drawingMenu.addAction(circle)
drawingMenu.addAction(square)
self.agDrawShape.triggered.connect(self.changeDrawingShape)
zoomMenu = menubar.addMenu('Zoom')
select1Act = QAction('1.0', self, checkable=True)
select15Act = QAction('1.5', self, checkable=True)
select2Act = QAction('2.0', self, checkable=True)
select4Act = QAction('4.0', self, checkable=True)
select8Act = QAction('8.0', self, checkable=True)
self.agZoom = QActionGroup(self)
one = self.agZoom.addAction(select1Act)
onefive = self.agZoom.addAction(select15Act)
two = self.agZoom.addAction(select2Act)
four = self.agZoom.addAction(select4Act)
eight = self.agZoom.addAction(select8Act)
self.agZoom.setExclusive(True)
one.setChecked(True)
zoomMenu.addAction(one)
zoomMenu.addAction(onefive)
zoomMenu.addAction(two)
zoomMenu.addAction(four)
zoomMenu.addAction(eight)
self.agZoom.triggered.connect(self.changeZoom)
flipMenu = menubar.addMenu('Flip')
selectAxis0Act = QAction('Axial', self, checkable=True)
selectAxis1Act = QAction('Coronal', self, checkable=True)
selectAxis2Act = QAction('Sagittal', self, checkable=True)
self.agFlip = QActionGroup(self)
axis0 = self.agFlip.addAction(selectAxis0Act)
axis1 = self.agFlip.addAction(selectAxis1Act)
axis2 = self.agFlip.addAction(selectAxis2Act)
self.agFlip.setExclusive(False)
flipMenu.addAction(axis0)
flipMenu.addAction(axis1)
flipMenu.addAction(axis2)
self.agFlip.triggered.connect(self.changeFlip)
self.selectExamAct = menubar.addAction('Change exam...')
self.selectExamAct.setVisible(False)
self.selectExamAct.triggered.connect(self.selectExam)
def _createLabels(self):
self.currentDICOMPathLabel = QLabel("DICOM folder: None", self)
self.gridLayout.addWidget(self.currentDICOMPathLabel, 3, 0, alignment=Qt.AlignmentFlag.AlignCenter)
self.currentSegmentationModelPathLabel = QLabel("Segmentation model folder: None", self)
self.gridLayout.addWidget(self.currentSegmentationModelPathLabel, 4, 0, alignment=Qt.AlignmentFlag.AlignCenter)
self.currentSavePathLabel = QLabel("Save folder: None", self)
self.gridLayout.addWidget(self.currentSavePathLabel, 5, 0, alignment=Qt.AlignmentFlag.AlignCenter)
self.currentPatientIDLabel = QLabel("Patient ID: None", self)
self.gridLayout.addWidget(self.currentPatientIDLabel, 6, 0, alignment=Qt.AlignmentFlag.AlignCenter)
self.currentPatientIDLabel.hide()
self.axialImageScene = CTGraphicsScene("axial", self)
self.axialImageLabel = QGraphicsView(self)
self.axialImageLabel.setScene(self.axialImageScene)
self.axialImageLabel.setCursor(QCursor(Qt.CursorShape.CrossCursor))
self.axialImageLabel.fitInView(self.axialImageScene.sceneRect(), Qt.AspectRatioMode.KeepAspectRatio)
self.gridLayout.addWidget(self.axialImageLabel, 0, 0)
self.coronalImageScene = CTGraphicsScene("coronal", self)
self.coronalImageLabel = QGraphicsView(self)
self.coronalImageLabel.setScene(self.coronalImageScene)
self.coronalImageLabel.setCursor(QCursor(Qt.CursorShape.CrossCursor))
self.coronalImageLabel.fitInView(self.coronalImageScene.sceneRect(), Qt.AspectRatioMode.KeepAspectRatio)
self.gridLayout.addWidget(self.coronalImageLabel, 0, 1)
self.sagittalImageScene = CTGraphicsScene("sagittal", self)
self.sagittalImageLabel = QGraphicsView(self)
self.sagittalImageLabel.setScene(self.sagittalImageScene)
self.sagittalImageLabel.setCursor(QCursor(Qt.CursorShape.CrossCursor))
