more informative pipeline defaults.py file to describe how to handle particle files; option to do relative or absolute subsampling

python_tools/pipeline_source/defaults.py

@@ -32,6 +32,9 @@ endAPStage = 5
 continueRun = True
 dataPortions = ["central"]
 
+# auto for AP analysis, "fixed" for catalog comparison
+stackMode = "fixed"
+
 # directory for the input simulation/observational particle files
 catalogDir = os.getenv("HOME")+"/workspace/Voids/catalog/"
 
@@ -60,11 +63,16 @@ useLightCone = False
 doPecVel = False
 
 # common filename of particle files
+# use a placeholder (such as NNNNN as shown below) to select the different
+#   filenames. For example, if we have partFile01, partFile02, etc., 
+#   then particleFileBase = 'partFileNN'
+#        particleFileDummy = 'NN'
+#        fileNums = ["01", "02"] 
 particleFileBase = "mf_4s_1G_512_NNNNN"
 particleFileDummy = 'NNNNN'
 
 # list of file numbers for the particle files
-# to get particle file name, we take particleFileBase+fileNum
+# to get particle file name, we replace particleFileDummy with fileNum
 fileNums = ["0.667", "0.500"]
 
 # redshift of each file in the above list
@@ -80,9 +88,15 @@ numSubvolumes = 1
 # prefix to give all outputs
 prefix = "mt_"
 
-# list of desired subsamples - these are in unts of h Mpc^-3!
+# list of desired subsamples - see subSamplingMode parameter
 subSamples = [1.0]
+
 doSubSampling = True # do the subsampling in preparation script?
+                     # if False, generateMock will do the subsampling
+
+# if 'absolute', subSamples are given in particles per cubic Mpc/h
+# if 'relative', subSamples are given as a fraction of input particles
+subSampleMode = "absolute" 
 
 # common filename of halo files, leave blank to ignore halos
 haloFileBase = "mf_4s_1G_512_bgc2_NNNNN.sdf"

python_tools/pipeline_source/prepareCatalogs.in.py

@@ -87,13 +87,22 @@ def getNickName(sampleName):
   
   if "ss" in splitName[1]:
     nickName = "Subsample = " + splitName[1].replace("ss","")
-    nickName += ", z = " + splitName[2].replace("z","")
+    if "pv" in splitName[2]: 
+      nickName += ", z = " + splitName[3].replace("z","") + ", Pev.Vel."
+    else:
+      nickName += ", z = " + splitName[2].replace("z","")
   elif "hod" in splitName[1]:
     nickName = "HOD = " + splitName[2]
-    nickName += ", z = " + splitName[3].replace("z","")
+    if "pv" in splitName[3]: 
+      nickName += ", z = " + splitName[4].replace("z","") + ", Pec.Vel."
+    else:
+      nickName += ", z = " + splitName[3].replace("z","")
   elif "halos" in splitName[1]:
     nickName = "Halos, min mass = " + splitName[2].replace("min","")
-    nickName += ", z = " + splitName[3].replace("z","")
+    if "pv" in splitName[3]: 
+      nickName += ", z = " + splitName[4].replace("z","") + ", Pec.Vel."
+    else:
+      nickName += ", z = " + splitName[3].replace("z","")
   else:
     nickName = sampleName
 
@@ -185,6 +194,12 @@ newSample = Sample(dataFile = "{dataFile}",
                    useLightCone = {useLightCone},
                    subsample = "{subsample}")
 dataSampleList.append(newSample)
+  """
+
+  if stackMode == "fixed":
+    stackInfo = """
+# {zMin}, {zMax}, {minRadius}
+newSample.addStack(0.0, 5.0, 5 , 10, False, False)
 newSample.addStack(0.0, 5.0, 10, 15, False, False)
 newSample.addStack(0.0, 5.0, 15, 20, False, False)
 newSample.addStack(0.0, 5.0, 20, 25, False, False)
@@ -195,13 +210,22 @@ newSample.addStack(0.0, 5.0, 60, 65, False, False)
 newSample.addStack(0.0, 5.0, 70, 75, False, False)
 newSample.addStack(0.0, 5.0, 80, 85, False, False)
 newSample.addStack(0.0, 5.0, 90, 95, False, False)
-#newSample.addStack({zMin}, {zMax}, 2*{minRadius}  , 2*{minRadius}+2, True, False)
-#newSample.addStack({zMin}, {zMax}, 2*{minRadius}  , 2*{minRadius}+4, True, False)
-#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False)
-#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False)
-#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False)
-#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False)
+  """
+
+  elif stackMode == "auto":
+    stackInfo = """
+newSample.addStack({zMin}, {zMax}, 2*{minRadius}  , 2*{minRadius}+2, True, False)
+newSample.addStack({zMin}, {zMax}, 2*{minRadius}  , 2*{minRadius}+4, True, False)
+newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False)
+newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False)
+newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False)
+newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False)
                """
+  else:
+    stackInfo = """
+# {zMin}, {zMax}, {minRadius}
+"""
+
   for (iFile, redshift) in enumerate(redshifts):
     fileNum = fileNums[iFile]
 
@@ -271,6 +295,11 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False)
                                          useLightCone=useLightCone,
                                          subsample=str(subsample).strip('[]')))
 
+          scriptFile.write(stackInfo.format(zMin=sliceMin,
+                                           zMax=sliceMax,
+                                           minRadius=minRadius))
+
+
   scriptFile.close()
   return
 
@@ -293,7 +322,13 @@ for iSubSample in xrange(len(subSamples)):
 
   keepFractionList = []
   for subSample in subSampleList:
-    keepFractionList.append(float(subSample) / baseResolution)
+    if subSampleMode == 'absolute':
+      keepFractionList.append(float(subSample) / baseResolution)
+    elif subSampleMode == 'relative':
+      keepFractionList.append(float(subSample))
+    else:
+      print "Unrecognized subSampleMode = ", subSampleMode
+      exit(-1)
   thisSubSample = subSamples[iSubSample]
   maxKeep = keepFractionList[-1] * numPart
   minRadius = int(np.ceil(lbox/maxKeep**(1./3)))