------------------------------------------------------------------------
r1594 | sauter | 2009-08-26 13:15:29 -0700 (Wed, 26 Aug 2009) | 1 line
Changed paths:
   M /trunk/array_family/flex_distl_spot.cpp
   M /trunk/distltbx/__init__.py
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/boost_python/hough_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/distltbx/hough.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/dptbx/boost_python/dptbx_ext.cpp

Migration of header files from labelit to spotfinder.
------------------------------------------------------------------------
r1593 | sauter | 2009-08-26 11:22:26 -0700 (Wed, 26 Aug 2009) | 1 line
Changed paths:
   M /trunk/SConscript
   M /trunk/distltbx/boost_python/singlemask.h
   M /trunk/distltbx/distl.h
   M /trunk/distltbx/ll.h
   M /trunk/distltbx/spotfilter.h
   M /trunk/dptbx/latticescorer.h
   M /trunk/libtbx_config

distl package now moved to sourceforge repository spotfinder
------------------------------------------------------------------------
r1586 | rwgk | 2009-08-19 16:27:46 -0700 (Wed, 19 Aug 2009) | 1 line
Changed paths:
   M /trunk/SConscript
   M /trunk/array_family/SConscript
   M /trunk/detectors/SConscript
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/dptbx/boost_python/SConscript
   M /trunk/hidden_symmetry/SConscript
   M /trunk/hidden_symmetry/boost_python/SConscript
   M /trunk/mathsupport/SConscript
   M /trunk/strategy/SConscript
   M /trunk/symmetry/SConscript
   M /trunk/webice_support/SConscript

global SConscript changes: env_base now pre-defines CCFLAGS, CXXFLAGS, SHCCFLAGS, SHCXXFLAGS
------------------------------------------------------------------------
r1559 | bkpoon | 2009-07-08 00:25:38 -0700 (Wed, 08 Jul 2009) | 1 line
Changed paths:
   M /trunk/distltbx/hough.cpp
   M /trunk/distltbx/hough.h

Updated comments
------------------------------------------------------------------------
r1557 | sauter | 2009-07-02 17:09:44 -0700 (Thu, 02 Jul 2009) | 1 line
Changed paths:
   M /trunk/distltbx/__init__.py
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/distltbx/distl.h

Expose spotfinder submethods individually to Python for fine-grained profiling and testing.
------------------------------------------------------------------------
r1503 | sauter | 2009-05-13 13:09:54 -0700 (Wed, 13 May 2009) | 1 line
Changed paths:
   M /trunk/diffraction/geometry.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/performance.py

Fig bugs in multiplatform build and run_tests
------------------------------------------------------------------------
r1501 | sauter | 2009-05-08 15:27:29 -0700 (Fri, 08 May 2009) | 1 line
Changed paths:
   M /trunk/distltbx/__init__.py
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.h

Distl scanbox tiling now permits special Pilatus definition so that inactive areas are not tiled.
------------------------------------------------------------------------
r1498 | sauter | 2009-05-06 22:32:10 -0700 (Wed, 06 May 2009) | 1 line
Changed paths:
   A /trunk/diffraction/geometry.cpp
   M /trunk/diffraction/geometry.py
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/performance.py

Fraction of the thin resolution shell intersected by the detector area, pushed into C++ for significant performance boost.
------------------------------------------------------------------------
r1359 | sauter | 2009-02-20 15:42:58 -0800 (Fri, 20 Feb 2009) | 1 line
Changed paths:
   M /trunk/SConscript

Allow compiles where labelit and distl sources are in location specified by libtbx/configure.py --repository=
------------------------------------------------------------------------
r1357 | sauter | 2009-02-19 20:01:39 -0800 (Thu, 19 Feb 2009) | 1 line
Changed paths:
   M /trunk/SConscript
   A /trunk/array_family/SConscript (from /trunk/array_family/boost_python/SConscript:1355)
   D /trunk/array_family/boost_python/SConscript
   D /trunk/array_family/boost_python/flex_distl_spot.cpp
   D /trunk/array_family/boost_python/flex_ext.cpp
   A /trunk/array_family/flex_distl_spot.cpp (from /trunk/array_family/boost_python/flex_distl_spot.cpp:1355)
   A /trunk/array_family/flex_ext.cpp (from /trunk/array_family/boost_python/flex_ext.cpp:1355)
   A /trunk/detectors/SConscript (from /trunk/detectors/boost_python/SConscript:1355)
   D /trunk/detectors/boost_python/SConscript
   D /trunk/detectors/boost_python/detectors_ext.cpp
   A /trunk/detectors/detectors_ext.cpp (from /trunk/detectors/boost_python/detectors_ext.cpp:1355)
   A /trunk/mathsupport/SConscript (from /trunk/mathsupport/boost_python/SConscript:1355)
   D /trunk/mathsupport/boost_python/SConscript
   D /trunk/mathsupport/boost_python/mathsupport_ext.cpp
   A /trunk/mathsupport/mathsupport_ext.cpp (from /trunk/mathsupport/boost_python/mathsupport_ext.cpp:1355)
   A /trunk/strategy/SConscript (from /trunk/strategy/boost_python/SConscript:1355)
   D /trunk/strategy/boost_python/SConscript
   D /trunk/strategy/boost_python/strategy_ext.cpp
   A /trunk/strategy/strategy_ext.cpp (from /trunk/strategy/boost_python/strategy_ext.cpp:1355)
   A /trunk/symmetry/SConscript (from /trunk/symmetry/boost_python/SConscript:1355)
   D /trunk/symmetry/boost_python/SConscript
   D /trunk/symmetry/boost_python/symmetry_ext.cpp
   A /trunk/symmetry/symmetry_ext.cpp (from /trunk/symmetry/boost_python/symmetry_ext.cpp:1355)
   A /trunk/webice_support/SConscript (from /trunk/webice_support/boost_python/SConscript:1355)
   D /trunk/webice_support/boost_python/SConscript
   D /trunk/webice_support/boost_python/webice_support_ext.cpp
   A /trunk/webice_support/webice_support_ext.cpp (from /trunk/webice_support/boost_python/webice_support_ext.cpp:1355)