self.sagittalImageLabel.fitInView(self.sagittalImageScene.sceneRect(), Qt.AspectRatioMode.KeepAspectRatio)
self.gridLayout.addWidget(self.sagittalImageLabel, 0, 2)
self.labelTable = LabelTable(self)
self.labelTable.setFixedWidth(280)
self.vLayout.addWidget(self.labelTable, alignment=Qt.AlignmentFlag.AlignTrailing)
self.axialIndexLabel = QLabel(self)
self.gridLayout.addWidget(self.axialIndexLabel, 1, 0, alignment=Qt.AlignmentFlag.AlignCenter)
self.coronalIndexLabel = QLabel(self)
self.gridLayout.addWidget(self.coronalIndexLabel, 1, 1, alignment=Qt.AlignmentFlag.AlignCenter)
self.sagittalIndexLabel = QLabel(self)
self.gridLayout.addWidget(self.sagittalIndexLabel, 1, 2, alignment=Qt.AlignmentFlag.AlignCenter)
self.segmentationIndexLabel = QLabel(self)
self.gridLayout.addWidget(self.segmentationIndexLabel, 6, 1, alignment=Qt.AlignmentFlag.AlignCenter)
self.segmentationIndexLabel.hide()
def _createButtons(self):
self.removeOutliersButton = QPushButton("Remove outliers from drawn mask")
self.gridLayout.addWidget(self.removeOutliersButton, 3, 1)
self.removeOutliersButton.clicked.connect(self.removeOutliersFunc)
self.removeOutliersButton.hide()
self.fillContoursButton = QPushButton("Fill masks")
self.fillContoursButton.clicked.connect(self.fillContoursFunc)
self.gridLayout.addWidget(self.fillContoursButton, 4, 1)
self.fillContoursButton.hide()
self.doSegmentationButton = QPushButton("Do segmentation")
self.gridLayout.addWidget(self.doSegmentationButton, 5, 1)
self.doSegmentationButton.clicked.connect(self.doSegmentation)
self.doSegmentationButton.hide()
def _createSliders(self):
self.axialSlider = QSlider(Qt.Orientation.Horizontal, self)
self.axialSlider.setRange(0, 100)
self.axialSlider.valueChanged[int].connect(self.changeAxialImageIndex)
self.gridLayout.addWidget(self.axialSlider, 2, 0)
self.axialSlider.hide()
self.coronalSlider = QSlider(Qt.Orientation.Horizontal, self)
self.coronalSlider.setRange(0, 511)
self.coronalSlider.valueChanged[int].connect(self.changeCoronalImageIndex)
self.gridLayout.addWidget(self.coronalSlider, 2, 1)
self.coronalSlider.hide()
self.sagittalSlider = QSlider(Qt.Orientation.Horizontal, self)
self.sagittalSlider.setRange(0, 511)
self.sagittalSlider.valueChanged[int].connect(self.changeSagittalImageIndex)
self.gridLayout.addWidget(self.sagittalSlider, 2, 2)
self.sagittalSlider.hide()
self.setOpacitySlider = QSlider(Qt.Orientation.Horizontal, self)
self.setOpacitySlider.setRange(0, 255)
self.setOpacitySlider.setValue(self.maskOpacity)
self.setOpacitySlider.valueChanged[int].connect(self.changeOpacity)
self.gridLayout.addWidget(self.setOpacitySlider, 3, 2)
self.setOpacitySlider.hide()
self.setSegmentationIndexSlider = RangeSlider(Qt.Orientation.Horizontal, self)
self.setSegmentationIndexSlider.setRange(0, 100)
self.setSegmentationIndexSlider.setLow(0)
self.setSegmentationIndexSlider.setHigh(100)
self.setSegmentationIndexSlider.sliderMoved.connect(self.changeSegmentationIndex)
self.gridLayout.addWidget(self.setSegmentationIndexSlider, 4, 2)
self.setSegmentationIndexSlider.hide()
def _createStatusBar(self):
self.statusbar = self.statusBar()
def _createProgressBar(self):
self.progressBar = QProgressBar(self)
self.progressBar.setRange(0, 100)
self.gridLayout.addWidget(self.progressBar, 8, 0, 1, 3)
self.progressBar.hide()
def changeAxialImageIndex(self, sliderValue):
self.brightness = 0
self.contrast = 1
