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Merge branch 'master' of bitbucket.org:cosmicvoids/void_identification

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Guilhem Lavaux 2013-03-03 16:26:09 +01:00
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31
README
View file

@ -1,5 +1,36 @@
\ / / |-\ -----
\ / | | \ |
\ / / | | |--
\ / | | / |
\/ / |-/ -----
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
This is VIDE. The Void IDEntifier pipeline.
License/Copyright information
-----------------------------
Copyright (C) 2010-2013 Guilhem Lavaux, 2011-2013 Paul M. Sutter.
This software is put under the GNU Public License. Please see LICENSE
for further information.
Parts of the pipeline includes ZOBOV. See zobov/zobov_readme.txt for
copyright/license information
Building
--------
After compiling, go to the pipeline directory.
Using the pipeline
------------------
Create a dataset parameter file. Look at datasets/multidark.py for
an example. Describe the simulation, where to put outputs, how many
redshift slices, subvolumes, etc. etc.

112
build_tools/gather_sources.py Normal file
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@ -0,0 +1,112 @@
#+
# VIDE -- Void IDEntification pipeline -- ./build_tools/gather_sources.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
import shutil
import tempfile
import re
from git import Repo,Tree,Blob
def apply_license(license, relimit, filename):
header = re.sub(r'@FILENAME@', filename, license)
f = file(filename)
lines = f.read()
f.close()
lines = re.sub(relimit, '', lines)
lines = header + lines
with tempfile.NamedTemporaryFile(delete=False) as tmp_sources:
tmp_sources.write(lines)
shutil.move(tmp_sources.name, filename)
def apply_python_license(filename):
license="""#+
# VIDE -- Void IDEntification pipeline -- @FILENAME@
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
"""
print("Shell/Python file: %s" % filename)
relimit=r'^#\+\n(#.*\n)*#\+\n'
apply_license(license, relimit, filename)
def apply_cpp_license(filename):
license="""/*+
VIDE -- Void IDEntification pipeline -- @FILENAME@
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
"""
relimit = r'^(?s)/\*\+.*\+\*/'
print("C++ file: %s" % filename)
apply_license(license, relimit, filename)
def analyze_tree(prefix, t):
for ename,entry in t.items():
if ename == 'external' or ename == 'zobov':
continue
if type(entry) == Tree:
analyze_tree(prefix + "/" + ename, entry)
elif type(entry) == Blob:
if re.match(".*\.(sh|py|pyx)$",ename) != None:
fname=prefix+"/"+ename
apply_python_license(fname)
if re.match('.*\.(cpp|hpp|h)$', ename) != None:
fname=prefix+"/"+ename
apply_cpp_license(fname)
if __name__=="__main__":
repo = Repo(".")
assert repo.bare == False
t = repo.tree()
analyze_tree(".", t)

21
c_tools/analysis/voidOverlap.cpp
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@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/analysis/voidOverlap.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
// =============================================================================
//
// Program: voidOverlap

21
c_tools/libzobov/contour_pixels.cpp
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@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/contour_pixels.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <vector>
#include <healpix_map.h>
#include <healpix_map_fitsio.h>

21
c_tools/libzobov/contour_pixels.hpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/contour_pixels.hpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#ifndef __CONTOUR_PIXELS_HPP
#define __CONTOUR_PIXELS_HPP

21
c_tools/libzobov/gslIntegrate.hpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/gslIntegrate.hpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#ifndef __MYGSL_INTEGRATE_HPP
#define __MYGSL_INTEGRATE_HPP

21
c_tools/libzobov/loadZobov.cpp
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@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/loadZobov.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <cassert>
#include <string>
#include <fstream>

21
c_tools/libzobov/loadZobov.hpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/loadZobov.hpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#ifndef __LOAD_ZOBOV_HPP
#define __LOAD_ZOBOV_HPP

21
c_tools/libzobov/particleInfo.cpp
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@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/particleInfo.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <cstdlib>
#include <netcdfcpp.h>
#include <CosmoTool/fortran.hpp>

21
c_tools/libzobov/particleInfo.hpp
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@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/particleInfo.hpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#ifndef _PARTICLE_INFO_HEADER_HPP
#define _PARTICLE_INFO_HEADER_HPP

21
c_tools/libzobov/voidTree.hpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/voidTree.hpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#ifndef _VOID_TREE_HPP
#define _VOID_TREE_HPP

21
c_tools/mock/generateFromCatalog.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateFromCatalog.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <healpix_map.h>
#include <healpix_map_fitsio.h>
#include <boost/format.hpp>

31
c_tools/mock/generateMock.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateMock.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <gsl/gsl_rng.h>
#include <boost/function.hpp>
#include <boost/bind.hpp>
@ -349,6 +370,8 @@ void buildBox(SimuData *simu, long num_targets, long loaded,
for (uint32_t i = 0; i < num_targets; i++, loaded++)
{
long pid = particle_id[loaded];
assert(pid < simu->NumPart);
assert(loaded < boxed->NumPart);
for (int j = 0; j < 3; j++)
{
@ -513,7 +536,7 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
{
particle_id[pid_write] = particle_id[pid_read];
uniqueID[pid_write] = uniqueID[pid_read];
expansion_fac[pid_write] = uniqueID[pid_read];
expansion_fac[pid_write] = expansion_fac[pid_read];
pid_write++;
}
pid_read++;
@ -618,6 +641,12 @@ int main(int argc, char **argv)
{
loader = multidarkLoader(args_info.multidark_arg, preselector);
}
#ifdef SDF_SUPPORT
else if (args_info.sdf_given)
{
loader = sdfLoader(args_info.sdf_arg, args_info.sdf_splitting_arg, NEED_POSITION|NEED_VELOCITY|NEED_GADGET_ID, preselector);
}
#endif
else
{
cerr << "A simulation snapshot is required to generate a mock catalog." << endl;

