cctbx-cvs Mailing List for Computational Crystallography Toolbox (Page 976)

Update of /cvsroot/cctbx/cctbx/maptbx/boost_python
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16697/maptbx/boost_python

Modified Files:
	maptbx_ext.cpp tst_maptbx.py 
Log Message:
new maptbx::copy(map_unit_cell, first, last) for copying blocks

Index: tst_maptbx.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/maptbx/boost_python/tst_maptbx.py,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** tst_maptbx.py	7 Dec 2004 01:21:26 -0000	1.23
--- tst_maptbx.py	29 Jan 2005 09:25:39 -0000	1.24
***************
*** 14,22 ****
      m = flex_type((1,2,3,4))
      m.resize(flex.grid(2,2))
!     c = maptbx.copy(m, m.accessor())
      assert tuple(m) == tuple(c)
!     c = maptbx.copy(m, flex.grid(2,3).set_focus(2,2))
      assert approx_equal(tuple(c), (1,2,0,3,4,0))
!     n = maptbx.copy(c, m.accessor())
      assert approx_equal(tuple(m), tuple(n))
      c = maptbx.copy(m, flex.grid(3,2).set_focus(2,2))
--- 14,22 ----
      m = flex_type((1,2,3,4))
      m.resize(flex.grid(2,2))
!     c = maptbx.copy(map=m, result_grid=m.accessor())
      assert tuple(m) == tuple(c)
!     c = maptbx.copy(map=m, result_grid=flex.grid(2,3).set_focus(2,2))
      assert approx_equal(tuple(c), (1,2,0,3,4,0))
!     n = maptbx.copy(c, result_grid=m.accessor())
      assert approx_equal(tuple(m), tuple(n))
      c = maptbx.copy(m, flex.grid(3,2).set_focus(2,2))
***************
*** 36,39 ****
--- 36,55 ----
      n = maptbx.copy(c, m.accessor())
      assert approx_equal(tuple(m), tuple(n))
+     #
+     m = flex_type()
+     for i in xrange(2):
+      for j in xrange(3):
+        for k in xrange(5):
+          m.append(i*100+j*10+k)
+     m.resize(flex.grid(2,3,5).set_focus((2,3,4)))
+     for i in xrange(-5,5):
+      for j in xrange(-5,5):
+        for k in xrange(-5,5):
+          c = maptbx.copy(map_unit_cell=m, first=(i,j,k), last=(i,j,k))
+          assert c.size() == 1
+          assert c[(i,j,k)] == m[(i%2,j%3,k%4)]
+     c = maptbx.copy(map_unit_cell=m, first=(-1,1,-2), last=(1,2,0))
+     assert list(c) == [112, 113, 110, 122, 123, 120,  12,  13,  10,
+                         22,  23,  20, 112, 113, 110, 122, 123, 120]
  
  def exercise_statistics():

Index: maptbx_ext.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/maptbx/boost_python/maptbx_ext.cpp,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** maptbx_ext.cpp	7 Dec 2004 01:21:26 -0000	1.12
--- maptbx_ext.cpp	29 Jan 2005 09:25:38 -0000	1.13
***************
*** 39,50 ****
      def("copy",
        (af::versa<float, af::flex_grid<> >(*)
!         (af::const_ref<float, af::flex_grid<> > const& map,
!          af::flex_grid<> const& result_grid))
!            maptbx::copy);
      def("copy",
        (af::versa<double, af::flex_grid<> >(*)
!         (af::const_ref<double, af::flex_grid<> > const& map,
!          af::flex_grid<> const& result_grid))
!            maptbx::copy);
  
      def("eight_point_interpolation",
--- 39,68 ----
      def("copy",
        (af::versa<float, af::flex_grid<> >(*)
!         (af::const_ref<float, af::flex_grid<> > const&,
!          af::flex_grid<> const&)) maptbx::copy, (
!       arg_("map"),
!       arg_("result_grid")));
      def("copy",
        (af::versa<double, af::flex_grid<> >(*)
!         (af::const_ref<double, af::flex_grid<> > const&,
!          af::flex_grid<> const&)) maptbx::copy, (
!       arg_("map"),
!       arg_("result_grid")));
!     def("copy",
!       (af::versa<float, af::flex_grid<> >(*)
!         (af::const_ref<float, c_grid_padded_p1<3> > const&,
!          af::int3 const&,
!          af::int3 const&)) maptbx::copy, (
!       arg_("map_unit_cell"),
!       arg_("first"),
!       arg_("last")));
!     def("copy",
!       (af::versa<double, af::flex_grid<> >(*)
!         (af::const_ref<double, c_grid_padded_p1<3> > const&,
!          af::int3 const&,
!          af::int3 const&)) maptbx::copy, (
!       arg_("map_unit_cell"),
!       arg_("first"),
!       arg_("last")));
  
      def("eight_point_interpolation",

Update of /cvsroot/cctbx/cctbx/include/cctbx/maptbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16697/include/cctbx/maptbx

Modified Files:
	copy.h 
Log Message:
new maptbx::copy(map_unit_cell, first, last) for copying blocks

Index: copy.h
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/maptbx/copy.h,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** copy.h	21 Jan 2004 07:33:34 -0000	1.4
--- copy.h	29 Jan 2005 09:25:37 -0000	1.5
***************
*** 57,60 ****
--- 57,82 ----
    }
  
+   template <typename OutFloatType, typename InpFloatType>
+   af::versa<OutFloatType, af::flex_grid<> >
+   copy(
+     af::const_ref<InpFloatType, c_grid_padded_p1<3> > const& map_unit_cell,
+     af::int3 const& first,
+     af::int3 const& last)
+   {
+     CCTBX_ASSERT(first.all_le(last));
+     af::flex_grid_default_index_type first_(af::adapt(first));
+     af::flex_grid_default_index_type last_(af::adapt(last));
+     af::versa<OutFloatType, af::flex_grid<> > result(
+       af::flex_grid<>(first_, last_, false));
+     OutFloatType* out_ptr = result.begin();
+     typename c_grid_padded_p1<3>::index_type out_pt;
+     for (out_pt[0] = first[0]; out_pt[0] <= last[0]; out_pt[0]++) {
+     for (out_pt[1] = first[1]; out_pt[1] <= last[1]; out_pt[1]++) {
+     for (out_pt[2] = first[2]; out_pt[2] <= last[2]; out_pt[2]++) {
+       *out_ptr++ = static_cast<OutFloatType>(map_unit_cell(out_pt));
+     }}}
+     return result;
+   }
+ 
  }} // namespace cctbx::maptbx
  

Update of /cvsroot/cctbx/iotbx/iotbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1213

Modified Files:
	tst_reflection_statistics.py 
Log Message:
attempt to work around strange Python 2.2.1 C assert failure

Index: tst_reflection_statistics.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/regression/tst_reflection_statistics.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** tst_reflection_statistics.py	3 Jan 2005 19:55:01 -0000	1.3
--- tst_reflection_statistics.py	28 Jan 2005 19:22:30 -0000	1.4
***************
*** 1,2 ****
--- 1,3 ----
+ from cctbx.array_family import flex
  from iotbx.command_line import reflection_statistics
  from iotbx import mtz
***************
*** 6,10 ****
  from cctbx.sgtbx import subgroups
  from cctbx.development import debug_utils
- from cctbx.array_family import flex
  from cStringIO import StringIO
  import sys
--- 7,10 ----

Update of /cvsroot/cctbx/cctbx/cctbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29621

Modified Files:
	tst_reflection_statistics.py 
Log Message:
fixed random seed to avoid rare failures

Index: tst_reflection_statistics.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_reflection_statistics.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** tst_reflection_statistics.py	4 Jan 2005 20:48:11 -0000	1.3
--- tst_reflection_statistics.py	28 Jan 2005 17:06:12 -0000	1.4
***************
*** 12,16 ****
  import sys
  
! if (0):
    random.seed(0)
    flex.set_random_seed(0)
--- 12,16 ----
  import sys
  
! if (1): # fixed random seed to avoid rare failures
    random.seed(0)
    flex.set_random_seed(0)

Update of /cvsroot/cctbx/cctbx/dox/rst
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25684

Modified Files:
	versions.txt 
Log Message:
newsletter link to cci web server

Index: versions.txt
===================================================================
RCS file: /cvsroot/cctbx/cctbx/dox/rst/versions.txt,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** versions.txt	28 Jan 2005 01:42:38 -0000	1.9
--- versions.txt	28 Jan 2005 16:52:38 -0000	1.10
***************
*** 26,30 ****
    - `No. 4, 2004/08 <http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf>`_
  
!   - `No. 5, 2005/01 <http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2005jan/>`_
  
  - Python interfaces:
--- 26,30 ----
    - `No. 4, 2004/08 <http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf>`_
  
!   - `No. 5, 2005/01 <http://cci.lbl.gov/publications/download/iucrcompcomm_jan2005.pdf>`_
  
  - Python interfaces:

Update of /cvsroot/cctbx/cctbx/cctbx/xray
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22039

Modified Files:
	target_functors.py 
Log Message:
step for integration is hidden now in fmodel

Index: target_functors.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/xray/target_functors.py,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** target_functors.py	14 Jan 2005 03:31:30 -0000	1.14
--- target_functors.py	28 Jan 2005 16:38:36 -0000	1.15
***************
*** 25,29 ****
                       flags,
                       abcd                   = None,
-                      step_for_integration   = None,
                       weights                = None,
                       use_sigmas_as_weights  = False,
--- 25,28 ----
***************
*** 39,43 ****
        self.f_obs_t = self.f_obs
      if(self.target_name == "mlhl"):
!       assert self.abcd is not None and self.step_for_integration
      if(self.abcd is not None):
        if(self.target_name == "mlhl"):
--- 38,42 ----
        self.f_obs_t = self.f_obs
      if(self.target_name == "mlhl"):
!       assert self.abcd is not None
      if(self.abcd is not None):
        if(self.target_name == "mlhl"):
***************
*** 86,91 ****
        return maximum_likelihood_criterion_hl(
                                f_obs                = f_obs,
!                               abcd                 = abcd.data(),
!                               step_for_integration = self.step_for_integration)
  
    def target_functor_t(self, selection = None):
--- 85,89 ----
        return maximum_likelihood_criterion_hl(
                                f_obs                = f_obs,
!                               abcd                 = abcd.data())
  
    def target_functor_t(self, selection = None):
***************
*** 112,117 ****
        return maximum_likelihood_criterion_hl(
                                f_obs                = f_obs,
!                               abcd                 = abcd.data(),
!                               step_for_integration = self.step_for_integration)
  
  
--- 110,114 ----
        return maximum_likelihood_criterion_hl(
                                f_obs                = f_obs,
!                               abcd                 = abcd.data())
  
  
***************
*** 206,210 ****
    def __init__(self, f_obs,
                       abcd,
!                      step_for_integration):
      adopt_init_args(self, locals(), hide=True)
  
--- 203,207 ----
    def __init__(self, f_obs,
                       abcd,
!                      step_for_integration = 5.0):
      adopt_init_args(self, locals(), hide=True)
  

Update of /cvsroot/cctbx/cctbx/sgtbx/boost_python
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14605/sgtbx/boost_python

Modified Files:
	space_group.cpp tst_sgtbx.py 
Log Message:
new space_group.average_u_star(); generic average_tensor(), used by the new function, site_symmetry.average_u_star() and space_group.average_metrical_matrix()

Index: space_group.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/boost_python/space_group.cpp,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** space_group.cpp	22 Dec 2004 00:24:54 -0000	1.12
--- space_group.cpp	28 Jan 2005 06:19:21 -0000	1.13
***************
*** 144,147 ****
--- 144,151 ----
            &w_t::is_compatible_unit_cell,
            is_compatible_unit_cell_overloads())
+         .def("average_u_star",
+           (scitbx::sym_mat3<double>(w_t::*)(
+             scitbx::sym_mat3<double> const&) const) &w_t::average_u_star, (
+           arg_("u_star")))
          .def("build_derived_acentric_group",
            &w_t::build_derived_acentric_group)

Index: tst_sgtbx.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/boost_python/tst_sgtbx.py,v
retrieving revision 1.61
retrieving revision 1.62
diff -C2 -d -r1.61 -r1.62
*** tst_sgtbx.py	28 Jan 2005 04:27:10 -0000	1.61
--- tst_sgtbx.py	28 Jan 2005 06:19:21 -0000	1.62
***************
*** 668,671 ****
--- 668,673 ----
    g = space_group("C 2y (x+y,-x+y+z,z)")
    assert g.is_compatible_unit_cell(u)
+   assert approx_equal(g.average_u_star(u_star=range(6,0,-1)),
+     (6.5, 5.5, 4.0, 3.5, 2.5, 1.5))
    g = space_group("C 2 -2c")
    h = g.build_derived_reflection_intensity_group(anomalous_flag=True)

Update of /cvsroot/cctbx/cctbx/include/cctbx/sgtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14605/include/cctbx/sgtbx

Modified Files:
	rt_mx.h site_symmetry.h space_group.h 
Log Message:
new space_group.average_u_star(); generic average_tensor(), used by the new function, site_symmetry.average_u_star() and space_group.average_metrical_matrix()

Index: space_group.h
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/sgtbx/space_group.h,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** space_group.h	22 Dec 2004 00:24:53 -0000	1.11
--- space_group.h	28 Jan 2005 06:19:20 -0000	1.12
***************
*** 477,481 ****
         */
        uc_sym_mat3
!       average_metrical_matrix(uc_sym_mat3 const& g) const;
  
        //! Computes a unit cell compatible with the space group symmetry.
--- 477,484 ----
         */
        uc_sym_mat3
!       average_metrical_matrix(uc_sym_mat3 const& g) const
!       {
!         return average_tensor(smx_.const_ref(), g, false);
!       }
  
        //! Computes a unit cell compatible with the space group symmetry.
***************
*** 504,507 ****
--- 507,524 ----
        }
  
+       /*! \brief Averages symmetrically equivalent u_star tensors to
+           obtain a tensor that satisfies the symmetry constraints.
+        */
+       /*! The averaged tensor is equivalent to beta_inv
+           of Giacovazzo, Fundamentals of Crystallography 1992,
+           p. 189.
+        */
+       template <class FloatType>
+       scitbx::sym_mat3<FloatType>
+       average_u_star(scitbx::sym_mat3<FloatType> const& u_star) const
+       {
+         return average_tensor(smx_.const_ref(), u_star, true);
+       }
+ 
        //! The translation parts of the symmetry operations are set to 0.
        /*! If discard_z = false, the lattice translation vectors are not

Index: rt_mx.h
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/sgtbx/rt_mx.h,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** rt_mx.h	16 Dec 2004 02:53:44 -0000	1.8
--- rt_mx.h	28 Jan 2005 06:19:20 -0000	1.9
***************
*** 4,7 ****
--- 4,8 ----
  #include <cctbx/sgtbx/rot_mx.h>
  #include <cctbx/sgtbx/parse_string.h>
+ #include <scitbx/sym_mat3.h>
  #include <scitbx/array_family/tiny_types.h>
  #include <cctbx/import_scitbx_af.h>
***************
*** 488,491 ****
--- 489,528 ----
    };
  
+   //! Symmetry-averaged tensor.
+   /*! reciprocal_space = false:
+         sum[tensor.tensor_transpose_transform(r)] / matrices.size()
+ 
+       reciprocal_space = true:
+         sum[tensor.tensor_transform(r)] / matrices.size()
+ 
+       over all rotation parts r of matrices.
+ 
+       See also:
+         Giacovazzo, Fundamentals of Crystallography 1992, p. 189.
+ 
+       Not available in Python.
+    */
+   template <class FloatType>
+   scitbx::sym_mat3<FloatType>
+   average_tensor(
+     af::const_ref<rt_mx> const& matrices,
+     scitbx::sym_mat3<FloatType> const& tensor,
+     bool reciprocal_space)
+   {
+     scitbx::sym_mat3<FloatType> result(0,0,0,0,0,0);
+     for (std::size_t i=0;i<matrices.size();i++) {
+       scitbx::mat3<FloatType>
+         r = matrices[i].r()
+               .as_floating_point(scitbx::type_holder<FloatType>());
+       if (reciprocal_space) {
+         result += tensor.tensor_transform(r);
+       }
+       else {
+         result += tensor.tensor_transpose_transform(r);
+       }
+     }
+     return result / static_cast<FloatType>(matrices.size());
+   }
+ 
  }} // namespace cctbx::sgtbx
  

Index: site_symmetry.h
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/sgtbx/site_symmetry.h,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** site_symmetry.h	4 Jul 2004 04:47:43 -0000	1.9
--- site_symmetry.h	28 Jan 2005 06:19:20 -0000	1.10
***************
*** 106,110 ****
        template <class FloatType>
        scitbx::sym_mat3<FloatType>
!       average_u_star(scitbx::sym_mat3<FloatType> const& u_star) const;
  
        /*! \brief Construct a new site_symmetry_ops instance with the
--- 106,113 ----
        template <class FloatType>
        scitbx::sym_mat3<FloatType>
!       average_u_star(scitbx::sym_mat3<FloatType> const& u_star) const
!       {
!         return average_tensor(matrices_.const_ref(), u_star, true);
!       }
  
        /*! \brief Construct a new site_symmetry_ops instance with the
***************
*** 182,200 ****
    }
  
