Resolving merge errors in getData.py

pythonScripts/config.py

@@ -102,6 +102,54 @@ def decode(code,xconfig):
    vid=values[1]
    return {getPatientField(xconfig):fid,getVisitField(xconfig):vid}
 
+#standardized file names
+def getPattern(ftype,code,nclass=0,ir=0,ic=0,fitType='global',qaName='fits',timepoint=0,iseg=0,qLambda=0):
+   qLambdaString='{:.3f}'.format(qLambda).replace('.','p')
+   replacePatterns={
+      '_code_':code,
+      '_nclass_':nclass,
+      '_ir_':ir,
+      '_ic_':ic,
+      '_fitType_':fitType,
+      '_qaName_':qaName,
+      '_timepoint_':timepoint,
+      '_iseg_':iseg,
+      '_qLambda_':qLambdaString}
+   map={'CT':'_code__CT.nrrd',
+      'SPECT':'_code__Volume_timepoint_.nrrd',
+      'Dummy':'_code__Dummy.mcsv',
+      'centerMap':'_code___nclass___ir__centerMap.txt',
+      'centerWeight':'_code___nclass___ir__center_ic__centerWeight.nrrd',
+      'centerNRRD':'_code___nclass___ir__centerMap__qaName_.nrrd',
+      'center':'_code___nclass___ir__center_ic__center.txt',
+      'fitParFinal':'_code___nclass___ir___fitType__fitParFinal.txt',
+      'fitPNG':'_code___nclass___ir___fitType__centers_ic_.png',
+      'pixelFitParFinal':'_code___nclass___ir__Pixel__fitType__fitParFinal.txt',
+      'pixelFitPNG':'_code___nclass___ir__Pixel__fitType__centers_ic_.png',
+      'fitIVF':'_code___nclass___ir___qLambda__fitParIVF.txt',
+      'plotIVF':'_code___nclass___ir___qLambda__plotIVF__qaName_.png',
+      'fitCompartment':'_code___nclass___ir___qLambda__fitCompartment__iseg___qaName_.txt',
+      'plotCompartment':'_code___nclass___ir___qLambda__plotCompartment__iseg___qaName_.png'}
+   w=map[ftype]
+   for x in replacePatterns:
+      w=re.sub(x,'{}'.format(replacePatterns[x]),w)
+   return w
+
+
+
+      
+
+#pixels corresponding to a particular c-means class
+def getCenterWeight(r,setup,nclass,ir,i):
+   code=getCode(r,setup)
+   return f'{code}_{nclass}_{ir}_center{i}_centerWeight.nrrd'
+
+#1D TAC for a particular group center 
+def getCenter(r,setup,nclass,ir,i):
+   code=getCode(r,setup)
+   return f'{code}_{nclass}_{ir}_center{i}_center.txt'
+
+#all names for determination of TAC, obsolete
 def printRowCenterNames(r,setup):
    names=[]
    nr=setup['nr']
@@ -111,11 +159,12 @@ def printRowCenterNames(r,setup):
    for nc in nclass:
       for j in range(nr):
          for i in range(nc): 
-            fCode='{}_{}_{}_center{}'.format(code,nc,j+1,i+1)
-            names.append('{}_center.txt'.format(fCode))
-            names.append('{}_centerWeight.nrrd'.format(fCode))
+            names.append(getCenter(r,setup,nc,j+1,i+1))
+            names.append(getCenterWeight(r,setup,nc,j+1,i+1))
    return names
- 
+
+
+#fit of a compartment 
 def getFitParFinalName(code,nc,j,aType):
    fCode='{}_{}_{}'.format(code,nc,j+1)
    if aType!='global':
@@ -123,6 +172,19 @@ def getFitParFinalName(code,nc,j,aType):
    
    return '{}_fitParFinal.txt'.format(fCode)
 
+#fit of the IVF
+def getFitIVFParName(r,setup,nc,j):
+   code=getCode(r,setup)
+   fCode='{}_{}_{}'.format(code,nc,j+1)
+   return f'{fCode}_fitParIVF.txt' 
+
+#status report of the IVF fit (three images)
+def getFitIVFReportPNG(r,setup,nc,j,name):
+   code=getCode(r,setup)
+   fCode=f'{code}_{nc}_{j+1}_fitParIVF_{name}.png'
+   return fCode
+
+#
 def getFitPNGNames(code,nc,j,aType):
    if aType=='global':
       return []

pythonScripts/getData.py

@@ -116,12 +116,9 @@ def uploadPixelFitParFinal(fb,r,xsetup,m='IVF'):
 
 
 def copyToServer(fb,r,setup,names):
-   tempDir=config.getTempDir(setup)
-   code=config.getCode(r,setup)
-   project=setup['project']
-   remoteDir=fb.buildPathURL(project,config.getPathList(r,setup))
+   remoteDir=fb.buildPathURL(setup['project'],config.getPathList(r,setup))
    for n in names:
-      localPath=os.path.join(tempDir,code,n)
+      localPath=getLocalPath(r,setup,n)
       remotePath='{}/{}'.format(remoteDir,n)
       fb.writeFileToFile(localPath,remotePath)
 
@@ -131,22 +128,22 @@ def copyFromServer(fb,r,setup,names):
    except KeyError:
       forceReload=False
 
-   tempDir=config.getTempDir(setup)
-   code=config.getCode(r,setup)
-   project=setup['project']
-   remoteDir=fb.buildPathURL(project,config.getPathList(r,setup))
+   getLocalDir(r,setup,createIfMissing=True)
+   remoteDir=fb.buildPathURL(setup['project'],config.getPathList(r,setup))
    for n in names:
-      localDir=os.path.join(tempDir,code)
-      if not os.path.isdir(localDir):
-         os.makedirs(localDir)
-      #n may contain slash, and localPath should be without it
-      fName=n[n.rfind('/')+1:]
-      localPath=os.path.join(localDir,fName)
+      localPath=getLocalPath(r,setup,n)
       if os.path.isfile(localPath) and not forceReload:
          continue
-      remotePath='{}/{}'.format(remoteDir,n)
+      remotePath='/'.join([remoteDir,n])
       fb.readFileToFile(remotePath,localPath)
 
+def getLocalDir(r,setup,createIfMissing=False):
+   localDir=os.path.join(config.getTempDir(setup),config.getCode(r,setup))
+   if createIfMissing:
+      if not os.path.isdir(localDir):
+         os.makedirs(localDir)
+   return localDir
+
 def getLocalPath(r,setup,name):
    tempDir=config.getTempDir(setup)
    code=config.getCode(r,setup)