6
c_tools/mock/generateMock.ggo
View file

@ -11,6 +11,9 @@ option "gadget" - "Base name of gadget snapshot (without parallel writing ex
option "flash" - "Base name for FLASH snapshot" string optional
option "multidark" - "Base name for multidark snapshot" string optional
option "sdf" - "SDF snapshot name" string optional
option "sdf_splitting" - "Number of artificial splitting of the SDF snapshot" int optional default="20"
option "axis" - "Redshift axis (X=0, Y=1, Z=2)" int optional default="2"
option "output" - "Output filename for particles" string required
@ -28,7 +31,7 @@ option "peculiarVelocities" - "Added peculiar velocities distortion" flag off
option "cosmo" - "Apply cosmological redshift" flag off
option "subsample" - "Subsample the input simulation by the specified amount" double optional
option "subsample" - "Subsample the input simulation by the specified amount" double optional default="1.0"
option "inputParameter" - "Input geometry (optional, warning!)" string optional
option "gadgetUnit" - "Unit of length in gadget file in Mpc/h" double optional default="0.001"
@ -37,3 +40,4 @@ option "subsample_seed" - "Seed for random number generation to select the subsa
option "resubsample" - "Resubsampling factor compared to the subsampled simulation" double optional
option "resubsample_seed" - "Seed for resubsampling from a subsampled simulation" int optional default="20132011"

21
c_tools/mock/generateTestMock.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateTestMock.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <iostream>
#include <cstdlib>
#include <CosmoTool/fortran.hpp>

21
c_tools/mock/loaders/basic_loader.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/basic_loader.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <cassert>
#include <string>
#include <iostream>

21
c_tools/mock/loaders/flash_loader.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/flash_loader.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <cassert>
#include <string>
#include <CosmoTool/loadFlash.hpp>

21
c_tools/mock/loaders/gadget_loader.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/gadget_loader.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <vector>
#include <cassert>
#include <string>

21
c_tools/mock/loaders/multidark_loader.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/multidark_loader.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <cassert>
#include <string>
#include <fstream>

21
c_tools/mock/loaders/ramses_loader.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/ramses_loader.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <cassert>
#include <string>
#include <CosmoTool/loadRamses.hpp>

21
c_tools/mock/loaders/sdf_loader.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/sdf_loader.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <iostream>
#include <boost/format.hpp>
#include <vector>

21
c_tools/mock/loaders/sdfloader_internal.hpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/sdfloader_internal.hpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#ifndef __VOID_SDF_LOADER_INTERNAL_HPP
#define __VOID_SDF_LOADER_INTERNAL_HPP

21
c_tools/mock/loaders/simulation_loader.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/simulation_loader.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#include <cmath>
#include <CosmoTool/loadSimu.hpp>
#include "simulation_loader.hpp"

21
c_tools/mock/loaders/simulation_loader.hpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/simulation_loader.hpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
#ifndef _MOCK_SIMULATION_LOADER_HPP
#define _MOCK_SIMULATION_LOADER_HPP

29
c_tools/stacking/pruneVoids.cpp
View file

@ -1,3 +1,24 @@
/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/stacking/pruneVoids.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 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.
+*/
// Reads in the void catalog and removes any void that could potentially
// be affected by a mock particle. It does this by computing the longest
// particle distance within each void and comparing it to the distance
@ -548,7 +569,7 @@ int main(int argc, char **argv) {
}
}
voids.resize(iGood);
printf(" 1st filter: reiGoodected %d obviously bad\n", numWrong);
printf(" 1st filter: rejected %d obviously bad\n", numWrong);
iGood = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
@ -559,7 +580,7 @@ int main(int argc, char **argv) {
}
}
voids.resize(iGood);
printf(" 2nd filter: reiGoodected %d too small\n", numTooSmall);
printf(" 2nd filter: rejected %d too small\n", numTooSmall);
iGood = 0;
@ -572,7 +593,7 @@ int main(int argc, char **argv) {
}
}
voids.resize(iGood);
printf(" 3rd filter: reiGoodected %d too close to high redshift boundaries\n", numNearZ);
printf(" 3rd filter: rejected %d too close to high redshift boundaries\n", numNearZ);
numNearZ = 0;
iGood = 0;
@ -586,7 +607,7 @@ int main(int argc, char **argv) {
}
}
voids.resize(iGood);
printf(" 4th filter: reiGoodected %d too close to low redshift boundaries\n", numNearZ);
printf(" 4th filter: rejected %d too close to low redshift boundaries\n", numNearZ);
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
if (voids[iVoid].centralDen > args.maxCentralDen_arg) {