self.axialDICOMIndex = sliderValue
self.updateSingleImage(imageType="axial")
def changeCoronalImageIndex(self, sliderValue):
self.coronalDICOMIndex = sliderValue
self.updateSingleImage(imageType="coronal")
def changeSagittalImageIndex(self, sliderValue):
self.sagittalDICOMIndex = sliderValue
self.updateSingleImage(imageType="sagittal")
def changeOpacity(self, sliderValue):
self.maskOpacity = sliderValue
self.updateImages()
def changeSegmentationIndex(self, sliderLow, sliderHigh):
self.indexesToSegment = list(range(sliderLow, sliderHigh + 1))
self.segmentationIndexLabel.setText(f"Slices to segment: {sliderLow} - {sliderHigh}")
def changeWindowing(self, act):
if self.currentDICOMStack is not None:
if act.text() == "Tissue 1":
self.dicomWindowCenter = 50
self.dicomWindowWidth = 400
elif act.text() == "Tissue 2":
self.dicomWindowCenter = 50
self.dicomWindowWidth = 250
elif act.text() == "Tissue 3":
self.dicomWindowCenter = 30
self.dicomWindowWidth = 150
elif act.text() == "Lungs":
self.dicomWindowCenter = -600
self.dicomWindowWidth = 1500
elif act.text() == "Bone":
self.dicomWindowCenter = 400
self.dicomWindowWidth = 1800
elif act.text() == "Custom...":
customWindowDialog = CustomWindowDialog(parent=self)
if customWindowDialog.exec():
try:
widthValue = int(customWindowDialog.setWidthValue.text())
centerValue = int(customWindowDialog.setCenterValue.text())
if widthValue > 0:
self.dicomWindowCenter = centerValue
self.dicomWindowWidth = widthValue
else:
self.statusbar.showMessage("Invalid values!")
self.agWindowing.actions()[0].setChecked(True)
self.dicomWindowCenter = 50
self.dicomWindowWidth = 400
except ValueError:
self.statusbar.showMessage("Invalid values!")
self.agWindowing.actions()[0].setChecked(True)
self.dicomWindowCenter = 50
self.dicomWindowWidth = 400
self.currentDICOMStack = None
self.showImages(imagesChanged=False)
if self.showMasks:
self.updateImages()
else:
self.agWindowing.actions()[0].setChecked(True)
self.dicomWindowCenter = 50
self.dicomWindowWidth = 400
self.statusbar.showMessage("Windowing cannot be changed without DICOMs! (Window changed back to default)")
def changeDevice(self, act):
if act.text() == "GPU":
self.device = "cuda"
elif act.text() == "CPU":
self.device = "cpu"
def changeOptions(self, act):
if self.agOptions.actions()[0].isChecked():
self.currentDICOMPathLabel.show()
else:
self.currentDICOMPathLabel.hide()
if self.agOptions.actions()[1].isChecked():
self.currentSegmentationModelPathLabel.show()
else:
self.currentSegmentationModelPathLabel.hide()
if self.agOptions.actions()[2].isChecked():
self.currentSavePathLabel.show()
else:
self.currentSavePathLabel.hide()
if self.agOptions.actions()[3].isChecked():
self.currentPatientIDLabel.show()
else:
self.currentPatientIDLabel.hide()
if self.agOptions.actions()[4].isChecked():
self.removeOutliers = True
else:
self.removeOutliers = False
if self.agOptions.actions()[5].isChecked():
self.fillContours = True
else:
self.fillContours = False
if self.agOptions.actions()[6].isChecked():
self.saveImages = True
else:
self.saveImages = False
if self.agOptions.actions()[7].isChecked():
self.saveFlipped = True
else:
self.saveFlipped = False
if self.agOptions.actions()[8].isChecked():
self.useFileOrder = True
else:
self.useFileOrder = False
if act.text() == 'Show DICOMs by filename order':
self.currentDICOMStack = None
