cctbx-cvs Mailing List for Computational Crystallography Toolbox (Page 972)

Update of /cvsroot/cctbx/libtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7100

Modified Files:
	dispatcher_front_end.c dispatcher_front_end.exe 
Log Message:
support application prefix in Windows dispatcher_front_end

Index: dispatcher_front_end.exe
===================================================================
RCS file: /cvsroot/cctbx/libtbx/dispatcher_front_end.exe,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
Binary files /tmp/cvsr8soJ1 and /tmp/cvsYcjTKO differ

Index: dispatcher_front_end.c
===================================================================
RCS file: /cvsroot/cctbx/libtbx/dispatcher_front_end.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** dispatcher_front_end.c	13 Jun 2004 05:11:57 -0000	1.2
--- dispatcher_front_end.c	19 Feb 2005 01:50:10 -0000	1.3
***************
*** 1,8 ****
  #include <process.h>
  #include <errno.h>
  #include <stdlib.h>
  #include <string.h>
  #include <ctype.h>
- #include <assert.h>
  
  int
--- 1,8 ----
  #include <process.h>
  #include <errno.h>
+ #include <stdio.h>
  #include <stdlib.h>
  #include <string.h>
  #include <ctype.h>
  
  int
***************
*** 37,45 ****
  }
  
  int
  main(int argc, char *const argv[])
  {
!   char* libtbx_python_exe;
!   char* libtbx_build;
    char* dispatcher;
    char** extended_argv;
--- 37,78 ----
  }
  
+ char*
+ getenv_certain(const char* argv0, const char* var_name)
+ {
+   char* var_value = getenv(var_name);
+   if (var_value == NULL) {
+     fprintf(stderr, "%s: environment variable is not defined: %s\n",
+       argv0, var_name);
+     exit(1);
+   }
+   return var_value;
+ }
+ 
+ void*
+ malloc_certain(const char* argv0, unsigned long n)
+ {
+   void* ptr;
+   errno = 0;
+   ptr = malloc(n);
+   if (ptr == NULL) {
+     fprintf(stderr, "%s: error allocating %lu bytes", argv0, n);
+     if (errno) {
+       fprintf(stderr, ": %s", strerror(errno));
+     }
+     fprintf(stderr, "\n");
+     exit(2);
+   }
+   return ptr;
+ }
+ 
+ static const char* /* APPLICATION PREFIX interleaved with random digits */
+ application_prefix = "3A7P0P0L4I8C3A5T5I6O3N490P0R7E6F8I6X4";
+ 
  int
  main(int argc, char *const argv[])
  {
!   char env_var_name[256];
!   char* env_python_exe;
!   char* env_build;
    char* dispatcher;
    char** extended_argv;
***************
*** 47,63 ****
    const char* dispatcher_name = "\\dispatcher";
    _putenv("PYTHONHOME=");
!   libtbx_python_exe = getenv("LIBTBX_PYTHON_EXE");
!   assert(libtbx_python_exe != NULL);
!   extended_argv = malloc((argc + 3) * sizeof(char*));
!   assert(extended_argv != NULL);
!   extended_argv[0] = libtbx_python_exe;
    n = 1;
    i = 1;
    if (!is_python_exe(argv[0])) {
!     libtbx_build = getenv("LIBTBX_BUILD");
!     assert(libtbx_build != NULL);
!     dispatcher = malloc(strlen(libtbx_build) + strlen(dispatcher_name) + 1);
!     assert(dispatcher != NULL);
!     strcpy(dispatcher, libtbx_build);
      strcat(dispatcher, dispatcher_name);
      extended_argv[n++] = dispatcher;
--- 80,97 ----
    const char* dispatcher_name = "\\dispatcher";
    _putenv("PYTHONHOME=");
!   strcpy(env_var_name, application_prefix);
!   strcat(env_var_name, "_PYTHON_EXE");
!   env_python_exe = getenv_certain(argv[0], env_var_name);
!   extended_argv = malloc_certain(argv[0], (argc + 3) * sizeof(char*));
!   extended_argv[0] = env_python_exe;
    n = 1;
    i = 1;
    if (!is_python_exe(argv[0])) {
!     strcpy(env_var_name, application_prefix);
!     strcat(env_var_name, "_BUILD");
!     env_build = getenv_certain(argv[0], env_var_name);
!     dispatcher = malloc_certain(
!       argv[0], strlen(env_build) + strlen(dispatcher_name) + 1);
!     strcpy(dispatcher, env_build);
      strcat(dispatcher, dispatcher_name);
      extended_argv[n++] = dispatcher;
***************
*** 65,70 ****
    }
    for(;i<argc;i++,n++) {
!     extended_argv[n] = malloc(strlen(argv[i]) + 3);
!     assert(extended_argv[n] != NULL);
      strcpy(extended_argv[n], "\"");
      strcat(extended_argv[n], argv[i]);
--- 99,103 ----
    }
    for(;i<argc;i++,n++) {
!     extended_argv[n] = malloc_certain(argv[0], strlen(argv[i]) + 3);
      strcpy(extended_argv[n], "\"");
      strcat(extended_argv[n], argv[i]);
***************
*** 74,79 ****
    spawnv(P_WAIT, extended_argv[0], extended_argv);
    if (errno) {
!     perror(argv[0]);
!     return 1;
    }
    return 0;
--- 107,113 ----
    spawnv(P_WAIT, extended_argv[0], extended_argv);
    if (errno) {
!     fprintf(stderr, "%s: error starting %s: %s\n",
!       argv[0], extended_argv[0], strerror(errno));
!     exit(3);
    }
    return 0;

Update of /cvsroot/cctbx/libtbx/libtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7100/libtbx

Modified Files:
	config.py 
Log Message:
support application prefix in Windows dispatcher_front_end

Index: config.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/config.py,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** config.py	17 Nov 2004 19:40:45 -0000	1.24
--- config.py	19 Feb 2005 01:50:13 -0000	1.25
***************
*** 115,119 ****
  class env:
  
!   def __init__(self):
      libtbx_build = os.environ["LIBTBX_BUILD"]
      file_name = join(libtbx_build, "libtbx_env")
--- 115,120 ----
  class env:
  
!   def __init__(self, application_prefix="LIBTBX"):
!     self.application_prefix = application_prefix
      libtbx_build = os.environ["LIBTBX_BUILD"]
      file_name = join(libtbx_build, "libtbx_env")
***************
*** 154,162 ****
      return norm(os.getcwd()) == self.LIBTBX_BUILD
  
!   def dispatcher_front_end_exe(self):
      if (    os.name == "nt"
          and self._dispatcher_front_end_exe is None):
        self._dispatcher_front_end_exe = open(join(
          self.dist_path("libtbx"), "dispatcher_front_end.exe"), "rb").read()
      return self._dispatcher_front_end_exe
  
--- 155,173 ----
      return norm(os.getcwd()) == self.LIBTBX_BUILD
  
!   def dispatcher_front_end_exe(self,
!        application_prefix_placeholder="3A7P0P0L4I8C3A5T5I6O3N490P0R7E6F8I6X4"):
      if (    os.name == "nt"
          and self._dispatcher_front_end_exe is None):
        self._dispatcher_front_end_exe = open(join(
          self.dist_path("libtbx"), "dispatcher_front_end.exe"), "rb").read()
+       application_prefix_index = self._dispatcher_front_end_exe.find(
+         application_prefix_placeholder)
+       assert application_prefix_index >= 0
+       assert len(self.application_prefix) <= len(application_prefix_placeholder)
+       self._dispatcher_front_end_exe \
+         = self._dispatcher_front_end_exe[:application_prefix_index] \
+         + self.application_prefix + "\0" \
+         + self._dispatcher_front_end_exe[
+             application_prefix_index+len(self.application_prefix)+1:]
      return self._dispatcher_front_end_exe
  

Update of /cvsroot/cctbx/libtbx/libtbx/bundle
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7100/libtbx/bundle

Modified Files:
	copy_build_libtbx.py 
Log Message:
support application prefix in Windows dispatcher_front_end

Index: copy_build_libtbx.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/bundle/copy_build_libtbx.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** copy_build_libtbx.py	6 Sep 2004 07:32:09 -0000	1.3
--- copy_build_libtbx.py	19 Feb 2005 01:50:13 -0000	1.4
***************
*** 36,40 ****
      if (    self.dispatcher_front_end_exe is not None
          and name.endswith(".exe")):
!       if (open(path, "rb").read() == self.dispatcher_front_end_exe):
          return True
      else:
--- 36,41 ----
      if (    self.dispatcher_front_end_exe is not None
          and name.endswith(".exe")):
!       if (open(path, "rb").read(len(self.dispatcher_front_end_exe)+1)
!           == self.dispatcher_front_end_exe):
          return True
      else:

Update of /cvsroot/cctbx/cctbx/include/cctbx/crystal
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24371

