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+import os
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+import json
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+import re
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+import subprocess
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+import nibabel
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+import shutil
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+import sys
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+import pathlib
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+import SimpleITK
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+import numpy
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+
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+#nothing gets done if you do import
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+
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+def getPatientLabel(row,participantField='PatientId'):
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+ return row[participantField].replace('/','_')
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+
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+def getVisitLabel(row):
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+ return 'VISIT_'+str(int(row['SequenceNum']))
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+
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+def getStudyLabel(row,participantField='PatientId'):
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+ return getPatientLabel(row,participantField)+'-'+getVisitLabel(row)
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+
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+
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+def updateRow(project,dataset,row,imageResampledField,gzFileNames,\
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+ participantField='PatientId'):
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+ row['patientCode']=getPatientLabel(row,participantField)
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+ row['visitCode']=getVisitLabel(row)
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+ for im in imageResampledField:
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+ row[imageResampledField[im]]=gzFileNames[im]
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+ db.modifyRows('update',project,'study',dataset,[row])
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+
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+def replacePatterns(infile,outfile,replacePatterns):
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+ of=open(outfile,'w')
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+ with open(infile,'r') as f:
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+ data=f.read()
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+ for p in replacePatterns:
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+ val=replacePatterns[p]
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+ data=re.sub(p,val,data)
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+ of.write(data)
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+ of.close()
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+
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+def valueSubstitution(pars,val):
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+ if val.find('__home__')>-1:
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+ val=re.sub(r'__home__',os.path.expanduser('~'),val)
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+
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+ return path
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+
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+def getSuffix(tempFile):
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+ p=pathlib.Path(tempFile)
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+ return ''.join(p.suffixes)
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+
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+def getSegmImagePath(tempFile):
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+ sfx=getSuffix(tempFile)
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+ return re.sub(sfx,'_Segm'+sfx,tempFile)
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+
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+def addVersion(tempFile,version):
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+ sfx=getSuffix(tempFile)
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+ return re.sub(sfx,'_'+version+sfx,tempFile)
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+
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+def addnnUNetCode(tempFile,fileNumber=0):
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+ sfx=getSuffix(tempFile)
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+ return re.sub(sfx,'_'+'{:04d}'.format(fileNumber)+sfx,tempFile)
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+
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+def runnnUNet(setup,pars):
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+ args=[]
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+ #set the environment
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+ args.append(setup['paths']['nnUNetRunInference'])
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+ #location of input images
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+ args.extend(['-i',os.path.join(pars['tempBase'],'CT')])
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+ #output path is segmentations
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+ args.extend(['-o',os.path.join(pars['tempBase'],'segmentations')])
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+ #modelid, nnUNet internal rules.
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+ args.extend(['-t',pars['nnUNet']['ModelId']])
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+ #specify configuration (3d_fullres)
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+ args.extend(['-m',pars['nnUNet']['configuration']])
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+ print(args)
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+ my_env = os.environ
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+ for key in pars['nnUNet']['env']:
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+ my_env[key]=pars['nnUNet']['env'][key]
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+
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+ print(subprocess.run(args,env=my_env,check=True,stdout=subprocess.PIPE).stdout)
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+
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+def getSegmentationFile(pars):
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+ #this is how deep medic stores files
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+ return os.path.join(pars['tempBase'],'segmentations',\
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+ pars['images']['CT']['tempFile'])
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+
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+
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+def runSegmentation(fb,row,pars,setup):
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+
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+
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+ #download to temp file (could be a fixed name)
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+ project=pars['project']
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+ images=pars['images']
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+ participantField=pars['participantField']
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+ baseDir=fb.formatPathURL(project,pars['imageDir']+'/'+\
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+ getPatientLabel(row,participantField)+'/'+\
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+ getVisitLabel(row))
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+
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+ #download CT
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+ ctDir=os.path.join(pars['tempBase'],'CT')
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+ if not os.path.isdir(ctDir):
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+ os.mkdir(ctDir)
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+ fullFile=os.path.join(ctDir,images['CT']['tempFile'])
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+
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+ fullFile=addnnUNetCode(fullFile)
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+ fb.readFileToFile(baseDir+'/'+row[images['CT']['queryField']],fullFile)
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+
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+ #debug
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+
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+ #run deep medic
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+ runnnUNet(setup,pars)
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+
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+ #processed file is
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+ segFile=getSegmentationFile(pars)
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+ #SimpleITK.WriteImage(outImg,segFile)
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+ return segFile
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+
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+
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+def test(parameterFile):
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+
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+ fhome=os.path.expanduser('~')
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+
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+
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+ with open(os.path.join(fhome,".labkey","setup.json")) as f:
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+ setup=json.load(f)
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+
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+ sys.path.insert(0,setup["paths"]["nixWrapper"])