Migration path
------------------------------------------------------------------------
r1353 | sauter | 2009-02-19 16:46:32 -0800 (Thu, 19 Feb 2009) | 1 line
Changed paths:
   A /trunk/__init__.py (from /trunk/labelit/__init__.py:1352)
   A /trunk/application (from /trunk/labelit/application:1352)
   A /trunk/array_family/__init__.py (from /trunk/labelit/array_family/__init__.py:1352)
   A /trunk/array_family/flex.py (from /trunk/labelit/array_family/flex.py:1352)
   A /trunk/assert_vars.py (from /trunk/labelit/assert_vars.py:1352)
   A /trunk/beamline (from /trunk/labelit/beamline:1352)
   A /trunk/command_line (from /trunk/labelit/command_line:1352)
   A /trunk/config_detector.py (from /trunk/labelit/config_detector.py:1352)
   A /trunk/detectors/__init__.py (from /trunk/labelit/detectors/__init__.py:1352)
   A /trunk/detectors/convention.py (from /trunk/labelit/detectors/convention.py:1352)
   A /trunk/detectors/header.txt (from /trunk/labelit/detectors/header.txt:1352)
   A /trunk/detectors/jpeg.py (from /trunk/labelit/detectors/jpeg.py:1352)
   A /trunk/detectors/mar.py (from /trunk/labelit/detectors/mar.py:1352)
   A /trunk/detectors/tolerance.py (from /trunk/labelit/detectors/tolerance.py:1352)
   A /trunk/diffraction (from /trunk/labelit/diffraction:1352)
   A /trunk/distltbx/__init__.py (from /trunk/labelit/distltbx/__init__.py:1352)
   A /trunk/distltbx/close_spots_detail.py (from /trunk/labelit/distltbx/close_spots_detail.py:1352)
   A /trunk/distltbx/ice2.py (from /trunk/labelit/distltbx/ice2.py:1352)
   A /trunk/distltbx/ice_nztt.py (from /trunk/labelit/distltbx/ice_nztt.py:1352)
   A /trunk/distltbx/method2.py (from /trunk/labelit/distltbx/method2.py:1352)
   A /trunk/distltbx/pickle_support.py (from /trunk/labelit/distltbx/pickle_support.py:1352)
   A /trunk/distltbx/spotlist_example.py (from /trunk/labelit/distltbx/spotlist_example.py:1352)
   A /trunk/dps.py (from /trunk/labelit/dps.py:1352)
   A /trunk/dptbx/__init__.py (from /trunk/labelit/dptbx/__init__.py:1352)
   A /trunk/dptbx/autoindex.py (from /trunk/labelit/dptbx/autoindex.py:1352)
   A /trunk/dptbx/basis_choice.py (from /trunk/labelit/dptbx/basis_choice.py:1352)
   A /trunk/dptbx/basis_refinement.py (from /trunk/labelit/dptbx/basis_refinement.py:1352)
   A /trunk/dptbx/beam_plot.py (from /trunk/labelit/dptbx/beam_plot.py:1352)
   A /trunk/dptbx/beam_rigorous.py (from /trunk/labelit/dptbx/beam_rigorous.py:1352)
   A /trunk/dptbx/constrainment.py (from /trunk/labelit/dptbx/constrainment.py:1352)
   A /trunk/dptbx/error.py (from /trunk/labelit/dptbx/error.py:1352)
   A /trunk/dptbx/lattice_likelihood.py (from /trunk/labelit/dptbx/lattice_likelihood.py:1352)
   A /trunk/dptbx/lepage.py (from /trunk/labelit/dptbx/lepage.py:1352)
   A /trunk/dptbx/mosaicity.py (from /trunk/labelit/dptbx/mosaicity.py:1352)
   A /trunk/dptbx/mosflm.py (from /trunk/labelit/dptbx/mosflm.py:1352)
   A /trunk/dptbx/next_layer_support.py (from /trunk/labelit/dptbx/next_layer_support.py:1352)
   A /trunk/dptbx/pickle_support.py (from /trunk/labelit/dptbx/pickle_support.py:1352)
   A /trunk/dptbx/profile_support.py (from /trunk/labelit/dptbx/profile_support.py:1352)
   A /trunk/dptbx/refinement.py (from /trunk/labelit/dptbx/refinement.py:1352)
   A /trunk/dptbx/refinement_mode.py (from /trunk/labelit/dptbx/refinement_mode.py:1352)
   A /trunk/dptbx/reindex.py (from /trunk/labelit/dptbx/reindex.py:1352)
   A /trunk/dptbx/sampling.py (from /trunk/labelit/dptbx/sampling.py:1352)
   A /trunk/dptbx/status.py (from /trunk/labelit/dptbx/status.py:1352)
   A /trunk/dptbx/sublattice.py (from /trunk/labelit/dptbx/sublattice.py:1352)
   A /trunk/dptbx/test_cases_lattice_symmetry.py (from /trunk/labelit/dptbx/test_cases_lattice_symmetry.py:1352)
   A /trunk/dptbx/test_reindex.py (from /trunk/labelit/dptbx/test_reindex.py:1352)
   A /trunk/dptbx/tools.py (from /trunk/labelit/dptbx/tools.py:1352)
   A /trunk/dptbx/tst_predict.py (from /trunk/labelit/dptbx/tst_predict.py:1352)
   A /trunk/exception.py (from /trunk/labelit/exception.py:1352)
   A /trunk/graphics (from /trunk/labelit/graphics:1352)
   A /trunk/hidden_symmetry (from /trunk/labelit/hidden_symmetry:1352)
   A /trunk/interface.py (from /trunk/labelit/interface.py:1352)
   D /trunk/labelit/__init__.py
   D /trunk/labelit/application
   D /trunk/labelit/array_family/__init__.py
   D /trunk/labelit/array_family/flex.py
   D /trunk/labelit/assert_vars.py
   D /trunk/labelit/beamline
   D /trunk/labelit/command_line
   D /trunk/labelit/config_detector.py
   D /trunk/labelit/detectors/__init__.py
   D /trunk/labelit/detectors/convention.py
   D /trunk/labelit/detectors/header.txt
   D /trunk/labelit/detectors/jpeg.py
   D /trunk/labelit/detectors/mar.py
   D /trunk/labelit/detectors/tolerance.py
   D /trunk/labelit/diffraction
   D /trunk/labelit/distltbx/__init__.py
   D /trunk/labelit/distltbx/close_spots_detail.py
   D /trunk/labelit/distltbx/ice2.py
   D /trunk/labelit/distltbx/ice_nztt.py
   D /trunk/labelit/distltbx/method2.py
   D /trunk/labelit/distltbx/pickle_support.py
   D /trunk/labelit/distltbx/spotlist_example.py
   D /trunk/labelit/dps.py
   D /trunk/labelit/dptbx/__init__.py
   D /trunk/labelit/dptbx/autoindex.py
   D /trunk/labelit/dptbx/basis_choice.py
