Delegating filter parsing to config

pythonScripts/analysis.py

@@ -222,8 +222,10 @@ def getWeights(db,r,setup,nclass,realizationId,sigma2,na):
 def getPixelFitPar(fb,r,setup,nc,s2,mode):
    code=config.getCode(r,setup)
    f=config.getPixelFitParFinalName(code,nc,s2,mode)
+   print('getPixelFitPar {}'.format(f))
    getData.copyFromServer(fb,r,setup,[f])
    fName=getData.getLocalPath(r,setup,f)
+   print('getPixelFitPar {}'.format(fName))
    return numpy.genfromtxt(fName,delimiter='\t')
 
 def getFitPar(fb,r,setup,nclass,realizationId,mode):
@@ -354,11 +356,7 @@ def storeSummary(db,setup,summary,sigma2,na):
                     
 def summaryPixelIVF(db,fb,setup):
     #for second type of analysis (pixel based regions)
-    qfilter=[]
-    try:
-      qfilter=setup['patientFilter']
-    except KeyError:
-      pass
+    qfilter=config.getFilter(setup)
     rows=getData.getPatients(db,setup,qfilter)
     sigma2=setup['sigma2']
     return \
@@ -406,5 +404,6 @@ def getPixelIVF(db,fb,r,setup,sigma2):
     #nclassIVF=segmentation.getNC(r,setup)
     #fitPar=getFitPar(r,setup,nclassIVF,sigma2,'PixelIVF')
     fitPar=getPixelFitPar(fb,r,setup,nclassIVF,sigma2,'IVF')
+    print(fitPar)
     k1={r['regionId']:getK1(fitPar,r['regionId']) for r in rows}
     return k1