19
crossCompare/analysis/datasetsToAnalyze.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/datasetsToAnalyze.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
#!/usr/bin/env python

19
crossCompare/analysis/mergerTree.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/mergerTree.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
#!/usr/bin/env python
# plots cumulative distributions of number counts

19
crossCompare/plotting/datasetsToPlot.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/datasetsToPlot.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
#!/usr/bin/env python

19
crossCompare/plotting/plotCompareDensCon.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotCompareDensCon.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
#!/usr/bin/env python
# plots cumulative distributions of number counts versus density contrast

19
crossCompare/plotting/plotDensConVsR.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotDensConVsR.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
#!/usr/bin/env python
# plots cumulative distributions of number counts versus density contrast

19
crossCompare/plotting/plotNumberFunc.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./crossCompare/plotting/plotNumberFunc.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
#!/usr/bin/env python
# plots cumulative distributions of number counts

5
external/external_build.cmake vendored
View file

@ -321,7 +321,8 @@ SET(QHULL_LIBRARIES ${QHULL_CPP_LIBRARY} ${QHULL_LIBRARY} )
# Build libSDF
###############
IF(SDF_SUPPORT)
SET(LIBSDF_ARCH x86_64)
SET(LIBSDF_ARCH x86_64 CACHE STRING "SDF architecture to activate")
mark_as_advanced(LIBSDF_ARCH)
SET(LIBSDF_PATH ${CMAKE_SOURCE_DIR}/external/libsdf)
ExternalProject_Add(libSDF
@ -329,7 +330,7 @@ IF(SDF_SUPPORT)
SOURCE_DIR ${LIBSDF_PATH}
CONFIGURE_COMMAND echo No configure
BUILD_COMMAND ${CMAKE_MAKE_PROGRAM} ARCH=${LIBSDF_ARCH}
INSTALL_COMMAND echo No install
INSTALL_COMMAND ${CMAKE_COMMAND} -DDEST_DIR=${CMAKE_BINARY_DIR}/ext_build/sdf -DLIBSDF_ARCH=${LIBSDF_ARCH} -DLIBSDF_PATH=${LIBSDF_PATH} -P ${CMAKE_SOURCE_DIR}/external/install_sdf.cmake
BUILD_IN_SOURCE 1
)
SET(LIBSDF_INCLUDE_PATH ${LIBSDF_PATH}/include)

4
external/install_sdf.cmake vendored Normal file
View file

@ -0,0 +1,4 @@
file(MAKE_DIRECTORY ${DEST_DIR})
file(MAKE_DIRECTORY ${DEST_DIR}/bin)
file(INSTALL ${LIBSDF_PATH}/apps/SDFcvt/SDFcvt.${LIBSDF_ARCH} DESTINATION ${DEST_DIR}/bin PERMISSIONS OWNER_EXECUTE OWNER_READ OWNER_WRITE GROUP_EXECUTE GROUP_READ)
file(RENAME ${DEST_DIR}/bin/SDFcvt.${LIBSDF_ARCH} ${DEST_DIR}/bin/SDFcvt)

2
external/libsdf/GNUmakefile vendored
View file

@ -20,7 +20,7 @@ all: All
# spell them a little differently in this file...
include Make-common/Make.generic
subdirs:= libSDF libmpmy libsw
subdirs:= libSDF libmpmy libsw apps/SDFcvt
All:
for dir in $(subdirs); do (cd $$dir; $(MAKE) ARCH=$(ARCH) all); done

15
external/libsdf/apps/SDFcvt/GNUmakefile vendored Normal file
View file

@ -0,0 +1,15 @@
TREEHOME=../..
##### Application-specific stuff goes here
treedir=$(TREEHOME)
programname=SDFcvt
src=SDFcvt.c
#### end of application-specific stuff
include $(treedir)/Make-common/Make.$(ARCH)
include $(treedir)/Make-common/Make.generic
# DO NOT DELETE THIS LINE -- make depend depends on it.