-   template <class FloatType>
-   scitbx::sym_mat3<FloatType>
-   site_symmetry_ops::
-   average_u_star(scitbx::sym_mat3<FloatType> const& u_star) const
-   {
-     scitbx::sym_mat3<FloatType> sum_r_u_rt(0,0,0,0,0,0);
-     for (std::size_t i=0;i<matrices_.size();i++) {
-       scitbx::mat3<FloatType>
-         r = matrices_[i].r()
-               .as_floating_point(scitbx::type_holder<FloatType>());
-       sum_r_u_rt += u_star.tensor_transform(r);
-     }
-     return sum_r_u_rt / static_cast<FloatType>(matrices_.size());
-   }
- 
    //! Numerically robust algorithm for the determination of site-symmetries.
    class site_symmetry : public site_symmetry_ops
--- 185,188 ----

Update of /cvsroot/cctbx/cctbx/sgtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14605/sgtbx

Modified Files:
	space_group.cpp 
Log Message:
new space_group.average_u_star(); generic average_tensor(), used by the new function, site_symmetry.average_u_star() and space_group.average_metrical_matrix()

Index: space_group.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/space_group.cpp,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** space_group.cpp	22 Dec 2004 00:24:54 -0000	1.9
--- space_group.cpp	28 Jan 2005 06:19:21 -0000	1.10
***************
*** 565,581 ****
    }
  
-   uc_sym_mat3
-   space_group::
-   average_metrical_matrix(uc_sym_mat3 const& g) const
-   {
-     typedef uc_sym_mat3::value_type float_type;
-     uc_sym_mat3 sum_r_g_rt(0,0,0,0,0,0);
-     for(std::size_t i_smx=0;i_smx<n_smx();i_smx++) {
-       uc_mat3 r(smx_[i_smx].r().as_double());
-       sum_r_g_rt += g.tensor_transpose_transform(r);
-     }
-     return sum_r_g_rt / float_type(n_smx());
-   }
- 
    af::shared<rt_mx>
    space_group::all_ops(int mod, bool cancel) const
--- 565,568 ----

Update of /cvsroot/cctbx/cctbx/cctbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14605/cctbx/regression

Modified Files:
	tst_sgtbx.py 
Log Message:
new space_group.average_u_star(); generic average_tensor(), used by the new function, site_symmetry.average_u_star() and space_group.average_metrical_matrix()

Index: tst_sgtbx.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_sgtbx.py,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** tst_sgtbx.py	28 Jan 2005 02:27:04 -0000	1.14
--- tst_sgtbx.py	28 Jan 2005 06:19:20 -0000	1.15
***************
*** 66,69 ****
--- 66,70 ----
    from cctbx import crystal
    from cctbx import adptbx
+   from scitbx import matrix
    site_symmetry = crystal.special_position_settings(
      crystal_symmetry).site_symmetry(site=(0,0,0))
***************
*** 72,79 ****
    assert site_symmetry.n_matrices() == group.order_p()
    adp_constraints = group.adp_constraints()
!   u_cart = adptbx.random_rotate_ellipsoid(
      u_cart=[random.random() for i in xrange(3)] + [0,0,0])
!   u_star = adptbx.u_cart_as_u_star(unit_cell, u_cart)
!   u_star = site_symmetry.average_u_star(u_star)
    independent_params = adp_constraints.independent_params(u_star)
    assert adp_constraints.n_independent_params() == independent_params.size()
--- 73,84 ----
    assert site_symmetry.n_matrices() == group.order_p()
    adp_constraints = group.adp_constraints()
!   u_cart_p1 = adptbx.random_rotate_ellipsoid(
      u_cart=[random.random() for i in xrange(3)] + [0,0,0])
!   u_star_p1 = adptbx.u_cart_as_u_star(unit_cell, u_cart_p1)
!   u_star = site_symmetry.average_u_star(u_star_p1)
!   f = unit_cell.volume()**(2/3.)
!   assert approx_equal(
!     list(matrix.col(group.average_u_star(u_star=u_star_p1))*f),
!     list(matrix.col(u_star)*f))
    independent_params = adp_constraints.independent_params(u_star)
    assert adp_constraints.n_independent_params() == independent_params.size()

Update of /cvsroot/cctbx/cctbx/cctbx/sgtbx/direct_space_asu
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25615/cctbx/sgtbx/direct_space_asu

Modified Files:
	facet_analysis.py 
Log Message:
second step of move cctbx::sgtbx::row_echelon -> scitbx::matrix::row_echelon: use code from new location; old implementation removed

Index: facet_analysis.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/sgtbx/direct_space_asu/facet_analysis.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** facet_analysis.py	6 Sep 2004 07:40:50 -0000	1.6
--- facet_analysis.py	28 Jan 2005 04:26:57 -0000	1.7
***************
*** 1,8 ****
  from cctbx.sgtbx.direct_space_asu import cut_plane
- from cctbx import sgtbx
  from cctbx.array_family import flex
  from scitbx import matrix
! from boost import rational
  from scitbx.python_utils import list_algebra
  
  def intersection(facets):
--- 1,8 ----
  from cctbx.sgtbx.direct_space_asu import cut_plane
  from cctbx.array_family import flex
  from scitbx import matrix
! import scitbx.math
  from scitbx.python_utils import list_algebra
+ from boost import rational
  
  def intersection(facets):
***************
*** 18,27 ****
    m.resize(flex.grid(3,3))
    t.resize(flex.grid(3,1))
!   r = sgtbx.row_echelon_form_t(m, t)
    assert r in (2,3)
    if (r != 3): return None
    t.resize(flex.grid(3))
    sol = flex.int(3)
!   d = sgtbx.row_echelon_back_substitution(m, t, sol)
    assert d > 0
    return tuple([rational.int(s,d) for s in sol])
--- 18,27 ----
    m.resize(flex.grid(3,3))
    t.resize(flex.grid(3,1))
!   r = scitbx.math.row_echelon_form_t(m, t)
    assert r in (2,3)
    if (r != 3): return None
    t.resize(flex.grid(3))
    sol = flex.int(3)
!   d = scitbx.math.row_echelon_back_substitution_int(m, t, sol)
    assert d > 0
    return tuple([rational.int(s,d) for s in sol])

Update of /cvsroot/cctbx/cctbx/cctbx/sgtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25615/cctbx/sgtbx

Modified Files:
	__init__.py 
Log Message:
second step of move cctbx::sgtbx::row_echelon -> scitbx::matrix::row_echelon: use code from new location; old implementation removed

Index: __init__.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/sgtbx/__init__.py,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** __init__.py	28 Jan 2005 01:42:38 -0000	1.29
--- __init__.py	28 Jan 2005 04:26:56 -0000	1.30
***************
*** 176,182 ****
      return uctbx.unit_cell(params)
  
- def row_echelon_back_substitution(rt_mx, v=None, sol=None, indep=None):
-   return ext.row_echelon_back_substitution(rt_mx, v, sol, indep)
- 
  class _tr_vec(boost.python.injector, tr_vec):
  
--- 176,179 ----

Update of /cvsroot/cctbx/cctbx/include/cctbx/sgtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25615/include/cctbx/sgtbx

Modified Files:
	row_echelon_solve.h smith_normal_form.h 
Removed Files:
	row_echelon.h 
Log Message:
second step of move cctbx::sgtbx::row_echelon -> scitbx::matrix::row_echelon: use code from new location; old implementation removed

Index: smith_normal_form.h
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/sgtbx/smith_normal_form.h,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** smith_normal_form.h	9 Nov 2002 00:46:59 -0000	1.2
--- smith_normal_form.h	28 Jan 2005 04:26:58 -0000	1.3
***************
*** 1,15 ****
- /* Copyright (c) 2001-2002 The Regents of the University of California
-    through E.O. Lawrence Berkeley National Laboratory, subject to
-    approval by the U.S. Department of Energy.
-    See files COPYRIGHT.txt and LICENSE.txt for further details.
- 
-    Revision history:
-      2002 Sep: Refactored part of sgtbx/math.cpp (rwgk)
-  */
- 
  #ifndef CCTBX_SGTBX_SMITH_NORMAL_FORM_H
  #define CCTBX_SGTBX_SMITH_NORMAL_FORM_H
  
! #include <cctbx/sgtbx/row_echelon.h>
  
  namespace cctbx { namespace sgtbx {
--- 1,6 ----
  #ifndef CCTBX_SGTBX_SMITH_NORMAL_FORM_H
  #define CCTBX_SGTBX_SMITH_NORMAL_FORM_H
  
! #include <scitbx/matrix/row_echelon.h>
  
  namespace cctbx { namespace sgtbx {
***************
*** 26,34 ****
      for (;;)
      {
!       row_echelon::form_t(m, p);
        if (m.is_diagonal()) break;
        m.transpose_in_place();
  
!       row_echelon::form_t(m, q);
        if (m.is_diagonal()) break;
        m.transpose_in_place();
--- 17,25 ----
      for (;;)
      {
!       scitbx::matrix::row_echelon::form_t(m, p);
        if (m.is_diagonal()) break;
        m.transpose_in_place();
  
!       scitbx::matrix::row_echelon::form_t(m, q);
        if (m.is_diagonal()) break;
        m.transpose_in_place();