   D /trunk/labelit/dptbx/basis_refinement.py
   D /trunk/labelit/dptbx/beam_plot.py
   D /trunk/labelit/dptbx/beam_rigorous.py
   D /trunk/labelit/dptbx/constrainment.py
   D /trunk/labelit/dptbx/error.py
   D /trunk/labelit/dptbx/lattice_likelihood.py
   D /trunk/labelit/dptbx/lepage.py
   D /trunk/labelit/dptbx/mosaicity.py
   D /trunk/labelit/dptbx/mosflm.py
   D /trunk/labelit/dptbx/next_layer_support.py
   D /trunk/labelit/dptbx/pickle_support.py
   D /trunk/labelit/dptbx/profile_support.py
   D /trunk/labelit/dptbx/refinement.py
   D /trunk/labelit/dptbx/refinement_mode.py
   D /trunk/labelit/dptbx/reindex.py
   D /trunk/labelit/dptbx/sampling.py
   D /trunk/labelit/dptbx/status.py
   D /trunk/labelit/dptbx/sublattice.py
   D /trunk/labelit/dptbx/test_cases_lattice_symmetry.py
   D /trunk/labelit/dptbx/test_reindex.py
   D /trunk/labelit/dptbx/tools.py
   D /trunk/labelit/dptbx/tst_predict.py
   D /trunk/labelit/exception.py
   D /trunk/labelit/graphics
   D /trunk/labelit/hidden_symmetry
   D /trunk/labelit/interface.py
   D /trunk/labelit/linreg.py
   D /trunk/labelit/mathsupport/__init__.py
   D /trunk/labelit/mathsupport/erf.py
   D /trunk/labelit/mathsupport/statistics.py
   D /trunk/labelit/performance.py
   D /trunk/labelit/phil_preferences.py
   D /trunk/labelit/preferences.py
   D /trunk/labelit/preferences_base.py
   D /trunk/labelit/procedure.py
   D /trunk/labelit/publications
   D /trunk/labelit/scope.py
   D /trunk/labelit/site_preferences.py
   D /trunk/labelit/steps.py
   D /trunk/labelit/strategy/systematic_absences.py
   D /trunk/labelit/sublattice_support
   D /trunk/labelit/symmetry/__init__.py
   D /trunk/labelit/symmetry/mark3_cluster.py
   D /trunk/labelit/symmetry/metricsym
   D /trunk/labelit/symmetry/mtz_data.py
   D /trunk/labelit/symmetry/patterson_choice.py
   D /trunk/labelit/symmetry/patterson_mark3.py
   D /trunk/labelit/symmetry/pickle_support.py
   D /trunk/labelit/symmetry/screw_axis.py
   D /trunk/labelit/symmetry/sgtbx_adaptor.py
   D /trunk/labelit/symmetry/subgroup.py
   D /trunk/labelit/symmetry/symmetry_operator.py
   D /trunk/labelit/tnear2.py
   D /trunk/labelit/tnear_support.py
   D /trunk/labelit/utilities.py
   D /trunk/labelit/webice_support/__init__.py
   D /trunk/labelit/webice_support/parallel_distl.py
   D /trunk/labelit/webice_support/runtestpng.csh
   D /trunk/labelit/webice_support/spotfinder.py
   D /trunk/labelit/webice_support/tst_imports.py
   A /trunk/linreg.py (from /trunk/labelit/linreg.py:1352)
   A /trunk/mathsupport/__init__.py (from /trunk/labelit/mathsupport/__init__.py:1352)
   A /trunk/mathsupport/erf.py (from /trunk/labelit/mathsupport/erf.py:1352)
   A /trunk/mathsupport/statistics.py (from /trunk/labelit/mathsupport/statistics.py:1352)
   A /trunk/performance.py (from /trunk/labelit/performance.py:1352)
   A /trunk/phil_preferences.py (from /trunk/labelit/phil_preferences.py:1352)
   A /trunk/preferences.py (from /trunk/labelit/preferences.py:1352)
   A /trunk/preferences_base.py (from /trunk/labelit/preferences_base.py:1352)
   A /trunk/procedure.py (from /trunk/labelit/procedure.py:1352)
   A /trunk/publications (from /trunk/labelit/publications:1352)
   M /trunk/run_tests.py
   A /trunk/scope.py (from /trunk/labelit/scope.py:1352)
   A /trunk/site_preferences.py (from /trunk/labelit/site_preferences.py:1352)
   A /trunk/steps.py (from /trunk/labelit/steps.py:1352)
   A /trunk/strategy/systematic_absences.py (from /trunk/labelit/strategy/systematic_absences.py:1352)
   A /trunk/sublattice_support (from /trunk/labelit/sublattice_support:1352)
   A /trunk/symmetry/__init__.py (from /trunk/labelit/symmetry/__init__.py:1352)
   A /trunk/symmetry/mark3_cluster.py (from /trunk/labelit/symmetry/mark3_cluster.py:1352)
   A /trunk/symmetry/metricsym (from /trunk/labelit/symmetry/metricsym:1352)
   A /trunk/symmetry/mtz_data.py (from /trunk/labelit/symmetry/mtz_data.py:1352)
   A /trunk/symmetry/patterson_choice.py (from /trunk/labelit/symmetry/patterson_choice.py:1352)
   A /trunk/symmetry/patterson_mark3.py (from /trunk/labelit/symmetry/patterson_mark3.py:1352)
   A /trunk/symmetry/pickle_support.py (from /trunk/labelit/symmetry/pickle_support.py:1352)
   A /trunk/symmetry/screw_axis.py (from /trunk/labelit/symmetry/screw_axis.py:1352)
   A /trunk/symmetry/sgtbx_adaptor.py (from /trunk/labelit/symmetry/sgtbx_adaptor.py:1352)
   A /trunk/symmetry/subgroup.py (from /trunk/labelit/symmetry/subgroup.py:1352)
   A /trunk/symmetry/symmetry_operator.py (from /trunk/labelit/symmetry/symmetry_operator.py:1352)
   A /trunk/tnear2.py (from /trunk/labelit/tnear2.py:1352)
   A /trunk/tnear_support.py (from /trunk/labelit/tnear_support.py:1352)
   A /trunk/utilities.py (from /trunk/labelit/utilities.py:1352)
   A /trunk/webice_support/__init__.py (from /trunk/labelit/webice_support/__init__.py:1352)
   A /trunk/webice_support/parallel_distl.py (from /trunk/labelit/webice_support/parallel_distl.py:1352)
   A /trunk/webice_support/runtestpng.csh (from /trunk/labelit/webice_support/runtestpng.csh:1352)
   A /trunk/webice_support/spotfinder.py (from /trunk/labelit/webice_support/spotfinder.py:1352)
   A /trunk/webice_support/tst_imports.py (from /trunk/labelit/webice_support/tst_imports.py:1352)