Modified Files:
	direct_space_asu.h direct_space_asu_bpl.cpp tst_ext.py 
Log Message:
array versions: float_asu::is_inside_frac(), float_asu::is_inside_cart()

Index: tst_ext.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/crystal/tst_ext.py,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** tst_ext.py	4 Feb 2005 02:57:57 -0000	1.19
--- tst_ext.py	18 Feb 2005 20:34:44 -0000	1.20
***************
*** 114,117 ****
--- 114,124 ----
      site_symmetry_ops=site_symmetry) is asu_mappings
    assert asu_mappings.mappings().size() == 2
+   sites_frac = flex.vec3_double([m[1-i].mapped_site()
+     for i,m in enumerate(asu_mappings.mappings())])
+   assert list(asu_mappings.asu().is_inside_frac(
+     sites_frac=sites_frac)) == [False, True]
+   assert list(asu_mappings.asu().is_inside_cart(
+     sites_cart=asu_mappings.asu().unit_cell().orthogonalization_matrix()
+               *sites_frac)) == [False, True]
    assert asu_mappings.n_sites_in_asu_and_buffer() == 11
    assert not asu_mappings.is_locked()

Index: direct_space_asu.h
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/crystal/direct_space_asu.h,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** direct_space_asu.h	16 Oct 2004 01:24:24 -0000	1.37
--- direct_space_asu.h	18 Feb 2005 20:34:28 -0000	1.38
***************
*** 129,132 ****
--- 129,161 ----
        }
  
+       //! Array version of is_inside(), given fractional coordinates.
+       af::shared<bool>
+       is_inside_frac(
+         af::const_ref<scitbx::vec3<FloatType> > const& sites_frac)
+       {
+         af::shared<bool>
+           result(sites_frac.size(), af::init_functor_null<bool>());
+         bool* res = result.begin();
+         for(std::size_t i=0;i<sites_frac.size();i++) {
+           *res++ = is_inside(sites_frac[i]);
+         }
+         return result;
+       }
+ 
+       //! Array version of is_inside(), given cartesian coordinates.
+       af::shared<bool>
+       is_inside_cart(
+         af::const_ref<scitbx::vec3<FloatType> > const& sites_cart)
+       {
+         af::shared<bool>
+           result(sites_cart.size(), af::init_functor_null<bool>());
+         scitbx::mat3<FloatType> frac = unit_cell().fractionalization_matrix();
+         bool* res = result.begin();
+         for(std::size_t i=0;i<sites_cart.size();i++) {
+           *res++ = is_inside(frac * sites_cart[i]);
+         }
+         return result;
+       }
+ 
        /*! \brief New asymmetric unit with all facets shifted by the distance
            specified as thickness.

Index: direct_space_asu_bpl.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/crystal/direct_space_asu_bpl.cpp,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** direct_space_asu_bpl.cpp	16 Oct 2004 01:24:24 -0000	1.5
--- direct_space_asu_bpl.cpp	18 Feb 2005 20:34:44 -0000	1.6
***************
*** 74,77 ****
--- 74,79 ----
          .def("is_inside_epsilon", &w_t::is_inside_epsilon)
          .def("is_inside", &w_t::is_inside, (arg_("point")))
+         .def("is_inside_frac", &w_t::is_inside_frac, (arg_("sites_frac")))
+         .def("is_inside_cart", &w_t::is_inside_cart, (arg_("sites_cart")))
          .def("_add_buffer", &w_t::add_buffer)
          .def("volume_vertices", &w_t::volume_vertices,

Update of /cvsroot/cctbx/libtbx/libtbx/command_line
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv27794/libtbx/command_line

Added Files:
	find_non_ascii.py 
Log Message:
Initial


--- NEW FILE: find_non_ascii.py ---
import os, sys, string

def visit(arg, dirname, names):
  if not os.path.basename(dirname)=='CVS':
    for name in names:
      if not name.endswith('.py'):
        continue
      filename = os.path.join(dirname,name)
      dot_filename = filename[len(working_dir)+1:]
      try:
        f = file(filename, 'r')
        lines = f.readlines()
        f.close()
      except IOError, e:
        continue

      for j, line in enumerate(lines):
        for i, l in enumerate(line):
          if not l in string.printable:
            print '-'*80
            print "Non-ASCII letter at position %d in line %d of file\n\t%s" \
                  % (i, j, dot_filename)
            print line
            print "%s^" % (' '*i)
            break

def run(dir):
  global working_dir
  working_dir = dir
  os.path.walk(dir, visit, 'show')

if (__name__ == "__main__"):
  try:
    run(sys.argv[1])
  except:
    run(os.getcwd())

Update of /cvsroot/cctbx/iotbx/iotbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23725/iotbx

Modified Files:
	reflection_file_converter.py reflection_file_utils.py 
	tst_reflection_file_utils.py 
Log Message:
support for --label=# removed

Index: tst_reflection_file_utils.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/tst_reflection_file_utils.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** tst_reflection_file_utils.py	4 Feb 2005 06:34:48 -0000	1.6
--- tst_reflection_file_utils.py	17 Feb 2005 07:20:18 -0000	1.7
***************
*** 93,114 ****
  """
      err = reflection_file_srv.err = StringIO()
-   f_obs = reflection_file_srv.get_xray_data(
-     file_name=None,
-     labels=["1"],
-     ignore_all_zeros=True,
-     parameter_scope="xray_data")
-   assert str(f_obs.info()) == "tmp2.mtz:F0,SIGF0"
-   f_obs = reflection_file_srv.get_xray_data(
-     file_name=None,
-     labels=["2"],
-     ignore_all_zeros=True,
-     parameter_scope="xray_data")
-   assert str(f_obs.info()) == "tmp2.mtz:F1,SIGF1"
-   f_obs = reflection_file_srv.get_xray_data(
-     file_name="tmp2.mtz",
-     labels=["2"],
-     ignore_all_zeros=True,
-     parameter_scope="xray_data")
-   assert str(f_obs.info()) == "tmp2.mtz:F1,SIGF1"
    assert len(reflection_file_srv.file_name_miller_arrays) == 1
    f_obs = reflection_file_srv.get_xray_data(
--- 93,96 ----

Index: reflection_file_converter.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/reflection_file_converter.py,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** reflection_file_converter.py	16 Feb 2005 08:08:26 -0000	1.11
--- reflection_file_converter.py	17 Feb 2005 07:20:18 -0000	1.12
***************
*** 92,97 ****
      print
      print "Please use --label to select a reflection array."
!     print "For example: --label=2"
!     print "         or: --label=%s" % str(
        all_miller_arrays[1].info()).split(":")[-1]
      print
--- 92,96 ----
      print
      print "Please use --label to select a reflection array."
!     print "For example: --label=%s" % str(
        all_miller_arrays[1].info()).split(":")[-1]
      print

Index: reflection_file_utils.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/reflection_file_utils.py,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** reflection_file_utils.py	17 Feb 2005 03:14:54 -0000	1.14
--- reflection_file_utils.py	17 Feb 2005 07:20:18 -0000	1.15
***************
*** 38,50 ****
      else:
        assert len(labels) > 0
-       label = labels[0]
-     if (len(labels) == 1):
-       try: i = int(label)-1
-       except (TypeError, ValueError): pass
-       else:
-         if (0 <= i < len(self.miller_arrays)):
-           result = [0]*len(self.miller_arrays)
-           result[i] = 2
-           return result
      result = []
      labels_lower = [lbl.lower() for lbl in labels]
--- 38,41 ----

Update of /cvsroot/cctbx/iotbx/iotbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8588

Modified Files:
	reflection_file_utils.py 
Log Message:
bug fix in match_data_label

Index: reflection_file_utils.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/reflection_file_utils.py,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** reflection_file_utils.py	26 Jan 2005 07:47:00 -0000	1.13
--- reflection_file_utils.py	17 Feb 2005 03:14:54 -0000	1.14
***************
*** 92,96 ****
      scores = self.scores(label=label)
      selected_array = None
!     for high_score in [2,1]:
        if (scores.count(high_score) > 0):
          if (scores.count(high_score) > 1):
--- 92,96 ----
      scores = self.scores(label=label)
      selected_array = None
!     for high_score in xrange(max(scores),0,-1):
        if (scores.count(high_score) > 0):
          if (scores.count(high_score) > 1):

Update of /cvsroot/cctbx/iotbx/iotbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5399

Modified Files:
	reflection_file_reader.py 
Log Message:
better exception message: "=intensities can only be used for SHELX reflection files."