461
external/libsdf/apps/SDFcvt/SDFcvt.c vendored Normal file
View file

@ -0,0 +1,461 @@
/* Convert SDF to ascii
Usage:
SDFcvt [-s skip][-n nrecout][-h hdrfile] [-bfv] sdffile name ...
Not too fancy, but it should handle most SDF files, including
non-unit arrcnt. By using -s and -n is is possible to skip
to a place in the file and examine pieces of files
that would otherwise be too big to handle. We do NOT read the
whole file into memory. We process output lines one at a time,
reading one value of each of the names into memory at a time.
Thrashing is possible. We do nothing to prevent it.
With -v it prints a potentially useful pair of header lines
starting with '#'.
CHANGELOG:
6/28/94: Added the FORMAT_NATIVE option, and made it the default.
This will write SDF_INTS as ints, SDF_SHORTS as shorts, etc. It's
useful for post-processing by programs that can handle mixed types,
e.g., perl, but not AVS.
10/18/93: Added the -S (Swapping) flag to write binary data swapped.
Use limits.h/INT_MAX instead of SunOS values.h/MAXINT.
8/1/93: add the AT_A_TIME construction. We no longer process lines
one at a time. Instead, we read up to AT_A_TIME to beat the
excessive overhead in each SDFrdvecs call. One of these days
I'll add a hash table to SDF's symbol-lookup functions. Until
then, reading one element at a time will be extremely slow.
8/20/93: added the option to produce output in binary. This is MUCH
faster. With a little luck, perl (and presumably other programs)
can read it MUCH faster too (perl uses read and unpack).
*/
#define AT_A_TIME 512 /* read this many values at a time */
#include <stdio.h>
#include <stdlib.h>
#include <limits.h>
#include <string.h>
#include "SDF.h"
#include "protos.h"
#include "byteswap.h"
#include "error.h"
#include "Malloc.h"
#ifndef __SUN5__
extern int getopt(int, char**, const char *);
extern char *optarg;
extern int optind, opterr;
#endif
#define FORMAT_FLOAT 1
#define FORMAT_DOUBLE 2
#define FORMAT_INT 3
#define FORMAT_NATIVE 4
int binary = 0;
int format = FORMAT_NATIVE;
int swap_out = 0;
int fwrite_maybe_swap(void *p, size_t sz, size_t n, FILE *fp){
if( swap_out )
Byteswap(sz, n, p, p);
return fwrite(p, sz, n, fp);
}
void output_char(short c){
float f;
double d;
int i;
if( binary ){
switch(format){
case FORMAT_DOUBLE:
d = c;
fwrite_maybe_swap(&d, sizeof(d), 1, stdout);
break;
case FORMAT_FLOAT:
f = c;
fwrite_maybe_swap(&f, sizeof(f), 1, stdout);
break;
case FORMAT_INT:
i = c;
fwrite_maybe_swap(&i, sizeof(i), 1, stdout);
break;
case FORMAT_NATIVE:
fwrite_maybe_swap(&c, sizeof(c), 1, stdout);
break;
}
}else{
printf("%d", c);
}
}
void output_short(short s){
float f;
double d;
int i;
if( binary ){
switch(format){
case FORMAT_DOUBLE:
d = s;
fwrite_maybe_swap(&d, sizeof(d), 1, stdout);
break;
case FORMAT_FLOAT:
f = s;
fwrite_maybe_swap(&f, sizeof(f), 1, stdout);
break;
case FORMAT_INT:
i = s;
fwrite_maybe_swap(&i, sizeof(i), 1, stdout);
break;
case FORMAT_NATIVE:
fwrite_maybe_swap(&s, sizeof(s), 1, stdout);
break;
}
}else{
printf("%d", s);
}
}
void output_int(int i){
float f;
double d;
if( binary ){
switch(format){
case FORMAT_DOUBLE:
d = i;
fwrite_maybe_swap(&d, sizeof(d), 1, stdout);
break;
case FORMAT_FLOAT:
f = i;
fwrite_maybe_swap(&f, sizeof(f), 1, stdout);
break;
case FORMAT_NATIVE:
case FORMAT_INT:
fwrite_maybe_swap(&i, sizeof(i), 1, stdout);
break;
}
}else{
printf("%d", i);
}
}
void output_long(long l){
float f;
double d;
if( binary ){
switch(format){
case FORMAT_DOUBLE:
d = l;
fwrite_maybe_swap(&d, sizeof(d), 1, stdout);
break;
case FORMAT_FLOAT:
f = l;
fwrite_maybe_swap(&f, sizeof(f), 1, stdout);
break;
case FORMAT_NATIVE:
case FORMAT_INT:
fwrite_maybe_swap(&l, sizeof(l), 1, stdout);
break;
}
}else{
printf("%ld", l);
}
}
void output_int64(int64_t i64){
float f;
double d;
if( binary ){
switch(format){
case FORMAT_DOUBLE:
d = i64;
fwrite_maybe_swap(&d, sizeof(d), 1, stdout);
break;
case FORMAT_FLOAT:
f = i64;
fwrite_maybe_swap(&f, sizeof(f), 1, stdout);
break;
case FORMAT_NATIVE:
case FORMAT_INT:
fwrite_maybe_swap(&i64, sizeof(i64), 1, stdout);
break;
}
}else{
#if __WORDSIZE==64
printf("%ld", i64);
#else
printf("%lld", i64);
#endif
}
}
void output_float(float f){
double d;
int i;
if( binary ){
switch(format){
case FORMAT_DOUBLE:
d = f;
fwrite_maybe_swap(&d, sizeof(d), 1, stdout);
break;
case FORMAT_FLOAT:
case FORMAT_NATIVE:
