SlicerLabkeyExtension/labkeySlicerPythonExtension/loadDicom.py

import slicer
import os
import subprocess
import re

dicomModify="/afs/f9.ijs.si/home/studen/software/install/"
dicomModify+="dicomModify/bin/dicomModify"

class loadDicom(slicer.ScriptedLoadableModule.ScriptedLoadableModule):
    def __init__(self,parent):
        slicer.ScriptedLoadableModule.ScriptedLoadableModule.__init__(self, parent)
        self.className="loadDicom"
        self.parent.title="loadDicom"
        self.parent.categories = ["Examples"]
        self.parent.dependencies = []
        self.parent.contributors = ["Andrej Studen (UL/FMF)"] # replace with "Firstname Lastname (Organization)"
        self.parent.helpText = """
            utilities for parsing dicom entries
            """
        self.parent.acknowledgementText = """
            Developed within the medical physics research programme of the Slovenian research agency.
            """ # replace with organization, grant and thanks.

class loadDicomWidget(slicer.ScriptedLoadableModule.ScriptedLoadableModuleWidget):
  """Uses ScriptedLoadableModuleWidget base class, available at:
  https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
  """

  def setup(self):
    slicer.ScriptedLoadableModule.ScriptedLoadableModuleWidget.setup(self)


class loadDicomLogic(slicer.ScriptedLoadableModule.ScriptedLoadableModuleLogic):
    def __init__(self,parent):
      slicer.ScriptedLoadableModule.ScriptedLoadableModuleLogic.__init__(self, parent)

    def load(self,sNet,dir,doRemove=True):
        dicomFiles=sNet.listDir(dir)
        #filelist=[os.path.join(dir,f) for f in os.listdir(dir)]
        filelist=[]
        for f in dicomFiles:
                localPath=sNet.GetFile(f)
                f0=localPath
                f1=f0+"1"
                subprocess.call(dicomModify+" "+f0+" "+f1+" && mv "+f1+" "+f0+";", shell=True)
                filelist.append(localPath)

        try:
            loadables=self.volumePlugin.examineForImport([filelist])
        except AttributeError:
            self.volumePlugin=slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
            loadables=self.volumePlugin.examineForImport([filelist])


        for loadable in loadables:
            #TODO check if it makes sense to load a particular loadable
            if loadable.name.find('imageOrientationPatient')>-1:
                continue
            volumeNode=self.volumePlugin.load(loadable)
            if volumeNode != None:
                vName='Series'+dicomValue(loadable.files[0],"0020,0011")
                volumeNode.SetName(vName)

        try:
            loadableRTs=self.RTPlugin.examineForImport([filelist])
        except:
            self.RTPlugin=plugin=slicer.modules.dicomPlugins['DicomRtImportExportPlugin']()
            loadableRTs=self.RTPlugin.examineForImport([filelist])

        for loadable in loadableRTs:
            segmentationNode=self.RTPlugin.load(loadable)
            #if segmentationNode!= None:
            #    segmentationNode.SetName('SegmentationBR')

        if not doRemove:
            return

        for f in filelist:
            os.remove(f)

def dicomValue(file,tag):
    dcmdump=os.path.join(os.environ['SLICER_HOME'],"bin")
    dcmdump=os.path.join(dcmdump,"dcmdump")
    try:
        out=subprocess.check_output([dcmdump,'+P',tag,file])
        out=re.sub(r'^.*\[(.*)\].*\n$',r'\1',out)
        return out
    except:
        return None

def clearNodes():
    nodes=[]
    nodes.extend(slicer.util.getNodesByClass("vtkMRMLScalarVolumeNode"))
    nodes.extend(slicer.util.getNodesByClass("vtkMRMLScalarVolumeDisplayNode"))
    nodes.extend(slicer.util.getNodesByClass("vtkMRMLSegmentationNode"))
    nodes.extend(slicer.util.getNodesByClass("vtkMRMLSegmentationDisplayNode"))
    for node in nodes:
        slicer.mrmlScene.RemoveNode(node)