From 0ef211a1ccb450ddd422a6e62dc72b49bd770689 Mon Sep 17 00:00:00 2001
From: "P.M. Sutter" <sutter@iap.fr>
Date: Fri, 16 Nov 2012 09:48:02 -0600
Subject: [PATCH] some small bug fixes, also prepared prunveVoids to
 potentially remove voids based on density contrast criteria

---
 c_tools/stacking/pruneVoids.cpp                   |  9 ++++++++-
 pipeline/prepareCatalogs.py                       |  1 +
 plotting/plotCompareDist.py                       | 15 +++++++++++----
 .../void_python_tools/backend/launchers.py        |  5 +++--
 4 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/c_tools/stacking/pruneVoids.cpp b/c_tools/stacking/pruneVoids.cpp
index 1390f3c..466151a 100644
--- a/c_tools/stacking/pruneVoids.cpp
+++ b/c_tools/stacking/pruneVoids.cpp
@@ -447,6 +447,13 @@ int main(int argc, char **argv) {
   }
 
   for (iVoid = 0; iVoid < numVoids; iVoid++) {
+// TEST
+    //if (voids[iVoid].densCon > 1.5) {
+    //  voids[iVoid].accepted = 0;
+    //}
+// END TEST
+
+
     if (strcmp(args_info.dataPortion_arg, "edge")  == 0 &&
         tolerance*voids[iVoid].maxRadius < voids[iVoid].nearestMock) {
       voids[iVoid].accepted = 0;
@@ -582,6 +589,6 @@ int main(int argc, char **argv) {
   clock1 = clock();
 
 
-  printf("Done!\n");
+  printf("Done!");
   return 0;
 } // end main
diff --git a/pipeline/prepareCatalogs.py b/pipeline/prepareCatalogs.py
index 9ef7697..17c9dc5 100755
--- a/pipeline/prepareCatalogs.py
+++ b/pipeline/prepareCatalogs.py
@@ -480,6 +480,7 @@ if args.hod or args.all:
   for (iRedshift, redshift) in enumerate(redshifts):
     print "  z = ", redshift
 
+    # these parameters come from Manera et al 2012, eq. 26
     parFileName = "./hod.par"
     parFile = open(parFileName, 'w')
     haloFile = catalogDir+"/mdr1_halos_z"+fileNums[iRedshift]
diff --git a/plotting/plotCompareDist.py b/plotting/plotCompareDist.py
index b2c47bd..b837173 100755
--- a/plotting/plotCompareDist.py
+++ b/plotting/plotCompareDist.py
@@ -17,15 +17,20 @@ import argparse
 workDir = "/home/psutter2/workspace/Voids/"
 figDir  = "./figs"
 
-sampleDirList = [ "multidark/md_halos/sample_md_halos_z0.03_d00/",
-                  "multidark/md_ss0.1/sample_md_ss0.1_z0.03_d00/",
-                  "multidark/md_hod_dr9mid/sample_md_hod_dr9mid_z0.03_d00/",
+sampleDirList = [ "multidark/md_ss0.1_pv/sample_md_ss0.1_pv_z0.56_d00/",
+                  "multidark/md_halos_pv/sample_md_halos_pv_z0.56_d00/",
+                  "random/ran_ss0.0004/sample_ran_ss0.0004_z0.56_d00/",
+                  "random/ran_ss0.1/sample_ran_ss0.1_z0.56_d00/",
+                  "multidark/md_hod_dr9mid_pv/sample_md_hod_dr9mid_pv_z0.56_d00/",
+                  "multidark/md_ss0.0004_pv/sample_md_ss0.0004_pv_z0.56_d00/",
                   "sdss_dr9/sample_lss.dr9cmassmid.dat/" ]
 
 plotNameBase = "compdist"
 
 dataPortion = "central"
 
+obsFudgeFactor = .66 # what fraction of the volume are we *reall* capturing?
+
 parser = argparse.ArgumentParser(description='Plot.')
 parser.add_argument('--show', dest='showPlot', action='store_const',
                    const=True, default=False,
@@ -47,6 +52,7 @@ plt.clf()
 plt.xlabel("Void Radius (Mpc/h)")
 plt.ylabel(r"N > R [$h^3$ Gpc$^{-3}$]")
 plt.yscale('log')
+plt.xlim(xmax=80.)
 
 plotName = plotNameBase
 
@@ -60,6 +66,7 @@ for (iSample,sample) in enumerate(dataSampleList):
                                sample.zBoundary[0], sample.zBoundary[1], 
                                sample.zRange[0], sample.zRange[1], "all",
                                selectionFuncFile=sample.selFunFile)[0]
+    boxVol *= obsFudgeFactor
   else:
     boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1] - 
                                           sample.zBoundaryMpc[0])
@@ -84,7 +91,7 @@ for (iSample,sample) in enumerate(dataSampleList):
            label=lineTitle, color=colorList[iSample],
            linewidth=linewidth)
 
-plt.legend(title = "Samples", loc = "upper right")
+plt.legend(title = "Samples", loc = "upper right", prop={'size':8})
 #plt.title(plotTitle)
 
 plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py
index e15e8fb..be2de94 100755
--- a/python_tools/void_python_tools/backend/launchers.py
+++ b/python_tools/void_python_tools/backend/launchers.py
@@ -245,7 +245,7 @@ def launchPrune(sample, binPath, thisDataPortion=None,
     totalPart = open(zobovDir+"/total_particles.txt", "r").read()
     maxDen = 0.2*float(mockIndex)/float(totalPart)
     observationLine = " --isObservation"
-    periodicLine = "--periodic=''"
+    periodicLine = " --periodic=''"
   else:
     mockIndex = -1
     maxDen = 0.2
@@ -297,7 +297,8 @@ def launchPrune(sample, binPath, thisDataPortion=None,
     cmd += " >& " + logFile
     os.system(cmd)
 
-    if jobSuccessful(logFile, "NetCDF: Not a valid ID\n") or jobSuccessful(logFile, "Done!") or jobSuccessful(logFile, ""):
+    if jobSuccessful(logFile, "NetCDF: Not a valid ID\n") or \
+       jobSuccessful(logFile, "Done!"):
       print "done"
     else:
       print "FAILED!"