Migration path, labelit directory reorganization
------------------------------------------------------------------------
r1352 | sauter | 2009-02-19 16:02:04 -0800 (Thu, 19 Feb 2009) | 1 line
Changed paths:
   D /trunk/array_family/boost_python/distl.h
   M /trunk/detectors/boost_python/detectors_ext.cpp
   A /trunk/detectors/detectors.h (from /trunk/include/labelit/detectors.h:1350)
   M /trunk/detectors/detectorsquick.cpp
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/boost_python/hough_ext.cpp
   A /trunk/distltbx/boost_python/singlemask.h (from /trunk/include/labelit/singlemask.h:1350)
   M /trunk/distltbx/distl.cpp
   A /trunk/distltbx/distl.h (from /trunk/array_family/boost_python/distl.h:1351)
   M /trunk/distltbx/hough.cpp
   A /trunk/distltbx/hough.h (from /trunk/include/labelit/hough.h:1350)
   A /trunk/distltbx/ll.h (from /trunk/include/labelit/ll.h:1350)
   M /trunk/distltbx/spotfilter.cpp
   A /trunk/distltbx/spotfilter.h (from /trunk/include/labelit/spotfilter.h:1350)
   M /trunk/dptbx/basis_refine.cpp
   A /trunk/dptbx/basis_refine.h (from /trunk/include/labelit/basis_refine.h:1350)
   M /trunk/dptbx/beamplotter.cpp
   A /trunk/dptbx/beamplotter.h (from /trunk/include/labelit/beamplotter.h:1350)
   M /trunk/dptbx/boost_python/dptbx_ext.cpp
   M /trunk/dptbx/boost_python/resolution_ext.cpp
   A /trunk/dptbx/directional_fft.h (from /trunk/include/labelit/directional_fft.h:1350)
   M /trunk/dptbx/dptbx.cpp
   A /trunk/dptbx/dptbx.h (from /trunk/include/labelit/dptbx.h:1350)
   A /trunk/dptbx/dptbx_debug.h (from /trunk/include/labelit/dptbx_debug.h:1350)
   A /trunk/dptbx/latticescorer.h (from /trunk/include/labelit/latticescorer.h:1350)
   M /trunk/dptbx/model_details.cpp
   A /trunk/dptbx/model_details.h (from /trunk/include/labelit/model_details.h:1350)
   M /trunk/dptbx/modelcalculator.cpp
   A /trunk/dptbx/modelcalculator.h (from /trunk/include/labelit/modelcalculator.h:1350)
   M /trunk/dptbx/mosaicity.cpp
   A /trunk/dptbx/mosaicity.h (from /trunk/include/labelit/mosaicity.h:1350)
   M /trunk/dptbx/orientation.cpp
   M /trunk/dptbx/possible_reflections.cpp
   A /trunk/dptbx/possible_reflections.h (from /trunk/include/labelit/possible_reflections.h:1350)
   M /trunk/dptbx/resolution.cpp
   A /trunk/dptbx/resolution.h (from /trunk/include/labelit/resolution.h:1350)
   M /trunk/dptbx/sublatticescorer.cpp
   D /trunk/include/labelit/basis_refine.h
   D /trunk/include/labelit/beamplotter.h
   D /trunk/include/labelit/detectors.h
   D /trunk/include/labelit/directional_fft.h
   D /trunk/include/labelit/dptbx.h
   D /trunk/include/labelit/dptbx_debug.h
   D /trunk/include/labelit/hough.h
   D /trunk/include/labelit/latticescorer.h
   D /trunk/include/labelit/ll.h
   D /trunk/include/labelit/model_details.h
   D /trunk/include/labelit/modelcalculator.h
   D /trunk/include/labelit/mosaicity.h
   D /trunk/include/labelit/possible_reflections.h
   D /trunk/include/labelit/resolution.h
   D /trunk/include/labelit/rmerge.h
   D /trunk/include/labelit/singlemask.h
   D /trunk/include/labelit/spotfilter.h
   D /trunk/include/labelit/strategy.h
   D /trunk/include/labelit/symmetry.h
   M /trunk/strategy/boost_python/strategy_ext.cpp
   M /trunk/strategy/strategy.cpp
   A /trunk/strategy/strategy.h (from /trunk/include/labelit/strategy.h:1350)
   M /trunk/symmetry/boost_python/symmetry_ext.cpp
   M /trunk/symmetry/mark3.cpp
   M /trunk/symmetry/rmerge.cpp
   A /trunk/symmetry/rmerge.h (from /trunk/include/labelit/rmerge.h:1350)
   A /trunk/symmetry/symmetry.h (from /trunk/include/labelit/symmetry.h:1350)