fwrite_maybe_swap(&f, sizeof(f), 1, stdout);
break;
case FORMAT_INT:
i = f;
fwrite_maybe_swap(&i, sizeof(i), 1, stdout);
break;
}
}else{
switch(format){
case FORMAT_DOUBLE:
printf("%.15e", f);
break;
case FORMAT_FLOAT:
case FORMAT_NATIVE:
printf("%.6e", f);
break;
case FORMAT_INT:
printf("%.0f", f);
break;
}
}
}
void output_double(double d){
float f;
int i;
if( binary ){
switch(format){
case FORMAT_NATIVE:
case FORMAT_DOUBLE:
fwrite_maybe_swap(&d, sizeof(d), 1, stdout);
break;
case FORMAT_FLOAT:
f = d;
fwrite_maybe_swap(&f, sizeof(f), 1, stdout);
break;
case FORMAT_INT:
i = d;
fwrite_maybe_swap(&i, sizeof(i), 1, stdout);
break;
}
}else{
switch(format){
case FORMAT_DOUBLE:
case FORMAT_NATIVE:
printf("%.15e", d);
break;
case FORMAT_FLOAT:
printf("%.6e", d);
break;
case FORMAT_INT:
printf("%.0f", d);
break;
}
}
}
void output_string(const char *s){
fwrite(s, strlen(s), 1, stdout);
}
void output_separator(void){
if( !binary )
putchar(' ');
}
void output_record_terminator(void){
if( !binary )
putchar('\n');
}
int main(int argc, char **argv){
int c;
char *fname, *hdr;
SDF *sdfp;
int64_t n, start;
int nnames, nn, i, j, k, kk;
int at_a_time;
int64_t nrecs, minnrecs, maxnrecs;
char *newname;
char **names;
void **addrs;
int *nread;
int *acnt;
int *strides;
enum SDF_type_enum *types, t;
int verbose;
hdr = NULL;
start = 0;
n = 0;
verbose = 0;
at_a_time = 0;
while((c=getopt(argc, argv, "a:h:s:n:vbfdiS")) != -1)
switch(c){
case 'h':
hdr = optarg;
break;
case 's':
start = atoll(optarg);
break;
case 'n':
n = atoll(optarg);
break;
case 'a':
at_a_time = atoi(optarg);
break;
case 'v':
verbose = 1;
break;
case 'b':
binary = 1;
break;
case 'f':
format = FORMAT_FLOAT;
break;
case 'S':
swap_out = 1;
break;
case 'd':
format = FORMAT_DOUBLE;
break;
case 'i':
format = FORMAT_INT;
break;
case '?':
fprintf(stderr, "Usage: %s [-s start][-n number][-a at-a-time][-v<erbose>][-h hdrfile][-b<inary>][-f<loat>][-d<ouble>][-i<nt>][-S<wap>] sdffile name ...\n", argv[0]);
}
fname = argv[optind];
optind++;
sdfp = SDFopen(hdr, fname);
if( sdfp == NULL ){
Error("Could not SDFopen(%s, %s): %s\n",
hdr?hdr:"<null>",
fname?fname:"<null>",
SDFerrstring);
}
if( at_a_time == 0 )
at_a_time = AT_A_TIME;
nnames = argc - optind;
names = Malloc(nnames*sizeof(char*));
addrs = Malloc(nnames*sizeof(void*));
nread = Malloc(nnames*sizeof(int));
types = Malloc(nnames*sizeof(enum SDF_type_enum));
strides = Malloc(nnames*sizeof(int));
acnt = Malloc(nnames*sizeof(int));
nn = 0;
minnrecs = INT64_MAX;
maxnrecs = 0;
for(; optind < argc; optind++){
newname = argv[optind];
if( !SDFhasname(newname, sdfp) ){
Error("%s not in %s\n", newname, fname);
}
t = SDFtype(newname, sdfp);
acnt[nn] = SDFarrcnt(newname, sdfp);
addrs[nn] = Malloc(SDFtype_sizes[t] * acnt[nn] * at_a_time);
strides[nn] = SDFtype_sizes[t]*acnt[nn];
names[nn] = newname;
types[nn] = t;
nrecs = SDFnrecs(newname, sdfp);
if( nrecs < minnrecs )
minnrecs = nrecs;
if( nrecs > maxnrecs )
maxnrecs = nrecs;
nread[nn] = at_a_time;
nn++;
}
if( n==0 ){
n = maxnrecs - start;
}
if( start+n > minnrecs ){
Error("Not enough records to start at %ld\n", start);
}
if( start ){
for(j=0; j<nnames; j++){
SDFseek(names[j], start, SDF_SEEK_SET, sdfp);
}
}
if( verbose ){
putchar('#');
for(i=0; i<argc; i++){
printf("%s%c", argv[i], (i<argc-1)?' ':'\n');
}
putchar('#');
for(j=0; j<nnames; j++){
printf("%s%c", names[j], (j<nnames-1)?' ':'\n');
}
}
while( n>0 ){
if( n < at_a_time ){
at_a_time = n;
for(j=0; j<nnames; j++){
nread[j] = at_a_time;
}
}
if( SDFrdvecsarr(sdfp, nnames, names, nread, addrs, strides) )
Error("SDFrdvecsarr failed n=%ld: %s\n", n, SDFerrstring);
n -= at_a_time;
for(i=0; i<at_a_time; i++){
for(j=0; j<nnames; j++){
for(k=0; k<acnt[j]; k++){
kk = acnt[j]*i + k;
if(j||k)
output_separator();
switch(types[j]){
case SDF_CHAR:
output_char( ((char *)addrs[j])[kk] );
break;
case SDF_SHORT:
output_short( ((short *)addrs[j])[kk] );
break;
case SDF_INT:
output_int( ((int *)addrs[j])[kk] );
break;
case SDF_LONG:
output_long( ((long *)addrs[j])[kk] );
break;
case SDF_INT64:
output_int64( ((int64_t *)addrs[j])[kk] );
break;
case SDF_FLOAT:
output_float( ((float *)addrs[j])[kk] );
break;
case SDF_DOUBLE:
output_double( ((double *)addrs[j])[kk] );
break;
case SDF_STRING:
output_string((char *)addrs[j]);
break;
default:
Error("Unrecognized type\n");
}
}
}
output_record_terminator();
}
}
exit(0);
}

