EMBRACE/dataExplorer/loadPatient.py

import slicer
import loadDicom
import re
import slicerNetwork
import os
import subprocess
import importDicom

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

class loadPatient(slicer.ScriptedLoadableModule.ScriptedLoadableModule):
    def __init__(self,parent):
        slicer.ScriptedLoadableModule.ScriptedLoadableModule.__init__(self, parent)
        self.className="loadPatient"
        self.parent.title="loadPatient"
        self.parent.categories = ["EMBRACE"]
        self.parent.contributors = ["Andrej Studen (UL/FMF)"] 

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

       #self.plugin=slicer.modules.dicomPlugins['DicomRtImportExportPlugin']()
       #self.volumePlugin=slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
       self.dicomLoader=loadDicom.loadDicomLogic(self)
       self.dicomImporter=importDicom.importDicomLogic(self)
       self.dicomImporter.local=self.local
       self.dicomImporter.basePath=self.basePath
       self.dicomLoader.local=self.local
       self.dicomLoader.basePath=self.basePath
       self.project="EMBRACE/Studija"
       self.imagingDataset="ImagingVisitsManaged"
       self.idDataset="PopisneStevilke"
       self.dicomProject="Test/Transfer"
       self.dicomDataset="Imaging"
       self.dicomPath=self.dicomProject+'/%40files/dicom'


       #self.rtReader=slicer.vtkSlicerDicomRtReader()

       #start SSL/TLS configuration

    def setURIHandler(self, net):
        self.sNet=net

    def setLocal(self,basePath):
        self.dicomImporter.setLocal(basePath)
        self.dicomLoader.setLocal(basePath)
       
    def getOICode(self, label):
        filter=[]
        filterID={"variable":"EMBRACE_ID",
            "oper":"eq",
            "value":label}
        filter.append(filterID)
        fSet=self.sNet.filterDataset(self.project,self.idDataset,filter)
        try:
            row=fSet["rows"][0]
        except:
            print("OI code for {} not found").format(label)
            return None
        return row["OICode"]


    def load(self,label):
        #clear previous data
        debug=True
        loadDicom.clearNodes()

        dirUrl=self.project+"/@files"
        dir=dirUrl+'/'+label
        #load segmentations
        rs=dir+"/RS/DICOM";
        self.dicomLoader.load(self.sNet,rs)


        rsMatch='None'
        filter=[]
        filterID={"variable":"EMBRACE_ID",
            "oper":"eq",
            "value":label}
        filter.append(filterID)
        filterType={"variable":"Type",
                "oper":"eq",
                "value":"RS"}
        filter.append(filterType)
        fSet=self.sNet.filterDataset(self.project,self.dataset,filter)
        fData=fSet['rows']
        row=fData[0] #first match

        if row['rsMatch']==None:
            return

        if row['rsMatch']=='NONE':
            return

        dicomDir=dir+'/'+row['rsMatch']+'/DICOM'
        if debug:
            print "Loading {}".format(dicomDir)
        self.dicomLoader.load(self.sNet,dicomDir)

    def findEmbrace(self,embraceId,imageType):
        filter=[]
        filterID={"variable":"EMBRACE_ID",
            "oper":"eq",
            "value":embraceId}
        filter.append(filterID)
        filterType={"variable":"Type",
                "oper":"eq",
                "value":imageType}
        filter.append(filterType)
        fSet=self.sNet.filterDataset(self.project,self.imagingDataset,filter)
        try:
            seqNum=fSet["rows"][0]["pseudoTransverseID"]
        except:
            print("CT data for patient {} not found").format(label)
            return None

        OIcode=self.getOICode(embraceId)
        dicomFilter=[]
        filterID={"variable":"PatientId",
            "oper":"eq",
            "value":OIcode}
        dicomFilter.append(filterID)
        filterSeq={"variable":"SequenceNum",
            "oper":"eq",
            "value":str(seqNum)}
        dicomFilter.append(filterSeq)
        fSet=self.sNet.filterDataset(self.dicomProject,self.dicomDataset,dicomFilter)
        try:
            row=fSet['rows'][0]
        except:
            print("Dicom for patient {}/{} not found").format(label,OIcode)
            return None
        return {'Study':row['Study'],'Series':row['Series']}

    def loadCT(self,label):
        studySeries=self.findEmbrace(label,"CT")
        if studySeries==None:
            return
        relativePath=self.dicomPath+'/'+studySeries['Study']+'/'+studySeries['Series']
        dicomReadFilter={'seriesNumber':"SeriesLabel",
                        'studyInstanceUid':None,
                        'frameOfReferenceInstanceUid':None}
        return self.dicomImporter.loadVolumes(self.sNet,relativePath,dicomReadFilter)

    def loadCTRS(self,label):
        studySeries=self.findEmbrace(label,"CT-RS")
        if studySeries==None:
            return
        relativePath=self.dicomPath+'/'+studySeries['Study']+'/'+studySeries['Series']
        dicomReadFilter={'seriesNumber':"SeriesLabel",
                        'studyInstanceUid':None,
                        'frameOfReferenceInstanceUid':None}
        print("Loading segmentation: {}").format(relativePath)
        return self.dicomLoader.loadSegmentations(self.sNet,relativePath,dicomReadFilter)


    def loadDMR(self,label):
        #clear previous data
        debug=True

        dirUrl=self.project+"/@files"
        dir=dirUrl+'/'+label
        #load segmentations
        rs=dir+"/DMR/DICOM";

        dicomReadFilter={'seriesNumber':"SeriesLabel",
                        'sequenceName':"*tse2d1_3",
                        'percentPhaseFieldOfView':90,
                        'studyInstanceUid':None,
                        'frameOfReferenceInstanceUid':None}

        return self.dicomImporter.loadVolumes(self.sNet,rs,dicomReadFilter)