Cleaning up listCreatedFiles in workflow

pythonScripts/workflow.py

@@ -95,56 +95,70 @@ def listRequiredFiles(stage,r,setup,db=None):
    return {}
 
 def listCreatedFiles(stage,r,setup):
-    code=config.getCode(r,setup)
-    nclass=setup['nclass'][0]
-    qLambda=getRobust(setup,'qLambda')
-    qLambdaC=getRobust(setup,'qLambdaC')
-    nr=setup['nr']
-    nseg=getRobust(setup,'nseg')
-    names={}
+   code=config.getCode(r,setup)
+   nclass=setup['nclass'][0]
+   qLambda=getRobust(setup,'qLambda')
+   qLambdaC=getRobust(setup,'qLambdaC')
+   nr=setup['nr']
+   nseg=getRobust(setup,'nseg')
+   print(f'List created files nseg={nseg}')
+   names={}
+   getPattern=config.getPattern
                                 
-    if stage=='setCenters':
-        names['center']=[]
-        for ir in range(nr):
-            rel=[config.getPattern('center',code=code,nclass=nclass,ir=ir,ic=i) for i in range(nclass)]
-            names['center'].extend(rel)
-            #rel=[config.getPattern('centerWeight',code=code,nclass=nclass,ir=ir,ic=i) for i in range(nclass)]
-            #names['center'].extend(rel)
-            names['center'].append(config.getPattern('centerMap',code=code,nclass=nclass,ir=ir))
-            rel=[config.getPattern('centerNRRD',code=code,nclass=nclass,ir=ir,qaName=x) for x in ['CT','SPECT']]
-            names['center'].extend(rel)
+   if stage=='setCenters':
+      names['center']=[]
+      for ir in range(nr):
+         rel=[getPattern('center',code=code,nclass=nclass,ir=ir,ic=i) for i in range(nclass)]
+         names['center'].extend(rel)
+         #rel=[config.getPattern('centerWeight',code=code,nclass=nclass,ir=ir,ic=i) for i in range(nclass)]
+         #names['center'].extend(rel)
+         names['center'].append(getPattern('centerMap',code=code,nclass=nclass,ir=ir))
+         rel=[getPattern('centerNRRD',code=code,nclass=nclass,ir=ir,qaName=x) for x in ['CT','SPECT']]
+         names['center'].extend(rel)
             
-        return names
-    if stage=='fitIVF':
-        names['fitIVF']=[]
-        for ir in range(nr):
-            names['fitIVF'].append(config.getPattern('fitIVF',code=code,nclass=nclass,ir=ir,qLambda=qLambda))
-        return names
-    if stage=='plotIVF':
-        names['plotIVF']=[]
-        for ir in range(nr):
-            x=[config.getPattern('plotIVF',code=code,nclass=nclass,ir=ir,qaName=y,qLambda=qLambda) 
-               for y in ['fits','diff','generatedIVF','centerIVFSPECT','centerIVFCT']]
-            names['plotIVF'].extend(x)
-        return names
-    if stage=='fitCompartment':
-        xc='fitCompartment'
-        names[xc]=[]
-        sNames=['kmeansFit','localFit','kmeansTAC','localTAC']
-        for ir in range(nr):
-            for iseg in range(nseg):
-                rel=[config.getPattern(xc,code=code,nclass=nclass,ir=ir,qaName=qn,iseg=iseg,qLambda=qLambda,qLambdaC=qLambdaC) for qn in sNames]
-                names[xc].extend(rel)
-    if stage=='plotCompartment':
-        xc='plotCompartment'
-        names[xc]=[]
-        sNames=['realizations','diff']
-        for ir in range(nr):
-            for iseg in range(nseg):
-                rel=[config.getPattern(xc,code=code,nclass=nclass,ir=ir,qaName=qn,iseg=iseg,qLambda=qLambda,qLambdaC=qLambdaC) for qn in sNames]
-                names[xc].extend(rel)
+      return names
+   if stage=='fitIVF':
+      names['fitIVF']=[]
+      for ir in range(nr):
+         names['fitIVF'].append(getPattern('fitIVF',code=code,nclass=nclass,ir=ir,qLambda=qLambda))
+      return names
+
+
+   if stage=='plotIVF':
+      names['plotIVF']=[]
+      sNames=['fits','diff','generatedIVF','centerIVFSPECT','centerIVFCT']
+      for ir in range(nr):
+         x=[getPattern('plotIVF',code=code,nclass=nclass,ir=ir,qaName=y,qLambda=qLambda) for y in sNames]
+         names['plotIVF'].extend(x)
+      return names
+
+
+   if stage=='fitCompartment':
+      xc='fitCompartment'
+      names[xc]=[]
+      sNames=['kmeansFit','localFit','kmeansTAC','localTAC']
+      for ir in range(nr):
+         for iseg in range(nseg):
+            _q=qLambda
+            _qC=qLambdaC
+            rel=[getPattern(xc,code=code,nclass=nclass,ir=ir,qaName=qn,iseg=iseg,qLambda=_q,qLambdaC=_qC) for qn in sNames]
+            names[xc].extend(rel)
+      return names
+
+   if stage=='plotCompartment':
+      xc=stage
+      names[xc]=[]
+      sNames=['realizations','diff']
+      for ir in range(nr):
+         for s in range(nseg):
+            iseg=s+1
+            _q=qLambda
+            _qC=qLambdaC
+            rel=[getPattern(xc,code=code,nclass=nclass,ir=ir,qaName=qn,iseg=iseg,qLambda=_q,qLambdaC=_qC) for qn in sNames]
+            names[xc].extend(rel)
+      return names
     