self.showImages()
def changeDrawingErasing(self, act):
self.clickType = dict.fromkeys(self.clickType, False)
self.clickType[act.text()] = True
if self.clickType["Dragging"]:
self.axialImageLabel.setDragMode(QGraphicsView.DragMode.ScrollHandDrag)
self.sagittalImageLabel.setDragMode(QGraphicsView.DragMode.ScrollHandDrag)
self.coronalImageLabel.setDragMode(QGraphicsView.DragMode.ScrollHandDrag)
else:
self.axialImageLabel.setDragMode(QGraphicsView.DragMode.NoDrag)
self.sagittalImageLabel.setDragMode(QGraphicsView.DragMode.NoDrag)
self.coronalImageLabel.setDragMode(QGraphicsView.DragMode.NoDrag)
if self.clickType["Erasing"]:
self.erasingOrDrawing = -1
elif self.clickType["Drawing"]:
self.erasingOrDrawing = 1
def changeDrawingSize(self, act):
if act.text() == "1x1":
self.axialImageScene.drawingSize = 1
self.axialImageScene.drawingHigh = 1
self.axialImageScene.drawingLow = 0
elif act.text() == "3x3":
self.axialImageScene.drawingSize = 3
self.axialImageScene.drawingHigh = 2
self.axialImageScene.drawingLow = 1
elif act.text() == "5x5":
self.axialImageScene.drawingSize = 5
self.axialImageScene.drawingHigh = 3
self.axialImageScene.drawingLow = 2
elif act.text() == "7x7":
self.axialImageScene.drawingSize = 7
self.axialImageScene.drawingHigh = 4
self.axialImageScene.drawingLow = 3
if self.agDrawShape.actions()[0].isChecked():
self.axialImageScene.drawingShape = circles[str(self.axialImageScene.drawingSize)]
else:
self.axialImageScene.drawingShape = squares[str(self.axialImageScene.drawingSize)]
def changeDrawingShape(self, act):
if act.text().lower() == "circle":
self.axialImageScene.drawingShape = circles[str(self.axialImageScene.drawingSize)]
else:
self.axialImageScene.drawingShape = squares[str(self.axialImageScene.drawingSize)]
def changeDrawnLabel(self, labelName, row):
QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
if labelName in self.hiddenLabels:
self.hiddenLabels.remove(labelName)
labelAmount = len(self.currentMaskStack)
if labelAmount == 0:
self.statusbar.showMessage("No labels!")
else:
for oldRow in range(self.labelTable.rowCount()):
if self.labelTable.item(oldRow, 0).text() == self.drawnMaskType:
self.labelTable.item(oldRow, 0).setBackground(QColor(255, 255, 255))
self.drawnMaskType = labelName
self.axialImageScene.drawnMaskType = labelName
self.labelTable.item(row, 0).setBackground((QColor(0, 0, 255, 80)))
self.updateImages()
QApplication.restoreOverrideCursor()
def changeZoom(self, act):
self.imageScale = float(act.text())
self.scaleChanged = True
self.updateImages()
self.scaleChanged = False
def changeFlip(self, act):
if self.currentDICOMStack is None:
pass
else:
self.flip[act.text()] = True
self.updateImages()
self.flip = {"Axial": False, "Coronal": False, "Sagittal": False}
def addLabel(self):
addLabelDialog = AddLabelDialog(parent=self)
if addLabelDialog.exec():
try:
label = addLabelDialog.setLabelName.text().lower()
red = int(addLabelDialog.setRedValue.text())
green = int(addLabelDialog.setGreenValue.text())
blue = int(addLabelDialog.setBlueValue.text())
if label == "":
raise ValueError
elif label in self.currentMaskStack.keys():
raise NameError
if red > 255:
red = 255
if green > 255:
green = 255
if blue > 255:
blue = 255
except ValueError:
self.statusbar.showMessage("Invalid value!")
except NameError:
self.statusbar.showMessage("Label name already taken!")
