Merge branch 'master' of https://bitbucket.org/cosmicvoids/vide_public

CMakeLists.txt

@@ -10,6 +10,7 @@ check_c_compiler_flag(-march=native SUPPORT_ARCH_NATIVE )
 
 
 find_library(MATH_LIB m)
+find_library(DL_LIB dl)
 
 macro(add_genopt _sourcelist _ggofile _basefile)
 

c_tools/CMakeLists.txt

@@ -32,7 +32,7 @@ ENDIF (CAIROMMCONFIG_INCLUDE_PATH AND CAIROMM_INCLUDE_PATH AND SIGC_INCLUDE_PATH
 
 SET(ZOB_LIBS zobovTool 
   ${COSMOTOOL_LIBRARY} ${GSL_LIBRARIES}
-  ${NETCDF_LIBRARIES})
+  ${NETCDF_LIBRARIES} ${DL_LIB})
 
 
 include_directories(

c_tools/stacking/pruneVoids.cpp

@@ -920,7 +920,22 @@ int main(int argc, char **argv) {
     }
   }
   voids.resize(iGood);
-  printf("  4th filter: rejected %d below redshift boundaries\n", numNearZ); 
+
+/*
+  iGood = 0;
+  for (iVoid = 0; iVoid < voids.size(); iVoid++) {
+    // just in case
+    if (args.isObservation_flag && 
+        voids[iVoid].redshift > args.zMax_arg) {
+      numNearZ++;
+     } else {
+      voids[iGood++] = voids[iVoid];
+    }
+  }
+  voids.resize(iGood);
+*/
+
+  printf("  4th filter: rejected %d outside redshift boundaries\n", numNearZ); 
 
   // take only top-level voids
   numAreParents = 0;
@@ -1156,11 +1171,18 @@ void outputVoids(string outputDir, string sampleName, string prefix,
              outVoid.numChildren,
              outVoid.centralDen);
 
+     double phi = atan2(outVoid.macrocenter[1]-boxLen[1]/2.,
+                        outVoid.macrocenter[0]-boxLen[0]/2.);
+     if (phi < 0) phi += 2.*M_PI;
+     double RA = phi * 180./M_PI;
+           
+     double theta = acos((outVoid.macrocenter[2]-boxLen[2]/2.) / 
+                          outVoid.redshiftInMpc);
+     double dec = (M_PI/2. - theta) * 180./M_PI;
+             
      fprintf(fpSkyPositions, "%.2f %.2f %.5f %.2f %d\n",
-             atan((outVoid.macrocenter[1]-boxLen[1]/2.) / 
+             RA,                  
-                  (outVoid.macrocenter[0]-boxLen[0]/2.)) * 180/M_PI + 180,  
+             dec,
-             asin((outVoid.macrocenter[2]-boxLen[2]/2.) / 
-                   outVoid.redshiftInMpc) * 180/M_PI,  
              outVoid.redshift,
              outVoid.radius,
              outVoid.voidID);

external/cosmotool/src/h5_readFlash.hpp

@@ -14,7 +14,8 @@ This file has been developped by P. M. Sutter.
 #include <stdio.h>
 #include <stdlib.h>
 #include <stddef.h>
-#include <string.h>
+#include <string>
+#include <cstring>
 #include "hdf5_flash.h"
 #include "H5Cpp.h"
 

external/external_build.cmake

@@ -27,7 +27,7 @@ IF(INTERNAL_GENGETOPT)
 ENDIF(INTERNAL_GENGETOPT)
 
 IF(INTERNAL_HDF5)
-  SET(HDF5_URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.9/src/hdf5-1.8.9.tar.gz" CACHE STRING "URL to download HDF5 from")
+  SET(HDF5_URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.15/src/hdf5-1.8.15.tar.gz" CACHE STRING "URL to download HDF5 from")
   mark_as_advanced(HDF5_URL)
 ENDIF(INTERNAL_HDF5)
 
