Adding comments and redirecting gzip to setup.json indicated binary in preprocess.py

pythonScripts/preprocess.py

@@ -18,7 +18,7 @@ def getStudyLabel(row,participantField='PatientId'):
     return getPatientLabel(row,participantField)+'-'+getVisitLabel(row)
 
 def runPreprocess_DM(matlab,generalCodes,niftiTools,studyDir):
-
+    print("Running matlab")
     #run after all directories have been assembled
     script="addpath('"+generalCodes+"');"
     script+="addpath('"+niftiTools+"');"
@@ -46,7 +46,7 @@ def getDicom(ofb,row,zipDir,rawDir,im,imageSelector,\
     if seriesId=="0":
         return False
 
-    print("{}: {}".format(im,seriesId))
+    print("getDicom: {}: {}".format(im,seriesId))
     fname=os.path.join(zipDir,\
             getStudyLabel(row,participantField)+'_'+im+".zip");
 
@@ -54,7 +54,7 @@ def getDicom(ofb,row,zipDir,rawDir,im,imageSelector,\
     if os.path.isfile(fname):
         print("Data already loaded. Skipping")
     else:
-        print("Loading data from orthanc")
+        print("getDicom: Loading data from orthanc")
         ofb.getZip('series',seriesId,fname)
 
     #unzip the zipped dicom series
@@ -111,6 +111,7 @@ def main(parameterFile):
     matlab=setup["paths"]["matlab"]
     generalCodes=setup["paths"]["generalCodes"]
     niftiTools=setup["paths"]["niftiTools"]
+    gzip=setup['paths']['gzip']
 
     net=labkeyInterface.labkeyInterface()
     net.init(fconfig)
@@ -148,7 +149,7 @@ def main(parameterFile):
 
     i=0
     for row in ds["rows"]:
-
+        print("Starting row id:{} seq:{}".format(row[participantField],row['SequenceNum']))
         #interesting files are processedDir/studyName_CT_notCropped_2mmVoxel.nii
         #asn processedDir/studyName_PET_notCropped_2mmVoxel.nii
         volumeFileNames={im:\
@@ -181,6 +182,8 @@ def main(parameterFile):
     
         #setup the directory structure for preprocess_DM
         studyDir=os.path.join(tempBase,getStudyLabel(row,participantField))
+        print("Making local directories in {}".format(studyDir))
+
         if not os.path.isdir(studyDir):
             os.mkdir(studyDir)
 
@@ -224,7 +227,7 @@ def main(parameterFile):
 
             for f in volumeFiles.values():
                 print("Running gzip {}".format(f))
-                outText=subprocess.check_output(["/bin/gzip",f])
+                outText=subprocess.check_output([gzip,f])
                 print(outText.decode('utf-8'))
 
         #upload local files to remote