Index: row_echelon_solve.h
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/sgtbx/row_echelon_solve.h,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** row_echelon_solve.h	9 Nov 2002 00:46:59 -0000	1.2
--- row_echelon_solve.h	28 Jan 2005 04:26:58 -0000	1.3
***************
*** 1,15 ****
- /* Copyright (c) 2001-2002 The Regents of the University of California
-    through E.O. Lawrence Berkeley National Laboratory, subject to
-    approval by the U.S. Department of Energy.
-    See files COPYRIGHT.txt and LICENSE.txt for further details.
- 
-    Revision history:
-      2002 Sep: Created (rwgk)
-  */
- 
  #ifndef CCTBX_SGTBX_ROW_ECHELON_SOLVE_H
  #define CCTBX_SGTBX_ROW_ECHELON_SOLVE_H
  
! #include <cctbx/sgtbx/row_echelon.h>
  
  namespace cctbx { namespace sgtbx { namespace row_echelon { namespace solve {
--- 1,8 ----
  #ifndef CCTBX_SGTBX_ROW_ECHELON_SOLVE_H
  #define CCTBX_SGTBX_ROW_ECHELON_SOLVE_H
  
! #include <cctbx/sgtbx/basic.h>
! #include <cctbx/import_scitbx_af.h>
! #include <scitbx/matrix/row_echelon.h>
  
  namespace cctbx { namespace sgtbx { namespace row_echelon { namespace solve {
***************
*** 17,21 ****
    af::tiny<sg_vec3, 4>
    homog_rank_1(scitbx::mat_const_ref<int> const& re_mx,
!                row_echelon::independent<int> const& indep);
  
    af::tiny<sg_vec3, 4>
--- 10,14 ----
    af::tiny<sg_vec3, 4>
    homog_rank_1(scitbx::mat_const_ref<int> const& re_mx,
!                scitbx::matrix::row_echelon::independent<int> const& indep);
  
    af::tiny<sg_vec3, 4>

--- row_echelon.h DELETED ---

Update of /cvsroot/cctbx/cctbx/sgtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25615/sgtbx

Modified Files:
	find_affine.cpp rot_mx_info.cpp row_echelon_solve.cpp 
	rt_mx.cpp seminvariant.cpp space_group_type.cpp 
Log Message:
second step of move cctbx::sgtbx::row_echelon -> scitbx::matrix::row_echelon: use code from new location; old implementation removed

Index: row_echelon_solve.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/row_echelon_solve.cpp,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** row_echelon_solve.cpp	9 Nov 2002 00:47:01 -0000	1.2
--- row_echelon_solve.cpp	28 Jan 2005 04:26:59 -0000	1.3
***************
*** 1,11 ****
- /* Copyright (c) 2001-2002 The Regents of the University of California
-    through E.O. Lawrence Berkeley National Laboratory, subject to
-    approval by the U.S. Department of Energy.
-    See files COPYRIGHT.txt and LICENSE.txt for further details.
- 
-    Revision history:
-      2002 Sep: Created with fragments from several files (rwgk)
-  */
- 
  #include <cctbx/sgtbx/row_echelon_solve.h>
  
--- 1,2 ----
***************
*** 14,18 ****
    af::tiny<sg_vec3, 4>
    homog_rank_1(scitbx::mat_const_ref<int> const& re_mx,
!                row_echelon::independent<int> const& indep)
    {
      CCTBX_ASSERT(re_mx.n_rows() == 1);
--- 5,9 ----
    af::tiny<sg_vec3, 4>
    homog_rank_1(scitbx::mat_const_ref<int> const& re_mx,
!                scitbx::matrix::row_echelon::independent<int> const& indep)
    {
      CCTBX_ASSERT(re_mx.n_rows() == 1);
***************
*** 31,36 ****
        }
        int* n_a = 0;
!       CCTBX_ASSERT(
!         row_echelon::back_substitution(re_mx, n_a, sol[i_tv].begin()) > 0);
      }
      return sol;
--- 22,27 ----
        }
        int* n_a = 0;
!       CCTBX_ASSERT(scitbx::matrix::row_echelon::back_substitution_int(
!         re_mx, n_a, sol[i_tv].begin()) > 0);
      }
      return sol;
***************
*** 40,44 ****
    homog_rank_1(scitbx::mat_const_ref<int> const& re_mx)
    {
!     row_echelon::independent<int> indep(re_mx);
      return homog_rank_1(re_mx, indep);
    }
--- 31,35 ----
    homog_rank_1(scitbx::mat_const_ref<int> const& re_mx)
    {
!     scitbx::matrix::row_echelon::independent<int> indep(re_mx);
      return homog_rank_1(re_mx, indep);
    }
***************
*** 66,76 ****
    {
      CCTBX_ASSERT(re_mx.n_rows() == 2);
!     row_echelon::independent<int> indep(re_mx);
      CCTBX_ASSERT(indep.indices.size() == 1);
      sg_vec3 ev(0,0,0);
      ev[indep.indices[0]] = 1;
      int* n_a = 0;
!     CCTBX_ASSERT(
!       row_echelon::back_substitution(re_mx, n_a, ev.begin()) >= 1);
      if (sign_hemisphere(ev) < 0) ev *= -1;
      return ev;
--- 57,67 ----
    {
      CCTBX_ASSERT(re_mx.n_rows() == 2);
!     scitbx::matrix::row_echelon::independent<int> indep(re_mx);
      CCTBX_ASSERT(indep.indices.size() == 1);
      sg_vec3 ev(0,0,0);
      ev[indep.indices[0]] = 1;
      int* n_a = 0;
!     CCTBX_ASSERT(scitbx::matrix::row_echelon::back_substitution_int(
!       re_mx, n_a, ev.begin()) >= 1);
      if (sign_hemisphere(ev) < 0) ev *= -1;
      return ev;

Index: rt_mx.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/rt_mx.cpp,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** rt_mx.cpp	16 Dec 2004 02:53:44 -0000	1.6
--- rt_mx.cpp	28 Jan 2005 04:26:59 -0000	1.7
***************
*** 1,4 ****
  #include <cctbx/sgtbx/rt_mx.h>
! #include <cctbx/sgtbx/row_echelon.h>
  #include <ctype.h>
  #include <string.h>
--- 1,4 ----
  #include <cctbx/sgtbx/rt_mx.h>
! #include <scitbx/matrix/row_echelon.h>
  #include <ctype.h>
  #include <string.h>
***************
*** 282,289 ****
      scitbx::mat_ref<int> ref_rmi(rmi.num().begin(), 3, 3);
      scitbx::mat_ref<int> ref_p(p.num().begin(), 3, 3);
!     row_echelon::form_t(ref_rmi, ref_p);
      tr_vec pwl = p * wl;
      tr_vec sh(0);
!     sh.den() = row_echelon::back_substitution(
        ref_rmi, pwl.num().begin(), sh.num().begin());
      CCTBX_ASSERT(sh.den() > 0);
--- 282,289 ----
      scitbx::mat_ref<int> ref_rmi(rmi.num().begin(), 3, 3);
      scitbx::mat_ref<int> ref_p(p.num().begin(), 3, 3);
!     scitbx::matrix::row_echelon::form_t(ref_rmi, ref_p);
      tr_vec pwl = p * wl;
      tr_vec sh(0);
!     sh.den() = scitbx::matrix::row_echelon::back_substitution_int(
        ref_rmi, pwl.num().begin(), sh.num().begin());
      CCTBX_ASSERT(sh.den() > 0);

Index: space_group_type.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/space_group_type.cpp,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** space_group_type.cpp	6 Dec 2004 15:34:54 -0000	1.4
--- space_group_type.cpp	28 Jan 2005 04:27:03 -0000	1.5
***************
*** 178,182 ****
        rot_mx cum_mx = r[0].accumulate(ord[0]);
        scitbx::mat_ref<int> re_mx(cum_mx.num().begin(), 3, 3);
!       CCTBX_ASSERT(row_echelon::form(re_mx) == 1);
        af::tiny<sg_vec3, 4> sol = row_echelon::solve::homog_rank_1(re_mx);
        std::size_t n_ix = 1; if (ord[0] == 2) n_ix++;
--- 178,182 ----
        rot_mx cum_mx = r[0].accumulate(ord[0]);
        scitbx::mat_ref<int> re_mx(cum_mx.num().begin(), 3, 3);
!       CCTBX_ASSERT(scitbx::matrix::row_echelon::form(re_mx) == 1);
        af::tiny<sg_vec3, 4> sol = row_echelon::solve::homog_rank_1(re_mx);
        std::size_t n_ix = 1; if (ord[0] == 2) n_ix++;

