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- import os
- import sys
- import json
- import pathlib
- import slicer
- import subprocess
- import shutil
- def main(configFile):
- print('Running with {}'.format(configFile))
- with open(configFile) as f:
- config=json.load(f)
- fsetup=os.path.join(os.path.expanduser('~'),'.labkey','setup.json')
- with open(fsetup) as f:
- setup=json.load(f)
- sys.path.append(setup['paths']['nixWrapper'])
- import nixWrapper
- nixWrapper.loadLibrary('labkeyInterface')
- import labkeyInterface
- import labkeyDatabaseBrowser
- import labkeyFileBrowser
-
- nixWrapper.loadLibrary('orthancInterface')
- import orthancInterface
- import orthancDatabaseBrowser
- import orthancFileBrowser
- net=labkeyInterface.labkeyInterface()
- fnet=os.path.join(os.path.expanduser('~'),'.labkey',config['network'])
- net.init(fnet)
- net.getCSRF()
- fb=labkeyFileBrowser.labkeyFileBrowser(net)
- db=labkeyDatabaseBrowser.labkeyDB(net)
- onet=orthancInterface.orthancInterface()
- onet.init(fnet)
- ofb=orthancFileBrowser.orthancFileBrowser(onet)
- odb=orthancDatabaseBrowser.orthancDB(onet)
- qFilter=[]
- ds=db.selectRows(config['project'],config['schemaName'],config['queryName'],qFilter)
- try:
- rows=ds['rows']
- except KeyError:
- print('No rows returned')
- return
- for r in rows:
- print("Loading {}/{}".format(patientId(r,config),visitId(r,config)))
- nNames=nodeNames(r,config)
- rPath=fb.formatPathURL(config['project'],outputDir(r,config))
- rPath+='/'+nNames['CT']+'.nrrd'
- entryDone=fb.entryExists(rPath)
- if entryDone:
- try:
- if not config['recalculate']:
- print('Entry done')
- continue
- except KeyError:
- print('Entry done')
- continue
- print('Forced recalculation')
-
- print('{} available:{}'.format(nNames['CT'],fb.entryExists(rPath)))
- #loadPatient into slicer
- patient=loadPatient(ofb,r,config)
- #convert to nodes
- addCT(r,patient,config)
- addFrames(r,patient,config)
- addDummyInputFunction(r,patient,config)
-
- nodes=slicer.mrmlScene.GetNodesByClass('vtkMRMLScalarVolumeNode')
- print('Nodes')
- for node in nodes:
- print('\t{}'.format(node.GetName()))
- storeNode(fb,r,config,node)
- nodes=slicer.mrmlScene.GetNodesByClass('vtkMRMLDoubleArrayNode')
- print('Nodes (double array)')
- for node in nodes:
- print('\t{}'.format(node.GetName()))
- storeNode(fb,r,config,node)
- clearNodes(r,config)
-
- def patientId(row,config):
- return row[config['ParticipantField']]
- def visitId(row,config):
- return row['visitName']
- def code(row,config):
- return '{}_{}'.format(patientId(row,config),visitId(row,config))
- def pathList(row,config):
- return [config['baseDir'],patientId(row,config),visitId(row,config)]
- def outputDir(row,config):
- return '/'.join(pathList(row,config))
- def localDir(row,config):
- return os.path.join(config['tempDir'],code(row,config))
- def nodeNames(row,config):
- names={}
- x=code(row,config)
- names['NM']=['{}_Volume{}'.format(x,i) for i in range(20)]
- names['CT']='{}_CT'.format(x)
- return names
- def clearNodes(row,config):
- nodes=slicer.mrmlScene.GetNodesByClass('vtkMRMLScalarVolumeNode')
- nodes1=slicer.mrmlScene.GetNodesByClass('vtkMRMLDoubleArrayNode')
- for n in nodes1:
- nodes.AddItem(n)
- res=[slicer.mrmlScene.RemoveNode(f) for f in nodes]
- def loadPatient(ofb,r,config):
- sys.path.append('../pythonScripts')
- import parseDicom
- import vtkInterface
- pd=parseDicom.parseDicom()
- masterPath=downloadAndUnzip(ofb,r,"nmMaster",config)
- pd.readMasterDirectory(masterPath,False)
- print('Time [{} .. {}]'.format(pd.frame_start,pd.frame_stop))
- nmPath=downloadAndUnzip(ofb,r,"nmCorrData",config)
- frame_data, frame_time, frame_duration, frame_origin, \
- frame_pixel_size, frame_orientation=\
- pd.readNMDirectory(nmPath,False)
- print('Frame time {}'.format(frame_time))
- ctPath=downloadAndUnzip(ofb,r,"ct",config)
- ct_data,ct_origin,ct_pixel_size, \
- ct_orientation=pd.readCTDirectory(ctPath,False)
- print('CT pixel {}'.format(ct_pixel_size))
- ct_orientation=vtkInterface.completeOrientation(ct_orientation)
- frame_orientation=vtkInterface.completeOrientation(frame_orientation)
- ct={'data':ct_data,'origin':ct_origin,'pixel_size':ct_pixel_size,