else:
self.maskColors[label] = [red, green, blue]
if self.currentDICOMStack is None:
self.currentMaskStack[label] = None
self.axialImageScene.mask[label] = None
else:
self.currentMaskStack[label] = np.zeros(self.currentDICOMStack.shape)
self.axialImageScene.createMask(label)
rowPosition = self.labelTable.rowCount()
self.modelClasses[label] = rowPosition
self.labelTable.insertRow(rowPosition)
self.labelTable.setItem(rowPosition, 0, QTableWidgetItem(label))
self.labelTable.setItem(rowPosition, 1, QTableWidgetItem(str(rowPosition)))
self.labelTable.setItem(rowPosition, 2, QTableWidgetItem(""))
self.labelTable.item(rowPosition, 2).setBackground(QColor(red, green, blue))
def showHideLabel(self, labelName, row):
if labelName in self.hiddenLabels:
self.hiddenLabels.remove(labelName)
self.labelTable.item(row, 0).setBackground((QColor(255, 255, 255)))
else:
self.hiddenLabels.append(labelName)
self.labelTable.item(row, 0).setBackground((QColor(128, 128, 128)))
if self.drawnMaskType == labelName:
self.drawnMaskType = None
self.axialImageScene.drawnMaskType = None
self.updateImages()
def removeLabel(self, labelName, row):
mb = QMessageBox()
text = "Are you sure you want to remove label \"" + labelName + "\"?"
yesNo = mb.question(self, '', text, QMessageBox.StandardButton.Yes, QMessageBox.StandardButton.No)
if yesNo is QMessageBox.StandardButton.Yes:
self.labelTable.removeRow(row)
for i in range(self.labelTable.rowCount()):
self.labelTable.item(i, 1).setText("")
self.maskColors.pop(labelName)
if labelName in self.hiddenLabels:
self.hiddenLabels.remove(labelName)
self.currentMaskStack.pop(labelName)
self.axialImageScene.mask.pop(labelName)
self.modelClasses.pop(labelName)
if self.drawnMaskType == labelName:
self.drawnMaskType = None
self.axialImageScene.drawnMaskType = None
self.updateImages()
self.labelTable.resizeRowsToContents()
self.labelTable.verticalHeader().setSectionResizeMode(QHeaderView.ResizeMode.Stretch)
def resetLabelColor(self, labelName, rowPosition):
resetLabelColor = ResetLabelColorDialog(parent=self)
if resetLabelColor.exec():
red = int(resetLabelColor.setRedValue.text())
green = int(resetLabelColor.setGreenValue.text())
blue = int(resetLabelColor.setBlueValue.text())
if red > 255:
red = 255
if green > 255:
green = 255
if blue > 255:
blue = 255
self.maskColors[labelName] = [red, green, blue]
self.labelTable.item(rowPosition, 2).setBackground(QColor(red, green, blue))
self.updateImages()
def selectExam(self):
annotableAmount = len(self.annotableFolders)
if annotableAmount == 0:
self.statusbar.showMessage("Invalid amount of exams!")
else:
selectExamDialog = SelectExamDialog(parent=self)
if selectExamDialog.exec():
try:
index = int(selectExamDialog.setIndexValue.text())
if index >= annotableAmount or index < 0:
self.statusbar.showMessage("Invalid number!")
else:
self.annotableIndex = index
self.changeAnnotable(True)
except ValueError:
self.statusbar.showMessage("Invalid number!")
def setClasses(self):
labelAmount = len(self.currentMaskStack)
if labelAmount == 0:
self.statusbar.showMessage("No labels!")
else:
setClassesDialog = SetClassesDialog(parent=self)
if setClassesDialog.exec():
segmentationClasses = setClassesDialog.segmentationClasses
num = list(range(len(segmentationClasses)))
classList = []
try:
for i in segmentationClasses:
classList.append(int(i.text()))
if set(classList) != set(num):
self.statusbar.showMessage("Invalid classes!")
else:
for k, v in self.currentMaskStack.items():
self.modelClasses[k] = None
for j, maskType in enumerate(self.modelClasses):
self.modelClasses[maskType] = int(segmentationClasses[j].text())
if maskType == self.labelTable.item(j, 0).text():
self.labelTable.item(j, 1).setText(segmentationClasses[j].text())
except ValueError:
self.statusbar.showMessage("Empty value in classes!")