Index: seminvariant.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/seminvariant.cpp,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** seminvariant.cpp	22 Apr 2004 21:21:00 -0000	1.29
--- seminvariant.cpp	28 Jan 2005 04:26:59 -0000	1.30
***************
*** 72,77 ****
        af::tiny<int, 3 * 3 * 3> gen_rmi = construct_gen_rmi(gen, false);
        scitbx::mat_ref<int> re_mx(gen_rmi.begin(), gen.n_all() * 3, 3);
!       CCTBX_ASSERT(row_echelon::form(re_mx) <= 3);
!       row_echelon::independent<int> indep(re_mx);
        if (indep.indices.size() != 2) {
          for (std::size_t i_indep=0;i_indep<indep.indices.size();i_indep++) {
--- 72,77 ----
        af::tiny<int, 3 * 3 * 3> gen_rmi = construct_gen_rmi(gen, false);
        scitbx::mat_ref<int> re_mx(gen_rmi.begin(), gen.n_all() * 3, 3);
!       CCTBX_ASSERT(scitbx::matrix::row_echelon::form(re_mx) <= 3);
!       scitbx::matrix::row_echelon::independent<int> indep(re_mx);
        if (indep.indices.size() != 2) {
          for (std::size_t i_indep=0;i_indep<indep.indices.size();i_indep++) {
***************
*** 80,85 ****
            vm.v[indep.indices[i_indep]] = 1;
            int* n_a = 0;
!           CCTBX_ASSERT(
!             row_echelon::back_substitution(re_mx, n_a, vm.v.begin()) > 0);
            vm.m = 0;
            result.push_back(vm);
--- 80,85 ----
            vm.v[indep.indices[i_indep]] = 1;
            int* n_a = 0;
!           CCTBX_ASSERT(scitbx::matrix::row_echelon::back_substitution_int(
!             re_mx, n_a, vm.v.begin()) > 0);
            vm.m = 0;
            result.push_back(vm);

Index: find_affine.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/find_affine.cpp,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** find_affine.cpp	13 Dec 2004 18:11:10 -0000	1.3
--- find_affine.cpp	28 Jan 2005 04:26:59 -0000	1.4
***************
*** 1,4 ****
  #include <cctbx/sgtbx/find_affine.h>
! #include <cctbx/sgtbx/row_echelon.h>
  #include <scitbx/math/unimodular_generator.h>
  #include <scitbx/array_family/loops.h>
--- 1,4 ----
  #include <cctbx/sgtbx/find_affine.h>
! #include <scitbx/matrix/row_echelon.h>
  #include <scitbx/math/unimodular_generator.h>
  #include <scitbx/array_family/loops.h>
***************
*** 71,76 ****
      }
      scitbx::mat_ref<int> m_ref(&*m.begin(), n_rows, 9);
!     std::size_t r = row_echelon::form(m_ref);
!     row_echelon::independent<int, 9> indep(m_ref);
      typedef af::nested_loop<af::small<int, 9> > loop_t;
      af::small<int, 9> loop_begin(indep.indices.size(), -range);
--- 71,76 ----
      }
      scitbx::mat_ref<int> m_ref(&*m.begin(), n_rows, 9);
!     std::size_t r = scitbx::matrix::row_echelon::form(m_ref);
!     scitbx::matrix::row_echelon::independent<int, 9> indep(m_ref);
      typedef af::nested_loop<af::small<int, 9> > loop_t;
      af::small<int, 9> loop_begin(indep.indices.size(), -range);
***************
*** 81,85 ****
          c[indep.indices[i]] = loop()[i];
        }
!       int den = row_echelon::back_substitution(
          m_ref,
          static_cast<int*>(0),
--- 81,85 ----
          c[indep.indices[i]] = loop()[i];
        }
!       int den = scitbx::matrix::row_echelon::back_substitution_int(
          m_ref,
          static_cast<int*>(0),

Index: rot_mx_info.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/rot_mx_info.cpp,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** rot_mx_info.cpp	9 Nov 2002 00:47:01 -0000	1.2
--- rot_mx_info.cpp	28 Jan 2005 04:26:59 -0000	1.3
***************
*** 56,60 ****
        rot_mx rmi = proper_r.minus_unit_mx();
        scitbx::mat_ref<int> re_mx(rmi.num().begin(), 3, 3);
!       if (row_echelon::form(re_mx) != 2) {
          throw error("Cannot determine Eigenvector of rotation matrix.");
        }
--- 56,60 ----
        rot_mx rmi = proper_r.minus_unit_mx();
        scitbx::mat_ref<int> re_mx(rmi.num().begin(), 3, 3);
!       if (scitbx::matrix::row_echelon::form(re_mx) != 2) {
          throw error("Cannot determine Eigenvector of rotation matrix.");
        }

Update of /cvsroot/cctbx/cctbx/sgtbx/boost_python
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25615/sgtbx/boost_python

Modified Files:
	SConscript sgtbx_ext.cpp tst_sgtbx.py 
Removed Files:
	row_echelon.cpp 
Log Message:
second step of move cctbx::sgtbx::row_echelon -> scitbx::matrix::row_echelon: use code from new location; old implementation removed

Index: sgtbx_ext.cpp
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/boost_python/sgtbx_ext.cpp,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** sgtbx_ext.cpp	5 Jul 2004 07:21:44 -0000	1.15
--- sgtbx_ext.cpp	28 Jan 2005 04:27:10 -0000	1.16
***************
*** 18,22 ****
    void wrap_reciprocal_space_asu();
    void wrap_rot_mx();
-   void wrap_row_echelon();
    void wrap_rt_mx();
    void wrap_search_symmetry();
--- 18,21 ----
***************
*** 101,105 ****
      wrap_reciprocal_space_asu();
      wrap_rot_mx();
-     wrap_row_echelon();
      wrap_rt_mx();
      wrap_search_symmetry();
--- 100,103 ----

Index: SConscript
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/boost_python/SConscript,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** SConscript	17 Apr 2004 08:04:46 -0000	1.11
--- SConscript	28 Jan 2005 04:27:09 -0000	1.12
***************
*** 11,15 ****
    "reciprocal_space_asu.cpp",
    "rot_mx.cpp",
-   "row_echelon.cpp",
    "rt_mx.cpp",
    "search_symmetry.cpp",
--- 11,14 ----

--- row_echelon.cpp DELETED ---

Index: tst_sgtbx.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/sgtbx/boost_python/tst_sgtbx.py,v
retrieving revision 1.60
retrieving revision 1.61
diff -C2 -d -r1.60 -r1.61
*** tst_sgtbx.py	22 Dec 2004 00:24:54 -0000	1.60
--- tst_sgtbx.py	28 Jan 2005 04:27:10 -0000	1.61
***************
*** 1427,1457 ****
    assert ss_discrete.vectors_and_moduli()[1].v == (0,1,0)
  
- def exercise_row_echelon():
-   m = flex.int((1,1,1,1))
-   m.resize(flex.grid(2,2))
-   t = flex.int((2,3))
-   t.resize(flex.grid(2,1))
-   assert sgtbx.row_echelon_form_t(m, t) == 1
-   assert m.focus() == (1,2)
-   assert tuple(m) == (1,1)
-   assert tuple(t) == (2,1)
-   assert sgtbx.row_echelon_form(m) == 1
-   assert m.focus() == (1,2)
-   assert tuple(m) == (1,1)
-   m = flex.int((0,-24,0,0,0,-24,24,0,24))
-   m.resize(flex.grid(3,3))
-   t = flex.int((-3, -6, 0))
-   t.resize(flex.grid(3,1))
-   assert sgtbx.row_echelon_form_t(m, t) == 3
-   assert tuple(m) == (24,0,24,0,24,0,0,0,24)
-   assert tuple(t) == (0,3,6)
-   t.resize(flex.grid(3))
-   sol = flex.int(3)
-   assert sgtbx.row_echelon_back_substitution(m, t, sol) == 8
-   assert tuple(sol) == (-2,1,2)
-   indep = flex.bool((True,True,True))
-   assert sgtbx.row_echelon_back_substitution(m, indep=indep) == 1
-   assert tuple(indep) == (False,False,False)
- 
  def exercise_lattice_symmetry():
    niggli_cell = uctbx.unit_cell((12,13,14,80,83,86))
--- 1427,1430 ----
***************
*** 1641,1645 ****
    exercise_sym_equiv_sites()
    exercise_seminvariant()
-   exercise_row_echelon()
    exercise_lattice_symmetry()
    exercise_find_affine()
--- 1614,1617 ----

Update of /cvsroot/cctbx/cctbx/cctbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1099/regression

Modified Files:
	tst_sgtbx.py 
Log Message:
adp_constraints.n_independent_params(), n_dependent_params() convenience methods

Index: tst_sgtbx.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_sgtbx.py,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** tst_sgtbx.py	28 Jan 2005 01:42:38 -0000	1.13
--- tst_sgtbx.py	28 Jan 2005 02:27:04 -0000	1.14
***************
*** 77,80 ****
--- 77,83 ----
    u_star = site_symmetry.average_u_star(u_star)
    independent_params = adp_constraints.independent_params(u_star)
+   assert adp_constraints.n_independent_params() == independent_params.size()
+   assert adp_constraints.n_independent_params() \
+        + adp_constraints.n_dependent_params() == 6
    u_star_vfy = adp_constraints.all_params(independent_params)
    u_cart = adptbx.u_star_as_u_cart(unit_cell, u_star)