Index: reflection_file_reader.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/reflection_file_reader.py,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** reflection_file_reader.py	16 Feb 2005 08:08:26 -0000	1.26
--- reflection_file_reader.py	17 Feb 2005 02:56:50 -0000	1.27
***************
*** 46,50 ****
        except KeyboardInterrupt: raise
        except:
!         raise UserError("Not a SHELX reflection file: %s" % file_name)
        else: self._file_type = "shelx_hklf"
      else:
--- 46,52 ----
        except KeyboardInterrupt: raise
        except:
!         raise UserError("Not a SHELX reflection file: %s\n"
!           "  =%s can only be used for SHELX reflection files."
!           % (file_name, self._observation_type))
        else: self._file_type = "shelx_hklf"
      else:

Update of /cvsroot/cctbx/boost_adaptbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20165

Modified Files:
	SConscript 
Log Message:
adjust to latest Jamfile

Index: SConscript
===================================================================
RCS file: /cvsroot/cctbx/boost_adaptbx/SConscript,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** SConscript	16 Dec 2004 01:56:05 -0000	1.32
--- SConscript	16 Feb 2005 08:32:28 -0000	1.33
***************
*** 115,120 ****
      m = md5.new()
      m.update(jamfile)
!     # based on boost/libs/python/test/Jamfile revision 1.79
!     jamfile_md5 = "1af054a4ee426478ce85a0683fa29c1b"
      if (m.hexdigest() != jamfile_md5):
        print "***************************************************"
--- 115,120 ----
      m = md5.new()
      m.update(jamfile)
!     # based on boost/libs/python/test/Jamfile revision 1.80
!     jamfile_md5 = "43a3311d27c605839e1bc08c2e864944"
      if (m.hexdigest() != jamfile_md5):
        print "***************************************************"
***************
*** 122,125 ****
--- 122,129 ----
        print "New md5 signature:", m.hexdigest()
        print "***************************************************"
+     if (env_etc.compiler in ["irix_CC", "tru64_cxx"]):
+       disabled = "#"
+     else:
+       disabled = ""
      bpl_tests = Split("""
  staticmethod
***************
*** 173,177 ****
  return_arg
  keywords,keywords,keywords_test
! properties
  map_indexing_suite;int_map_indexing_suite,map_indexing_suite_ext,map_indexing_suite
  injected
--- 177,181 ----
  return_arg
  keywords,keywords,keywords_test
! %sproperties
  map_indexing_suite;int_map_indexing_suite,map_indexing_suite_ext,map_indexing_suite
  injected
***************
*** 179,183 ****
  const_argument
  raw_ctor
! """)
      Import("env_boost_python_ext")
      all_tst = []
--- 183,187 ----
  const_argument
  raw_ctor
! """ % disabled)
      Import("env_boost_python_ext")
      all_tst = []

Update of /cvsroot/cctbx/iotbx/iotbx/command_line
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15112/command_line

Modified Files:
	reflection_statistics.py 
Log Message:
iotbx.reflection_file_reader: special treatment of SHELX reflection files: =amplitudes, =intensities, =hklf3, =hklf4

Index: reflection_statistics.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/command_line/reflection_statistics.py,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** reflection_statistics.py	16 Feb 2005 01:56:42 -0000	1.19
--- reflection_statistics.py	16 Feb 2005 08:08:26 -0000	1.20
***************
*** 7,10 ****
--- 7,11 ----
  import cctbx.sgtbx.cosets
  from cctbx.array_family import flex
+ from libtbx.utils import UserError
  from libtbx.itertbx import count
  import math
***************
*** 269,274 ****
          miller_arrays = reflection_file.as_miller_arrays(
            crystal_symmetry=command_line.symmetry)
!       except:
!         pass
      if (miller_arrays is None):
        print >> sys.stderr, "Warning: unknown file format:", file_name
--- 270,275 ----
          miller_arrays = reflection_file.as_miller_arrays(
            crystal_symmetry=command_line.symmetry)
!       except UserError, KeyboardInterrupt: raise
!       except: pass
      if (miller_arrays is None):
        print >> sys.stderr, "Warning: unknown file format:", file_name

Update of /cvsroot/cctbx/iotbx/iotbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15112

Modified Files:
	reflection_file_converter.py reflection_file_reader.py 
Log Message:
iotbx.reflection_file_reader: special treatment of SHELX reflection files: =amplitudes, =intensities, =hklf3, =hklf4

Index: reflection_file_reader.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/reflection_file_reader.py,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** reflection_file_reader.py	16 Feb 2005 01:39:43 -0000	1.25
--- reflection_file_reader.py	16 Feb 2005 08:08:26 -0000	1.26
***************
*** 21,98 ****
  
    def __init__(self, file_name):
!     self._file_name = file_name
      open(file_name) # test read access
      self._file_type = None
!     if (self._file_type is None):
!       try: self._file_content = mtz.object(file_name=file_name)
!       except RuntimeError: pass
!       else: self._file_type = "ccp4_mtz"
!     if (self._file_type is None):
!       try: self._file_content = cns_reflection_reader.cns_reflection_file(
!         open(file_name))
!       except cns_reflection_reader.CNS_input_Error: pass
!       else: self._file_type = "cns_reflection_file"
!     if (self._file_type is None):
!       try: self._file_content = cns_index_fobs_sigma_reader.reader(
!         file_name=file_name)
!       except RuntimeError: pass
!       else: self._file_type = "cns_index_fobs_sigma"
!     if (self._file_type is None):
!       try: self._file_content = scalepack_merge.reader(
!         open(file_name))
!       except scalepack_merge.FormatError: pass
!       else: self._file_type = "scalepack_merge"
!     if (self._file_type is None):
!       try: self._file_content = scalepack_no_merge.reader(file_name)
!       except KeyboardInterrupt: raise
!       except: pass
!       else: self._file_type = "scalepack_no_merge_original_index"
!     if (self._file_type is None):
!       try: self._file_content = dtrek_reflnlist_reader.reflnlist(
!         open(file_name))
!       except KeyboardInterrupt: raise
!       except: pass
!       else: self._file_type = "dtrek_reflnlist"
!     if (self._file_type is None):
        try: self._file_content = shelx_hklf.reader(
          open(file_name))
        except KeyboardInterrupt: raise
!       except: pass
        else: self._file_type = "shelx_hklf"
!     if (self._file_type is None):
!       try: self._file_content = xds_ascii_reader(
!         open(file_name))
!       except KeyboardInterrupt: raise
!       except: pass
!       else: self._file_type = "xds_ascii"
!     if (self._file_type is None):
!       try: self._file_content = solve_fpfm_reader(file_name=file_name)
!       except KeyboardInterrupt: raise
!       except: pass
!       else: self._file_type = "solve_fpfm"
!     if (self._file_type is None):
!       try: self._file_content = easy_pickle.load(file_name)
!       except KeyboardInterrupt: raise
!       except: pass
!       else:
!         if (isinstance(self._file_content, miller.array)):
!           self._file_content = [self._file_content]
          else:
!           miller_arrays = []
!           try:
!             for miller_array in self._file_content:
!               if (isinstance(miller_array, miller.array)):
!                 if (hasattr(miller_array.info(), "source")):
!                   miller_array.info().source = os.path.abspath(self._file_name)
!                 miller_arrays.append(miller_array)
!           except KeyboardInterrupt: raise
!           except: pass
            else:
!             if (len(miller_arrays) == 0):
!               self._file_content = None
              else:
!               self._file_content = miller_arrays
!         if (self._file_content is not None):
!           self._file_type = "cctbx.miller.array"
  