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+
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+ import nixWrapper
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+
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+ nixWrapper.loadLibrary("labkeyInterface")#force reload
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+ import labkeyInterface
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+ import labkeyDatabaseBrowser
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+ import labkeyFileBrowser
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+
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+ nixWrapper.loadLibrary("parseConfig")
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+ import parseConfig
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+
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+ with open(parameterFile) as f:
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+ pars=json.load(f)
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+
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+ pars=parseConfig.convert(pars)
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+ pars=parseConfig.convertValues(pars)
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+ #print(pars)
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+
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+
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+
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+
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+def doSegmentation(parameterFile):
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+ fhome=os.path.expanduser('~')
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+
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+
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+ with open(os.path.join(fhome,".labkey","setup.json")) as f:
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+ setup=json.load(f)
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+
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+ sys.path.insert(0,setup["paths"]["nixWrapper"])
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+
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+ import nixWrapper
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+
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+ nixWrapper.loadLibrary("labkeyInterface")#force reload
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+ import labkeyInterface
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+ import labkeyDatabaseBrowser
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+ import labkeyFileBrowser
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+
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+ nixWrapper.loadLibrary("parseConfig")
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+ import parseConfig
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+
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+ with open(parameterFile) as f:
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+ pars=json.load(f)
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+
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+ pars=parseConfig.convert(pars)
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+ pars=parseConfig.convertValues(pars)
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+
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+ project=pars['project']
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+ dataset=pars['targetQuery']
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+ schema=pars['targetSchema']
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+ view=pars['viewName']
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+
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+
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+ tempBase=pars['tempBase']
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+ if not os.path.isdir(tempBase):
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+ os.makedirs(tempBase)
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+
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+ #start the database interface
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+ fconfig=os.path.join(fhome,'.labkey','network.json')
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+ net=labkeyInterface.labkeyInterface()
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+ net.init(fconfig)
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+ db=labkeyDatabaseBrowser.labkeyDB(net)
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+ fb=labkeyFileBrowser.labkeyFileBrowser(net)
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+
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+
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+ #all images from database
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+ ds=db.selectRows(project,schema,dataset,[],view)
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+
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+ #input
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+ #use webdav to transfer file (even though it is localhost)
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+
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+
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+ i=0
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+ rows=[ds['rows'][0]]
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+ rows=ds['rows']
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+ for row in rows:
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+
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+
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+ #check if file is already there
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+ #dummy tf to get the suffix
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+ sfx=pars['images']['segmentation']['suffix']
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+ outpath=fb.buildPathURL(pars['project'],[pars['imageDir'],row['patientCode'],row['visitCode']])
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+ outName=addVersion(\
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+ getSegmImagePath(\
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+ getStudyLabel(row,pars['participantField'])+sfx),\
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+ pars['version'])
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+
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+ outFile=outpath+'/'+outName
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+
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+ #check if file is there
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+ if not fb.entryExists(outFile):
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+
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+
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+ segFile=getSegmentationFile(pars)
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+ #remove existing file
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+ if os.path.isfile(segFile):
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+ os.remove(segFile)
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+
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+ segFile=runSegmentation(fb,row,pars,setup)
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+ #copy file to file
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+ #normally I would update the targetQuery, but it contains previously set images
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+ #copy to labkey
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+ fb.writeFileToFile(segFile,outFile)
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+ print(segFile)
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+ #debug
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+
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+ #update database
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+ copyFields=[pars['participantField'],'SequenceNum','patientCode','visitCode']
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+ row['SequenceNum']+=0.001*float(pars['versionNumber'])
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+ filters=[{'variable':v,'value':str(row[v]),'oper':'eq'} for v in copyFields]
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+ filters.append({'variable':'Version','value':pars['version'],'oper':'eq'})
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+
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+ ds1=db.selectRows(pars['project'],pars['segmentationSchema'],pars['segmentationQuery'],filters)
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+
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+ if len(ds1['rows'])>0:
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+ mode='update'
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+ outRow=ds1['rows'][0]
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+ else:
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+ mode='insert'
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+ outRow={v:row[v] for v in copyFields}
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+ outRow['Version']= pars['version']
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+ outRow['Segmentation']= outName
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+ print(db.modifyRows(mode,pars['project'],pars['segmentationSchema'],pars['segmentationQuery'],[outRow]))
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+ #pull results back to LabKey
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+ print("Done")
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+
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+
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+if __name__ == '__main__':
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+ #test(sys.argv[1])
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+ doSegmentation(sys.argv[1])
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+ #sys.exit()
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+
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Andrej Studen