@@ -121,6 +121,7 @@ else(INTERNAL_HDF5)
   find_library(HDF5HL_LIBRARY hdf5_hl)
 endif (INTERNAL_HDF5)
 SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${HDF5_INCLUDE_PATH}")
+SET(CONFIGURE_LIBS_FLAGS "${DL_LIB}")
 mark_as_advanced(HDF5_INCLUDE_PATH HDF5_LIBRARY HDF5_CPP_LIBRARY HDF5HL_LIBRARY HDF5HL_CPP_LIBRARY)
 
 ###############
@@ -133,7 +134,7 @@ if (INTERNAL_NETCDF)
   SET(NETCDF_BIN_DIR ${CMAKE_BINARY_DIR}/ext_build/netcdf)
   SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${NETCDF_BIN_DIR}/include")
   SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${NETCDF_BIN_DIR}/lib")
-  SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_LDFLAGS})
+  SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_LDFLAGS} LIBS=${CONFIGURE_LIBS_FLAGS})
   ExternalProject_Add(netcdf
     DEPENDS ${hdf5_built}
     PREFIX ${BUILD_PREFIX}/netcdf-prefix
@@ -239,7 +240,7 @@ ExternalProject_Add(cosmotool
 	-DGSLCBLAS_LIBRARY=${GSLCBLAS_LIBRARY}
 	-DNETCDF_LIBRARY=${NETCDF_LIBRARY}
 	-DNETCDFCPP_LIBRARY=${NETCDFCPP_LIBRARY}
-        -DENABLE_SHARP=OFF
+  -DENABLE_SHARP=OFF
 )
 SET(COSMOTOOL_LIBRARY ${CMAKE_BINARY_DIR}/ext_build/cosmotool/lib/libCosmoTool.a)
 set(COSMOTOOL_INCLUDE_PATH ${CMAKE_BINARY_DIR}/ext_build/cosmotool/include)

pipeline/datasets/example_observation.py

@@ -33,21 +33,17 @@ continueRun = False
 startCatalogStage = 1
 endCatalogStage   = 3
 
-# a global name to give 
-#catalogName = "lcdm"
-
-
 # directory for input data files
-inputDataDir = os.getenv("HOME")+"/workspace/Voids/catalogs/nyuvagc/"
+inputDataDir = os.getenv("PWD")+"/../examples/"
 
 # void catalog output directory
-workDir      = os.getenv("HOME")+"/workspace/Voids/sdss_dr7LCDM/"
+workDir = os.getenv("PWD")+"/../examples/example_observation/"
 
 # output directory for log files
-logDir = os.getenv("PWD")+"/../logs/sdss_dr7LCDM"
+logDir = os.getenv("PWD")+"/../logs/example_observation/"
 
 # output directory for figures
-figDir = os.getenv("PWD")+"/../figs/sdss_dr7LCDM"
+figDir = os.getenv("PWD")+"/../figs/example_observation/"
 
 # you need to set these manually: point to ZOBOV and C_TOOLS in VIDE directory
 ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
@@ -68,38 +64,39 @@ dataSampleList = []
 # define your volume-limited samples
 newSample = Sample(
                    # path to galaxy file is inputDataDir+dataFile
-                   dataFile = "filename.dat"
+                   dataFile = "example_observation.dat",
 
                    # full name for this sample
-                   fullName = "lss.dr72dim1.dat",
+                   fullName = "example_observation",
 
                    # a convenient nickname
-                   nickName = "dim1",
+                   nickName = "exobs",
 
                    # don't change this
                    dataType = "observation",
 
-                   # assume volume-limites?
+                   # assume sample is volume-limited?
                    volumeLimited = True,
 
                    # HEALpix mask file
-                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   maskFile = inputDataDir+"/example_observation_mask.fits",
 
                    # radial selection function (if not volume limited)
                    selFunFile = None,
 
                    # max and min redshifts of galaxies in your sample
-                   zBoundary = (0.0, 0.05),
+                   zBoundary = (0.0, 0.15),
 
                    # max and min redshifts where you want to find voids
-                   zRange = (0.0, 0.05),
+                   zRange = (0.1, 0.15),
  