    def file_name(self):
--- 21,124 ----
  
    def __init__(self, file_name):
!     if (   file_name.startswith("amplitudes=")
!         or file_name.startswith("hklf3=")
!         or file_name.startswith("intensities=")
!         or file_name.startswith("hklf4=")):
!       self._observation_type, self._file_name = file_name.split("=", 1)
!     elif (   file_name.endswith("=amplitudes")
!           or file_name.endswith("=hklf3")
!           or file_name.endswith("=intensities")
!           or file_name.endswith("=hklf4")):
!       self._file_name, self._observation_type = file_name.split("=", 1)
!     else:
!       self._file_name = file_name
!       self._observation_type = None
!     if (self._observation_type == "hklf3"):
!       self._observation_type = "amplitudes"
!     elif (self._observation_type == "hklf4"):
!       self._observation_type = "intensities"
!     file_name = self._file_name
      open(file_name) # test read access
      self._file_type = None
!     if (self._observation_type is not None):
        try: self._file_content = shelx_hklf.reader(
          open(file_name))
        except KeyboardInterrupt: raise
!       except:
!         raise UserError("Not a SHELX reflection file: %s" % file_name)
        else: self._file_type = "shelx_hklf"
!     else:
!       if (self._file_type is None):
!         try: self._file_content = mtz.object(file_name=file_name)
!         except RuntimeError: pass
!         else: self._file_type = "ccp4_mtz"
!       if (self._file_type is None):
!         try: self._file_content = cns_reflection_reader.cns_reflection_file(
!           open(file_name))
!         except cns_reflection_reader.CNS_input_Error: pass
!         else: self._file_type = "cns_reflection_file"
!       if (self._file_type is None):
!         try: self._file_content = cns_index_fobs_sigma_reader.reader(
!           file_name=file_name)
!         except RuntimeError: pass
!         else: self._file_type = "cns_index_fobs_sigma"
!       if (self._file_type is None):
!         try: self._file_content = scalepack_merge.reader(
!           open(file_name))
!         except scalepack_merge.FormatError: pass
!         else: self._file_type = "scalepack_merge"
!       if (self._file_type is None):
!         try: self._file_content = scalepack_no_merge.reader(file_name)
!         except KeyboardInterrupt: raise
!         except: pass
!         else: self._file_type = "scalepack_no_merge_original_index"
!       if (self._file_type is None):
!         try: self._file_content = dtrek_reflnlist_reader.reflnlist(
!           open(file_name))
!         except KeyboardInterrupt: raise
!         except: pass
!         else: self._file_type = "dtrek_reflnlist"
!       if (self._file_type is None):
!         try: self._file_content = shelx_hklf.reader(
!           open(file_name))
!         except KeyboardInterrupt: raise
!         except: pass
!         else: self._file_type = "shelx_hklf"
!       if (self._file_type is None):
!         try: self._file_content = xds_ascii_reader(
!           open(file_name))
!         except KeyboardInterrupt: raise
!         except: pass
!         else: self._file_type = "xds_ascii"
!       if (self._file_type is None):
!         try: self._file_content = solve_fpfm_reader(file_name=file_name)
!         except KeyboardInterrupt: raise
!         except: pass
!         else: self._file_type = "solve_fpfm"
!       if (self._file_type is None):
!         try: self._file_content = easy_pickle.load(file_name)
!         except KeyboardInterrupt: raise
!         except: pass
          else:
!           if (isinstance(self._file_content, miller.array)):
!             self._file_content = [self._file_content]
            else:
!             miller_arrays = []
!             try:
!               for miller_array in self._file_content:
!                 if (isinstance(miller_array, miller.array)):
!                   if (hasattr(miller_array.info(), "source")):
!                     miller_array.info().source = os.path.abspath(
!                       self._file_name)
!                   miller_arrays.append(miller_array)
!             except KeyboardInterrupt: raise
!             except: pass
              else:
!               if (len(miller_arrays) == 0):
!                 self._file_content = None
!               else:
!                 self._file_content = miller_arrays
!           if (self._file_content is not None):
!             self._file_type = "cctbx.miller.array"
  
    def file_name(self):
***************
*** 121,129 ****
          source=source,
          source_type=self.file_type())
!     return self._file_content.as_miller_arrays(
        crystal_symmetry=crystal_symmetry,
        force_symmetry=force_symmetry,
        merge_equivalents=merge_equivalents,
        base_array_info=base_array_info)
  
  def collect_arrays(file_names,
--- 147,186 ----
          source=source,
          source_type=self.file_type())
!     result = self._file_content.as_miller_arrays(
        crystal_symmetry=crystal_symmetry,
        force_symmetry=force_symmetry,
        merge_equivalents=merge_equivalents,
        base_array_info=base_array_info)
+     if (self.file_type() == "shelx_hklf"):
+       if (self._observation_type == "intensities"):
+         result[0].set_info(result[0].info().customized_copy(
+           labels=["Iobs", "SigIobs"]))
+         result[0].set_observation_type_xray_intensity()
+       elif (self._observation_type == "amplitudes"):
+         result[0].set_info(result[0].info().customized_copy(
+           labels=["Fobs", "SigFobs"]))
+         result[0].set_observation_type_xray_amplitude()
+       else:
+         raise UserError("Unresolved amplitude/intensity ambiguity: %s\n"
+           "  SHELX reflection files may contain amplitudes or intensities.\n"
+           "  Please append   =amplitudes\n"
+           "             or   =hklf3\n"
+           "             or   =intensities\n"
+           "             or   =hklf4\n"
+           "  to the file name to resolve the ambiguity.\n"
+           "  If a corresponding .ins file is available, look for the"
+           " HKLF codeword.\n"
+           "  Alternatively, run the iotbx.iotbx.reflection_statistics"
+           " command twice,\n"
+           "  once with =amplitudes and once with =intensities. Inspect"
+           " the <I^2>/(<I>)^2\n"
+           "  statistics. For acentric structures the values should"
+           " fluctuate around\n"
+           "  2.0, for centric structures around 3.0. If the statistics"
+           " are not conclusive\n"
+           "  it will be best to recover the original reflection data, such"
+           " as SCALEPACK,\n"
+           "  SCALA MTZ, XDS, or d*TREK files." % self._file_name)
+     return result
  
  def collect_arrays(file_names,

Index: reflection_file_converter.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/reflection_file_converter.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** reflection_file_converter.py	11 Feb 2005 23:39:58 -0000	1.10
--- reflection_file_converter.py	16 Feb 2005 08:08:26 -0000	1.11
***************
*** 24,30 ****
        help="Substring of reflection data label or number",
        metavar="STRING")
-     .option(None, "--observation_type",
-       choices=("amplitude", "intensity"),
-       metavar="amplitude|intensity")
      .option(None, "--scale_max",
        action="store",
--- 24,27 ----
***************
*** 117,134 ****
      print
      return None
-   if (selected_array.observation_type() is None):
-     if (command_line.options.observation_type is None):
-       command_line.parser.show_help()
-       print "Observation type is unknown. Please use --observation_type."
-       print
-       return None
-     if (command_line.options.observation_type == "amplitude"):
-       selected_array.set_observation_type_xray_amplitude()
-     else:
-       selected_array.set_observation_type_xray_intensity()
    print "Selected data:"
    print " ", selected_array.info()
    print "  Observation type:", selected_array.observation_type()
    print
    d_max = command_line.options.low_resolution
    d_min = command_line.options.resolution
--- 114,122 ----
      print
      return None
    print "Selected data:"
    print " ", selected_array.info()
    print "  Observation type:", selected_array.observation_type()
    print
+   selected_array_info = selected_array.info()
    d_max = command_line.options.low_resolution
    d_min = command_line.options.resolution
***************
*** 156,160 ****
    if (command_line.options.sca is not None):
      file_name = reflection_file_utils.construct_output_file_name(
!       input_file_names=command_line.args,
        user_file_name=command_line.options.sca,
        file_type_label="Scalepack",
--- 144,148 ----
    if (command_line.options.sca is not None):
      file_name = reflection_file_utils.construct_output_file_name(
!       input_file_names=[selected_array_info.source],
        user_file_name=command_line.options.sca,
        file_type_label="Scalepack",
***************
*** 168,172 ****
    if (command_line.options.mtz is not None):
      file_name = reflection_file_utils.construct_output_file_name(
!       input_file_names=command_line.args,
        user_file_name=command_line.options.mtz,
        file_type_label="MTZ",
--- 156,160 ----
    if (command_line.options.mtz is not None):
      file_name = reflection_file_utils.construct_output_file_name(
!       input_file_names=[selected_array_info.source],
        user_file_name=command_line.options.mtz,
        file_type_label="MTZ",
***************
*** 182,186 ****
    if (command_line.options.cns is not None):
      file_name = reflection_file_utils.construct_output_file_name(
!       input_file_names=command_line.args,
        user_file_name=command_line.options.cns,
        file_type_label="CNS",
--- 170,174 ----
    if (command_line.options.cns is not None):
      file_name = reflection_file_utils.construct_output_file_name(
!       input_file_names=[selected_array_info.source],
        user_file_name=command_line.options.cns,
        file_type_label="CNS",
***************
*** 192,196 ****
    if (command_line.options.shelx is not None):
      file_name = reflection_file_utils.construct_output_file_name(
!       input_file_names=command_line.args,
        user_file_name=command_line.options.shelx,
        file_type_label="SHELX",
--- 180,184 ----
    if (command_line.options.shelx is not None):
      file_name = reflection_file_utils.construct_output_file_name(
!       input_file_names=[selected_array_info.source],
        user_file_name=command_line.options.shelx,
        file_type_label="SHELX",

Update of /cvsroot/cctbx/cctbx/cctbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29727/regression

Modified Files:
	tst_miller.py 
Log Message:
new miller.array.as_intensity_array()

Index: tst_miller.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_miller.py,v
retrieving revision 1.70
retrieving revision 1.71
diff -C2 -d -r1.70 -r1.71
*** tst_miller.py	16 Feb 2005 01:16:41 -0000	1.70
--- tst_miller.py	16 Feb 2005 01:58:05 -0000	1.71
***************
*** 264,267 ****
--- 264,270 ----
    aa = ac.as_amplitude_array()
    assert aa.as_amplitude_array() is aa
+   ai = aa.as_intensity_array()
+   assert approx_equal(ai.data(), ac.data())
+   assert ai.as_intensity_array() is ai
    assert aa.eliminate_sys_absent() is aa
    aa = miller.array(