Update of /cvsroot/cctbx/cctbx/cctbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1099

Modified Files:
	adptbx.py 
Log Message:
adp_constraints.n_independent_params(), n_dependent_params() convenience methods

Index: adptbx.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/adptbx.py,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** adptbx.py	28 Jan 2005 01:42:37 -0000	1.7
--- adptbx.py	28 Jan 2005 02:27:04 -0000	1.8
***************
*** 23,26 ****
--- 23,32 ----
        independent_flags=self.independent_flags)
  
+   def n_independent_params(self):
+     return self.independent_flags.count(True)
+ 
+   def n_dependent_params(self):
+     return self.independent_flags.count(False)
+ 
    def independent_params(self, u_star):
      return flex.double(u_star).select(self.independent_flags)

Update of /cvsroot/cctbx/cctbx/dox/rst
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24843/dox/rst

Modified Files:
	versions.txt 
Log Message:
new cctbx.sgtbx.space_group.adp_constraints() method

Index: versions.txt
===================================================================
RCS file: /cvsroot/cctbx/cctbx/dox/rst/versions.txt,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** versions.txt	25 Aug 2004 00:16:53 -0000	1.8
--- versions.txt	28 Jan 2005 01:42:38 -0000	1.9
***************
*** 26,29 ****
--- 26,31 ----
    - `No. 4, 2004/08 <http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf>`_
  
+   - `No. 5, 2005/01 <http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2005jan/>`_
+ 
  - Python interfaces:
    `libtbx <current_cvs/python/libtbx/>`_

Update of /cvsroot/cctbx/cctbx/cctbx/sgtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24843/cctbx/sgtbx

Modified Files:
	__init__.py 
Log Message:
new cctbx.sgtbx.space_group.adp_constraints() method

Index: __init__.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/sgtbx/__init__.py,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** __init__.py	21 Jan 2005 08:59:08 -0000	1.28
--- __init__.py	28 Jan 2005 01:42:38 -0000	1.29
***************
*** 9,12 ****
--- 9,13 ----
  
  from cctbx.array_family import flex
+ import scitbx.math
  from scitbx import matrix
  from boost import rational
***************
*** 14,17 ****
--- 15,49 ----
  import sys
  
+ class _space_group(boost.python.injector, ext.space_group):
+ 
+   def tensor_constraints(self, reciprocal_space):
+     """row-reduced echelon form of coefficients
+          r.transpose() * t * r - t = 0
+        Mathematica code:
+          r={{r0,r1,r2},{r3,r4,r5},{r6,r7,r8}}
+          t={{t0,t3,t4},{t3,t1,t5},{t4,t5,t2}}
+          FortranForm[Expand[Transpose[r].t.r - t]]
+     """
+     result = flex.int()
+     for i_smx in xrange(1,self.n_smx()):
+       r = self(i_smx).r()
+       if (reciprocal_space):
+         r = r.transpose()
+       r0,r1,r2,r3,r4,r5,r6,r7,r8 = r.num()
+       result.extend(flex.int((
+         r0*r0-1, r3*r3,   r6*r6,   2*r0*r3, 2*r0*r6, 2*r3*r6,
+         r1*r1,   r4*r4-1, r7*r7,   2*r1*r4, 2*r1*r7, 2*r4*r7,
+         r2*r2,   r5*r5,   r8*r8-1, 2*r2*r5, 2*r2*r8, 2*r5*r8,
+         r0*r1, r3*r4, r6*r7, r1*r3+r0*r4-1, r1*r6+r0*r7,   r4*r6+r3*r7,
+         r0*r2, r3*r5, r6*r8, r2*r3+r0*r5,   r2*r6+r0*r8-1, r5*r6+r3*r8,
+         r1*r2, r4*r5, r7*r8, r2*r4+r1*r5,   r2*r7+r1*r8,   r5*r7+r4*r8-1)))
+     result.resize(flex.grid(result.size()//6,6))
+     scitbx.math.row_echelon_form(result)
+     return result
+ 
+   def adp_constraints(self):
+     from cctbx import adptbx
+     return adptbx.constraints(space_group=self)
+ 
  class space_group_info:
  

Update of /cvsroot/cctbx/cctbx/cctbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24843/cctbx/regression

Modified Files:
	tst_sgtbx.py 
Log Message:
new cctbx.sgtbx.space_group.adp_constraints() method

Index: tst_sgtbx.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_sgtbx.py,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** tst_sgtbx.py	6 Sep 2004 07:40:49 -0000	1.12
--- tst_sgtbx.py	28 Jan 2005 01:42:38 -0000	1.13
***************
*** 1,4 ****
--- 1,6 ----
  from cctbx import sgtbx
+ import cctbx.sgtbx.bravais_types
  from libtbx.test_utils import approx_equal
+ import random
  import pickle
  
***************
*** 61,67 ****
--- 63,99 ----
                     (212, 213)]
  
+ def exercise_tensor_constraints_core(crystal_symmetry):
+   from cctbx import crystal
+   from cctbx import adptbx
+   site_symmetry = crystal.special_position_settings(
+     crystal_symmetry).site_symmetry(site=(0,0,0))
+   unit_cell = crystal_symmetry.unit_cell()
+   group = crystal_symmetry.space_group()
+   assert site_symmetry.n_matrices() == group.order_p()
+   adp_constraints = group.adp_constraints()
+   u_cart = adptbx.random_rotate_ellipsoid(
+     u_cart=[random.random() for i in xrange(3)] + [0,0,0])
+   u_star = adptbx.u_cart_as_u_star(unit_cell, u_cart)
+   u_star = site_symmetry.average_u_star(u_star)
+   independent_params = adp_constraints.independent_params(u_star)
+   u_star_vfy = adp_constraints.all_params(independent_params)
+   u_cart = adptbx.u_star_as_u_cart(unit_cell, u_star)
+   u_cart_vfy = adptbx.u_star_as_u_cart(unit_cell, list(u_star_vfy))
+   assert approx_equal(u_cart_vfy, u_cart)
+ 
+ def exercise_tensor_constraints():
+   from cctbx import crystal
+   for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
+     space_group_info = sgtbx.space_group_info(symbol=symbol)
+     crystal_symmetry = crystal.symmetry(
+       unit_cell=space_group_info.any_compatible_unit_cell(volume=1000),
+       space_group_info=space_group_info)
+     exercise_tensor_constraints_core(crystal_symmetry)
+     exercise_tensor_constraints_core(crystal_symmetry.minimum_cell())
+ 
  def run():
    exercise_space_group_info()
    test_enantiomorphic_pairs()
+   exercise_tensor_constraints()
    print "OK"
  

Update of /cvsroot/cctbx/cctbx/cctbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24843/cctbx

Modified Files:
	adptbx.py 
Log Message:
new cctbx.sgtbx.space_group.adp_constraints() method

Index: adptbx.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/adptbx.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** adptbx.py	18 Mar 2004 18:09:12 -0000	1.6
--- adptbx.py	28 Jan 2005 01:42:37 -0000	1.7
***************
*** 1,3 ****
! import cctbx.array_family.flex # for tuple mappings
  
  import boost.python
--- 1,3 ----
! from cctbx.array_family import flex # for tuple mappings
  
  import boost.python
***************
*** 5,13 ****
  from cctbx_adptbx_ext import *
  
! from scitbx.math import euler_angles_as_matrix
  import random
  
  def random_rotate_ellipsoid(u_cart):
!   c = euler_angles_as_matrix(
      [random.uniform(0,360) for i in xrange(3)]).elems
    return c_u_c_transpose(c, u_cart)
--- 5,34 ----
  from cctbx_adptbx_ext import *
  
! import scitbx.math
  import random
  
  def random_rotate_ellipsoid(u_cart):
!   c = scitbx.math.euler_angles_as_matrix(
      [random.uniform(0,360) for i in xrange(3)]).elems
    return c_u_c_transpose(c, u_cart)
+ 
+ class constraints:
+ 
+   def __init__(self, space_group):
+     self.row_echelon_form = space_group.tensor_constraints(
+       reciprocal_space=True)
+     self.independent_flags = flex.bool(6, True)
+     scitbx.math.row_echelon_back_substitution_int(
+       row_echelon_form=self.row_echelon_form,
+       independent_flags=self.independent_flags)
+ 
+   def independent_params(self, u_star):
+     return flex.double(u_star).select(self.independent_flags)
+ 
+   def all_params(self, independent_params):
+     result = flex.double(6, 0)
+     result.set_selected(self.independent_flags, independent_params)
+     scitbx.math.row_echelon_back_substitution_float(
+       row_echelon_form=self.row_echelon_form,
+       solution=result)
+     return result

Update of /cvsroot/cctbx/scitbx/scitbx/math
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24532/scitbx/math

