From ccc469aa6e925cab074e1a12388d4c389263e5cf Mon Sep 17 00:00:00 2001
From: Guilhem Lavaux <guilhem.lavaux@iap.fr>
Date: Thu, 25 Feb 2021 14:14:33 +0200
Subject: [PATCH] Add an option to change the merging threshold

---
 python_tools/vide/backend/launchers.py               | 12 ++++++------
 python_tools/void_pipeline/__main__.py               |  4 ++--
 .../void_pipeline/datasets/example_observation.py    |  5 +++++
 .../void_pipeline/datasets/example_simulation.py     |  5 +++++
 4 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/python_tools/vide/backend/launchers.py b/python_tools/vide/backend/launchers.py
index 84b0681..1d0502c 100644
--- a/python_tools/vide/backend/launchers.py
+++ b/python_tools/vide/backend/launchers.py
@@ -323,7 +323,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
 
 # -----------------------------------------------------------------------------
 def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
-                 numZobovDivisions=None, numZobovThreads=None):
+                 numZobovDivisions=None, numZobovThreads=None, mergingThreshold=0.2):
 
   sampleName = sample.fullName
 
@@ -339,10 +339,10 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
   if sample.dataType == "observation":
     maskIndex = open(zobovDir+"/mask_index.txt", "r").read()
     totalPart = open(zobovDir+"/total_particles.txt", "r").read()
-    maxDen = 0.2*float(maskIndex)/float(totalPart)
+    maxDen = mergingThreshold*float(maskIndex)/float(totalPart)
   else:
     maskIndex = -1
-    maxDen = 0.2
+    maxDen = mergingThreshold
     if numZobovDivisions == 1:
       print("  WARNING! You are using a single ZOBOV division with a simulation. Periodic boundaries will not be respected!")
 
@@ -466,7 +466,7 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
 # -----------------------------------------------------------------------------
 def launchPrune(sample, binPath,
                 summaryFile=None, logFile=None, zobovDir=None,
-                continueRun=None, useComoving=False):
+                continueRun=None, useComoving=False, mergingThreshold=0.2):
 
   sampleName = sample.fullName
 
@@ -477,12 +477,12 @@ def launchPrune(sample, binPath,
   if sample.dataType == "observation":
     mockIndex = open(zobovDir+"/mask_index.txt", "r").read()
     totalPart = open(zobovDir+"/total_particles.txt", "r").read()
-    maxDen = 0.2*float(mockIndex)/float(totalPart)
+    maxDen = mergingThreshold*float(mockIndex)/float(totalPart)
     observationLine = " --isObservation"
     #periodicLine = " --periodic=''"
   else:
     mockIndex = -1
-    maxDen = 0.2
+    maxDen = mergingThreshold
     observationLine = ""
 
   periodicLine = " --periodic='" + getPeriodic(sample) + "'"
diff --git a/python_tools/void_pipeline/__main__.py b/python_tools/void_pipeline/__main__.py
index af3797c..304a5db 100644
--- a/python_tools/void_pipeline/__main__.py
+++ b/python_tools/void_pipeline/__main__.py
@@ -105,7 +105,7 @@ for sample in dataSampleList:
 
     launchZobov(sample, ZOBOV_PATH, zobovDir=zobovDir, logDir=logDir, 
                 continueRun=continueRun, numZobovDivisions=numZobovDivisions,
-                 numZobovThreads=numZobovThreads)
+                 numZobovThreads=numZobovThreads, mergingThreshold=mergingThreshold)
 
   # -------------------------------------------------------------------------
   if (startCatalogStage <= 3) and (endCatalogStage >= 3) and not sample.isCombo:
@@ -119,7 +119,7 @@ for sample in dataSampleList:
 
     launchPrune(sample, PRUNE_PATH, 
                 logFile=logFile, zobovDir=zobovDir, 
-                useComoving=sample.useComoving, continueRun=continueRun)
+                useComoving=sample.useComoving, continueRun=continueRun, mergingThreshold=mergingThreshold)
 
 # -------------------------------------------------------------------------
 if (startCatalogStage <= 4) and (endCatalogStage >= 4):
diff --git a/python_tools/void_pipeline/datasets/example_observation.py b/python_tools/void_pipeline/datasets/example_observation.py
index 81f2ca3..b6dec36 100644
--- a/python_tools/void_pipeline/datasets/example_observation.py
+++ b/python_tools/void_pipeline/datasets/example_observation.py
@@ -54,6 +54,11 @@ numZobovThreads = 2
 # optimization: number of subdivisions of the box
 numZobovDivisions = 2
 
+# Maximum density for merging voids
+#   0 (equivalent to infinitely large value) -> Merge everything (no threshold)
+#   1e-9 (or smaller != 0) -> Do not merge anything
+mergingThreshold = 1e-9
+
 # don't change this
 dataSampleList = []
 
diff --git a/python_tools/void_pipeline/datasets/example_simulation.py b/python_tools/void_pipeline/datasets/example_simulation.py
index 27ddfda..0efcf23 100644
--- a/python_tools/void_pipeline/datasets/example_simulation.py
+++ b/python_tools/void_pipeline/datasets/example_simulation.py
@@ -71,6 +71,11 @@ numZobovThreads = 2
 # optimization: number of subdivisions of the box
 numZobovDivisions = 2
 
+# maximum density for merging voids
+#   0 (equivalent to infinitely large value) -> Merge everything (no threshold)
+#   1e-9 (or smaller != 0) -> Do not merge anything
+mergingThreshold = 1e-9
+
 # prefix to give all outputs
 prefix = "sim_"