Migration path, reorganized labelit directory structure
------------------------------------------------------------------------
r1351 | sauter | 2009-02-19 14:41:01 -0800 (Thu, 19 Feb 2009) | 1 line
Changed paths:
   A /trunk/array_family/boost_python/distl.h (from /trunk/include/labelit/distl.h:1350)
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   D /trunk/include/labelit/distl.h

migration path, labelit directory structure
------------------------------------------------------------------------
r1346 | sauter | 2009-02-15 19:11:38 -0800 (Sun, 15 Feb 2009) | 1 line
Changed paths:
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/labelit/diffraction/sublattice.py

Fix two potential divide-by-zero conditions
------------------------------------------------------------------------
r1272 | sauter | 2008-08-07 14:28:33 -0700 (Thu, 07 Aug 2008) | 1 line
Changed paths:
   M /trunk/detectors/boost_python/SConscript
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/mathsupport/boost_python/SConscript
   M /trunk/strategy/boost_python/SConscript
   M /trunk/symmetry/boost_python/SConscript
   M /trunk/webice_support/boost_python/SConscript

link against libomptbx across the board to avoid import errors
------------------------------------------------------------------------
r1244 | sauter | 2008-06-17 23:02:13 -0700 (Tue, 17 Jun 2008) | 1 line
Changed paths:
   M /trunk/array_family/boost_python/SConscript
   M /trunk/array_family/boost_python/flex_ext.cpp
   D /trunk/array_family/boost_python/flex_labelit_arrays.cpp
   M /trunk/labelit/array_family/flex.py

Migration path to rstbx namespace
------------------------------------------------------------------------
r1240 | sauter | 2008-06-16 14:29:21 -0700 (Mon, 16 Jun 2008) | 1 line
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

wts is the ADC pixel height above local background; new data is part of distl::spot
------------------------------------------------------------------------
r1218 | sauter | 2008-04-27 15:02:08 -0700 (Sun, 27 Apr 2008) | 1 line
Changed paths:
   M /trunk/distltbx/hough.cpp

clean clutter
------------------------------------------------------------------------
r1213 | bkpoon | 2008-04-01 13:35:17 -0700 (Tue, 01 Apr 2008) | 1 line
Changed paths:
   M /trunk/distltbx/hough.cpp
   M /trunk/include/labelit/hough.h
   M /trunk/labelit/distltbx/ice_nztt.py

Fixed compatibility issue in Hough Transform with IRIX
------------------------------------------------------------------------
r1210 | bkpoon | 2008-03-25 11:05:32 -0700 (Tue, 25 Mar 2008) | 1 line
Changed paths:
   M /trunk/distltbx/hough.cpp

Fixed infinite loop for older compilers
------------------------------------------------------------------------
r1185 | sauter | 2008-03-10 11:48:26 -0700 (Mon, 10 Mar 2008) | 1 line
Changed paths:
   M /trunk/distltbx/hough.cpp

clean clutter
------------------------------------------------------------------------
r1177 | bkpoon | 2008-02-20 01:24:41 -0800 (Wed, 20 Feb 2008) | 1 line
Changed paths:
   M /trunk/distltbx/hough.cpp
   M /trunk/include/labelit/hough.h

Fixed namespace issue for Tru64 compilers
------------------------------------------------------------------------
r1172 | bkpoon | 2008-02-14 15:22:46 -0800 (Thu, 14 Feb 2008) | 1 line
Changed paths:
   M /trunk/SConscript
   M /trunk/distltbx/boost_python/SConscript
   A /trunk/distltbx/boost_python/hough_ext.cpp
   A /trunk/distltbx/hough.cpp
   A /trunk/include/labelit/hough.h
   M /trunk/labelit/distltbx/__init__.py
   A /trunk/labelit/distltbx/ice_nztt.py
   M /trunk/labelit/tnear2.py

For non-zero two theta cases, ice ring detection is performed using the Hough transform through the RingFinder_nztt class
------------------------------------------------------------------------
r1124 | sauter | 2007-11-20 20:24:50 -0800 (Tue, 20 Nov 2007) | 1 line
Changed paths:
   M /trunk/distltbx/spotfilter.cpp

vampire code (dead code that still bites) eliminated
------------------------------------------------------------------------
r1098 | sauter | 2007-09-18 23:21:41 -0700 (Tue, 18 Sep 2007) | 1 line
Changed paths:
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/include/labelit/spotfilter.h
   M /trunk/labelit/tnear2.py

clean up unused code related to two-theta implementation
------------------------------------------------------------------------
r1097 | sauter | 2007-09-18 22:55:30 -0700 (Tue, 18 Sep 2007) | 1 line
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/dptbx/boost_python/dptbx_ext.cpp
   M /trunk/dptbx/dptbx.cpp
   M /trunk/dptbx/modelcalculator.cpp
   M /trunk/dptbx/mosaicity.cpp
   M /trunk/include/labelit/dptbx.h
   M /trunk/include/labelit/model_details.h
   M /trunk/include/labelit/modelcalculator.h
   M /trunk/include/labelit/mosaicity.h
   M /trunk/include/labelit/spotfilter.h
   M /trunk/labelit/command_line/imagefiles.py
   M /trunk/labelit/command_line/mosflm_script.py
   M /trunk/labelit/command_line/overlay_distl.py
   M /trunk/labelit/command_line/overlay_mosflm.py
   M /trunk/labelit/command_line/stats_index.py
   M /trunk/labelit/dptbx/__init__.py
   M /trunk/labelit/dptbx/autoindex.py
   M /trunk/labelit/dptbx/refinement.py
   A /trunk/labelit/dptbx/refinement_mode.py
   A /trunk/labelit/dptbx/test_two_theta.py
   M /trunk/labelit/interface.py
   M /trunk/labelit/procedure.py
   M /trunk/labelit/symmetry/metricsym/constrained.py
   M /trunk/labelit/tnear2.py

Initial support for non-zero two theta. Infrastructure for two-theta refinement, but this refinement is turned off.
------------------------------------------------------------------------
r1091 | sauter | 2007-08-10 15:41:03 -0700 (Fri, 10 Aug 2007) | 1 line
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/include/labelit/distl.h

An integer array of zeroes, for any user-defined purpose, intended as a scratchpad for overlap detection in the sublattice procedure
------------------------------------------------------------------------
r1090 | sauter | 2007-08-10 15:34:06 -0700 (Fri, 10 Aug 2007) | 1 line
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/tnear2.py

To support sublattice detection, make DISTL's pixel-wise Z-score persistent
------------------------------------------------------------------------
r1089 | sauter | 2007-08-10 15:16:53 -0700 (Fri, 10 Aug 2007) | 1 line
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   A /trunk/include/labelit/singlemask.h
   M /trunk/labelit/tnear2.py

To support sublattice detection, singlemask estimates a conservative rectangular spot box for one image
------------------------------------------------------------------------
r1060 | sauter | 2007-04-20 10:17:19 -0700 (Fri, 20 Apr 2007) | 2 lines
Changed paths:
   M /trunk/labelit/distltbx/__init__.py
   M /trunk/labelit/webice_support/tst_imports.py
   D /trunk/labelit/webice_support/tst_modules.py
   M /trunk/run_tests.py

Bugfix-now webice do_distl imports can be tested to confirm no extraneous modules.

