Delegating and implementing filter parsing in config.py

pythonScripts/calculateCenters.py

@@ -10,10 +10,9 @@ def main(configFile):
    with open(configFile,'r') as f:
       xsetup=json.load(f)
    db,fb=getData.connectDB(xsetup['network'])
-   try:
-      qfilter=xsetup['patientFilter']
-   except KeyError:
-      qfilter=[]
+
+   qfilter=config.getFilter(xsetup)
+
    #getData.downloadPatientFiles(db,fb,xsetup,qfilter)
    rows=getData.getPatients(db,xsetup,qfilter)
    try:

pythonScripts/config.py

@@ -38,12 +38,29 @@ def getVisitFilter(row,xconfig):
       'value':getVisitId(row,xconfig),
       'oper':'eq'}
 
+def getFilter(xconfig):
+   row={}
+   fields={getPatientField(xconfig):getIdFilter,
+           getVisitField(xconfig):getVisitFilter}
+
+   qfilter=[]
+   for f in fields:
+      try:
+         row[f]=xconfig[f]
+         qfilter.append(fields[f](row,xconfig))
+      except KeyError:
+         continue
+   return qfilter
+
+
 def getCode(row,xconfig):
    return '{}_{}'.format(getPatientId(row,xconfig),getVisitId(row,xconfig))
 
 def getTargetSeqNum(row,xconfig):
    if getVisitId(row,xconfig)=='OBR':
       return 2
+   if getVisitId(row,xconfig)=='MIR1':
+      return 3
    return 1
 
 def getPathList(row,xconfig):
@@ -101,6 +118,16 @@ def getFitParFinalName(code,nc,j,aType):
    
    return '{}_fitParFinal.txt'.format(fCode)
 
+def getFitPNGNames(code,nc,j,aType):
+   fCode='{}_{}_{}'.format(code,nc,j+1)
+   if aType!='global':
+      fCode='{}_{}'.format(fCode,aType)
+   names=[]
+   for i in range(nc):
+      names.append('{}_centers{}.txt'.format(fCode,i+1))
+   return names
+
+
 def printFitParFinalRowNames(r,setup,aType):
    names=[]
    nr=setup['nr']
@@ -110,7 +137,9 @@ def printFitParFinalRowNames(r,setup,aType):
    for nc in nclass:
       for j in range(nr):
          names.append(getFitParFinalName(code,nc,j,aType))
-         #names.append('{}_centerWeight.nrrd'.format(fCode))
+#add pngs of the fit (good QA)
+#this are only partial fits, from which global parameters are taken
+         #names+=getFitPNGNames(code,nc,j,aType)
    return names
  
 def getPixelFitParFinalName(code,nc,s2,mode):

pythonScripts/doAnalysis.py

@@ -12,11 +12,8 @@ def main(configFile):
       xsetup=json.load(f)
    db,fb=getData.connectDB(xsetup['network'])
 
-   try:
-      qfilter=xsetup['patientFilter']
-   except KeyError:
-      qfilter=[]
-   
+   qfilter=config.getFilter(xsetup)
+
    rows=getData.getPatients(db,xsetup,qfilter)
 
    for r in rows:

pythonScripts/doPixelAnalysis.py

@@ -12,10 +12,7 @@ def main(configFile):
       xsetup=json.load(f)
    db,fb=getData.connectDB(xsetup['network'])
 
-   try:
-      qfilter=xsetup['patientFilter']
-   except KeyError:
-      qfilter=[]
+   qfilter=config.getFilter(xsetup)
    
    rows=getData.getPatients(db,xsetup,qfilter)
 

slicerScripts/convertToNRRD.py

@@ -53,7 +53,7 @@ def main(configFile):
    ofb=orthancFileBrowser.orthancFileBrowser(onet)
    odb=orthancDatabaseBrowser.orthancDB(onet)
 
-   qFilter=[]  
+   qFilter=config.getFilter(xconfig)
    ds=db.selectRows(xconfig['project'],xconfig['schemaName'],xconfig['queryName'],qFilter)