def getDICOMFolder(self):
QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
try:
self.DICOMFolderPath = QFileDialog.getExistingDirectory(self, 'Choose DICOM folder', directory=self.defaultDirectory)
except ValueError:
pass
else:
if not self.DICOMFolderPath or self.DICOMFolderPath is None:
pass
else:
self.currentPatientID = Path(self.DICOMFolderPath).name
self.dicoms = sorted(list(Path(self.DICOMFolderPath).rglob("*.dcm")))
if len(self.dicoms) > 1500 or len(self.dicoms) == 0:
self.dicoms = sorted(list(Path(self.DICOMFolderPath).rglob("*")))
if len(self.dicoms) > 1500 or len(self.dicoms) == 0:
self.statusbar.showMessage("Invalid folder (too many DICOMs (> 1500) or no DICOMs found)")
else:
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
self.axialSlider.setRange(0, len(self.dicoms) - 1)
self.currentDICOMStack = None
self.currentMaskStack = reset_mask_stack(self.currentMaskStack)
self.currentStudyID = None
validFolder = self.showImages()
if validFolder == 0:
self.DICOMFolderPath = "None"
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
self.annotableFolders = []
self.annotableDirectory = None
self.annotableIndex = 0
self.selectExamAct.setVisible(False)
else:
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
self.axialSlider.setRange(0, len(self.dicoms) - 1)
self.currentDICOMStack = None
self.currentMaskStack = reset_mask_stack(self.currentMaskStack)
self.currentStudyID = None
validFolder = self.showImages()
if validFolder == 0:
self.DICOMFolderPath = "None"
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
self.annotableFolders = []
self.annotableDirectory = None
self.annotableIndex = 0
self.selectExamAct.setVisible(False)
QApplication.restoreOverrideCursor()
def getSegmentationModelFolder(self):
QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
try:
self.segmentationModelFolderPath = QFileDialog.getExistingDirectory(self, 'Choose segmentation model folder', directory=self.defaultDirectory)
except ValueError:
pass
else:
if not self.segmentationModelFolderPath or self.segmentationModelFolderPath is None:
pass
else:
self.segmentationModelPath = list(Path(self.segmentationModelFolderPath).glob("*.p"))
if len(self.segmentationModelPath) == 0:
self.segmentationModelPath = list(Path(self.segmentationModelFolderPath).glob("*.pth"))
if len(self.segmentationModelPath) == 0:
self.statusbar.showMessage("No model(s) found")
self.segmentationModelPath = None
try:
if len(self.segmentationModelPath) > 0:
labelText = f"Segmentation model folder: {str(Path(self.segmentationModelFolderPath).name)}"
self.currentSegmentationModelPathLabel.setText(labelText)
self.segmentationModelType = str(Path(self.segmentationModelFolderPath).parents[0].name).lower()
self.doSegmentationButton.show()
self.setSegmentationIndexSlider.show()
self.segmentationIndexLabel.setText(f"Slices to segment: {self.setSegmentationIndexSlider.low()} - {self.setSegmentationIndexSlider.high()}")
self.segmentationIndexLabel.show()
except TypeError:
self.statusbar.showMessage("No model(s) found")
QApplication.restoreOverrideCursor()
def getSaveFolder(self):
QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
try:
self.saveDirectory = QFileDialog.getExistingDirectory(self, 'Choose save folder', directory=self.defaultDirectory)
except ValueError:
self.saveDirectory = None
else:
labelText = f"Save folder: {str(self.saveDirectory)}"
self.currentSavePathLabel.setText(labelText)
QApplication.restoreOverrideCursor()
def getAnnotableFolder(self):
QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
try:
if self.saveDirectory is None:
self.statusbar.showMessage("Select save folder before annotating!")
else:
self.annotableDirectory = QFileDialog.getExistingDirectory(self, 'Choose folder to annotate', directory=self.defaultDirectory)
except ValueError:
pass
else:
if not self.annotableDirectory or self.annotableDirectory is None:
pass
else:
self.annotableFolders = sorted(os.listdir(self.annotableDirectory))
if len(self.annotableFolders) == 0:
self.statusbar.showMessage("Folder is empty!")