Update of /cvsroot/cctbx/cctbx/cctbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29727

Modified Files:
	miller.py 
Log Message:
new miller.array.as_intensity_array()

Index: miller.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/miller.py,v
retrieving revision 1.119
retrieving revision 1.120
diff -C2 -d -r1.119 -r1.120
*** miller.py	11 Feb 2005 19:36:25 -0000	1.119
--- miller.py	16 Feb 2005 01:58:04 -0000	1.120
***************
*** 898,901 ****
--- 898,906 ----
      return self
  
+   def as_intensity_array(self):
+     if (not self.is_xray_intensity_array()):
+       return self.f_as_f_sq()
+     return self
+ 
    def map_to_asu(self):
      i = self.indices().deep_copy()

Update of /cvsroot/cctbx/iotbx/iotbx/command_line
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29352

Modified Files:
	reflection_statistics.py 
Log Message:
new show_second_moments_of_intensities(); in show_perfect_merohedral_twinning_test() divide amplitudes by epsilon

Index: reflection_statistics.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/command_line/reflection_statistics.py,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** reflection_statistics.py	22 Jan 2005 16:50:04 -0000	1.18
--- reflection_statistics.py	16 Feb 2005 01:56:42 -0000	1.19
***************
*** 109,116 ****
  
    def show_perfect_merohedral_twinning_test(self, n_bins=None):
!     if (self.input.space_group().is_centric()): return
      print "Perfect merohedral twinning test for %s:"%str(self.input.info())
!     acentric = self.input.select_acentric()
!     assert acentric.observation_type() is self.input.observation_type()
      if (n_bins is not None):
        acentric.setup_binner(n_bins=n_bins)
--- 109,118 ----
  
    def show_perfect_merohedral_twinning_test(self, n_bins=None):
!     assert not self.input.space_group().is_centric()
      print "Perfect merohedral twinning test for %s:"%str(self.input.info())
!     acentric = self.input.select_acentric().as_intensity_array()
!     acentric = acentric.array(
!       data=acentric.data()/acentric.epsilons().data().as_double())
!     acentric.set_observation_type_xray_intensity()
      if (n_bins is not None):
        acentric.setup_binner(n_bins=n_bins)
***************
*** 131,134 ****
--- 133,149 ----
      print
  
+   def show_second_moments_of_intensities(self, n_bins=None):
+     print "Second moments of intensities for %s:"%str(self.input.info())
+     f = self.input.as_intensity_array()
+     f = f.array(data=f.data()/f.epsilons().data().as_double())
+     f.set_observation_type_xray_intensity()
+     if (n_bins is not None):
+       f.setup_binner(n_bins=n_bins)
+     else:
+       f.setup_binner(auto_binning=True)
+     print f.second_moment_of_intensities.__doc__.split()[0]
+     f.second_moment_of_intensities(use_binning=True).show()
+     print
+ 
    def unique_reindexing_operators(self,
          other,
***************
*** 234,237 ****
--- 249,259 ----
        help="Number of bins for twinning test",
        metavar="INT")
+     .option(None, "--bins_second_moments",
+       action="store",
+       type="int",
+       dest="n_bins_second_moments",
+       default=None,
+       help="Number of bins for second moments of intensities",
+       metavar="INT")
    ).process(args=args)
    if (len(command_line.args) == 0):
***************
*** 314,319 ****
      print
      cache_0.show_patterson_peaks()
!     cache_0.show_perfect_merohedral_twinning_test(
!       n_bins=command_line.options.n_bins_twinning_test)
      if (cache_0.input.anomalous_flag()):
        print "Anomalous signal of %s:" % str(cache_0.input.info())
--- 336,345 ----
      print
      cache_0.show_patterson_peaks()
!     if (not cache_0.input.space_group().is_centric()):
!       cache_0.show_perfect_merohedral_twinning_test(
!         n_bins=command_line.options.n_bins_twinning_test)
!     else:
!       cache_0.show_second_moments_of_intensities(
!         n_bins=command_line.options.n_bins_second_moments)
      if (cache_0.input.anomalous_flag()):
        print "Anomalous signal of %s:" % str(cache_0.input.info())

Update of /cvsroot/cctbx/iotbx/iotbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24654

Modified Files:
	reflection_file_reader.py 
Log Message:
re-raise KeyboardInterrupt

Index: reflection_file_reader.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/reflection_file_reader.py,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** reflection_file_reader.py	6 Jan 2005 20:21:44 -0000	1.24
--- reflection_file_reader.py	16 Feb 2005 01:39:43 -0000	1.25
***************
*** 45,48 ****
--- 45,49 ----
      if (self._file_type is None):
        try: self._file_content = scalepack_no_merge.reader(file_name)
+       except KeyboardInterrupt: raise
        except: pass
        else: self._file_type = "scalepack_no_merge_original_index"
***************
*** 50,53 ****
--- 51,55 ----
        try: self._file_content = dtrek_reflnlist_reader.reflnlist(
          open(file_name))
+       except KeyboardInterrupt: raise
        except: pass
        else: self._file_type = "dtrek_reflnlist"
***************
*** 55,58 ****
--- 57,61 ----
        try: self._file_content = shelx_hklf.reader(
          open(file_name))
+       except KeyboardInterrupt: raise
        except: pass
        else: self._file_type = "shelx_hklf"
***************
*** 60,71 ****
--- 63,77 ----
        try: self._file_content = xds_ascii_reader(
          open(file_name))
+       except KeyboardInterrupt: raise
        except: pass
        else: self._file_type = "xds_ascii"
      if (self._file_type is None):
        try: self._file_content = solve_fpfm_reader(file_name=file_name)
+       except KeyboardInterrupt: raise
        except: pass
        else: self._file_type = "solve_fpfm"
      if (self._file_type is None):
        try: self._file_content = easy_pickle.load(file_name)
+       except KeyboardInterrupt: raise
        except: pass
        else:
***************
*** 80,85 ****
                    miller_array.info().source = os.path.abspath(self._file_name)
                  miller_arrays.append(miller_array)
!           except:
!             pass
            else:
              if (len(miller_arrays) == 0):
--- 86,91 ----
                    miller_array.info().source = os.path.abspath(self._file_name)
                  miller_arrays.append(miller_array)
!           except KeyboardInterrupt: raise
!           except: pass
            else:
              if (len(miller_arrays) == 0):

Update of /cvsroot/cctbx/iotbx/iotbx/shelx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24377

Modified Files:
	crystal_symmetry_from_ins.py 
Log Message:
count number of codewords and return space group P1 if 3 or more codewords were found, even if there are not LATT and SYMM cards

Index: crystal_symmetry_from_ins.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/shelx/crystal_symmetry_from_ins.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** crystal_symmetry_from_ins.py	31 Jul 2003 17:31:14 -0000	1.3
--- crystal_symmetry_from_ins.py	16 Feb 2005 01:38:26 -0000	1.4
***************
*** 4,7 ****
--- 4,19 ----
  import sys
  
+ codewords = [
+   "ABSC", "ACTA", "AFIX", "AFLS", "ANIS", "BASF", "BIND", "BLOC", "BOND",
+   "BUMP", "CELL", "CGLS", "CHIV", "CONF", "CONN", "DAMP", "DANG", "DEFS",
+   "DELU", "DFIX", "DISP", "EADP", "EGEN", "EQIV", "ESEL", "EXTI", "EXYZ",
+   "FACE", "FEND", "FLAT", "FMAP", "FRAG", "FREE", "FVAR", "GRID", "HFIX",
+   "HKLF", "HOPE", "HTAB", "ILSF", "INIT", "ISOR", "L.S.", "LATT", "LAUE",
+   "LIST", "MERG", "MOLE", "MORE", "MOVE", "MPLA", "NCSY", "OMIT", "PART",
+   "PATT", "PHAN", "PHAS", "PLAN", "PSEE", "RESI", "RTAB", "SADI", "SAME",
+   "SFAC", "SHEL", "SIMU", "SIZE", "SLIM", "SPAG", "SPEC", "SPIN", "STIR",
+   "SUMP", "SWAT", "SYMM", "TEMP", "TEXP", "TIME", "TITL", "TREF", "TWIN",
+   "UNDO", "UNIT", "VECT", "VLEN", "VOID", "WGHT", "WPDB", "XHAB", "ZERR"]
+ 
  class read_shelx_latt:
  
