SlicerLabkeyExtension/DICOMtools/loadDicom.py

import slicer
import os
import subprocess
import re
import slicerNetwork
import ctk,qt
import json

dicomModify=os.getenv("HOME")
if not dicomModify==None:
    dicomModify+="/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 = ["LabKey"]
        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)
    self.logic=loadDicomLogic(self)
    self.network=slicerNetwork.labkeyURIHandler()
    
    connectionCollapsibleButton = ctk.ctkCollapsibleButton()
    connectionCollapsibleButton.text = "Connection"
    self.layout.addWidget(connectionCollapsibleButton)

    connectionFormLayout = qt.QFormLayout(connectionCollapsibleButton)
    
    self.loadConfigButton=qt.QPushButton("Load configuration")
    self.loadConfigButton.toolTip="Load configuration"
    self.loadConfigButton.connect('clicked(bool)',self.onLoadConfigButtonClicked)
    connectionFormLayout.addRow("Connection:",self.loadConfigButton)

    self.DICOMDirectory=qt.QLineEdit("Test/Temp/%40files/TEST/MLEM")
    connectionFormLayout.addRow("LabKey directory:",self.DICOMDirectory)


    loadDICOMButton=qt.QPushButton("Load")
    loadDICOMButton.toolTip="Load DICOM"
    loadDICOMButton.clicked.connect(self.onLoadDICOMButtonClicked)
    connectionFormLayout.addRow("DICOM:",loadDICOMButton)

    self.DICOMFilter=qt.QLineEdit('{"seriesNumber":"SeriesLabel"}')
    connectionFormLayout.addRow("Filter(JSON):",self.DICOMFilter)

    loadDICOMFilterButton=qt.QPushButton("Load with filter")
    loadDICOMFilterButton.toolTip="Load DICOM with filter"
    loadDICOMFilterButton.clicked.connect(self.onLoadDICOMFilterButtonClicked)
    connectionFormLayout.addRow("DICOM:",loadDICOMFilterButton)

    loadDICOMSegmentationFilterButton=qt.QPushButton("Load segmentation with filter")
    loadDICOMSegmentationFilterButton.toolTip="Load DICOM (RT contour) with filter"
    loadDICOMSegmentationFilterButton.clicked.connect(self.onLoadDICOMSegmentationFilterButtonClicked)
    connectionFormLayout.addRow("DICOM:",loadDICOMSegmentationFilterButton)


  def onLoadConfigButtonClicked(self):
       filename=qt.QFileDialog.getOpenFileName(None,'Open configuration file (JSON)',
            os.path.join(os.path.expanduser('~'),'.labkey'), '*.json')
       self.network.parseConfig(filename)
       self.network.initRemote()
       self.loadConfigButton.setText(os.path.basename(filename))
  
  def onLoadDICOMFilterButtonClicked(self):
      filter=json.loads(self.DICOMFilter.text)
      #print("Filter is {}".format(filter))
      self.logic.loadVolumes(self.network,self.DICOMDirectory.text,filter)
    
  def onLoadDICOMSegmentationFilterButtonClicked(self):
      filter=json.loads(self.DICOMFilter.text)
      #print("Filter is {}".format(filter))
      self.logic.loadSegmentations(self.network,self.DICOMDirectory.text,filter)
  
  def onLoadDICOMButtonClicked(self):
      self.logic.load(self.network,self.DICOMDirectory.text)
       

