Making convertToNRRD.py robust to starting it from anywhere in path, using __file__ variable to determine where to find pythonScripts

slicerScripts/convertToNRRD.py

@@ -6,6 +6,8 @@ import slicer
 import subprocess
 import shutil
 
+#for all rows in xconfig[queryName] import dicom and convert to nrrd
+
 def main(configFile):
    print('Running with {}'.format(configFile))
    with open(configFile) as f:
@@ -28,9 +30,15 @@ def main(configFile):
    import orthancInterface
    import orthancDatabaseBrowser
    import orthancFileBrowser
+   
+#one should be smart to figure this out if pwd is not the same as the directory of the script
 
-   sys.path.append('../pythonScripts')
+   pwd=os.path.dirname(os.path.abspath(__file__))
+   pwdUp=os.path.dirname(pwd)
+   pythonScripts=os.path.join(pwdUp,'pythonScripts')
+   sys.path.append(pythonScripts)
    import config
+   print('Config loaded')
 
    net=labkeyInterface.labkeyInterface()
    fnet=os.path.join(os.path.expanduser('~'),'.labkey',xconfig['network'])
@@ -151,10 +159,17 @@ def clearUnzipDir(r,xconfig):
 
 def downloadAndUnzip(ofb,r,code,xconfig):
    import config 
+   
+   pathList=xconfig['tempDir'].split('/')
+   pathList.insert(0,os.path.expanduser('~'))
+   tempDir=os.path.join(*pathList)
+   if not os.path.isdir(tempDir):
+      print('Creating {}'.format(tempDir))
+      os.makedirs(tempDir)
 
    orthancId=r[code+'OrthancId']
    fileCode='{}_{}'.format(config.getCode(r,xconfig),code)
-   zipFile=os.path.join(xconfig['tempDir'],fileCode+'.zip')
+   zipFile=os.path.join(tempDir,fileCode+'.zip')
    ofb.getZip('series',orthancId,zipFile)
    zipDir=clearUnzipDir(r,xconfig)
 
@@ -167,7 +182,6 @@ def downloadAndUnzip(ofb,r,code,xconfig):
    return zipDir
 
 def addCT(r,patient,xconfig):
-   sys.path.append('../pythonScripts')
    import config
    import vtkInterface
    ct=patient['CT']