-    return []
+   return []
     
 
 def getRequiredFiles(stage,r,setup,fb,names=None,db=None):
@@ -372,6 +386,7 @@ def workflow(r,setup,stage,fb=None,db=None):
         nclass=setup['nclass'][0]
         code=config.getCode(r,setup)
         setup['nseg']=len(segmentIds)
+        print('Setting setup[nseg]={}'.format(setup['nseg']))
         t,dt=loadData.loadTime(r,setup)
         for iseg in segmentIds:
             m,samplesC=loadData.readSamples(r,setup,'kmeansFit',ir=ir,iseg=iseg,qLambda=qLambda,qLambdaC=qLambdaC)
@@ -396,14 +411,16 @@ def workflow(r,setup,stage,fb=None,db=None):
             row['mean']=k1
             row['std']=stdK1
             row['regionId']=iseg
-            row['fitPlot']=config.getPattern(tag,code=code,ir=0,nclass=nclass,qaName='realizations',iseg=iseg,qLambda=qLambda,qLambdaC=qLambdaC)
-            row['diffPlot']=config.getPattern(tag,code=code,ir=0,nclass=nclass,qaName='diff',iseg=iseg,qLambda=qLambda,qLambdaC=qLambdaC)
+            row['qLambda']=qLambda
+            row['qLambdaC']=qLambdaC
+            row['fitPlot']=config.getPattern(tag,code=code,ir=0,nclass=nclass,qaName='realizations',\
+               iseg=iseg,qLambda=qLambda,qLambdaC=qLambdaC)
+            row['diffPlot']=config.getPattern(tag,code=code,ir=0,nclass=nclass,qaName='diff',\
+               iseg=iseg,qLambda=qLambda,qLambdaC=qLambdaC)
             row1={x:row[x] for x in row}
             row1['option']='localFit'
             row1['mean']=k11
             row1['std']=stdK11
-            row['qLambda']=qLambda
-            row['qLambdaC']=qLambdaC
             if db:
                 db.modifyRows('insert',setup['project'],'lists','Summary',[row,row1])
             
@@ -416,7 +433,8 @@ def workflow(r,setup,stage,fb=None,db=None):
             plotData.plotSamples(t,evalArray,file0=file0,file1=file1)
 
 
-
+    nseg=getRobust(setup,'nseg')
+    print(f'At upload nseg={nseg}')
     uploadCreatedFiles(stage,fb,r,setup)
    #setup could be modified
     return setup