***************
*** 20,23 ****
--- 32,37 ----
    unit_cell = None
    space_group = None
+   codew = dict([(w+" ",0) for w in codewords])
+   n_codew = 0
    n_characters = 0
    for line in file:
***************
*** 25,29 ****
        n_characters += len(line)
        if (n_characters > max_characters): break
!     l = line.strip()
      if (l.startswith("CELL ")):
        assert unit_cell is None
--- 39,43 ----
        n_characters += len(line)
        if (n_characters > max_characters): break
!     l = line.rstrip().split("!")[0]
      if (l.startswith("CELL ")):
        assert unit_cell is None
***************
*** 31,35 ****
        assert len(flds) == 8
        unit_cell = uctbx.unit_cell(" ".join(flds[2:]))
!     if (l.startswith("LATT ")):
        assert space_group is None
        latt = read_shelx_latt(l)
--- 45,49 ----
        assert len(flds) == 8
        unit_cell = uctbx.unit_cell(" ".join(flds[2:]))
!     elif (l.startswith("LATT ")):
        assert space_group is None
        latt = read_shelx_latt(l)
***************
*** 38,47 ****
          space_group.expand_inv(sgtbx.tr_vec((0,0,0)))
        space_group.expand_conventional_centring_type(latt.z)
!     if (l.startswith("SYMM ")):
        assert space_group is not None
        s = sgtbx.rt_mx(l[5:])
        space_group.expand_smx(s)
    assert unit_cell is not None
!   assert space_group is not None
    return crystal.symmetry(
      unit_cell=unit_cell,
--- 52,68 ----
          space_group.expand_inv(sgtbx.tr_vec((0,0,0)))
        space_group.expand_conventional_centring_type(latt.z)
!     elif (l.startswith("SYMM ")):
        assert space_group is not None
        s = sgtbx.rt_mx(l[5:])
        space_group.expand_smx(s)
+     else:
+       w = l[:5]
+       c = codew.get(w, -1)
+       if (c == 0):
+         codew[w] = 1
+         n_codew += 1
    assert unit_cell is not None
!   if (space_group is None and n_codew >= 3):
!     space_group = sgtbx.space_group()
    return crystal.symmetry(
      unit_cell=unit_cell,

Update of /cvsroot/cctbx/cctbx/cctbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17566

Modified Files:
	tst_miller.py 
Log Message:
bug fix in exercise_array_2()

Index: tst_miller.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_miller.py,v
retrieving revision 1.69
retrieving revision 1.70
diff -C2 -d -r1.69 -r1.70
*** tst_miller.py	11 Feb 2005 19:36:38 -0000	1.69
--- tst_miller.py	16 Feb 2005 01:16:41 -0000	1.70
***************
*** 588,593 ****
        #
        orig = m.array()
-       ave = orig.average_bijvoet_mates()
        if (not orig.anomalous_flag()):
          assert ave.correlation(orig).coefficient() > 1-1.e-6
          if (sigmas is not None):
--- 588,593 ----
        #
        orig = m.array()
        if (not orig.anomalous_flag()):
+         ave = orig.average_bijvoet_mates()
          assert ave.correlation(orig).coefficient() > 1-1.e-6
          if (sigmas is not None):
***************
*** 595,598 ****
--- 595,603 ----
              ave.sigmas(), orig.sigmas()).coefficient() > 1-1.e-6
        else:
+         if (sigmas is not None):
+           # merge_equivalents uses the sigmas as weights
+           orig = orig.customized_copy(
+             sigmas=flex.double(orig.sigmas().size(),1))
+         ave = orig.average_bijvoet_mates()
          asu, matches = orig.match_bijvoet_mates()
          vfy_indices = asu.indices().select(matches.pairs().column(0))
***************
*** 609,613 ****
              anomalous_flag=False),
            data=vfy_data).adopt_set(ave)
!         assert vfy.correlation(ave).coefficient() > 1-1.e-5
  
  def exercise_fft_map():
--- 614,618 ----
              anomalous_flag=False),
            data=vfy_data).adopt_set(ave)
!         assert vfy.correlation(ave).coefficient() > 1-1.e-6
  
  def exercise_fft_map():

Update of /cvsroot/cctbx/cctbx/cctbx/development
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16802/cctbx/development

Modified Files:
	debug_utils.py 
Log Message:
use libtbx.utils.format_cpu_times()

Index: debug_utils.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/development/debug_utils.py,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** debug_utils.py	20 Nov 2004 03:03:20 -0000	1.36
--- debug_utils.py	16 Feb 2005 01:12:51 -0000	1.37
***************
*** 1,4 ****
--- 1,5 ----
  from cctbx import sgtbx
  from scitbx.python_utils.command_line import parse_options
+ from libtbx.utils import format_cpu_times
  import sys, os, time, random
  
***************
*** 30,42 ****
    return space_group_info.change_basis(sgtbx.change_of_basis_op(xyz))
  
- def report_cpu_times():
-   t = os.times()
-   print "u+s,u,s: %.2f %.2f %.2f" % (t[0] + t[1], t[0], t[1]),
-   try: python_ticker = sys.gettickeraccumulation()
-   except AttributeError: pass
-   else:
-     print "micro-seconds/tick: %.3f" % ((t[0] + t[1]) / python_ticker * 1.e6),
-   print
- 
  def loop_space_groups(argv, flags, call_back, symbols_to_stdout=0):
    chunk_size = 1
--- 31,34 ----
***************
*** 88,92 ****
        time.sleep(1)
    sys.stdout.flush()
!   report_cpu_times()
  
  def parse_options_loop_space_groups(argv, call_back,
--- 80,84 ----
        time.sleep(1)
    sys.stdout.flush()
!   print format_cpu_times()
  
  def parse_options_loop_space_groups(argv, call_back,

Update of /cvsroot/cctbx/scitbx/array_family/boost_python
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14410/array_family/boost_python

Modified Files:
	tst_flex.py 
Log Message:
simple flex.histogram.show()

Index: tst_flex.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/array_family/boost_python/tst_flex.py,v
retrieving revision 1.85
retrieving revision 1.86
diff -C2 -d -r1.85 -r1.86
*** tst_flex.py	31 Jan 2005 21:17:43 -0000	1.85
--- tst_flex.py	16 Feb 2005 01:02:20 -0000	1.86
***************
*** 787,790 ****
--- 787,799 ----
    assert tuple(hy.slots()) == (7,4,4,4,7)
    assert hy.n_out_of_slot_range() == 0
+   s = StringIO()
+   hy.show(f=s, prefix="*")
+   assert s.getvalue() == """\
+ *0 - 3.8: 7
+ *3.8 - 7.6: 4
+ *7.6 - 11.4: 4
+ *11.4 - 15.2: 4
+ *15.2 - 19: 7
+ """
  
  def exercise_linear_regression():

Update of /cvsroot/cctbx/scitbx/scitbx/array_family
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14410/scitbx/array_family

Modified Files:
	flex.py 
Log Message:
simple flex.histogram.show()

Index: flex.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/scitbx/array_family/flex.py,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** flex.py	26 Jan 2005 02:52:21 -0000	1.27
--- flex.py	16 Feb 2005 01:02:21 -0000	1.28
***************
*** 146,149 ****
--- 146,160 ----
      print >> f, "coefficient:", self.coefficient()
  
+ class _histogram(boost.python.injector, ext.histogram):
+ 
+   def show(self, f=None, prefix=""):
+     if (f is None): f = sys.stdout
+     low_cutoff = self.data_min()
+     for i,n in enumerate(self.slots()):
+       high_cutoff = self.data_min() + self.slot_width() * (i+1)
+       print >> f, "%s%.8g - %.8g: %d" % (
+         prefix, low_cutoff, high_cutoff, n)
+       low_cutoff = high_cutoff
+ 
  def exercise_triple(flex_triple, flex_order=None, as_double=False):
    from libtbx.test_utils import approx_equal

Update of /cvsroot/cctbx/libtbx/libtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13529

Modified Files:
	utils.py 
Log Message:
new format_cpu_times()

Index: utils.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/utils.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** utils.py	18 Jan 2005 09:33:17 -0000	1.5
--- utils.py	16 Feb 2005 00:58:01 -0000	1.6
***************
*** 1,5 ****
  from __future__ import division
  import time
! import sys
  
  class Keep: pass
--- 1,5 ----
  from __future__ import division
  import time
! import sys, os
  
  class Keep: pass
***************
*** 39,40 ****
--- 39,50 ----
    return time.strftime("Date %Y-%m-%d Time %H:%M:%S", localtime) \
         + " %s %+03d%02d" % (tzname, offs//3600, offs//60%60)
+ 
+ def format_cpu_times(show_micro_seconds_per_tick=True):
+   t = os.times()
+   result = "u+s,u,s: %.2f %.2f %.2f" % (t[0] + t[1], t[0], t[1])
+   if (show_micro_seconds_per_tick):
+     try: python_ticker = sys.gettickeraccumulation()
+     except AttributeError: pass
+     else:
+       result += " micro-seconds/tick: %.3f" % ((t[0]+t[1])/python_ticker*1.e6)
+   return result

Update of /cvsroot/cctbx/scitbx/scitbx/math
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25986/scitbx/math