------------------------------------------------------------------------
r1041 | sauter | 2007-02-23 11:23:43 -0800 (Fri, 23 Feb 2007) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/labelit/distltbx/spotlist_example.py

Fix uninitialized variable in unit test, causing intermittent crash on irix.

------------------------------------------------------------------------
r1037 | rwgk | 2007-01-10 10:22:28 -0800 (Wed, 10 Jan 2007) | 2 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp

make scitbx/boost_python/pickle_double_buffered.h independent of Python.h

------------------------------------------------------------------------
r1029 | sauter | 2006-12-14 20:31:15 -0800 (Thu, 14 Dec 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

Expose distl pixel maxima so they can be rendered in the WebIce picture.

------------------------------------------------------------------------
r1028 | sauter | 2006-12-14 20:30:05 -0800 (Thu, 14 Dec 2006) | 3 lines
Changed paths:
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/distltbx/ice2.py
   M /trunk/labelit/tnear2.py

Add ice-ring_bounds data item to Spotfinder so WebIce can render a picture
of the ice-ring locations.

------------------------------------------------------------------------
r1027 | sauter | 2006-12-01 13:45:31 -0800 (Fri, 01 Dec 2006) | 2 lines
Changed paths:
   M /trunk/detectors/detectors.cpp
   M /trunk/detectors/detectorsquick.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/dptbx/directional_fft.cpp
   M /trunk/dptbx/dptbx.cpp
   M /trunk/dptbx/model_details.cpp
   M /trunk/dptbx/mosaicity.cpp
   M /trunk/include/labelit/model_details.h
   M /trunk/include/labelit/modelcalculator.h

Satisfy -Wall warnings on unix gcc 4.1

------------------------------------------------------------------------
r1023 | sauter | 2006-11-14 16:49:24 -0800 (Tue, 14 Nov 2006) | 3 lines
Changed paths:
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/labelit/tnear2.py

Reorganization of close spots analysis.  Identification of intensity outliers
now moved down to C++ level.

------------------------------------------------------------------------
r1020 | sauter | 2006-11-13 23:24:21 -0800 (Mon, 13 Nov 2006) | 5 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/labelit/tnear2.py

Filtering on skewness, important when using center-of-mass positions
for autoindexing.  The goal is to eliminate pairs of unresolved Bragg
spots.  Condition is flagged when the max_pixel to center-of-mass
vector is more than 45% of the semi-major axis

------------------------------------------------------------------------
r1019 | sauter | 2006-11-13 22:44:05 -0800 (Mon, 13 Nov 2006) | 4 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/labelit/tnear2.py

The old libdistl::eccentricity function is deprecated, replaced by the
new model_eccentricity function based on modelling the inertia tensor
with a uniform-density ellipse.

------------------------------------------------------------------------
r1014 | sauter | 2006-11-09 22:03:59 -0800 (Thu, 09 Nov 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

pass-by-value integers don't need to be constant

------------------------------------------------------------------------
r1009 | sauter | 2006-10-31 13:41:12 -0800 (Tue, 31 Oct 2006) | 3 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/labelit/tnear2.py

Image overlays and autoindexing maintain backward compatibility
with spot information pickled under the old maximum_pixel method.

------------------------------------------------------------------------
r1008 | sauter | 2006-10-30 17:08:35 -0800 (Mon, 30 Oct 2006) | 3 lines
Changed paths:
   M /trunk/distltbx/distl.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/labelit/preferences.py
   M /trunk/labelit/tnear2.py

Indexing algorithm is controlled by a new parameter,
distl_spotcenter_algorithm = 'maximum_pixel'|'center_of_mass'

------------------------------------------------------------------------
r1006 | rwgk | 2006-10-30 13:11:16 -0800 (Mon, 30 Oct 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

Visual C++ 8.0 also needs the const int workaround

------------------------------------------------------------------------
r1005 | rwgk | 2006-10-28 22:44:07 -0700 (Sat, 28 Oct 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

work around Visual C++ 7.1 bug

------------------------------------------------------------------------
r1004 | sauter | 2006-10-28 21:12:19 -0700 (Sat, 28 Oct 2006) | 3 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp

spotlist pickler inow converts (double) quantities to (float) to save disk
        space, but the gain is not as much as hoped.

------------------------------------------------------------------------
r1003 | sauter | 2006-10-27 23:40:37 -0700 (Fri, 27 Oct 2006) | 3 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/labelit/distltbx/spotlist_example.py

Bragg spots now modeled with an intrinsically 2-dimensional treatment
of the inertia tensor.

------------------------------------------------------------------------
r1002 | sauter | 2006-10-26 15:33:42 -0700 (Thu, 26 Oct 2006) | 4 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/labelit/distltbx/pickle_support.py
   A /trunk/labelit/distltbx/spotlist_example.py

Pickling interface for spotlists (version 2) now records a) the total
        pixel sum (background subtracted), b) center of mass x,y, c) inertia
        tensor eigenvalues, and d) principle axes.

------------------------------------------------------------------------
r1001 | sauter | 2006-10-25 14:18:03 -0700 (Wed, 25 Oct 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h

remove dead code from distltbx for N^2 nearest neighbor calculation

------------------------------------------------------------------------
r999 | sauter | 2006-10-25 10:46:20 -0700 (Wed, 25 Oct 2006) | 6 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/labelit/command_line/overlay_distl.py
   M /trunk/labelit/distltbx/pickle_support.py
   M /trunk/labelit/procedure.py
   M /trunk/labelit/tnear2.py

deprecate the spotlist_to_flexint() interface and the ['inlier_bpl']
        spot markup interface, while maintaining backward compatibility so that
        old-style DISTL_pickle files can still be used for image overlays.
        Now, the DISTL_pickle file no longer contains duplicated pixel markup
        information, thus saving disk space.

