dynamicSPECT/pythonScripts/config.py

import os
import json
import re

def cmdMatlab():
   pwd=os.path.dirname(os.path.abspath(__file__))
   pwdUp=os.path.dirname(pwd)
   mDir=os.path.join(pwdUp,'matlab')
   with open(os.path.join(os.path.expanduser('~'),'.labkey','setup.json'),'r') as f:
      siteSetup=json.load(f)
   mExec=siteSetup['paths']['matlab']

   cmds=[mExec]
   cmds.append('-sd')
   cmds.append(mDir)
   #cmds.append('-batch')
   return cmds
 
def getPatientId(row,xconfig):
   return row[getPatientField(xconfig)]

def getPatientField(xconfig):
   return xconfig['ParticipantField']

def getVisitField(xconfig):
   try:
      return xconfig['visitField']
   except KeyError:
      return 'visitName'

def getVisitId(row,xconfig):
   return row[getVisitField(xconfig)]

def getIdFilter(row,xconfig):
   return {'variable':getPatientField(xconfig),\
      'value':getPatientId(row,xconfig),
      'oper':'eq'}

def getVisitFilter(row,xconfig):
   return {'variable':getVisitField(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]
         if xconfig[f]!='NONE':
            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
   if getVisitId(row,xconfig)=='MIR2':
      return 4
   return 1

def getPathList(row,xconfig):
   return [xconfig['baseDir'],getPatientId(row,xconfig),getVisitId(row,xconfig)]

def getOutputDir(row,xconfig):
   return '/'.join(getPathList(row,xconfig))


def getTempDir(xconfig):
   tempDir=xconfig['tempDir']
   pathList=tempDir.split('/')
   pathList.insert(0,os.path.expanduser('~'))
   return os.path.join(*pathList)
 

def getLocalDir(row,xconfig):
   return os.path.join(getTempDir(xconfig),getCode(row,xconfig))

def getNodeName(row,xconfig,mode,i=0):
   if mode=='CT':
      return getCode(row,xconfig)+'_CT'
   if mode=='NM':
      return '{}_Volume{}'.format(getCode(row,xconfig),i)
   return getCode(row,xconfig)+'_Dummy'

def decode(code,xconfig):
   #invert code and return object equivalent to row with relevant
   #fields set that can be used in 
   #getPatientId, getVisitId,getIdFilter,getVisitFilter 
   #as an equivalent replacement for r
   values=code.split('_')
   fid=values[0]
   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,qLambdaC=0):
   qLambdaString='{:.3f}'.format(qLambda).replace('.','p')
   qLambdaCString='{:.3f}'.format(qLambdaC).replace('.','p')
   replacePatterns={
      '_code_':code,
      '_nclass_':nclass,
      '_ir_':ir,
      '_ic_':ic,
      '_fitType_':fitType,
      '_qaName_':qaName,
      '_timepoint_':timepoint,
      '_iseg_':iseg,
      '_qLambda_':qLambdaString,
      '_qLambdaC_':qLambdaCString}

   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___qLambdaC_.txt',
      'plotCompartment':'_code___nclass___ir___qLambda__plotCompartment__iseg___qaName___qLambdaC_.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']
   nclass=setup['nclass']
   code=getCode(r,setup)
   #tempDir=config.getTempDir(setup)
   for nc in nclass:
      for j in range(nr):
         for i in range(nc): 
            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':
      fCode='{}_{}'.format(fCode,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 []
   fCode='{}_{}_{}'.format(code,nc,j+1)
   #if aType!='global':
   fCode='{}_{}'.format(fCode,aType)
   names=[]
   for i in range(nc):
      names.append('{}_centers{}.png'.format(fCode,i+1))
   return names


def printFitParFinalRowNames(r,setup,aType):
   names=[]
   nr=setup['nr']
   nclass=setup['nclass']
   code=getCode(r,setup)
   #tempDir=config.getTempDir(setup)
   for nc in nclass:
      for j in range(nr):
         names.append(getFitParFinalName(code,nc,j,aType))
#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):
   sigmaCode='{:.2f}'.format(s2)
   sigmaCode=re.sub('\.','p',sigmaCode)
   fName='{}_{}_{}_Pixel'.format(code,nc,sigmaCode)
   if mode!='general':
      fName='{}{}'.format(fName,mode)
   fName='{}_fitParFinal.txt'.format(fName)
   return fName

def getPixelFitParFinalPngName(code,nc,i,s2,mode):
   sigmaCode='{:.2f}'.format(s2)
   sigmaCode=re.sub('\.','p',sigmaCode)
   fName='{}_{}_{}_Pixel'.format(code,nc,sigmaCode)
   if mode!='general':
      fName='{}{}'.format(fName,mode)
   fName='{}_centers{}.png'.format(fName,i)
   return fName


def printPixelFitParFinalRowNames(r,setup,nc,s2,mode):
   names=[]
   code=getCode(r,setup)
   names.append(getPixelFitParFinalName(code,nc,s2,mode))
   for i in range(nc):
      names.append(getPixelFitParFinalPngName(code,nc,i+1,s2,mode))
   return names