switched variable name useLCDM to less confusing useComoving; make it sample-level rather than dataset-level

c_tools/mock/generateFromCatalog.cpp

@@ -115,7 +115,7 @@ void loadData(const string& fname, NYU_VData & data)
 }
 
 void generateGalaxiesInCube(NYU_VData& data, ParticleData& output_data, 
-                            bool useLCDM)
+                            bool useComoving)
 {
   double d2r = M_PI/180;
 
@@ -163,7 +163,7 @@ void generateGalaxiesInCube(NYU_VData& data, ParticleData& output_data,
       double ra = data[i].ra*d2r, dec = data[i].dec*d2r;
       Position& p = output_data.pos[i];
 
-      if (useLCDM) {
+      if (useComoving) {
         //double pos = gsl_interp_eval(interp, redshifts, dL, data[i].cz, acc);
         gsl_integration_qng(&expanF, 1.e-6, data[i].cz/LIGHT_SPEED,
                                         1.e-6, 
@@ -587,7 +587,7 @@ int main(int argc, char **argv)
   // We compute a cube holding all the galaxies + the survey surface mask
 
   cout << "Placing galaxies..." << endl;
-  generateGalaxiesInCube(data, output_data, args_info.useLCDM_flag);
+  generateGalaxiesInCube(data, output_data, args_info.useComoving_flag);
   generateSurfaceMask(args_info, mask, pixel_list, full_mask_list,
                       data, output_data);
   

c_tools/mock/generateFromCatalog.ggo

@@ -14,4 +14,4 @@ option "zMax" - "Maximum redshift of data" double required
 option "output"	- "Filename of particle datafile" string required
 option "params" - "Output parameters of the datacube" string required
 
-option "useLCDM" - "Convert to real space using LCDM cosmology" flag off
+option "useComoving" - "Convert to real space using LCDM cosmology" flag off

c_tools/stacking/pruneVoids.cpp

@@ -724,7 +724,7 @@ int main(int argc, char **argv) {
       voids[iVoid].redshiftInMpc = voids[iVoid].redshiftInMpc;
 
 
-      if (args.useLCDM_flag) {
+      if (args.useComoving_flag) {
         redshift = gsl_interp_eval(interp, dL, redshifts,
                  voids[iVoid].redshiftInMpc, acc);
         //printf("HELLO %e %e\n", redshift, args.zMax_arg);

c_tools/stacking/pruneVoids.ggo

@@ -23,7 +23,7 @@ option "numVoids" - "Number of voids" int required
 
 option "isObservation" - "We are working with observational data" flag off
 
-option "useLCDM" - "Void positions are in comoving coordinates" flag off
+option "useComoving" - "Void positions are in comoving coordinates" flag off
 
 option "zMin" - "Minimum redshift of sample" double optional default="0.0"
 option "zMax" - "Maximum redshift of sample" double optional default="10.0"

pipeline/generateCatalog.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #+
-#   VIDE -- Void IDEntification pipeline -- ./pipeline/generateCatalog.py
+#   VIDE -- Void IDentification and Examination -- ./pipeline/generateCatalog.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #
@@ -91,7 +91,7 @@ for sample in dataSampleList:
 
     launchGenerate(sample, GENERATE_PATH, workDir=workDir, 
                    inputDataDir=inputDataDir, zobovDir=zobovDir,
-                   figDir=figDir, logFile=logFile, useLCDM=useLCDM,
+                   figDir=figDir, logFile=logFile, useComoving=sample.useComoving,
                    continueRun=continueRun, regenerate=regenerateFlag)
 
   # --------------------------------------------------------------------------
@@ -115,7 +115,7 @@ for sample in dataSampleList:
 
     launchPrune(sample, PRUNE_PATH, 
                 logFile=logFile, zobovDir=zobovDir, 
-                useLCDM=useLCDM, continueRun=continueRun)
+                useComoving=sample.useComoving, continueRun=continueRun)
 
 # -------------------------------------------------------------------------
 if (startCatalogStage <= 4) and (endCatalogStage >= 4):

python_tools/pipeline_source/prepareCatalogs.in.py

@@ -150,7 +150,7 @@ freshStack = True
 errorBars = "CALCULATED"
 numIncoherentRuns = 100
 ranSeed = 101010
-useLCDM = False
+useComoving = False
 bias = 1.16
 
 dataPortions = {dataPortions}

python_tools/void_python_tools/backend/classes.py

@@ -77,7 +77,7 @@ class Sample:
   includeInHubble = True
   partOfCombo  = False
   isCombo = False
-  useLCDM = False # if True, convert population to comoving coordinates
+  useComoving = False # if True, convert population to comoving coordinates
   
   comboList = []
 
