migration to project specific orthanc

pythonScripts/preprocess.py

@@ -5,6 +5,7 @@ import subprocess
 import nibabel
 import shutil
 import sys
+import nixWrapper
 
 #nothing gets done if you do import
 
@@ -35,13 +36,18 @@ def runPreprocess_DM(matlab,generalCodes,niftiTools,studyDir):
     return True
 
 
-def getDicom(ofb,row,zipDir,rawDir,im,imageSelector,\
-        participantField='PatientId'):
+def getDicom(pars,row,zipDir,rawDir,im,imageSelector):
 
     #Load the dicom zip file and unzips it. If zip file is already at the expected path, it skips the loading step
 
     #Return True for valid outcome and False for troubles in row formating or unzip failures
 
+    participantField=pars.get('participantField','PatientId')
+    ofb=pars['ofb']
+    if row['movedToProjectOrthanc']=='TRUE':
+      ofbStore=ofb.store()
+      ofb.set(pars['orthanc'])
+    
     seriesId=row[imageSelector[im]];
     if seriesId=="0":
         return False
@@ -55,8 +61,19 @@ def getDicom(ofb,row,zipDir,rawDir,im,imageSelector,\
         print("Data already loaded. Skipping")
     else:
         print("getDicom: Loading data from orthanc")
+
+#use study specific orthanc
+        if row['movedToProjectOrthanc']=='TRUE':
+            ofbStore=ofb.store()
+            ofb.set(pars['orthanc'])
+   
         ofb.getZip('series',seriesId,fname)
 
+#reset to global value
+        if row['movedToProjectOrthanc']=='TRUE':
+            ofb.set(ofbStore) 
+
+
     #unzip the zipped dicom series
 
     unzipDir=os.path.join(rawDir,im)
@@ -92,8 +109,6 @@ def main(parameterFile):
     with open(os.path.join(fhome,".labkey","setup.json")) as f:
         setup=json.load(f)
 
-    sys.path.insert(0,setup["paths"]["nixWrapper"])
-    import nixWrapper
 
     nixWrapper.loadLibrary("labkeyInterface")
 
@@ -135,7 +150,15 @@ def main(parameterFile):
 
 
     participantField=pars['Database']['participantField']
+    dicomPars={'participantField':participantField,'ofb':ofb}
+
+
+    ds=db.selectRows(project,'study','StudyProperties')
+    orthancObj={'server':ds['rows'][0]['orthancURL'],
+      'user':ds['rows'][0]['orthancUser'],
+      'password':ds['rows'][0]['orthancPassword']}
 
+    dicomPars['orhanc']=orthancObj
     #all images from database
     ds=db.selectRows(project,schema,dataset,[])
     imageSelector={"CT":"CT_orthancId","PET":"PETWB_orthancId"}
@@ -227,7 +250,7 @@ def main(parameterFile):
             #use imageSelector -> inputs
             for im in imageSelector:
                 #checks if raw files are already loaded
-                getDicom(ofb,row,zipDir,rawDir,im,imageSelector,\
+                getDicom(dicomPars,row,zipDir,rawDir,im,imageSelector,\
                     participantField)