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

build_tools/apply_license.py

@@ -1,26 +0,0 @@
-import shutil
-import tempfile
-import sys
-import re
-
-rex = "@FILENAME@"
-
-filename = sys.argv[1]
-
-
-fh = file("header.txt")
-header = fh.read()
-header_translated = re.sub(r'@FILENAME@', filename, header)
-fh.close()
-
-f = file(filename)
-lines = f.read()
-f.close()
-
-lines = re.sub(r'(?s)/\*\+.*\+\*/','',lines)
-lines = header_translated + lines
-
-with tempfile.NamedTemporaryFile(delete=False) as tmp_sources:
-  tmp_sources.write(lines)
-
-shutil.move(tmp_sources.name, filename)

build_tools/gather_sources.py

@@ -1,11 +1,112 @@
-from git import Repo
+#+
+#   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)
-
-for entry in t.travers():
-  print entry

build_tools/header.txt

@@ -1,19 +0,0 @@
-/*+
-    VIDE -- Void IDEntification pipeline -- @FILENAME@
-    Copyright (C) 2010-2013 Guilhem Lavaux
-    Copyright (C) 2011-2013 Paul 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; either version 2 of the License, or
-    (at your option) any later version.
-
-    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.
-+*/

c_tools/analysis/voidOverlap.cpp

@@ -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

c_tools/libzobov/contour_pixels.cpp

@@ -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>

c_tools/libzobov/contour_pixels.hpp

@@ -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
 

c_tools/libzobov/gslIntegrate.hpp

@@ -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
 

c_tools/libzobov/loadZobov.cpp

@@ -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>

c_tools/libzobov/loadZobov.hpp

@@ -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
 

c_tools/libzobov/particleInfo.cpp

@@ -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>

c_tools/libzobov/particleInfo.hpp

@@ -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
 

c_tools/libzobov/voidTree.hpp

@@ -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
 

c_tools/mock/generateFromCatalog.cpp

@@ -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>

c_tools/mock/generateMock.cpp

@@ -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>

c_tools/mock/generateTestMock.cpp

@@ -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>

c_tools/mock/loaders/basic_loader.cpp

@@ -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>

c_tools/mock/loaders/flash_loader.cpp

@@ -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>

c_tools/mock/loaders/gadget_loader.cpp

@@ -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>

c_tools/mock/loaders/multidark_loader.cpp

@@ -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>

c_tools/mock/loaders/ramses_loader.cpp

@@ -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>

c_tools/mock/loaders/sdf_loader.cpp

@@ -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>

c_tools/mock/loaders/sdfloader_internal.hpp

@@ -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
 

c_tools/mock/loaders/simulation_loader.cpp

@@ -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"

c_tools/mock/loaders/simulation_loader.hpp

@@ -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
 

c_tools/stacking/pruneVoids.cpp

@@ -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

crossCompare/analysis/datasetsToAnalyze.py

@@ -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
 
 

crossCompare/analysis/mergerTree.py

@@ -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

crossCompare/plotting/datasetsToPlot.py

@@ -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
 
 

crossCompare/plotting/plotCompareDensCon.py

@@ -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

crossCompare/plotting/plotDensConVsR.py

@@ -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

crossCompare/plotting/plotNumberFunc.py

@@ -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

external/external_build.cmake

@@ -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)

external/install_sdf.cmake

@@ -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)

external/libsdf/GNUmakefile

@@ -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

external/libsdf/apps/SDFcvt/GNUmakefile

@@ -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.
+
+

external/libsdf/apps/SDFcvt/SDFcvt.c

@@ -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);
+}
+

pipeline/datasets/mock_dr9mid.py

@@ -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
 
 # -----------------------------------------------------------------------------

pipeline/datasets/multidark.py

@@ -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
 
 # -----------------------------------------------------------------------------

pipeline/generateCatalog.py

@@ -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

python_tools/pipeline_source/prepareCatalogs.in.py

@@ -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

python_tools/setup.py

@@ -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

python_tools/void_python_tools/__init__.py

@@ -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 *

python_tools/void_python_tools/apTools/__init__.py

@@ -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 *

python_tools/void_python_tools/apTools/chi2/__init__.py

@@ -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 *

python_tools/void_python_tools/apTools/chi2/cosmologyTools.py

@@ -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
 

python_tools/void_python_tools/apTools/profiles/__init__.py

@@ -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 *

python_tools/void_python_tools/apTools/profiles/getSurveyProps.py

@@ -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

python_tools/void_python_tools/backend/__init__.py

@@ -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 *

python_tools/void_python_tools/backend/classes.py

@@ -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

python_tools/void_python_tools/backend/launchers.py

@@ -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 - 

python_tools/void_python_tools/plotting/__init__.py

@@ -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 *

python_tools/void_python_tools/plotting/plotDefs.py

@@ -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', 

python_tools/void_python_tools/plotting/plotTools.py

@@ -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']