bug fixed related to different boundary handling procedure. no guarantee that it's correct (yet) but it runs

c_source/prep/prepObservation.cpp

@@ -290,7 +290,7 @@ void generateSurfaceMask(prepObservation_info& args ,
   volume *= Rmax*Rmax*Rmax/3/1e6;
   numToInsert = (int)floor(volume*args.density_fake_arg);
   // TEST NOT USING MOCK PARTICLES
-  numToIntsert = 0
+  numToInsert = 0;
   // END TEST
   cout << format("3d volume to fill: %g (Mpc/h)^3") % volume << endl;
 

python_source/backend/classes.py

@@ -67,8 +67,9 @@ class Sample:
   dataUnit = 1
   fullName = "lss.dr72dim.dat"
   nickName = "dim"
-  zobovDir = ""
+  outputDir = ""
   maskFile = "rast_window_512.fits"
+  nsideForMask = 128
   selFunFile = "czselfunc.all.dr72dim.dat"
   zBoundary = (0.0, 0.1)
   zBoundaryMpc = (0., 300)
@@ -98,7 +99,7 @@ class Sample:
   stacks = []
 
   def __init__(self, dataFile="", fullName="", dataUnit=1,
-               nickName="", maskFile="", selFunFile="",
+               nickName="", maskFile="", nsideForMask=128, selFunFile="",
                zBoundary=(), zRange=(), zBoundaryMpc=(), shiftSimZ=False,
                minVoidRadius=-1, fakeDensity=0.01, volumeLimited=True,
                numAPSlices=1,
@@ -114,6 +115,7 @@ class Sample:
     self.fullName = fullName
     self.nickName = nickName
     self.maskFile = maskFile
+    self.nsideForMask = nsideForMask
     self.selFunFile = selFunFile
     self.zBoundary = zBoundary 
     self.zBoundaryMpc = zBoundaryMpc
@@ -127,7 +129,7 @@ class Sample:
     self.isCombo = isCombo
     self.comboList = comboList
     self.numAPSlices = numAPSlices
-    self.zobovDir = None
+    self.outputDir = None
     self.profileBinSize = profileBinSize
     self.dataType = dataType
     self.boxLen = boxLen

python_source/backend/cosmologyTools.py

@@ -23,7 +23,7 @@
 import numpy as np
 import scipy.integrate as integrate
 import os
-from backend import *
+#from backend import *
 
 __all__=['expansion', 'comovingDistance', 'aveExpansion']
 

python_source/backend/launchers.py

@@ -54,7 +54,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
     sampleName = sample.fullName
 
     if regenerate:
-      inputParameterFlag = "inputParameter " + outputDir + 
+      inputParameterFlag = "inputParameter " + outputDir + \
                            "/zobov_slice_"+sampleName+".par"
       outputFile = outputDir + "/regenerated_zobov_slice_" + sampleName
     else:
@@ -67,14 +67,12 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
       datafile = inputDataDir+"/"+sample.dataFile
 
     if sample.maskFile == "":
-      maskFile = outputDir + "/constructed_mask.fits"
+      sample.maskFile = outputDir + "/constructed_mask.fits"
-      figureOutMask(dataFile, sample.nsideForMask, maskFile)
+      figureOutMask(datafile, sample.nsideForMask, sample.maskFile)
-    else:
-      maskFile = sample.maskFile
 
     edgeGalFile = outputDir + "/galaxy_edge_flags.txt"
     edgeMaskFile = outputDir + "/mask_edge_map.fits"
-    findEdgeGalaxies(dataFile, maskFile, edgeGalFile, edgeMaskFile,
+    findEdgeGalaxies(datafile, sample.maskFile, edgeGalFile, edgeMaskFile,
                      sample.zBoundary[0], sample.zBoundary[1], sample.omegaM,
                      useComoving)
 
@@ -94,7 +92,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
       %s
       %s
       omegaM %g
-      """ % (datafile, maskFile, outputFile,
+      """ % (datafile, sample.maskFile, outputFile,
              outputDir+"/zobov_slice_"+sampleName+".par",
              sample.zBoundary[0], sample.zBoundary[1], sample.fakeDensity,
              useComovingFlag, inputParameterFlag, sample.omegaM)

python_source/backend/surveyTools.py

@@ -24,6 +24,7 @@ import numpy as np
 import healpy as healpy
 import os
 from backend import *
+from backend.cosmologyTools import *
 
 __all__=['getSurveyProps', 'getNside', 'figureOutMask', 'findEdgeGalaxies']
 
@@ -44,6 +45,8 @@ def getSurveyProps(maskFile, zmin, zmax, selFunMin, selFunMax, portion,
     zmin = zmin * LIGHT_SPEED/100.
     zmax = zmax * LIGHT_SPEED/100. 
 
+  volume = area * (zmax**3  - zmin**3) / 3
+
   if selectionFuncFile == None:
     nbar = 1.0
 
@@ -119,7 +122,7 @@ def figureOutMask(galFile, nside, outMaskFile):
     pix = healpy.ang2pix(nside, theta, phi)
     mask[pix] = 1.
  