------------------------------------------------------------------------
r993 | sauter | 2006-10-23 17:22:48 -0700 (Mon, 23 Oct 2006) | 6 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/labelit/tnear2.py

- in the spot interface, functions x() and y() are changed to
        maxpxl_x() and maxpxl_y().  This emphasizes that these are
        integer pixel positions of the spot's local maximum, as opposed to other
        kinds of position like center of mass.  More descriptive names easier
        for code maintenance.

------------------------------------------------------------------------
r885 | sauter | 2006-05-19 16:23:48 -0700 (Fri, 19 May 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

compatilbility with new spot_base / spot class hierarchy.

------------------------------------------------------------------------
r884 | sauter | 2006-05-18 16:04:46 -0700 (Thu, 18 May 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

Reorganization leading to SSRL compatibility

------------------------------------------------------------------------
r883 | sauter | 2006-05-18 15:31:15 -0700 (Thu, 18 May 2006) | 2 lines
Changed paths:
   M /trunk/SConscript
   M /trunk/distltbx/distl.cpp

Support a reorganization in the distl code leading toward SSRL compatibility.

------------------------------------------------------------------------
r882 | sauter | 2006-04-07 13:58:02 -0700 (Fri, 07 Apr 2006) | 8 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/command_line/stats_distl.py
   M /trunk/labelit/distltbx/__init__.py
   M /trunk/labelit/preferences.py
   M /trunk/labelit/tnear2.py

New preferences option "distl_report_overloads" causes distl to report
      candidate Bragg spots containing saturation overloads.  LABELIT takes
      the DISTL candidates, performs the usual ice ring and resolution filters,
      then counts the number of remaining overloaded spots (and reports them
      in stats_distl).  Overloaded spots are then removed prior to auto-
      indexing.  Previously "distl_report_overloads" was always False; now
      it is True by default.

-----------------------------------------------------------------------
r870 | sauter | 2006-03-19 20:40:48 -0800 (Sun, 19 Mar 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

Another attempt to fix the Windows compile bug.

------------------------------------------------------------------------
r867 | rwgk | 2006-03-19 08:07:43 -0800 (Sun, 19 Mar 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

colon restored (it wasn't stray; sorry), but with a leading blank

------------------------------------------------------------------------
r866 | rwgk | 2006-03-18 16:58:34 -0800 (Sat, 18 Mar 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

stray colon removed (to avoid Visual C++ failure)

------------------------------------------------------------------------
r857 | sauter | 2006-03-16 17:32:43 -0800 (Thu, 16 Mar 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

Fix a syntax error flagged by the Windows compiler

------------------------------------------------------------------------
r856 | sauter | 2006-03-16 17:12:45 -0800 (Thu, 16 Mar 2006) | 2 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp

Resolve pedantic warnings.

------------------------------------------------------------------------
r855 | sauter | 2006-03-16 17:10:56 -0800 (Thu, 16 Mar 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

Synonymous but more concise.

------------------------------------------------------------------------
r849 | sauter | 2006-03-06 10:56:46 -0800 (Mon, 06 Mar 2006) | 4 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

pixel values are now contained in the Distl::constmat<int> container.  The
memory is managed by the image reader, in this case iotbx/detectors.  Distl
no longer has a second copy of the image data.

------------------------------------------------------------------------
r848 | sauter | 2006-03-03 21:12:32 -0800 (Fri, 03 Mar 2006) | 5 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/include/labelit/spotfilter.h
   M /trunk/labelit/tnear2.py

Reorganize code so that the spot type is declared and defined within the
Distl namespace and file structure.  Boost.python directly wraps this; the
intermediate wrapper is merged into the Distl code and removed from the
labelit file tree.

------------------------------------------------------------------------
r847 | sauter | 2006-03-02 18:25:22 -0800 (Thu, 02 Mar 2006) | 2 lines
Changed paths:
   M /trunk/detectors/detectorsquick.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/dptbx/direction.cpp
   M /trunk/dptbx/modelcalculator.cpp
   M /trunk/dptbx/resolution.cpp
   M /trunk/include/labelit/resolution.h
   M /trunk/labelit/command_line/default_param.py
   M /trunk/labelit/command_line/fineprobe.py
   M /trunk/labelit/command_line/overlay_mosflm.py
   M /trunk/labelit/command_line/userprediction.py
   M /trunk/labelit/detectors/convention.py
   M /trunk/labelit/detectors/mar.py
   M /trunk/labelit/detectors/tolerance.py
   M /trunk/labelit/diffraction/decay.py
   M /trunk/labelit/diffraction/geometry.py
   M /trunk/labelit/diffraction/resolution.py
   M /trunk/labelit/distltbx/ice2.py
   M /trunk/labelit/dptbx/basis_choice.py
   M /trunk/labelit/dptbx/basis_refinement.py
   M /trunk/labelit/dptbx/beam_plot.py
   M /trunk/labelit/dptbx/constrainment.py
   M /trunk/labelit/dptbx/mosaicity.py
   M /trunk/labelit/dptbx/mvdr.py
   M /trunk/labelit/mathsupport/statistics.py
   M /trunk/labelit/symmetry/patterson_choice.py
   M /trunk/labelit/symmetry/pickle_support.py
   M /trunk/labelit/symmetry/screw_axis.py

clean whitespace clutter

------------------------------------------------------------------------
r846 | sauter | 2006-03-02 18:16:31 -0800 (Thu, 02 Mar 2006) | 3 lines
Changed paths:
   M /trunk/SConscript
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/include/labelit/spotfilter.h

For forward compatibility, migrate from the Diffspot namespace to the
newly-implemented Distl namespace (from SSRL).

------------------------------------------------------------------------
r841 | sauter | 2006-02-23 16:45:49 -0800 (Thu, 23 Feb 2006) | 9 lines
Changed paths:
   M /trunk/distltbx/distl.cpp
   M /trunk/labelit/tnear2.py

Large change in the method for calculating spot shape.  For each spot,
the major and minor axis is now determined by a pixel-by-pixel analysis.
This replaces the old (Zepu's) method using area and perimeter.  The
results are much more accurate, and permit reasonable spot rejections
within the tnear2.py procedure, which are now enabled.  Note:  a very
simple algorithm is used:  first the average pixel position is determined,
then the major axis is given by the largest displacement away from the
average position.  Minor axis is detected in the perpendicular direction.