19
pipeline/datasets/mock_dr9mid.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/mock_dr9mid.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
import os
# -----------------------------------------------------------------------------

19
pipeline/datasets/multidark.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/multidark.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
import os
# -----------------------------------------------------------------------------

19
pipeline/generateCatalog.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./pipeline/generateCatalog.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
#!/usr/bin/env python
# does full void analysis. Also generates 2d/1d stacked plots and hubble diagram

160
python_tools/pipeline_source/prepareCatalogs.in.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/pipeline_source/prepareCatalogs.in.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
#!/usr/bin/env python
# prepares input catalogs based on multidark simulations
@ -62,7 +81,7 @@ def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
def writeScript(setName, dataFileNameBase, dataFormat,
scriptDir, catalogDir, fileNums, redshifts, numSubvolumes,
numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0,
suffix=".dat"):
suffix=".dat", dataFileNameList=None):
if useVel: setName += "_pv"
@ -134,7 +153,7 @@ newSample = Sample(dataFile = "{dataFile}",
numSubvolumes = {numSubvolumes},
mySubvolume = "{mySubvolume}",
useLightCone = {useLightCone},
subsample = {subsample})
subsample = "{subsample}")
dataSampleList.append(newSample)
newSample.addStack(0.0, 5.0, 20, 25, False, False)
newSample.addStack(0.0, 5.0, 30, 35, False, False)
@ -165,33 +184,32 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False)
for i in xrange(len(zVsDY)):
zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
if useLightCone:
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
dzSafe = 0.03
else:
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
#boxWidthZ = lbox*100./LIGHT_SPEED
dzSafe = 0.0
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
for iSlice in xrange(numSlices):
sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices
sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices
if useLightCone:
dzSafe = 0.03
sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices
sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices
sliceMinMpc = sliceMin*LIGHT_SPEED/100.
sliceMaxMpc = sliceMax*LIGHT_SPEED/100.
else:
sliceMinMpc = LIGHT_SPEED/100.*vp.angularDiameter(sliceMin, Om=Om)
sliceMaxMpc = LIGHT_SPEED/100.*vp.angularDiameter(sliceMax, Om=Om)
sliceMinMpc = zBoxMpc + iSlice*lbox/numSlices
sliceMaxMpc = zBoxMpc + (iSlice+1)*lbox/numSlices
sliceMin = np.interp(sliceMinMpc*100./LIGHT_SPEED, zVsDX, zVsDY)
sliceMax = np.interp(sliceMaxMpc*100./LIGHT_SPEED, zVsDX, zVsDY)
sliceMin = "%0.2f" % sliceMin
sliceMax = "%0.2f" % sliceMax
sliceMinMpc = "%0.1f" % sliceMinMpc
sliceMaxMpc = "%0.1f" % sliceMaxMpc
dataFileName = dataFileNameBase + fileNum + suffix
if (dataFileNameList != None):
dataFileName = dataFileNameList[iFile]
else:
dataFileName = dataFileNameBase + fileNum + suffix
for iX in xrange(numSubvolumes):
for iY in xrange(numSubvolumes):
@ -216,7 +234,7 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False)
numSubvolumes=numSubvolumes,
mySubvolume=mySubvolume,
useLightCone=useLightCone,
subsample=subsample))
subsample=str(subsample).strip('[]')))
scriptFile.close()
return
@ -233,44 +251,60 @@ if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir)
# ss0.000175 ~ SDSS DR9 mid
baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
prevSubSample = -1
for thisSubSample in sorted(subSamples, reverse=True):
subSamples = sorted(subSamples, reverse=True)
for iSubSample in xrange(len(subSamples)):
keepFraction = float(thisSubSample) / baseResolution
maxKeep = keepFraction * numPart
subSampleList = subSamples[0:iSubSample+1]
keepFractionList = []
for subSample in subSampleList:
keepFractionList.append(float(subSample) / baseResolution)
thisSubSample = subSamples[iSubSample]
maxKeep = keepFractionList[-1] * numPart
minRadius = int(np.ceil(lbox/maxKeep**(1./3)))
partFileList = []
for (iRedshift, redshift) in enumerate(redshifts):
if particleFileDummy == '':
partFileList.append(particleFileBase+fileNums[iRedshift])
else:
partFileList.append(particleFileBase.replace(particleFileDummy,
fileNums[iRedshift]))
if args.script or args.all:
print " Doing subsample", thisSubSample, "scripts"
sys.stdout.flush()
setName = prefix+"ss"+str(thisSubSample)
if dataFormat == "multidark":
subSampleToUse = 1.0
fileToUse = prefix+"ss"+str(thisSubSample)+"_z"
suffix = ".dat"
elif dataFormat == "gadget":
subSampleToUse = keepFraction
#subSampleToUse = thisSubSample
fileToUse = particleFileBase
suffix = ""
elif dataFormat == "lanl":
subSampleToUse = keepFraction
#subSampleToUse = thisSubSample
fileToUse = particleFileBase
suffix = ""
elif dataFormat == "random":
if dataFormat == "random":
subSampleToUse = 1.0
fileToUse = "ran.ss"+str(thisSubSample)+"_z"
suffix = ".dat"
writeScript(setName, fileToUse, dataFormat,
writeScript(setName, fileToUse, dataFormat,
scriptDir, catalogDir, fileNums, redshifts,
numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
subsample=subSampleToUse, suffix=suffix)
writeScript(setName, fileToUse, dataFormat,
writeScript(setName, fileToUse, dataFormat,
scriptDir, catalogDir, fileNums, redshifts,
numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
subsample=subSampleToUse, suffix=suffix)
else:
subSampleToUse = keepFractionList
suffix = ""
fileToUse = partFileList[0]
writeScript(setName, fileToUse, dataFormat,
scriptDir, catalogDir, fileNums, redshifts,
numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
subsample=subSampleToUse, suffix=suffix,
dataFileNameList=partFileList)
writeScript(setName, fileToUse, dataFormat,
scriptDir, catalogDir, fileNums, redshifts,
numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
subsample=subSampleToUse, suffix=suffix,
dataFileNameList=partFileList)
if args.subsample or args.all:
print " Doing subsample", thisSubSample
sys.stdout.flush()
@ -411,31 +445,37 @@ if (args.halos or args.all) and haloFileBase != "":
sampleName = prefix+"halos_min"+str(minHaloMass)+"_z"+fileNums[iRedshift]
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
outFile.write("%f\n" %(lbox))
outFile.write("%s\n" %(omegaM))
outFile.write("%s\n" %(hubble))
outFile.write("%s\n" %(redshift))
outFile.write("%d\n" %(numPart))
inFile = open(dataFile, 'r')
for (iHalo,line) in enumerate(inFile):
if iHalo < haloFileNumComLines: continue
line = line.split(haloFileColSep)
if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
x = float(line[haloFileXCol])
y = float(line[haloFileYCol])
z = float(line[haloFileZCol])
vz = float(line[haloFileVZCol])
vy = float(line[haloFileVYCol])
vx = float(line[haloFileVXCol])
if dataFormat == "sdf":
# TODO process halo file with SDFcvt
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
outFile.close()
else:
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
inFile = open(dataFile, 'r')
for (iHalo,line) in enumerate(inFile):
if iHalo < haloFileNumComLines: continue
line = line.split(haloFileColSep)
if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
x = float(line[haloFileXCol])
y = float(line[haloFileYCol])
z = float(line[haloFileZCol])
vz = float(line[haloFileVZCol])
vy = float(line[haloFileVYCol])
vx = float(line[haloFileVXCol])
# write to output file
outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx))
# write to output file
outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx))
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
inFile.close()
outFile.close()
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
outFile.close()
inFile.close()
# -----------------------------------------------------------------------------
# now the HOD
@ -510,6 +550,14 @@ if (args.hod or args.all) and haloFileBase != "":
else:
haloFile = catalogDir+haloFileBase.replace(haloFileDummy,
fileNums[iRedshift])
if dataFormat == "sdf":
# TODO process halo file with SDFcvt
inFile = haloFile
outFile = haloFile+"_temp"
haloFile = outFile
parFile.write(parFileText.format(omegaM=omegaM,
hubble=hubble,
redshift=redshift,
@ -535,4 +583,6 @@ if (args.hod or args.all) and haloFileBase != "":
os.system("mv %s/hod.mock %s" % (catalogDir, outFileName))
os.system("rm %s/hod.*" % catalogDir)
os.system("rm %s" % haloFile)
print " Done!"