-  healpy.write_map(outMaskFile, mask, overwrite=True)
+  healpy.write_map(outMaskFile, mask, overwrite=True, dtype=np.dtype('float64'))
 
   return mask
 
@@ -129,12 +132,12 @@ def figureOutMask(galFile, nside, outMaskFile):
 def findEdgeGalaxies(galFile, maskFile, edgeGalFile, edgeMaskFile,
                      zmin, zmax, omegaM, useComoving=False):
 
-  if useComoving:
+  #if useComoving:
-    zmin = LIGHT_SPEED/100.*comovingDistance(zmin, Om=omegaM)
+  #  zmin = LIGHT_SPEED/100.*comovingDistance(zmin, Om=omegaM)
-    zmax = LIGHT_SPEED/100.*comovingDistance(zmax, Om=omegaM)
+  #  zmax = LIGHT_SPEED/100.*comovingDistance(zmax, Om=omegaM)
-  else:
+  #else:
-    zmin *= LIGHT_SPEED/100.
+  #  zmin *= LIGHT_SPEED/100.
-    zmax *= LIGHT_SPEED/100.
+  #  zmax *= LIGHT_SPEED/100.
 
 
   mask = healpy.read_map(maskFile)
@@ -151,32 +154,33 @@ def findEdgeGalaxies(galFile, maskFile, edgeGalFile, edgeMaskFile,
     z   = float(line[5])
 
     if useComoving:
-      z = LIGHT_SPEED/100.*comovingDistance(z, Om=omegaM)
+      z = comovingDistance(z/LIGHT_SPEED, Om=omegaM)
     else:
       z *= LIGHT_SPEED/100.
 
     phi, theta = convertAngle(RA, Dec)
 
     # check the mask edges
-    neighbors = healpy.get_all_neighbors(nside, theta, phi)
+    neighbors = healpy.get_all_neighbours(nside, theta, phi)
     isOnMaskEdge = any(p == 0 for p in neighbors)
   
     # check the redshift boundaries
     tol = 0.01 # TODO: made this user-adjustable
-    zBuffer = (zmax-zmin)*tol
+    zbuffer = (zmax-zmin)*tol
-    isOnHighZEdge = (z >= zmax-buffer)
+    isOnHighZEdge = (z >= zmax-zbuffer)
-    isOnLowZEdge  = (z <= zmin+buffer)
+    isOnLowZEdge  = (z <= zmin+zbuffer)
 
+    print("DOING %f %f %f %f\n" % (zbuffer, z, zmax, zmin) )
     if isOnMaskEdge:
-      edgeFile.write("1")
+      edgeFile.write("1\n")
     elif isOnHighZEdge:
-      edgeFile.write("2")
+      edgeFile.write("2\n")
     elif isOnLowZEdge:
-      edgeFile.write("3")
+      edgeFile.write("3\n")
     else:
-      edgeFile.write("0")
+      edgeFile.write("0\n")
 
   edgeFile.close()
-  healpy.write_map(edgeMaskFile, edgeMask, overwrite=True)
+  healpy.write_map(edgeMaskFile, edgeMask, overwrite=True, dtype=np.dtype('float64'))
 
   return

python_source/vide_pipeline/__main__.py

@@ -75,11 +75,11 @@ for sample in dataSampleList:
   sampleName = sample.fullName
 
   print(" Working with data set", sampleName, "...")
-  zobovDir = workDir+"/sample_"+sampleName+"/"
+  outputDir = workDir+"/sample_"+sampleName+"/"
-  sample.zobovDir = zobovDir
+  sample.outputDir = outputDir
 
-  if not os.access(zobovDir, os.F_OK):
+  if not os.access(outputDir, os.F_OK):
-    os.makedirs(zobovDir)
+    os.makedirs(outputDir)
 
 # ---------------------------------------------------------------------------
   if (startCatalogStage <= 1) and (endCatalogStage >= 1) and not sample.isCombo:
@@ -94,7 +94,7 @@ for sample in dataSampleList:
       GENERATE_PATH = CTOOLS_PATH+"/prepSimulation"
 
     launchPrep(sample, GENERATE_PATH, workDir=workDir, 
-               inputDataDir=inputDataDir, zobovDir=zobovDir,
+               inputDataDir=inputDataDir, outputDir=outputDir,
                figDir=figDir, logFile=logFile, useComoving=sample.useComoving,
                continueRun=continueRun, regenerate=regenerateFlag)
 
@@ -103,7 +103,7 @@ for sample in dataSampleList:
     print("  Extracting voids with ZOBOV...", end=' ')
     sys.stdout.flush()
 
-    launchZobov(sample, ZOBOV_PATH, zobovDir=zobovDir, logDir=logDir, 
+    launchZobov(sample, ZOBOV_PATH, outputDir=outputDir, logDir=logDir, 
                 continueRun=continueRun, numZobovDivisions=numZobovDivisions,
                  numZobovThreads=numZobovThreads,
                  mergingThreshold=mergingThreshold)
@@ -119,7 +119,7 @@ for sample in dataSampleList:
     PRUNE_PATH = CTOOLS_PATH+"/pruneVoids"
 
     launchPrune(sample, PRUNE_PATH, 
-                logFile=logFile, zobovDir=zobovDir, 
+                logFile=logFile, outputDir=outputDir, 
                 useComoving=sample.useComoving, continueRun=continueRun,
                 mergingThreshold=mergingThreshold,
                 boundaryTolerance=boundaryTolerance)