-                   # leave this at -1 for mean particle separation, or 
+                   # leave this at -1 for mean particle separation, 
-                   # specify your own in Mpc/h
+                   # or specify your own in Mpc/h
                    minVoidRadius = -1,
 
                    # density of mock particles in cubic Mpc/h
-                   fakeDensity = 0.01,
+                   # (make this as high as you can afford)
+                   fakeDensity = 0.05,
 
                    )
 dataSampleList.append(newSample)

pipeline/datasets/example_simulation.py

@@ -33,26 +33,26 @@ continueRun = False
 startCatalogStage = 1
 endCatalogStage   = 3
 
-# directory for the input simulation/observational particle files
+# directory for the input simulation files
-catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/mergertree1024/"
+catalogDir = os.getenv("PWD")+"/../examples/"
 
 # void catalog output directory
-voidOutputDir = os.getenv("HOME")+"/workspace/Voids/sim/"
+voidOutputDir = os.getenv("PWD")+"/../examples/example_simulation/"
 
 # output directory for log files
-logDir = os.getenv("PWD")+"/../logs/sim/"
+logDir = os.getenv("PWD")+"/../logs/example_simulation/"
 
 # output directory for figures
-figDir = os.getenv("PWD")+"/../figs/sim/"
+figDir = os.getenv("PWD")+"/../figs/example_simulation/"
 
 # where to place the pipeline scripts
-scriptDir = os.getenv("PWD")+"/sim/"
+scriptDir = os.getenv("PWD")+"/example_simulation/"
 
 # don't change
 dataType = "simulation"
 
 # available formats for simulation: gadget, sdf, multidark
-dataFormat = "sdf"
+dataFormat = "multidark"
 
 # units of position in Mpc/h
 dataUnit = 1
@@ -84,19 +84,19 @@ numSubvolumes = 1
 # Particles
 
 # common filename of particle files
-particleFileBase = "mf_4s_1G_1k_NNNNN"
+particleFileBase = "example_simulation_NNNN.dat"
 
 # this flag will be replaced by values in fileNums list below
-particleFileDummy = 'NNNNN'
+particleFileDummy = 'NNNN'
 
 # list of file numbers for the particle files
-fileNums = ["1.000"]
+fileNums = ["z0.0"]
 
 # redshift of each file in the above fileNums list
 redshifts = ["0.0"]
 
 # list of desired subsamples - these are in unts of h Mpc^-3!
-subSamples = [1.0, 0.5]
+subSamples = [1.0]
 
 # if True, do the subsampling in preparation (available for sdf and multidark)
 doSubSamplingInPrep = False
@@ -112,14 +112,17 @@ shiftSimZ = False
 # Halos
 
 # common filename of halo files, leave blank to ignore halos
-haloFileBase = "mf_4s_1G_1k_bgc2_NNNNN.sdf"
+haloFileBase = ""
+#haloFileBase = "mf_4s_1G_1k_bgc2_NNNNN.sdf"
 
 # this flag will be replaced by values in fileNums list above
-haloFileDummy = 'NNNNN'
+haloFileDummy = ''
+#haloFileDummy = 'NNNNN'
 
 # minimum halo mass cuts to apply for the halo catalog
 #   use "none" to get all halos
-minHaloMasses = ["none", 1.2e13]
+minHaloMasses = []
+#minHaloMasses = ["none", 1.2e13]
 
 # locations of data in the halo catalog
 haloFileMCol  = 6    # mass
@@ -147,14 +150,14 @@ hubble = 0.6962 # h_0
 
 # each of the HOD sets will be applied to each halo catalog defined above
 hodParmList = [
-  {'name'       : "LowRes", #BOSS: Manera et al. 2012, eq. 26
+  #{'name'       : "LowRes", #BOSS: Manera et al. 2012, eq. 26
-   'Mmin'       : 0.0,
+  # 'Mmin'       : 0.0,
-   'M1'         : 1.e14,
+  # 'M1'         : 1.e14,
-   'sigma_logM' : 0.596,
+  # 'sigma_logM' : 0.596,
-   'alpha'      : 1.0127,
+  # 'alpha'      : 1.0127,
-   'Mcut'       : 1.19399e13,
+  # 'Mcut'       : 1.19399e13,
-   'galDens'    : 0.0002,
+  # 'galDens'    : 0.0002,
-  },
+  #},
 ]
 