self.annotableFolders = []
else:
self.annotableIndex = 0
self.DICOMFolderPath = Path(self.annotableDirectory) / self.annotableFolders[self.annotableIndex]
self.currentPatientID = Path(self.DICOMFolderPath).name
self.dicoms = sorted(list(Path(self.DICOMFolderPath).rglob("*.dcm")))
if len(self.dicoms) > 1500 or len(self.dicoms) == 0:
self.dicoms = sorted(list(Path(self.DICOMFolderPath).rglob("*")))
if len(self.dicoms) > 1500 or len(self.dicoms) == 0:
self.statusbar.showMessage("Invalid folder (too many DICOMs (> 1500) or no DICOMs found)")
else:
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
self.axialSlider.setRange(0, len(self.dicoms) - 1)
self.currentDICOMStack = None
self.currentMaskStack = reset_mask_stack(self.currentMaskStack)
self.currentStudyID = None
validFolder = self.showImages()
if validFolder == 0:
self.DICOMFolderPath = "None"
self.annotableDirectory = None
self.annotableFolders = []
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
elif self.saveDirectory is not None:
self.loadAnnotations()
self.selectExamAct.setVisible(True)
else:
self.selectExamAct.setVisible(True)
else:
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
self.axialSlider.setRange(0, len(self.dicoms) - 1)
self.currentDICOMStack = None
self.currentMaskStack = reset_mask_stack(self.currentMaskStack)
self.currentStudyID = None
validFolder = self.showImages()
if validFolder == 0:
self.DICOMFolderPath = "None"
self.annotableDirectory = None
self.annotableFolders = []
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
elif self.saveDirectory is not None:
self.loadAnnotations()
self.selectExamAct.setVisible(True)
else:
self.selectExamAct.setVisible(True)
QApplication.restoreOverrideCursor()
def changeAnnotable(self, save=True):
QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
if save:
self.saveAnnotations()
self.DICOMFolderPath = Path(self.annotableDirectory) / self.annotableFolders[self.annotableIndex]
self.currentPatientID = Path(self.DICOMFolderPath).name
self.dicoms = sorted(list(Path(self.DICOMFolderPath).rglob("*.dcm")))
if len(self.dicoms) > 1500 or len(self.dicoms) == 0:
self.dicoms = sorted(list(Path(self.DICOMFolderPath).rglob("*")))
if len(self.dicoms) > 1500 or len(self.dicoms) == 0:
self.statusbar.showMessage("Invalid folder (too many DICOMs (> 1500) or no DICOMs found)")
else:
self.axialSlider.setRange(0, len(self.dicoms) - 1)
self.currentDICOMStack = None
self.currentMaskStack = reset_mask_stack(self.currentMaskStack)
self.currentStudyID = None
validFolder = self.showImages()
if validFolder == 0:
self.annotableIndex += 1
if self.annotableIndex >= len(self.annotableFolders):
self.annotableIndex = 0
self.statusbar.showMessage("Last annotable folder was invalid, switching to first folder")
else:
self.statusbar.showMessage("Invalid folder in annotables, switching to next folder")
self.changeAnnotable(save=False)
else:
self.loadAnnotations()
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
else:
self.axialSlider.setRange(0, len(self.dicoms) - 1)
self.currentDICOMStack = None
self.currentMaskStack = reset_mask_stack(self.currentMaskStack)
self.currentStudyID = None
validFolder = self.showImages()
if validFolder == 0:
self.annotableIndex += 1
if self.annotableIndex >= len(self.annotableFolders):
self.annotableIndex = 0
self.statusbar.showMessage("Last annotable folder was invalid, switching to first folder")
else:
self.statusbar.showMessage("Invalid folder in annotables, switching to next folder")
self.changeAnnotable(save=False)
else:
self.loadAnnotations()
labelText = f"DICOM folder: {str(Path(self.DICOMFolderPath))}"
self.currentDICOMPathLabel.setText(labelText)
QApplication.restoreOverrideCursor()
def saveMasks(self):
QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
for maskType, mask in self.currentMaskStack.items():
if self.currentMaskStack[maskType] is not None and self.currentStudyID is not None and self.saveDirectory is not None:
self.progressBar.show()