Modified Files:
	ext.py 
Log Message:
basic_statistics.show() method

Index: ext.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/scitbx/math/ext.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** ext.py	19 Dec 2003 05:04:57 -0000	1.4
--- ext.py	12 Feb 2005 12:14:00 -0000	1.5
***************
*** 2,3 ****
--- 2,30 ----
  ext = boost.python.import_ext("scitbx_math_ext")
  from scitbx_math_ext import *
+ 
+ import sys
+ 
+ class _basic_statistics(boost.python.injector, ext.basic_statistics):
+ 
+   def show(self, f=None, prefix=""):
+     if (f is None): f = sys.stdout
+     print >> f, prefix+"n:", self.n
+     if (self.n > 0):
+       print >> f, prefix+"min:", self.min
+       print >> f, prefix+"max:", self.max
+       print >> f, prefix+"max_absolute:", self.max_absolute
+       print >> f, prefix+"sum:", self.sum
+       print >> f, prefix+"mean:", self.mean
+       print >> f, prefix+"mean_absolute_deviation_from_mean:", \
+                      self.mean_absolute_deviation_from_mean
+       print >> f, prefix+"biased_variance:", self.biased_variance
+       print >> f, prefix+"biased_standard_deviation:", \
+                      self.biased_standard_deviation
+       if (self.n > 1):
+         print >> f, prefix+"bias_corrected_variance:", \
+                        self.bias_corrected_variance
+         print >> f, prefix+"bias_corrected_standard_deviation:", \
+                        self.bias_corrected_standard_deviation
+         print >> f, prefix+"skew:", self.skew
+         print >> f, prefix+"kurtosis:", self.kurtosis
+         print >> f, prefix+"kurtosis_excess:", self.kurtosis_excess

Update of /cvsroot/cctbx/scitbx/math/boost_python
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25986/math/boost_python

Modified Files:
	tst_math.py 
Log Message:
basic_statistics.show() method

Index: tst_math.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/tst_math.py,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** tst_math.py	12 Feb 2005 08:52:42 -0000	1.41
--- tst_math.py	12 Feb 2005 12:13:59 -0000	1.42
***************
*** 16,20 ****
  from libtbx.test_utils import approx_equal, eps_eq
  import pickle
! import StringIO
  import random
  import math
--- 16,20 ----
  from libtbx.test_utils import approx_equal, eps_eq
  import pickle
! from cStringIO import StringIO
  import random
  import math
***************
*** 413,421 ****
      4.297983))
    g = gaussian.sum((1,-2,3,-4,5), (-.1,.2,-.3,.4,-.5), 6)
!   s = StringIO.StringIO()
    g.show(s)
    assert len(s.getvalue().split()) == 14
    g = gaussian.sum((3,-2,1,-4,5), (-.3,.2,-.1,.4,-.5))
!   s = StringIO.StringIO()
    g.show(s)
    assert len(s.getvalue().split()) == 12
--- 413,421 ----
      4.297983))
    g = gaussian.sum((1,-2,3,-4,5), (-.1,.2,-.3,.4,-.5), 6)
!   s = StringIO()
    g.show(s)
    assert len(s.getvalue().split()) == 14
    g = gaussian.sum((3,-2,1,-4,5), (-.3,.2,-.1,.4,-.5))
!   s = StringIO()
    g.show(s)
    assert len(s.getvalue().split()) == 12
***************
*** 1037,1040 ****
--- 1037,1043 ----
    assert approx_equal(s.kurtosis, 1.7)
    assert approx_equal(s.kurtosis_excess, -1.3)
+   f = StringIO()
+   s.show(f=f)
+   assert len(f.getvalue().splitlines()) == 14
    for i_trial in xrange(10):
      x = flex.random_double(size=2+int(random.random()*10))

Update of /cvsroot/cctbx/scitbx/include/scitbx/math
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11880/include/scitbx/math

Added Files:
	basic_statistics.h 
Log Message:
new scitbx.math.basic_statistics

--- NEW FILE: basic_statistics.h ---
#ifndef SCITBX_MATH_BASIC_STATISTICS_H
#define SCITBX_MATH_BASIC_STATISTICS_H

#include <scitbx/array_family/misc_functions.h>
#include <cmath>

namespace scitbx { namespace math {

  //! Collection of basic statistics such as min, max, mean, variance.
  /*! See also:
        http://mathworld.wolfram.com/Variance.html
        http://mathworld.wolfram.com/Kurtosis.html
   */
  template <typename FloatType = double>
  class basic_statistics
  {
    public:
      typedef FloatType float_type;
      typedef std::size_t size_type;

      //! Default constructor. Some data members are not initialized!
      basic_statistics() {}

      //! Computation of all statistics.
      /*! The calculations involve two loops over the array of values.
          The memory requirements are minimal since large temporaries
          are avoided.
       */
      basic_statistics(af::const_ref<FloatType> values)
      {
        n = values.size();
        if (n == 0) {
          min = -1;
          max = -1;
          max_absolute = -1;
          sum = -1;
          mean = -1;
          mean_absolute_deviation_from_mean = -1;
          biased_variance = -1;
          biased_standard_deviation = -1;
          bias_corrected_variance = -1;
          bias_corrected_standard_deviation = -1;
          skew = -1;
          kurtosis = -1;
          kurtosis_excess = -1;
        }
        else {
          min = max = sum = values[0];
          for(std::size_t i=1;i<n;i++) {
            FloatType const& v = values[i];
            if (min > v) min = v;
            if (max < v) max = v;
            sum += v;
          }
          if (-min > max) max_absolute = -min;
          else            max_absolute = max;
          mean = sum / static_cast<FloatType>(n);
          FloatType sum_a = 0;
          FloatType sum_2 = 0;
          FloatType sum_3 = 0;
          FloatType sum_4 = 0;
          for(std::size_t i=0;i<n;i++) {
            FloatType const& v = values[i];
            FloatType vm = v - mean;
            FloatType vms = vm * vm;
            sum_a += fn::absolute(vm);
            sum_2 += vms;
            sum_3 += vms * vm;
            sum_4 += vms * vms;
          }
          FloatType nf = static_cast<FloatType>(n);
          mean_absolute_deviation_from_mean = sum_a / nf;
          biased_variance = sum_2 / nf;
          biased_standard_deviation = std::sqrt(biased_variance);
          if (n == 1) {
            bias_corrected_variance = -1;
            bias_corrected_standard_deviation = -1;
            skew = -1;
            kurtosis = -1;
            kurtosis_excess = -1;
          }
          else {
            bias_corrected_variance = sum_2 / static_cast<FloatType>(n-1);
            bias_corrected_standard_deviation = std::sqrt(
              bias_corrected_variance);
            skew = (sum_3 / nf) / fn::pow3(biased_standard_deviation);
            kurtosis = (sum_4 / nf) / fn::pow2(biased_variance);
            kurtosis_excess = kurtosis - 3;
          }
        }
      }

      //! Number of values.
      std::size_t n;
      //! Minimum of values.
      FloatType min;
      //! Maximum of values.
      FloatType max;
      //! Maximum of absolute values.
      FloatType max_absolute;
      //! sum(values)
      FloatType sum;
      //! sum(values) / n
      FloatType mean;
      //! sum(abs(value-mean)) / n
      FloatType mean_absolute_deviation_from_mean;
      //! sum((value-mean)**2) / n
      FloatType biased_variance;
      //! sqrt(sum((value-mean)**2) / n)
      FloatType biased_standard_deviation;
      //! sum((value-mean)**2) / (n-1)
      FloatType bias_corrected_variance;
      //! sqrt(sum((value-mean)**2) / (n-1))
      FloatType bias_corrected_standard_deviation;
      //! (sum((value-mean)**3)/n) / (sum((value-mean)**2)/n)**(3/2)
      FloatType skew;
      //! (sum((value-mean)**4)/n) / (sum((value-mean)**2)/n)**2
      FloatType kurtosis;
      //! (sum((value-mean)**4)/n) / (sum((value-mean)**2)/n)**2 - 3
      FloatType kurtosis_excess;
  };

}} // namespace scitbx::math

#endif // SCITBX_MATH_BASIC_STATISTICS_H

Update of /cvsroot/cctbx/scitbx/math/boost_python
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11880/math/boost_python

Modified Files:
	SConscript gaussian.cpp golay.cpp icosahedron.cpp math_ext.cpp 
	row_echelon.cpp tst_math.py 
Added Files:
	basic_statistics.cpp 
Log Message:
new scitbx.math.basic_statistics

--- NEW FILE: basic_statistics.cpp ---
#include <scitbx/array_family/boost_python/flex_fwd.h>