Modified Files:
	__init__.py 
Log Message:
row_echelon code moved from cctbx::sgtbx::row_echelon to scitbx::matrix::row_echelon

Index: __init__.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/scitbx/math/__init__.py,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** __init__.py	6 Sep 2004 07:40:17 -0000	1.9
--- __init__.py	28 Jan 2005 01:40:57 -0000	1.10
***************
*** 91,92 ****
--- 91,108 ----
    else:
      return minimum_covering_sphere_nd(points=points, epsilon=epsilon)
+ 
+ def row_echelon_back_substitution_int(
+       row_echelon_form,
+       v=None,
+       solution=None,
+       independent_flags=None):
+   return ext.row_echelon_back_substitution_int(
+     row_echelon_form, v, solution, independent_flags)
+ 
+ def row_echelon_back_substitution_float(
+       row_echelon_form,
+       v=None,
+       solution=None):
+   assert solution is not None
+   return ext.row_echelon_back_substitution_float(
+     row_echelon_form, v, solution)

Update of /cvsroot/cctbx/scitbx/math/boost_python
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24532/math/boost_python

Modified Files:
	SConscript math_ext.cpp tst_math.py 
Added Files:
	row_echelon.cpp 
Log Message:
row_echelon code moved from cctbx::sgtbx::row_echelon to scitbx::matrix::row_echelon

Index: SConscript
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/SConscript,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** SConscript	31 Mar 2004 05:32:09 -0000	1.12
--- SConscript	28 Jan 2005 01:40:57 -0000	1.13
***************
*** 8,11 ****
      "golay.cpp",
      "minimum_covering_sphere.cpp",
!     "principal_axes_of_inertia.cpp"],
  )
--- 8,12 ----
      "golay.cpp",
      "minimum_covering_sphere.cpp",
!     "principal_axes_of_inertia.cpp",
!     "row_echelon.cpp"]
  )

Index: math_ext.cpp
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/math_ext.cpp,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** math_ext.cpp	6 Dec 2004 21:20:38 -0000	1.20
--- math_ext.cpp	28 Jan 2005 01:40:57 -0000	1.21
***************
*** 19,22 ****
--- 19,23 ----
    void wrap_minimum_covering_sphere();
    void wrap_principal_axes_of_inertia();
+   void wrap_row_echelon();
  
  namespace {
***************
*** 89,92 ****
--- 90,94 ----
      wrap_minimum_covering_sphere();
      wrap_principal_axes_of_inertia();
+     wrap_row_echelon();
  
      def("time_eigensystem_real_symmetric", time_eigensystem_real_symmetric);

Index: tst_math.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/math/boost_python/tst_math.py,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** tst_math.py	6 Dec 2004 21:20:38 -0000	1.34
--- tst_math.py	28 Jan 2005 01:40:57 -0000	1.35
***************
*** 767,770 ****
--- 767,826 ----
        other=flex.double([345*f]), deg=deg), [-15*f])
  
+ def exercise_row_echelon():
+   m = flex.int((1,1,1,1))
+   m.resize(flex.grid(2,2))
+   t = flex.int((2,3))
+   t.resize(flex.grid(2,1))
+   assert scitbx.math.row_echelon_form_t(m, t) == 1
+   assert m.focus() == (1,2)
+   assert tuple(m) == (1,1)
+   assert tuple(t) == (2,1)
+   assert scitbx.math.row_echelon_form(m) == 1
+   assert m.focus() == (1,2)
+   assert tuple(m) == (1,1)
+   m = flex.int((0,-24,0,0,0,-24,24,0,24))
+   m.resize(flex.grid(3,3))
+   t = flex.int((-3, -6, 0))
+   t.resize(flex.grid(3,1))
+   assert scitbx.math.row_echelon_form_t(m, t) == 3
+   assert tuple(m) == (24,0,24,0,24,0,0,0,24)
+   assert tuple(t) == (0,3,6)
+   t.resize(flex.grid(3))
+   sol = flex.int(3)
+   assert scitbx.math.row_echelon_back_substitution_int(m, t, sol) == 8
+   assert tuple(sol) == (-2,1,2)
+   indep = flex.bool((True,True,True))
+   assert scitbx.math.row_echelon_back_substitution_int(
+     row_echelon_form=m, independent_flags=indep) == 1
+   assert tuple(indep) == (False,False,False)
+   #
+   for n_cols in xrange(1,5):
+     for n_rows in xrange(5):
+       for i_trial in xrange(10):
+         m = flex.int()
+         for i in xrange(n_rows):
+           coeffs = flex.int([random.randrange(-5,5) for j in xrange(n_cols)])
+           m.extend(coeffs)
+         m.resize(flex.grid(n_rows,n_cols))
+         rank = scitbx.math.row_echelon_form(m)
+         assert m.focus()[0] == rank
+         assert m.focus()[1] == n_cols
+         indep = flex.bool(n_cols, True)
+         scitbx.math.row_echelon_back_substitution_int(
+           row_echelon_form=m, independent_flags=indep)
+         mm = matrix.rec(m, m.focus())
+         s = matrix.col([random.random() for j in xrange(n_cols)])
+         sol = flex.double(n_cols, 0)
+         sol.set_selected(indep, flex.double(s).select(indep))
+         assert scitbx.math.row_echelon_back_substitution_float(
+           row_echelon_form=m, solution=sol, v=flex.double(mm * s))
+         assert approx_equal(sol, s)
+         sol = flex.double(n_cols, 0)
+         sol.set_selected(indep, flex.double(s).select(indep))
+         assert scitbx.math.row_echelon_back_substitution_float(
+           row_echelon_form=m, solution=sol)
+         zeros = mm * matrix.col(sol)
+         assert approx_equal(zeros, [0]*rank)
+ 
  def exercise_minimum_covering_sphere(epsilon=1.e-3):
    s3 = sphere_3d(center=[1,2,3], radius=4)
***************
*** 895,898 ****
--- 951,955 ----
    exercise_principal_axes_of_inertia()
    exercise_phase_error()
+   exercise_row_echelon()
    forever = "--Forever" in sys.argv[1:]
    while 1:

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

#include <scitbx/matrix/row_echelon.h>
#include <boost/python/def.hpp>

namespace scitbx { namespace matrix { namespace boost_python {

namespace {

  template <typename ElementType>
  scitbx::mat_ref<ElementType>
  flex_as_mat_ref(af::versa<ElementType, af::flex_grid<> >& a)
  {
    SCITBX_ASSERT(a.accessor().nd() == 2);
    SCITBX_ASSERT(a.accessor().is_0_based());
    SCITBX_ASSERT(!a.accessor().is_padded());
    return scitbx::mat_ref<ElementType>(
      a.begin(),
      a.accessor().all()[0],
      a.accessor().all()[1]);
  }

  std::size_t
  row_echelon_form_t(
    af::versa<int, af::flex_grid<> >& m,
    af::versa<int, af::flex_grid<> >& t)
  {
    scitbx::mat_ref<int> m_ref = flex_as_mat_ref(m);
    scitbx::mat_ref<int> t_ref = flex_as_mat_ref(t);
    std::size_t rank = row_echelon::form_t(m_ref, t_ref);
    m.resize(af::flex_grid<>(m_ref.n_rows(), m_ref.n_columns()));
    return rank;
  }

  std::size_t
  row_echelon_form(
    af::versa<int, af::flex_grid<> >& m)
  {
    scitbx::mat_ref<int> m_ref = flex_as_mat_ref(m);
    std::size_t rank = row_echelon::form(m_ref);
    m.resize(af::flex_grid<>(m_ref.n_rows(), m_ref.n_columns()));
    return rank;
  }

  int
  row_echelon_back_substitution_int(
    af::versa<int, af::flex_grid<> >& re_mx,
    af::const_ref<int> const& v,
    af::ref<int> const& sol,
    af::ref<bool> const& indep)
  {
    scitbx::mat_ref<int> re_mx_ref = flex_as_mat_ref(re_mx);
    const int* v_ptr = 0;
    int* sol_ptr = 0;
    bool* indep_ptr = 0;
    if (v.size()) {
      SCITBX_ASSERT(v.size() == re_mx_ref.n_rows());
      v_ptr = v.begin();
    }
    if (sol.size()) {
      SCITBX_ASSERT(sol.size() == re_mx_ref.n_columns());
      sol_ptr = sol.begin();
    }
    if (indep.size()) {
      SCITBX_ASSERT(indep.size() == re_mx_ref.n_columns());
      indep_ptr = indep.begin();
    }
    return row_echelon::back_substitution_int(
      re_mx_ref, v_ptr, sol_ptr, indep_ptr);
  }

  bool
  row_echelon_back_substitution_float(
    af::versa<int, af::flex_grid<> >& re_mx,
    af::const_ref<double> const& v,
    af::ref<double> const& sol)
  {
    scitbx::mat_ref<int> re_mx_ref = flex_as_mat_ref(re_mx);
    const double* v_ptr = 0;
    double* sol_ptr = 0;
    if (v.size()) {
      SCITBX_ASSERT(v.size() == re_mx_ref.n_rows());
      v_ptr = v.begin();
    }
    if (sol.size()) {
      SCITBX_ASSERT(sol.size() == re_mx_ref.n_columns());
      sol_ptr = sol.begin();
    }
    return row_echelon::back_substitution_float(
      re_mx_ref, v_ptr, sol_ptr);
  }

  void wrap_row_echelon()
  {
    using namespace boost::python;
    def("row_echelon_form_t", row_echelon_form_t);
    def("row_echelon_form", row_echelon_form);
    def("row_echelon_back_substitution_int",
      row_echelon_back_substitution_int);
    def("row_echelon_back_substitution_float",
      row_echelon_back_substitution_float);
  }

