Script to put segmentations at the correct places

pythonScripts/addSegmentations.py

@@ -0,0 +1,110 @@
+import os
+import json
+import re
+import subprocess
+import nibabel
+import shutil
+import sys
+
+shome=os.path.expanduser('~nixUser')
+fhome=os.path.expanduser('~')
+with open(os.path.join(fhome,".labkey","setup.json")) as f:
+    setup=json.load(f)
+
+sys.path.insert(0,setup["paths"]["labkeyInterface"])
+import labkeyInterface
+import labkeyDatabaseBrowser
+import labkeyFileBrowser
+
+#sys.path.insert(1,shome+'/software/src/IPNUMM/dicomUtils')
+#import loadDicom
+
+fconfig=os.path.join(fhome,'.labkey','network.json')
+
+net=labkeyInterface.labkeyInterface()
+net.init(fconfig)
+db=labkeyDatabaseBrowser.labkeyDB(net)
+fb=labkeyFileBrowser.labkeyFileBrowser(net)
+
+project='iPNUMMretro/Study'
+dataset='Imaging1'
+tempBase=os.path.join(fhome,'temp')
+
+#all images from database
+ds=db.selectRows(project,'study',dataset,[])
+#imageSelector={"CT":"CT","PET":"PETWB"};
+imageResampledField={"Segm":"Segmentation"}
+
+#projectNIfTIBase=os.path.join(labkeyBase,'files',project,'@files/nifti')
+#use webdav to transfer file (even though it is localhost)
+
+
+def getPatientLabel(row):
+    return row['PatientId'].replace('/','_') 
+
+def getVisitLabel(row):
+    return 'VISIT_'+str(int(row['SequenceNum']))
+
+def getStudyLabel(row):
+    return getPatientLabel(row)+'-'+getVisitLabel(row)
+
+def updateRow(project,dataset,row,imageResampledField,gzFileNames):
+    for im in imageResampledField:
+        row[imageResampledField[im]]=gzFileNames[im]
+    db.modifyRows('update',project,'study',dataset,[row])
+ 
+i=0
+for row in ds["rows"]:
+
+    #interesting files are processedDir/studyName_CT_notCropped_2mmVoxel.nii
+    #asn processedDir/studyName_PET_notCropped_2mmVoxel.nii
+    gzFileNames={im:\
+            getStudyLabel(row)+'_'+im+'.nii.gz'\
+                for im in imageResampledField}
+    
+    #build/check remote directory structure
+    remoteDir=fb.buildPathURL(project,\
+            ['preprocessedImages',getPatientLabel(row),getVisitLabel(row)])
+
+    gzRemoteFiles={im:remoteDir+'/'+f\
+            for (im,f) in gzFileNames.items()}
+
+    remoteFilePresent=[fb.entryExists(f)\
+            for f in gzRemoteFiles.values()]
+
+    for f in gzRemoteFiles.values():
+        print("[{}]: [{}]".format(f,fb.entryExists(f)))
+
+
+    if all(remoteFilePresent):
+        print("Entry for row done.")
+        updateRow(project,dataset,row,imageResampledField,\
+                gzFileNames)
+        continue
+
+    inputDir=fb.buildPathURL(project,['segmentations']) 
+    inputFiles={im:inputDir+'/'+f for (im,f) in gzFileNames.items()}
+    
+    for im in inputFiles:
+        f=inputFiles[im]
+        if not fb.entryExists(f):
+            print("Input file {} not found".format(f))
+            continue
+        print("Found {}".format(f))
+        localFile=os.path.join(tempBase,gzFileNames[im])
+        print("Local {}".format(localFile))
+        fb.readFileToFile(f,localFile)
+        fb.writeFileToFile(localFile,gzRemoteFiles[im])
+        print("Remote {}".format(gzRemoteFiles[im]))
+        os.remove(localFile)
+
+    #update row and let it know where the processed files are
+    updateRow(project,dataset,row,imageResampledField,gzFileNames)
+   
+
+    if i==-1:
+        break
+    i=i+1
+
+
+print("Done")