#include <scitbx/math/basic_statistics.h>
#include <boost/python/class.hpp>
#include <boost/python/args.hpp>

namespace scitbx { namespace math { namespace {

  struct basic_statistics_wrappers
  {
    typedef basic_statistics<> w_t;

    static void
    wrap()
    {
      using namespace boost::python;
      class_<w_t>("basic_statistics", no_init)
        .def(init<af::const_ref<double> const&>((arg_("values"))))
        .def_readonly("n", &w_t::n)
        .def_readonly("min", &w_t::min)
        .def_readonly("max", &w_t::max)
        .def_readonly("max_absolute", &w_t::max_absolute)
        .def_readonly("sum", &w_t::sum)
        .def_readonly("mean", &w_t::mean)
        .def_readonly("mean_absolute_deviation_from_mean",
          &w_t::mean_absolute_deviation_from_mean)
        .def_readonly("biased_variance", &w_t::biased_variance)
        .def_readonly("biased_standard_deviation",
          &w_t::biased_standard_deviation)
        .def_readonly("bias_corrected_variance", &w_t::bias_corrected_variance)
        .def_readonly("bias_corrected_standard_deviation",
          &w_t::bias_corrected_standard_deviation)
        .def_readonly("skew", &w_t::skew)
        .def_readonly("kurtosis", &w_t::kurtosis)
        .def_readonly("kurtosis_excess", &w_t::kurtosis_excess)
      ;
    }
  };

} // namespace <anonymous>

namespace boost_python {

  void wrap_basic_statistics()
  {
    basic_statistics_wrappers::wrap();
  }

}}} // namespace scitbx::math::boost_python

Index: tst_math.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/tst_math.py,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** tst_math.py	9 Feb 2005 09:09:00 -0000	1.40
--- tst_math.py	12 Feb 2005 08:52:42 -0000	1.41
***************
*** 988,991 ****
--- 988,1065 ----
        assert d/2 < m
  
+ def exercise_basic_statistics():
+   x = flex.double([])
+   s = scitbx.math.basic_statistics(values=x)
+   assert s.n == 0
+   assert approx_equal(s.min, -1)
+   assert approx_equal(s.max, -1)
+   assert approx_equal(s.max_absolute, -1)
+   assert approx_equal(s.sum, -1)
+   assert approx_equal(s.mean, -1)
+   assert approx_equal(s.mean_absolute_deviation_from_mean, -1)
+   assert approx_equal(s.biased_variance, -1)
+   assert approx_equal(s.biased_standard_deviation, -1)
+   assert approx_equal(s.bias_corrected_variance, -1)
+   assert approx_equal(s.bias_corrected_standard_deviation, -1)
+   assert approx_equal(s.skew, -1)
+   assert approx_equal(s.kurtosis, -1)
+   assert approx_equal(s.kurtosis_excess, -1)
+   x = flex.double([-7])
+   s = scitbx.math.basic_statistics(values=x)
+   assert s.n == 1
+   assert approx_equal(s.min, -7)
+   assert approx_equal(s.max, -7)
+   assert approx_equal(s.max_absolute, 7)
+   assert approx_equal(s.sum, -7)
+   assert approx_equal(s.mean, -7)
+   assert approx_equal(s.mean_absolute_deviation_from_mean, 0)
+   assert approx_equal(s.biased_variance, 0)
+   assert approx_equal(s.biased_standard_deviation, 0)
+   assert approx_equal(s.bias_corrected_variance, -1)
+   assert approx_equal(s.bias_corrected_standard_deviation, -1)
+   assert approx_equal(s.skew, -1)
+   assert approx_equal(s.kurtosis, -1)
+   assert approx_equal(s.kurtosis_excess, -1)
+   x = flex.double([1,2,3,4,5])
+   s = scitbx.math.basic_statistics(values=x)
+   assert s.n == 5
+   assert approx_equal(s.min, 1)
+   assert approx_equal(s.max, 5)
+   assert approx_equal(s.max_absolute, 5)
+   assert approx_equal(s.sum, 15)
+   assert approx_equal(s.mean, 3)
+   assert approx_equal(s.mean_absolute_deviation_from_mean, 1.2)
+   assert approx_equal(s.biased_variance, 2)
+   assert approx_equal(s.biased_standard_deviation, math.sqrt(2))
+   assert approx_equal(s.bias_corrected_variance, 2.5)
+   assert approx_equal(s.bias_corrected_standard_deviation, math.sqrt(2.5))
+   assert approx_equal(s.skew, 0)
+   assert approx_equal(s.kurtosis, 1.7)
+   assert approx_equal(s.kurtosis_excess, -1.3)
+   for i_trial in xrange(10):
+     x = flex.random_double(size=2+int(random.random()*10))
+     s = scitbx.math.basic_statistics(values=x)
+     assert s.n == x.size()
+     assert approx_equal(s.min, flex.min(x))
+     assert approx_equal(s.max, flex.max(x))
+     assert approx_equal(s.max_absolute, max(-flex.min(x), flex.max(x)))
+     assert approx_equal(s.sum, flex.sum(x))
+     assert approx_equal(s.mean, flex.mean(x))
+     d = x-flex.mean(x)
+     assert approx_equal(s.mean_absolute_deviation_from_mean,
+       flex.mean(flex.abs(d)))
+     assert approx_equal(s.biased_variance, flex.sum(d*d) / s.n)
+     assert approx_equal(s.biased_standard_deviation,
+       math.sqrt(s.biased_variance))
+     assert approx_equal(s.bias_corrected_variance,
+       flex.sum(flex.pow2(d)) / (s.n-1))
+     assert approx_equal(s.bias_corrected_standard_deviation,
+       math.sqrt(s.bias_corrected_variance))
+     assert approx_equal(s.skew,
+       (flex.sum(d*d*d)/s.n) / (flex.sum(d*d)/s.n)**(3/2.))
+     assert approx_equal(s.kurtosis,
+       (flex.sum(d*d*d*d)/s.n) / (flex.sum(d*d)/s.n)**2)
+     assert approx_equal(s.kurtosis_excess, s.kurtosis-3)
+ 
  def run():
    exercise_floating_point_epsilon()
***************
*** 1003,1006 ****
--- 1077,1081 ----
    exercise_row_echelon()
    exercise_icosahedron()
+   exercise_basic_statistics()
    forever = "--Forever" in sys.argv[1:]
    while 1:

Index: math_ext.cpp
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/math_ext.cpp,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** math_ext.cpp	9 Feb 2005 09:09:00 -0000	1.23
--- math_ext.cpp	12 Feb 2005 08:52:42 -0000	1.24
***************
*** 16,19 ****
--- 16,20 ----
  namespace boost_python {
  
+   void wrap_basic_statistics();
    void wrap_gaussian();
    void wrap_golay();
***************
*** 94,97 ****
--- 95,99 ----
      eigensystem_real_symmetric_wrappers::wrap();
  
+     wrap_basic_statistics();
      wrap_gaussian();
      wrap_golay();

Index: icosahedron.cpp
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/icosahedron.cpp,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** icosahedron.cpp	4 Feb 2005 02:57:41 -0000	1.3
--- icosahedron.cpp	12 Feb 2005 08:52:42 -0000	1.4
***************
*** 29,33 ****
    };
  
! } // namespace <anoymous>
  
  namespace boost_python {
--- 29,33 ----
    };
  
! } // namespace <anonymous>
  
  namespace boost_python {

Index: golay.cpp
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/golay.cpp,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** golay.cpp	23 Dec 2003 21:19:40 -0000	1.1
--- golay.cpp	12 Feb 2005 08:52:42 -0000	1.2
***************
*** 36,40 ****
    };
  
! } // namespace <anoymous>
  
  namespace boost_python {
--- 36,40 ----
    };
  
! } // namespace <anonymous>
  
  namespace boost_python {

Index: gaussian.cpp
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/gaussian.cpp,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** gaussian.cpp	15 Jan 2004 03:04:58 -0000	1.9
--- gaussian.cpp	12 Feb 2005 08:52:42 -0000	1.10
***************
*** 119,123 ****
    };
  
! }} // gaussian::namespace <anoymous>
  
  namespace boost_python {
--- 119,123 ----
    };
  
! }} // gaussian::namespace <anonymous>
  
  namespace boost_python {

Index: SConscript
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/SConscript,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** SConscript	3 Feb 2005 09:12:35 -0000	1.14
--- SConscript	12 Feb 2005 08:52:42 -0000	1.15
***************
*** 5,8 ****
--- 5,9 ----
    source=[
      "math_ext.cpp",
+     "basic_statistics.cpp",
      "gaussian.cpp",
      "golay.cpp",

Index: row_echelon.cpp
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/row_echelon.cpp,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** row_echelon.cpp	28 Jan 2005 01:40:57 -0000	1.1
--- row_echelon.cpp	12 Feb 2005 08:52:42 -0000	1.2
***************
*** 102,106 ****
    }
  
! }}} // namespace matrix::boost_python::<anoymous>
  
  namespace math { namespace boost_python {
--- 102,106 ----
    }
  
! }}} // namespace matrix::boost_python::<anonymous>
  
  namespace math { namespace boost_python {