19
python_tools/setup.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/setup.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext

19
python_tools/void_python_tools/__init__.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/__init__.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
from void_python_tools.backend import *
from void_python_tools.apTools import *
from void_python_tools.plotting import *

19
python_tools/void_python_tools/apTools/__init__.py
View file

@ -1,2 +1,21 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/__init__.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
from chi2 import *
from profiles import *

19
python_tools/void_python_tools/apTools/chi2/__init__.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/chi2/__init__.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
from velocityProfileFitNative import *
from likelihood import *
from cosmologyTools import *

19
python_tools/void_python_tools/apTools/chi2/cosmologyTools.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/chi2/cosmologyTools.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
# a suite of functions to compute expansion rates, angular diameter
# distances, and expected void stretching

19
python_tools/void_python_tools/apTools/profiles/__init__.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/profiles/__init__.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
from build import *
from draw import *
from fit import *

19
python_tools/void_python_tools/apTools/profiles/getSurveyProps.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/profiles/getSurveyProps.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
import numpy as np
import healpy as healpy
import scipy.integrate

19
python_tools/void_python_tools/backend/__init__.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/__init__.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
from classes import *
from launchers import *
from catalogPrep import *

19
python_tools/void_python_tools/backend/classes.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/classes.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
# classes and routines used to support scripts
import os