}}} // namespace matrix::boost_python::<anoymous>

namespace math { namespace boost_python {

  void wrap_row_echelon()
  {
    matrix::boost_python::wrap_row_echelon();
  }

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

Update of /cvsroot/cctbx/scitbx/include/scitbx/matrix
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24532/include/scitbx/matrix

Added Files:
	row_echelon.h 
Log Message:
row_echelon code moved from cctbx::sgtbx::row_echelon to scitbx::matrix::row_echelon

--- NEW FILE: row_echelon.h ---
#ifndef SCITBX_SCITBX_MATRIX_ROW_ECHELON_H
#define SCITBX_SCITBX_MATRIX_ROW_ECHELON_H

#include <scitbx/mat_ref.h>
#include <scitbx/array_family/small.h>
#include <scitbx/array_family/misc_functions.h>
#include <boost/rational.hpp>

namespace scitbx { namespace matrix { namespace row_echelon {

  namespace detail {

    template <typename AnyType>
    inline void
    swap(AnyType* a, AnyType* b, std::size_t n)
    {
      for(std::size_t i=0;i<n;i++) std::swap(a[i], b[i]);
    }

  } // namespace detail

  template <typename IntType>
  std::size_t
  form_t(scitbx::mat_ref<IntType>& m,
         scitbx::mat_ref<IntType> const& t)
  {
    // C++ version of RowEchelonFormT from the CrystGAP package
    //     (GAP Version 3.4.4).
    // B. Eick, F. Ga"hler and W. Nickel
    //     Computing Maximal Subgroups and Wyckoff Positions of Space Groups
    //     Acta Cryst. (1997). A53, 467 - 474
    using std::size_t;
    size_t mr = m.n_rows();
    size_t mc = m.n_columns();
    size_t tc = t.n_columns();
    if (tc) {
      SCITBX_ASSERT(t.begin() != 0 && t.n_rows() >= mr);
    }
    size_t i, j;
    for (i = j = 0; i < mr && j < mc;) {
      size_t k = i; while (k < mr && m(k,j) == 0) k++;
      if (k == mr)
        j++;
      else {
        if (i != k) {
                  detail::swap(&m(i,0), &m(k,0), mc);
          if (tc) detail::swap(&t(i,0), &t(k,0), tc);
        }
        for (k++; k < mr; k++) {
          IntType a = scitbx::fn::absolute(m(k, j));
          if (a != 0 && a < scitbx::fn::absolute(m(i,j))) {
                    detail::swap(&m(i,0), &m(k,0), mc);
            if (tc) detail::swap(&t(i,0), &t(k,0), tc);
          }
        }
        if (m(i,j) < 0) {
                  for(size_t ic=0;ic<mc;ic++) m(i,ic) *= -1;
          if (tc) for(size_t ic=0;ic<tc;ic++) t(i,ic) *= -1;
        }
        bool cleared = true;
        for (k = i+1; k < mr; k++) {
          IntType a = m(k,j) / m(i,j);
          if (a != 0) {
                    for(size_t ic=0;ic<mc;ic++) m(k,ic) -= a * m(i,ic);
            if (tc) for(size_t ic=0;ic<tc;ic++) t(k,ic) -= a * t(i,ic);
          }
          if (m(k,j) != 0) cleared = false;
        }
        if (cleared) { i++; j++; }
      }
    }
    m = scitbx::mat_ref<IntType>(m.begin(), i, mc);
    return i;
  }

  template <typename IntType>
  std::size_t
  form(scitbx::mat_ref<IntType>& m)
  {
    scitbx::mat_ref<IntType> t(0,0,0);
    return form_t(m, t);
  }

  template <typename IntType>
  IntType
  back_substitution_int(
    scitbx::mat_const_ref<IntType> const& re_mx,
    const IntType* v = 0,
    IntType* sol = 0,
    bool* flag_indep = 0)
  {
    using std::size_t;
    size_t nr = re_mx.n_rows();
    size_t nc = re_mx.n_columns();
    if (flag_indep) {
      for(size_t ic=0;ic<nc;ic++) flag_indep[ic] = true;
    }
    IntType d = 1;
    for (size_t ir = nr; ir > 0;)
    {
      ir--;
      size_t ic;
      for(ic=0;ic<nc;ic++) {
        if (re_mx(ir,ic)) goto set_sol_ic;
      }
      if (v && v[ir] != 0) return 0;
      continue;

      set_sol_ic:
      if (flag_indep) flag_indep[ic] = false;
      if (sol) {
                  size_t icp = ic + 1;
        size_t nv = nc - icp;
        if (nv) {
          scitbx::matrix::multiply(&re_mx(ir,icp), &sol[icp], 1, nv, 1,
                                   &sol[ic]);
          sol[ic] *= -1;
        }
        else {
          sol[ic] = 0;
        }
        if (v) sol[ic] += d * v[ir];
                                IntType mrc = re_mx(ir,ic);
        IntType f = boost::gcd(sol[ic], mrc);
        if (mrc < 0) f *= -1;
        sol[ic] /= f;
        f = mrc / f;
        if (f != 1) {
          for(size_t jc=0;jc<nc;jc++) if (jc != ic) sol[jc] *= f;
          d *= f;
        }
      }
    }
    return d;
  }

  template <typename IntType, typename FloatType>
  bool
  back_substitution_float(
    scitbx::mat_const_ref<IntType> const& re_mx,
    const FloatType* v,
    FloatType* sol)
  {
    SCITBX_ASSERT(sol != 0);
    using std::size_t;
    size_t nr = re_mx.n_rows();
    size_t nc = re_mx.n_columns();
    for (size_t ir = nr; ir > 0;)
    {
      ir--;
      size_t ic;
      for(ic=0;ic<nc;ic++) {
        if (re_mx(ir,ic)) goto set_sol_ic;
      }
      if (v && v[ir] != 0) return false;
      continue;

      set_sol_ic:
                size_t icp = ic + 1;
      size_t nv = nc - icp;
      if (nv) {
        scitbx::matrix::multiply(&re_mx(ir,icp), &sol[icp], 1, nv, 1,
                                 &sol[ic]);
        sol[ic] = -sol[ic];
      }
      else {
        sol[ic] = 0;
      }
      if (v) sol[ic] += v[ir];
      sol[ic] /= static_cast<FloatType>(re_mx(ir,ic));
    }
    return true;
  }

  template <typename IntType, std::size_t MaxIndependentIndices = 6>
  struct independent
  {
    independent() {}

    independent(scitbx::mat_const_ref<IntType> const& re_mx)
    {
      using std::size_t;
      size_t nc = re_mx.n_columns();
      SCITBX_ASSERT(nc <= MaxIndependentIndices);
      bool flag_indep[MaxIndependentIndices];
      IntType* n_a = 0;
      SCITBX_ASSERT(back_substitution_int(re_mx, n_a, n_a, flag_indep) >= 1);
      for(size_t ic=0;ic<nc;ic++) {
        if (flag_indep[ic]) indices.push_back(ic);
      }
    }

    af::small<std::size_t, MaxIndependentIndices> indices;
  };

}}} // namespace scitbx::matrix::row_echelon

#endif // SCITBX_SCITBX_MATRIX_ROW_ECHELON_H

Update of /cvsroot/cctbx/scitbx/scitbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29669

Modified Files:
	matrix.py 
Log Message:
mathematica_form bug fix: matrix with 0 rows -> {}

Index: matrix.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/scitbx/matrix.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** matrix.py	6 Dec 2004 21:20:38 -0000	1.10
--- matrix.py	27 Jan 2005 02:32:05 -0000	1.11
***************
*** 218,222 ****
        if (one_row_per_line): s += "\n  "
        else: s += " "
!     return s[:-2] + "}"
  
    def as_sym_mat3(self):
--- 218,223 ----
        if (one_row_per_line): s += "\n  "
        else: s += " "
!     if (self.n_rows() > 0): s = s[:-2]
!     return s + "}"
  
    def as_sym_mat3(self):
***************
*** 334,337 ****
--- 335,340 ----
    from libtbx.test_utils import approx_equal
    from boost import rational
+   a = rec((),(0,0))
+   assert a.mathematica_form() == "{}"
    a = rec(range(1,7), (3,2))
    assert len(a) == 6