Merge branch 'release/2.x' into guilhem/test_large_mask

README.md

@@ -56,6 +56,26 @@ python3 -m void_pipeline  your_config_file.py
 The VIDE tools are all packaged in the `vide` package. 
 
 
+Running with simulation
+-----------------------
+
+!! Temporary measure !!
+
+After build the vide package and installing it with `python3 setup.py install` (for example), it is possible to find the
+script to build the pipeline for simulations in `build/temp.[SOMETHING]/pipeline/prepareInputs.py`. Just copy that script where
+you want the analysis and execute it directly with the parameter file as an argument.
+
+For example:
+```
+mkdir $HOME/my_vide_test
+cp build/temp.[SOMETHING]/pipeline/prepareInputs.py $HOME/my_vide_test
+cp python_tools/void_pipeline/datasets/example_simulation.py $HOME/my_vide_test
+mkdir $HOME/my_vide_test/examples
+cp examples/example_simulation_z0.0.dat $HOME/my_vide_test/examples
+cd $HOME/my_vide_test
+python3 prepareInputs.py --all --parm example_simulation.py
+python3 -m void_pipeline example_simulation/sim_ss1.0.py
+```
 
 Notes for CONDA
 ---------------

c_tools/mock/generateMock.cpp

@@ -455,7 +455,7 @@ void saveBox(SimuData *&boxed, const std::string& outbox, generateMock_info& arg
 
   v.putVar({0}, {size_t(boxed->NumPart)}, particle_id);
   v2.putVar({0}, {size_t(boxed->NumPart)}, expansion_fac);  
-  v3.putVar({0}, {size_t(boxed->NumPart)}, snapshot_split);
+  v3.putVar({0}, {size_t(num_snapshots)}, snapshot_split);
   if (uniqueID != 0)
     {
       NcVar v4 = f.addVar("unique_ids_lsb", ncInt, NumPart_dim);

c_tools/stacking/pruneVoids.cpp

@@ -170,8 +170,8 @@ int main(int argc, char **argv) {
   double result, error;
   size_t nEval;
 
-  int iZ, numZ = 4000;
-  double maxZ = 5.0, z, *dL, *redshifts;
+  int iZ, numZ = 8000;
+  double maxZ = 10.0, z, *dL, *redshifts;
   dL = (double *) malloc(numZ * sizeof(double));  
   redshifts = (double *) malloc(numZ * sizeof(double));
   for (iZ = 0; iZ < numZ; iZ++) {
@@ -181,7 +181,7 @@ int main(int argc, char **argv) {
     //printf("HERE %e %e\n", z, dL[iZ]);
     redshifts[iZ] = z;
   }
-  gsl_interp *interp = gsl_interp_alloc(gsl_interp_linear, 4000);
+  gsl_interp *interp = gsl_interp_alloc(gsl_interp_linear, numZ);
   gsl_interp_init(interp, dL, redshifts, numZ);
   gsl_interp_accel *acc = gsl_interp_accel_alloc();
 

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) + "'"

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):

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 = []
 

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_"