121
python_tools/void_python_tools/backend/launchers.py Executable file → Normal file
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/launchers.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
# routines which communicate with individual data analysis portions -
@ -105,37 +124,43 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
datafile = inputDataDir+"/"+sample.dataFile
if regenerate:
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+sampleName+".par"
outputFile = zobovDir+"/regenerated_zobov_slice_" + sampleName
else:
inputParameterFlag = ""
outputFile = zobovDir+"/zobov_slice_" + sampleName
prevSubSample = -1
for thisSubSample in sample.subsample.split(', '):
if prevSubSample == -1:
inputParameterFlag = ""
outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + thisSubSample
keepFraction = float(thisSubSample)
subSampleLine = "subsample %g" % keepFraction
else:
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\
sampleName+"_ss"+prevSubSample+".par"
outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + thisSubSample
keepFraction = float(thisSubSample)/float(prevSubSample)
subSampleLine = "resubsample %g" % keepFraction
if sample.usePecVel:
includePecVelString = "peculiarVelocities"
else:
includePecVelString = ""
if sample.usePecVel: includePecVelString = "peculiarVelocities"
if sample.useLightCone:
useLightConeString = "cosmo"
else:
useLightConeString = ""
if sample.useLightCone: useLightConeString = "cosmo"
if sample.dataFormat == "multidark" or sample.dataFormat == "random":
dataFileLine = "multidark " + datafile
elif sample.dataFormat == "gadget":
dataFileLine = "gadget " + datafile
if sample.dataFormat == "multidark" or sample.dataFormat == "random":
dataFileLine = "multidark " + datafile
elif sample.dataFormat == "gadget":
dataFileLine = "gadget " + datafile
elif sample.dataFormat == "sdf":
dataFileLine = "sdf " + datafile
iX = float(sample.mySubvolume[0])
iY = float(sample.mySubvolume[1])
iX = float(sample.mySubvolume[0])
iY = float(sample.mySubvolume[1])
xMin = iX/sample.numSubvolumes * sample.boxLen
yMin = iY/sample.numSubvolumes * sample.boxLen
xMax = (iX+1)/sample.numSubvolumes * sample.boxLen
yMax = (iY+1)/sample.numSubvolumes * sample.boxLen
xMin = iX/sample.numSubvolumes * sample.boxLen
yMin = iY/sample.numSubvolumes * sample.boxLen
xMax = (iX+1)/sample.numSubvolumes * sample.boxLen
yMax = (iY+1)/sample.numSubvolumes * sample.boxLen
conf="""
conf="""
%s
output %s
outputParameter %s
@ -148,36 +173,52 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
rangeY_max %g
rangeZ_min %g
rangeZ_max %g
subsample %g
%s
%s
""" % (dataFileLine, outputFile,
zobovDir+"/zobov_slice_"+sampleName+".par",
outputFile+".par",
includePecVelString,
useLightConeString,
sample.dataUnit,
xMin, xMax, yMin, yMax,
sample.zBoundaryMpc[0], sample.zBoundaryMpc[1],
sample.subsample,inputParameterFlag)
subSampleLine,inputParameterFlag)
parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
file(parmFile, mode="w").write(conf)
file(parmFile, mode="w").write(conf)
if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
os.system(cmd)
if jobSuccessful(logFile, "Done!\n"):
print "done"
else:
print "FAILED!"
exit(-1)
doneLine = "Done! %5.2e\n" % keepFraction
print "TEST", doneLine
if not (continueRun and jobSuccessful(logFile, doneLine)):
if (prevSubSample == -1):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
else:
cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile)
os.system(cmd)
if not jobSuccessful(logFile, doneLine):
print "FAILED!"
exit(-1)
else:
print "already done!"
# remove intermediate files
if (prevSubSample != -1):
os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample+".par")
os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample)
prevSubSample = thisSubSample
if (continueRun and jobSuccessful(logFile, doneLine)): print "already done!"
if jobSuccessful(logFile, doneLine): print "done"
# place the final subsample
os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\
prevSubSample, zobovDir+"/zobov_slice_"+sampleName))
os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\
prevSubSample+".par", zobovDir+"/zobov_slice_"+sampleName+".par"))
if os.access("comoving_distance.txt", os.F_OK):
os.system("mv %s %s" % ("comoving_distance.txt", zobovDir))
#os.system("mv %s %s" % ("sample_info.txt", zobovDir))
if os.access(parmFile, os.F_OK):
os.unlink(parmFile)
@ -417,7 +458,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
maxDen = 0.2*float(maskIndex)/float(totalPart)
else:
maskIndex = 999999999
maxDen = -0.8
maxDen = 0.2
if INCOHERENT:
nullTestFlag = "INCOHERENT"

19
python_tools/void_python_tools/plotting/__init__.py
View file

@ -1,2 +1,21 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/__init__.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
from plotTools import *
from plotDefs import *

19
python_tools/void_python_tools/plotting/plotDefs.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/plotDefs.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
LIGHT_SPEED = 299792.458
colorList = ['r', 'b', 'g', 'y', 'c', 'm',

19
python_tools/void_python_tools/plotting/plotTools.py
View file

@ -1,3 +1,22 @@
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/plotTools.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 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.
#+
__all__=['plotRedshiftDistribution', 'plotSizeDistribution', 'plot1dProfiles',
'plotMarg1d', 'plotNumberDistribution']