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

        self.tag={
              'studyDate': {'tag':"0008,0020",'VR':'DA'},
              'studyTime': {'tag':"0008,0030",'VR':'TM'},
              'seriesTime': {'tag':"0008,0031",'VR':'TM'},
              'modality': {'tag':"0008,0060",'VR':'CS'},
              'presentationIntentType': {'tag':"0008,0068",'VR':'CS'},
              'manufacturer': {'tag':"0008,0070",'VR':'LO'},
              'institutionName': {'tag':"0008,0080",'VR':'LO'},
              'studyDescription': {'tag':"0008,1030",'VR':'LO'},
              'seriesDescription': {'tag':"0008,103e",'VR':'LO'},
              'manufacturerModelName': {'tag':"0008,1090",'VR':'LO'},
              'patientName': {'tag':"0010,0010",'VR':'PN'},
              'patientId': {'tag':"0010,0020",'VR':'LO'},
              'patientBirthDate': {'tag':"0010,0030",'VR':'DA'},
              'patientSex': {'tag':"0010,0040",'VR':'CS'},
              'patientAge': {'tag':"0010,1010",'VR':'AS'},
              'patientComments': {'tag':"0010,4000",'VR':'LT'},
              'sequenceName': {'tag':"0018,0024",'VR':'SH'},
              'kVP': {'tag':"0018,0060",'VR':'DS'},
              'percentPhaseFieldOfView': {'tag':"0018,0094",'VR':'DS'},
              'xRayTubeCurrent': {'tag':"0018,1151",'VR':'IS'},
              'exposure': {'tag':"0018,1152",'VR':'IS'},
              'imagerPixelSpacing': {'tag':"0018,1164",'VR':'DS'},
              'bodyPartThickness': {'tag':"0018,11a0",'VR':'DS'},
              'compressionForce': {'tag':"0018,11a2",'VR':'DS'},
              'viewPosition': {'tag':"0018,5101",'VR':'CS'},
              'fieldOfViewHorizontalFlip': {'tag':"0018,7034",'VR':'CS'},
              'studyInstanceUid': {'tag':"0020,000d",'VR':'UI'},
              'seriesInstanceUid': {'tag':"0020,000e",'VR':'UI'},
              'studyId': {'tag':"0020,0010",'VR':'SH'},
              'seriesNumber': {'tag':"0020,0011",'VR':'IS'},
              'instanceNumber': {'tag':"0020,0013",'VR':'IS'},
              'frameOfReferenceInstanceUid': {'tag':"0020,0052",'seqTag':"3006,0010",'VR':'UI'},
              'imageLaterality': {'tag':"0020,0062",'VR':'CS'},
              'imagesInAcquisition': {'tag':"0020,1002",'VR':'IS'},
              'photometricInterpretation': {'tag':"0028,0004",'VR':'CS'},
              'reconstructionMethod': {'tag':"0054,1103",'VR':'LO'}
        }
        self.tagPyDicom={
              'studyDate': 0x00080020,
              'studyTime': 0x00080030,
              'modality': 0x00080060,
              'presentationIntentType': 0x00080068,
              'manufacturer': 0x00080070,
              'studyDescription': 0x00081030,
              'seriesDescription': 0x0008103e,
              'patientName': 0x00100010,
              'patientId': 0x00100020,
              'patientBirthDate': 0x00100030,
              'patientSex': 0x00100040,
              'patientComments': 0x00104000,
              'sequenceName': 0x00180024,
              'kVP': 0x00180060,
              'percentPhaseFieldOfView': 0x00180094,
              'xRayTubeCurrent': 0x00181151,
              'exposure': 0x00181152,
              'imagerPixelSpacing': 0x00181164,
              'bodyPartThickness': 0x001811a0,
              'compressionForce': 0x001811a2,
              'viewPosition': 0x00185101,
              'studyInstanceUid': 0x0020000d,
              'seriesInstanceUid': 0x0020000e,
              'studyId': 0x00200010,
              'seriesNumber': 0x00200011,
              'instanceNumber': 0x00200013,
              'frameOfReferenceInstanceUid': 0x00200052
              }
      #new_dict_items={
      #        0x001811a0: ('DS','BodyPartThickness','Body Part Thickness')
      #}
      #dicom.datadict.add_dict_entries(new_dict_items)
        self.local=False

    def setLocal(self,basePath):
        self.local=True
        self.basePath=basePath
        

    def getHex(self,key):
        #convert string to hex key;
        fv=key.split(",")
        return int(fv[0],16)*0x10000+int(fv[1],16)

    def load(self,sNet,dir,doRemove=True):
        #load directory using DICOMLib tools

