Slight re-organization of C/C++ tools. Significant modifications to support observational data. Python and pipeline scripts added

pipeline/generateCatalog.py

@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+
+# does full void analysis. Also generates 2d/1d stacked plots and hubble diagram
+
+from void_python_tools.backend import *
+from void_python_tools.plotting import *
+import imp
+
+# ------------------------------------------------------------------------------
+
+def my_import(name):
+    mod = __import__(name)
+    components = name.split('.')
+    for comp in components[1:]:
+        mod = getattr(mod, comp)
+    return mod
+
+if (len(sys.argv) == 0):
+  print "Usage: ./anylyzeVoids.py parameter_file.py"
+  exit(-1)
+
+if (len(sys.argv) > 1):
+  filename = sys.argv[1]
+  print " Loading parameters from", filename
+  if not os.access(filename, os.F_OK):
+    print "  Cannot find parameter file!"
+    exit(-1)
+  #parms = __import__(filename[:-3], globals(), locals(), ['*'])
+  parms = imp.load_source("name", filename)
+  globals().update(vars(parms))
+else:
+  print " Using default parameters"
+
+# ------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
+
+if not os.access(logDir, os.F_OK):
+  os.makedirs(logDir)
+
+if not os.access(figDir, os.F_OK):
+  os.makedirs(figDir)
+
+if not continueRun:
+  print " Cleaning out log files..."
+
+  if startCatalogStage <= 1 and glob.glob(logDir+"/generate*") != []:
+    os.system("rm %s/generate*" % logDir)
+  if startCatalogStage <= 2 and glob.glob(logDir+"/zobov*") != []:
+    os.system("rm %s/zobov*" % logDir)
+  if startCatalogStage <= 3 and glob.glob(logDir+"/prune*") != []:
+    os.system("rm %s/prune*" % logDir)
+
+for sample in dataSampleList:
+
+  sampleName = sample.fullName
+
+  print " Working with data set", sampleName, "..."
+  zobovDir = workDir+"/sample_"+sampleName+"/"
+  sample.zobovDir = zobovDir
+
+  if not os.access(zobovDir, os.F_OK):
+    os.makedirs(zobovDir)
+
+# ---------------------------------------------------------------------------
+  if (startCatalogStage <= 1) and (endCatalogStage >= 1) and not sample.isCombo:
+    print "  Extracting tracers from catalog...",
+    sys.stdout.flush()
+
+    logFile = logDir+"/generate_"+sampleName+".out"
+
+    if sample.dataType == "observation":
+      GENERATE_PATH = CTOOLS_PATH+"/mock/generateFromCatalog"
+    else:
+      GENERATE_PATH = CTOOLS_PATH+"/mock/generateMock"
+
+    launchGenerate(sample, GENERATE_PATH, workDir=workDir, 
+                   inputDataDir=inputDataDir, zobovDir=zobovDir,
+                   figDir=figDir, logFile=logFile, useLCDM=useLCDM,
+                   continueRun=continueRun)
+
+  # --------------------------------------------------------------------------
+  if (startCatalogStage <= 2) and (endCatalogStage >= 2) and not sample.isCombo:
+    print "  Extracting voids with ZOBOV...",
+    sys.stdout.flush()
+
+    launchZobov(sample, ZOBOV_PATH, zobovDir=zobovDir, logDir=logDir, 
+                continueRun=continueRun)
+
+  # -------------------------------------------------------------------------
+  if (startCatalogStage <= 3) and (endCatalogStage >= 3) and not sample.isCombo:
+
+    for thisDataPortion in dataPortions:
+      print "  Taking data portion:", thisDataPortion, "...",
+      sys.stdout.flush()
+        
+      logFile = logDir+"/pruneVoids_"+sampleName+"_"+\
+                thisDataPortion+".out"
+
+      PRUNE_PATH = CTOOLS_PATH+"/stacking/pruneVoids"
+
+      launchPrune(sample, PRUNE_PATH, thisDataPortion=thisDataPortion, 
+                  logFile=logFile, zobovDir=zobovDir, continueRun=continueRun)
+
+# -------------------------------------------------------------------------
+if (startCatalogStage <= 4) and (endCatalogStage >= 4):
+
+  print "  Plotting...",
+  sys.stdout.flush()
+
+  for thisDataPortion in dataPortions:
+    plotNumberCounts(workDir, dataSampleList, figDir, showPlot=True, dataPortion=thisDataPortion, setName=setName)
+
+print "\n Done!"