gistfile1.txt

import os
import sys
import logging
import datetime
import slicer
import labels
from dotenv import load_dotenv
from pathlib import Path
from DICOMLib import DICOMUtils

def clear_scene():
    """Clear slicer scene""" 
    slicer.mrmlScene.Clear(0)

def load_dicom(dicomDataDir):
    """Load *.dcm to scene as volume""" 
    loadedNodeIDs = []  # this list will contain the list of all loaded node IDs
    with DICOMUtils.TemporaryDICOMDatabase() as db:
        DICOMUtils.importDicom(dicomDataDir, db)
        patientUIDs = db.patients()
        for patientUID in patientUIDs:
            loadedNodeIDs.extend(DICOMUtils.loadPatientByUID(patientUID))
    return loadedNodeIDs[0]

def get_avalible_labels_list(labelsPath):
    """Return labels list which avalibale in folder"""
    f_files=[]
    for root, dirs, file in os.walk(labelsPath):
        for f in file:
            f_files.append(root+'\\'+f)
    return f_files

def create_segment_editor_widget(segmentationNode, masterVolumeNode, show:bool=False):
    """Create segmentEditorWidget"""
    segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
    if show:
        segmentEditorWidget.show()
    segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
    segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
    slicer.mrmlScene.AddNode(segmentEditorNode)
    segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
    segmentEditorWidget.setSegmentationNode(segmentationNode)
    segmentEditorWidget.setSourceVolumeNode(slicer.mrmlScene.GetNodeByID(masterVolumeNode))
    return segmentEditorWidget

def create_segmentation_node():
    """Create segmentationNode"""
    segmentationNode=slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
    # segmentationNode.CreateDefaultDisplayNodes() # only needed for display
    return segmentationNode

def fill_background(segmentationNode, segmentEditorWidget, maskedVolume):
    segment = segmentationNode.GetSegmentation().AddEmptySegment("background")
    segmentEditorWidget.setCurrentSegmentID(segment)

    segmentEditorWidget.setActiveEffectByName("Mask volume")
    effect = segmentEditorWidget.activeEffect()
    effect.setParameter("Operation", "FILL_OUTSIDE")
    effect.setParameter("FillValue", '0')
    effect.self().outputVolumeSelector.setCurrentNode(maskedVolume)
    effect.self().onApply()

def load_avalible_labels(labels_stl_path, segmentationNode):
    for label in labels_stl_path:
        modelNode = slicer.modules.models.logic().AddModel(label)
        slicer.modules.segmentations.logic().ImportModelToSegmentationNode(modelNode, segmentationNode)
        # slicer.mrmlScene.RemoveNode(modelNode)

def fill_avalible_labels(segmentationNode,segmentEditorWidget,maskedVolume):
    segmentList=[]
    segmentationNode.GetSegmentation().GetSegmentIDs(segmentList)
    
    segmentEditorWidget.setActiveEffectByName("Mask volume")
    effect = segmentEditorWidget.activeEffect()
    effect.self().inputVolumeSelector.setCurrentNode(maskedVolume)
    effect.self().outputVolumeSelector.setCurrentNode(maskedVolume)
    
    for segment in segmentList:
        if segment == 'background':
            continue
        scalar_value = labels.get_label_scalar_value(segment)

        segmentEditorWidget.setCurrentSegmentID(segment)
        effect.setParameter("Operation", "FILL_INSIDE")
        effect.setParameter("FillValue", str(scalar_value))
        effect.self().onApply()

def main(uuid_path, stl_label_path):
    clear_scene()

    masterVolumeNode = load_dicom(uuid_path)
    maskedVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", "Temporary masked volume")
    segmentationNode = create_segmentation_node()
    segmentEditorWidget = create_segment_editor_widget(segmentationNode, masterVolumeNode)

    fill_background(segmentationNode, segmentEditorWidget, maskedVolume)

    labels_stl_path = get_avalible_labels_list(stl_label_path)
    load_avalible_labels(labels_stl_path, segmentationNode)

    fill_avalible_labels(segmentationNode,segmentEditorWidget,maskedVolume)

    slicer.util.exportNode(maskedVolume, stl_label_path+"\\multilabel.nii.gz", {"useCompression": 1})

uuid_path='c:\\Users\\xxxiN\\Documents\\tests\\original\\e1'
stl_label_path='c:\\Users\\xxxiN\\Documents\\tests\\Labels\\e1'

main(uuid_path, stl_label_path)

    # sys.exit('0')