        print("Loading dir {}").format(dir)
        dicomFiles=self.listdir(sNet,dir)
        
        filelist=[]
        for f in dicomFiles:
                localPath=self.getfile(sNet,f)
                f0=localPath
                f1=f0+"1"
                if not dicomModify==None:
                    try:
                        subprocess.call(dicomModify+" "+f0+" "+f1+" && mv "+f1+" "+f0+";", shell=True)
                    except OSError:
                        print("dicomModify failed")
                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:
            #check if it makes sense to load a particular loadable
            
            if loadable.name.find('imageOrientationPatient')>-1:
                continue
            filter={}
            filter['seriesNumber']=None 
            metadata={}
            if not self.applyFilter(loadable,filter,metadata):
                continue
            volumeNode=self.volumePlugin.load(loadable)
            if volumeNode != None:
                vName='Series'+metadata['seriesNumber']
                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 not doRemove:
            return

        for f in filelist:
            os.remove(f)

    def applyFilter(self,loadable,filter,nodeMetadata):
        #apply filter to loadable.file[0]. Return true if file matches prescribed filter and
        #false otherwise

        #filter is a directory with keys equal to pre-specified values listed above
        #if value associated to key equals None, that value gets set in nodeMetadata
        #if value is set, a match is attempted and result reported in return value
        #all filters should match for true output

        return applyFilterFile(self,loadable.files[0],filter,nodeMetadata)
    
    def applyFilterFile(self,file,filter,nodeMetadata,shell=False):
        #apply filter to file. Return true if file matches prescribed filter and
        #false otherwise

        #filter is a directory with keys equal to pre-specified values listed above
        #if value associated to key equals None, that value gets set in nodeMetadata
        #if value is set, a match is attempted and result reported in return value
        #all filters should match for true output

        filterOK=True
        
        for key in filter:
            try:
                fileValue=dicomValue(file,self.tag[key]['tag'],self.tag[key]['seqTag'],shell=shell)
            except KeyError:
                fileValue=dicomValue(file,self.tag[key]['tag'],shell=shell)


            if filter[key]=="SeriesLabel":
                nodeMetadata['seriesLabel']=fileValue
                continue

            if not filter[key]==None:
                if not fileValue==filter[key]:
                    print("File {} failed for tag {}: {}/{}").format(
                        file,key,fileValue,filter[key])
                    filterOK=False
                    break

            nodeMetadata[key]=fileValue


        return filterOK

    def listdir(self,sNet,dir):
        #list remote directory
        if self.local:
            dir1=os.path.join(self.basePath,dir)
            dirs=os.listdir(dir1)
            return [os.path.join(dir1,f) for f in dirs]
        return sNet.listRelativeDir(dir)

    def getfile(self,sNet,file):
        #get remote file
        if self.local:
            return file
        return sNet.DownloadFileToCache(file)

    def removeLocal(self,localFile):
        if self.local:
            return
        os.remove(localFile)
        

    def loadVolumes(self,sNet,dir,filter,doRemove=True):
    #returns all series from the directory, each as a separate node in a node list
    #filter is a dictionary of speciifed dicom values, if filter(key)=None, that values
    #get set, if it isn't, the file gets checked for a match

        print("Loading dir {}").format(dir)
        dicomFiles=self.listdir(sNet,dir)
        #filelist=[os.path.join(dir,f) for f in os.listdir(dir)]
        filelist=[]
        for f in dicomFiles:
            localPath=self.getfile(sNet,f)
            f0=localPath
            f1=f0+"1"
            if not dicomModify==None:
                try:
                    subprocess.call(dicomModify+" "+f0+" "+f1+" && mv "+f1+" "+f0+";", shell=False)
                except OSError:
                    print("dicomModify failed")
            filelist.append(localPath)