@@ -99,7 +99,7 @@ class Sample:
                comboList=(), profileBinSize=2.0, skyFraction=0.19,
                boxLen=1024, usePecVel=False, omegaM=0.27, 
                numSubvolumes=1, mySubvolume=1, dataFormat="sdss",
-               useLCDM=False,
+               useComoving=False,
                dataType="observation",
                subsample=1.0, useLightCone=True, autoNumInStack=-1):
     self.dataFile = dataFile
@@ -130,7 +130,7 @@ class Sample:
     self.subsample = subsample
     self.useLightCone = useLightCone
     self.dataUnit = dataUnit
-    self.useLCDM = useLCDM
+    self.useComoving = useComoving
     self.autoNumInStack = autoNumInStack
 
     self.stacks = []

python_tools/void_python_tools/backend/launchers.py

@@ -43,7 +43,7 @@ ncFloat = 'f8' # Double precision
 
 # -----------------------------------------------------------------------------
 def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, 
-                   zobovDir=None, figDir=None, logFile=None, useLCDM=False,
+                   zobovDir=None, figDir=None, logFile=None, useComoving=False,
                    continueRun=None,regenerate=False):
 
   if sample.dataType == "observation":
@@ -63,10 +63,10 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
 
     maskFile = sample.maskFile
 
-    if useLCDM:
+    if useComoving:
-      useLCDMFlag = "useLCDM"
+      useComovingFlag = "useComoving"
     else:
-      useLCDMFlag = ""
+      useComovingFlag = ""
 
     conf="""
       catalog %s
@@ -81,7 +81,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
       """ % (datafile, maskFile, outputFile,
              zobovDir+"/zobov_slice_"+sampleName+".par",
              sample.zBoundary[0], sample.zBoundary[1], sample.fakeDensity,
-             useLCDMFlag, inputParameterFlag)
+             useComovingFlag, inputParameterFlag)
 
     parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
 
@@ -244,7 +244,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
   if sample.dataType == "observation":
     (boxVol, nbar) = vp.getSurveyProps(sample.maskFile, sample.zRange[0],
      sample.zRange[1], sample.zRange[0], sample.zRange[1], "all", 
-     useLCDM=useLCDM)
+     useComoving=useComoving)
   else:
     iX = float(sample.mySubvolume[0])
     iY = float(sample.mySubvolume[1])
@@ -357,7 +357,7 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
 # -----------------------------------------------------------------------------
 def launchPrune(sample, binPath, 
                 summaryFile=None, logFile=None, zobovDir=None, 
-                continueRun=None, useLCDM=False):
+                continueRun=None, useComoving=False):
 
   sampleName = sample.fullName
 
@@ -385,10 +385,10 @@ def launchPrune(sample, binPath,
 
   periodicLine = " --periodic='" + getPeriodic(sample) + "'"
 
-  if useLCDM:
+  if useComoving:
-    useLCDMFlag = " --useLCDM"
+    useComovingFlag = " --useComoving"
   else:
-    useLCDMFlag = ""
+    useComovingFlag = ""
 
   if not (continueRun and (jobSuccessful(logFile, "NetCDF: Not a valid ID\n") \
           or jobSuccessful(logFile, "Done!\n"))):
@@ -410,7 +410,7 @@ def launchPrune(sample, binPath,
     cmd += " --numVoids=" + str(numVoids)
     cmd += observationLine
     cmd += periodicLine
-    cmd += useLCDMFlag
+    cmd += useComovingFlag
     cmd += " --outputDir=" + zobovDir
     cmd += " --sampleName=" + str(sampleName)
     cmd += " &> " + logFile
@@ -1460,7 +1460,6 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
       sys.stdout = open(logFile, 'w')
       sys.stderr = open(logFile, 'a')
       if doPlot:
-        print "DOING PLOT"
         if INCOHERENT:
           #plotTitle = "all samples, incoherent "+\
           #            thisDataPortion+" voids"
@@ -1486,7 +1485,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
         else:
           #plotTitle = "all samples, "+thisDataPortion+\
           #            " voids (systematics corrected)"
-          plotTitle = setName + "(sysematics corrected)"
+          plotTitle = setName + "(systematics corrected)"
         vp.do_all_obs(zbase, allExpList, aveDistList,
                       rlist, plotTitle=plotTitle, sampleNames=shortSampleNames,
                       plotAve=True, mulfac = 1.16,