Merged in python3 (pull request #5)

Port to python3, large code cleanup * Fixed command line for cosmotool * Fix path * Dump command line is log file * Fix important typo * Modify paths for example * Fix path again * Use an explicit constructor * Change file to open (python 2->3) * python3 fix for xrange in periodic_kdtree.py * Fixed index for Np, numPart, numZones, numZonesTot, partID, zoneID in catalogUtil.py
2025-07-04 15:21:11 +00:00 · 2020-12-29 08:56:33 +00:00 · 2020-12-29 08:56:33 +00:00 · affb56ff48
commit affb56ff48
parent 8249256508
392 changed files with 4092 additions and 260938 deletions
--- a/python_tools/void_pipeline/main.py
+++ b/python_tools/void_pipeline/main.py
@ -0,0 +1,140 @@
+#!/usr/bin/env python
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_pipeline/__init__.py
+#   Copyright (C) 2010-2014 Guilhem Lavaux
+#   Copyright (C) 2011-2014 P. M. Sutter
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; version 2 of the License.
+# 
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License along
+#   with this program; if not, write to the Free Software Foundation, Inc.,
+#   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#+
+
+# Stage 1 : generate particles
+# Stage 2 : find voids
+# Stage 3 : prune catalog
+
+from vide.backend import *
+import vide
+import imp
+import os
+import pickle
+
+# ------------------------------------------------------------------------------
+
+if (len(sys.argv) == 1):
+  print("Usage: ./generateCatalog.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 %s!" % filename)
+    exit(-1)
+  parms = imp.load_source("name", filename)
+  regenerateFlag = False
+  globals().update(vars(parms))
+  void_path = os.path.split(vide.__file__)[0]
+  ZOBOV_PATH=f'{void_path}/bin/'
+  CTOOLS_PATH=ZOBOV_PATH
+  print(f"ZOBOV_PATH is  {ZOBOV_PATH}")
+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...", end=' ')
+    sys.stdout.flush()
+
+    logFile = logDir+"/generate_"+sampleName+".out"
+
+    if sample.dataType == "observation":
+      GENERATE_PATH = CTOOLS_PATH+"/generateFromCatalog"
+    else:
+      GENERATE_PATH = CTOOLS_PATH+"/generateMock"
+
+    launchGenerate(sample, GENERATE_PATH, workDir=workDir, 
+                   inputDataDir=inputDataDir, zobovDir=zobovDir,
+                   figDir=figDir, logFile=logFile, useComoving=sample.useComoving,
+                   continueRun=continueRun, regenerate=regenerateFlag)
+
+  # --------------------------------------------------------------------------
+  if (startCatalogStage <= 2) and (endCatalogStage >= 2) and not sample.isCombo:
+    print("  Extracting voids with ZOBOV...", end=' ')
+    sys.stdout.flush()
+
+    launchZobov(sample, ZOBOV_PATH, zobovDir=zobovDir, logDir=logDir, 
+                continueRun=continueRun, numZobovDivisions=numZobovDivisions,
+                 numZobovThreads=numZobovThreads)
+
+  # -------------------------------------------------------------------------
+  if (startCatalogStage <= 3) and (endCatalogStage >= 3) and not sample.isCombo:
+
+    print("  Taking data portions", "...", end=' ')
+    sys.stdout.flush()
+        
+    logFile = logDir+"/pruneVoids_"+sampleName+".out"
+
+    PRUNE_PATH = CTOOLS_PATH+"/pruneVoids"
+
+    launchPrune(sample, PRUNE_PATH, 
+                logFile=logFile, zobovDir=zobovDir, 
+                useComoving=sample.useComoving, continueRun=continueRun)
+
+# -------------------------------------------------------------------------
+if (startCatalogStage <= 4) and (endCatalogStage >= 4):
+
+  print("  Plotting...", end=' ')
+  sys.stdout.flush()
+
+  #for thisDataPortion in dataPortions:
+    #plotRedshiftDistribution(workDir, dataSampleList, figDir, showPlot=False, 
+    #                         dataPortion=thisDataPortion, setName=setName)
+    #plotSizeDistribution(workDir, dataSampleList, figDir, showPlot=False, 
+    #                         dataPortion=thisDataPortion, setName=setName)
+    #plotNumberDistribution(workDir, dataSampleList, figDir, showPlot=False, 
+    #                         dataPortion=thisDataPortion, setName=setName)
+    #plotVoidDistribution(workDir, dataSampleList, figDir, showPlot=False, 
+    #                         dataPortion=thisDataPortion, setName=setName)
+
+print("\n Done!")