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


        volumeNodes=[]
        print("Number of loadables:{}").format(len(loadables))
        for loadable in loadables:
            #TODO check if it makes sense to load a particular loadable

            print "Loading {} number of files: {}".format(loadable.name,len(loadable.files))
            for f in loadable.files:
                print "\t {}".format(f)
            #perform checks
            nodeMetadata={}
            filterOK=self.applyFilter(loadable,filter,nodeMetadata)

            if not filterOK:
                #skip this loadable
                continue

            volumeNode=self.volumePlugin.load(loadable,"DCMTK")
            if volumeNode != None:
                vName='Series'+nodeMetadata['seriesLabel']
                volumeNode.SetName(vName)
                volume={'node':volumeNode,'metadata':nodeMetadata}
                volumeNodes.append(volume)

        if self.local:
            return volumeNodes

        if doRemove:
            for f in filelist:
                os.remove(f)

        return volumeNodes

    def loadSegmentations(self,net,dir,filter,doRemove=True):

        print("Loading dir {}").format(dir)
        dicomFiles=self.listdir(net,dir)
        filelist=[self.getfile(net,f) for f in dicomFiles]
        segmentationNodes=[]

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

        for loadable in loadableRTs:

            nodeMetadata={}
            filterOK=self.applyFilter(loadable,filter,nodeMetadata)

            if not filterOK:
                continue

            success=self.RTPlugin.load(loadable)

            if not success:
                print("Could not load RT structure set")
                return

            segNodes=slicer.util.getNodesByClass("vtkMRMLSegmentationNode")
            segmentationNode=segNodes[0]
            #assume we loaded the first node in list

            if segmentationNode != None:
                sName='Segmentation'+nodeMetadata['seriesLabel']
                segmentationNode.SetName(sName)
                segmentation={'node':segmentationNode,'metadata':nodeMetadata}
                segmentationNodes.append(segmentation)

        if self.local or not doRemove:
            return segmentationNodes
        
        for f in filelist:
            os.remove(f)

        return segmentationNodes

def isDicom(file):
    #check if file is a dicom file
    try:
        f=open(file,'rb')
    except IOError:
        return False

    f.read(128)
    dt=f.read(4)
    f.close()
    return dt=='DICM'


def dicomValue(file,tag,seqTag=None,shell=False):
    #query dicom value of file using dcmdump (DCMTK routine)
    dcmdump=os.path.join(os.environ['SLICER_HOME'],"bin","dcmdump")
    try:
        out=subprocess.check_output([dcmdump,'+p','+P',tag,file],shell=shell)
    except subprocess.CalledProcessError as e:
        return None
    
    debug=False
    
    if debug:
        print("Tag {} Line '{}'").format(tag,out)
    if len(out)==0:
        return out

    #parse multi-match outputs which appear as several lines
    lst=out.split('\n')
    return getTagValue(lst,tag,seqTag)
    
def getTagValue(lst,tag,seqTag=None):
    #report tag value from a list lst of lines reported by dcmdump        
    
    debug=False
    
    #parse output
    longTag="^\({}\)".format(tag)
    #combine sequence and actual tags to long tags
    if not seqTag==None:
        if debug:
            print("Tag:{} seqTag:{}").format(tag,seqTag)
        longTag="^\({}\).\({}\)".format(seqTag,tag)
    
    #pick the values
    pattern=r'^.*\[(.*)\].*$'
    
    #extract tag values
    rpl=[re.sub(pattern,r'\1',f) for f in lst]
    
    #logical whether the line can be matched to typical dcmdump output
    mtchPattern=[re.match(pattern,f) for f in lst]
    #find matching tags
    mtchTag=[re.match(longTag,f) for f in lst]
    
    #weed out non-matching lines and lines not matching longTag
    mtch=[None if x==None or y==None else x \
            for x,y in zip(mtchTag,mtchPattern)]
    #set values 
    out=[x for y,x in zip(mtch,rpl) if not y==None]
    if len(out)==0:
        return ''
    #return first match
    out=out[0]
    
    if debug:
        print("Tag {} Parsed value {}").format(tag,out)
    #split output to lists if values are DICOM lists
    if out.find('\\')>-1:
        out=out.split('\\')

    return out
        

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)