 # END CONFIGURATION

python_tools/void_python_tools/backend/launchers.py

@@ -37,7 +37,7 @@ from   netCDF4 import Dataset
 from void_python_tools.backend.classes import *
 import pickle
 import void_python_tools.apTools as vp
-import scipy.interpolate
+import scipy.interpolate as interpolate
 
 NetCDFFile = Dataset
 ncFloat = 'f8' # Double precision
@@ -374,7 +374,7 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
       File.close()
 
       # load redshifts
-      partFile = sampleDir+"/zobov_slice_"+sample.fullName
+      partFile = zobovDir+"/zobov_slice_"+sample.fullName
       File = file(partFile)
       chk = np.fromfile(File, dtype=np.int32,count=1)
       Np = np.fromfile(File, dtype=np.int32,count=1)
@@ -414,16 +414,20 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
       # build selection function interpolation
       selfuncData = np.genfromtxt(sample.selFunFile)
       selfunc = interpolate.interp1d(selfuncData[:,0], selfuncData[:,1],
-                                     kind='cubic')
+                                     kind='cubic', bounds_error=False,
+                                     fill_value=1.0)
       # re-weight and write
-      vols *= selfunc(redshifts)
+       ## TEST
+      #redshifts /= 10000.
+      for i in xrange(len(vols)):
+        vols[i] *= selfunc(redshifts[i])
 
-      volFile = zobovDir+"/vol_"+sampleName+".dat"
+      volFile = zobovDir+"/vol_weighted_"+sampleName+".dat"
       File = file(volFile, 'w')
-      chk.astype('np.int32').tofile(File)
+      numPartTot.astype(np.int32).tofile(File)
-      vols.astype('np.float32').tofile(File)
+      vols.astype(np.float32).tofile(File)
 
-      volFileToUse = zobovDir+"/vol_weighted"+sampleName+".dat"
+      volFileToUse = zobovDir+"/vol_weighted_"+sampleName+".dat"
     else:
       volFileToUse = zobovDir+"/vol_"+sampleName+".dat"
 

zobov/CMakeLists.txt

@@ -3,8 +3,8 @@ add_executable(voz1b1 voz1b1.c readfiles.c vozutil.c voz.h)
 target_link_libraries(voz1b1 ${QHULL_LIBRARY} ${MATH_LIB})
 
 
-add_executable(jozov jozov.c findrtop.c)
+#add_executable(jozov jozov.c findrtop.c)
-target_link_libraries(jozov ${MATH_LIB})
+#target_link_libraries(jozov ${MATH_LIB})
 
 add_executable(vozinit vozinit.c readfiles.c)
 target_link_libraries(vozinit ${MATH_LIB})

zobov/vozinit.c

@@ -173,10 +173,14 @@ int main(int argc, char *argv[]) {
   for (b[0]=0;b[0]<numdiv; b[0]++) {
    for (b[1] = 0; b[1] < numdiv; b[1]++) {
     for (b[2] = 0; b[2] < numdiv; b[2]++) {
+      //fprintf(scr,"%s/../c_tools/zobov2/voz1b1/voz1b1_2 %s %f %f %f %f %s %d %d %d %d %d %d %s&\n",
+     //   vobozPath,
+     //   posfile,border,boxsize,boxsize,boxsize,suffix,numdiv,numdiv, numdiv,b[0],b[1],b[2],
+     //   outDir);
       fprintf(scr,"%s/voz1b1 %s %f %f %s %d %d %d %d %s&\n",
-        vobozPath,
+              vobozPath,
-	      posfile,border,boxsize,suffix,numdiv,b[0],b[1],b[2], 
+              posfile,border,boxsize,suffix,numdiv,b[0],b[1],b[2], 
-        outDir);
+              outDir);
       p++;
       if ((p == numThreads)) { fprintf(scr, "wait\n"); p = 0; }
     }