- 'orientation':ct_orientation}
- nm={'data':frame_data,'time':frame_time,'duration':frame_duration,
- 'origin':frame_origin,'pixel_size':frame_pixel_size,
- 'orientation':frame_orientation}
- return {'CT':ct,'NM':nm}
-
- print('Done')
- def downloadAndUnzip(ofb,r,xcode,config):
- orthancId=r[xcode+'OrthancId']
- fileCode='{}_{}'.format(code(r,config),xcode)
- zipFile=os.path.join(config['tempDir'],fileCode+'.zip')
- ofb.getZip('series',orthancId,zipFile)
- zipDir=localDir(r,config)
- try:
- os.mkdir(zipDir)
- except FileExistsError:
- shutil.rmtree(zipDir)
- try:
- outTxt=subprocess.check_output(["unzip","-d",zipDir,"-xj",zipFile])
- except subprocess.CalledProcessError:
- print("unzip failed for {}".format(zipFile))
- return ""
- return zipDir
- def addCT(r,patient,config):
- sys.path.append('../pythonScripts')
- import vtkInterface
- ct=patient['CT']
- vtkData=vtkInterface.numpyToVTK(ct['data'],ct['data'].shape)
- nodeName=code(r,config)+'_CT'
- addNode(nodeName,vtkData,ct['origin'],ct['pixel_size'],ct['orientation'],0)
- def addFrames(r,patient,config):
- sys.path.append('../pythonScripts')
- import vtkInterface
- #convert data from numpy.array to vtkImageData
- #use time point it
- x=code(r,config)
- nm=patient['NM']
- print("NFrames: {}".format(nm['data'].shape[3]))
- for it in range(0,nm['data'].shape[3]):
- frame_data=nm['data'][:,:,:,it];
- nodeName=x+'_Volume'+str(it)
- vtkData=vtkInterface.numpyToVTK(frame_data,frame_data.shape)
- addNode(nodeName,vtkData,nm['origin'],nm['pixel_size'],nm['orientation'],1)
- def addNode(nodeName,v,origin,pixel_size,orientation,dataType):
- #origin,orientation in lps
- #dataType=0 is CT (to background)
- #dataType=1 is SPECT, view not adjusted, foreground,
- newNode=slicer.vtkMRMLScalarVolumeNode()
- newNode.SetName(nodeName)
- v.SetOrigin([0,0,0])
- v.SetSpacing([1,1,1])
- ijkToRAS = vtk.vtkMatrix4x4()
- #think how to do this with image orientation
- #orientation from lps to ras
- rasOrientation=[-orientation[i] if (i%3 < 2) else orientation[i]
- for i in range(0,len(orientation))]
- #origin from lps to ras
- rasOrigin=[-origin[i] if (i%3<2) else origin[i] for i in range(0,len(origin))]
- for i in range(0,3):
- for j in range(0,3):
- ijkToRAS.SetElement(i,j,pixel_size[i]*rasOrientation[3*j+i])
- ijkToRAS.SetElement(i,3,rasOrigin[i])
- newNode.SetIJKToRASMatrix(ijkToRAS)
- newNode.SetAndObserveImageData(v)
- slicer.mrmlScene.AddNode(newNode)
- def addDummyInputFunction(r,patient,config):
- nm=patient['NM']
- n=nm['data'].shape[3]
- dnsNodeName=code(r,config)+'_Dummy'
- dns = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLDoubleArrayNode',dnsNodeName)
- if dns.GetNumberOfItems() == 0:
- dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
- dn.SetName(dnsNodeName)
- else:
- dn = dns.GetItemAsObject(0)
- dn.SetSize(n)
- ft=nm['time']
- dt=nm['duration']
- for i in range(0,n):
- fx=ft[i]
- fy=dt[i]
- dn.SetValue(i, 0, fx)
- dn.SetValue(i, 1, fy)
- dn.SetValue(i, 2, 0)
- print('{} ({},{})'.format(i,fx,fy))
- def storeNode(fb,row,config,node):
- suffix=".nrrd"
- if node.__class__.__name__=="vtkMRMLDoubleArrayNode":
- suffix=".mcsv"
- if (node.__class__.__name__=="vtkMRMLTransformNode" or \
- node.__class__.__name__=="vtkMRMLGridTransformNode"):
- suffix=".h5"
- fileName=node.GetName()+suffix
- localPath=os.path.join(localDir(row,config),fileName)
- slicer.util.saveNode(node,localPath)
- print("Stored to: {}".format(localPath))
- labkeyPath=fb.buildPathURL(config['project'],pathList(row,config))
- print ("Remote: {}".format(labkeyPath))
- #checks if exists
- remoteFile=labkeyPath+'/'+fileName
- fb.writeFileToFile(localPath,remoteFile)
-
- def readPatient(fb,localDir,project,patientId):
- rDir=fb.formatPathURL(project,'/'.join([patientId]))
- lDir=os.path.join(localDir,patientId)
- if not os.path.isdir(lDir):
- os.makedirs(lDir)
- ok,files=fb.listRemoteDir(rDir)
- locFiles=[]
- for f in files:
- print(f)
- p=pathlib.Path(f)
- localFile=os.path.join(lDir,p.name)
- fb.readFileToFile(f,localFile)
- locFiles.append(localFile)
- print('Done')
- return locFiles
- if __name__=='__main__':
- main(sys.argv[1])
- quit()
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