------------------------------------------------------------------------
r839 | sauter | 2006-02-22 12:13:11 -0800 (Wed, 22 Feb 2006) | 6 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/include/labelit/spotfilter.h
   M /trunk/labelit/tnear2.py

The brute force nearest neighbor search is replaced by a k-d tree search.
This is a reference implementation showing that the two methods give the same
nearest neighbor distance (but not always the exact same neighbor), however
it is not fully functional in the spotpicking context.  The next version
will remove the dependency on the brute force approach.

------------------------------------------------------------------------
r837 | sauter | 2006-02-17 16:28:07 -0800 (Fri, 17 Feb 2006) | 2 lines
Changed paths:
   M /trunk/SConscript

Add background plane correction to spotfinder

------------------------------------------------------------------------
r831 | sauter | 2006-02-15 12:14:42 -0800 (Wed, 15 Feb 2006) | 5 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/tnear2.py

While introducing ListManager mechanism for maintaining a single C++ spotlist
that can be efficiently subsetted; also maintain backward compatibility so
that results previously pickled can still be viewed, and bright spots viewed
with labelit.overlay_distl.

------------------------------------------------------------------------
r829 | sauter | 2006-02-15 10:53:14 -0800 (Wed, 15 Feb 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/include/labelit/spotfilter.h

Fix EDG compiler Info messages

------------------------------------------------------------------------
r828 | sauter | 2006-02-15 10:42:01 -0800 (Wed, 15 Feb 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

Fix an EDG front end compiler warning

------------------------------------------------------------------------
r827 | sauter | 2006-02-14 20:43:15 -0800 (Tue, 14 Feb 2006) | 2 lines
Changed paths:
   M /trunk/distltbx/spotfilter.cpp

non-void function must have return value (some compilers)

------------------------------------------------------------------------
r826 | sauter | 2006-02-14 17:40:25 -0800 (Tue, 14 Feb 2006) | 4 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/distltbx/__init__.py

Ability to pickle flex_distl_spot, flex_icering, and SpotFilterAgent.
This will make it much easier to maintain a single master list of
spots, with subset nodes containing pointers to the master list.

------------------------------------------------------------------------
r825 | sauter | 2006-02-14 17:29:35 -0800 (Tue, 14 Feb 2006) | 4 lines
Changed paths:
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/include/labelit/spotfilter.h

Bugfix in filter agent; also, the minimum radius is no longer passed to the
constructor since it is only used in one test; instead, minradius is given
with the generalized "arguments" mechanism (function set_arguments()).

------------------------------------------------------------------------
r824 | sauter | 2006-02-14 11:49:01 -0800 (Tue, 14 Feb 2006) | 3 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/include/labelit/spotfilter.h

Provisional code to rank a subset of chosen spots by peak intensity.
Code will be tested and generalized later.

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r823 | sauter | 2006-02-14 11:46:48 -0800 (Tue, 14 Feb 2006) | 6 lines
Changed paths:
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h

Special method to reconstruct
the spot from a flex int.  Meant to be used for unpickling.
The const_iterator is intentionally meant to be incremented by
this constructor, so it can be used by the calling code to unpickle
the next spot.

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r820 | sauter | 2006-02-10 16:14:09 -0800 (Fri, 10 Feb 2006) | 9 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/spotfilter.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/include/labelit/spotfilter.h
   M /trunk/labelit/distltbx/ice2.py
   M /trunk/labelit/distltbx/method2.py
   M /trunk/labelit/procedure.py
   M /trunk/labelit/tnear2.py

A partially working improvement on the long-standing DISTL wrapper.  The
main improvements include a) push most of the array-intensive work down
below the Boost.Python boundary; b) reorganize process of subsetting the
spotlists; more indirection allows i) inserting and deleting tests,
ii) modular introduction of tests at C++ level, iii) en-bloc handling
of subsets, instead of instantiating separate code for each, iv) each
subset is now represented by pointers to the master list, which will be
separately pickled in the future.

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r819 | sauter | 2006-02-09 10:25:53 -0800 (Thu, 09 Feb 2006) | 5 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

Change the spotfinder background classification threshholds; the values
given in the paper don't make sense:  they should not increase in
subsequent passes.  There has been no testing to see if the regression tests
still work, so this modification may have to be rolled back.

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r818 | sauter | 2006-02-09 10:08:25 -0800 (Thu, 09 Feb 2006) | 5 lines
Changed paths:
   M /trunk/SConscript
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   A /trunk/distltbx/spotfilter.cpp
   A /trunk/include/labelit/spotfilter.h

Push many of the spot-filtering logic down into the C++ layer in an attempt
to improve performance of tnear2.  The underlying problem is that boost
python function calls were very numerous: many for each spot, and this
becomes prohibitive for large unit cells.

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r817 | sauter | 2006-02-08 20:31:13 -0800 (Wed, 08 Feb 2006) | 7 lines
Changed paths:
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h

w_Distl::mod_data() is an example function showing how the caller can
introspect the function of libdistl.  A modified data set is reported in
this case to show which pixels are being considered as candidate
background pixels.  This is a necessary tool for determining why the
background determination is failing. (Answer: too many pixels were being
excluded as underloads.)

------------------------------------------------------------------------
r816 | sauter | 2006-02-07 13:42:10 -0800 (Tue, 07 Feb 2006) | 4 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/labelit/distltbx/pickle_support.py

convert spotlist to a flex_int for pickling; very fast if done at C++ level
instead of in python (large performance hit from crossing boost.python boundary
many times.

------------------------------------------------------------------------
r798 | sauter | 2005-11-14 11:57:53 -0800 (Mon, 14 Nov 2005) | 4 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/include/labelit/distl.h

Remove dead code pertaining to DISTL's radial and angular anomalies.  This code
was in fact never used, and must be taken out before converging my DISTL cvs tree
to SSRL's current version.

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r692 | sauter | 2005-06-03 13:26:31 -0700 (Fri, 03 Jun 2005) | 5 lines
Changed paths:
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/distltbx/__init__.py

We can do much better during DISTL analysis of the Mar345 if we take into account
the true saturation value, which is much higher than 64K.  For one particular
test case provided by Ana Gonzalez, this makes the difference between yes or no
being able to index the dataset.

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r670 | rwgk | 2005-03-01 12:03:03 -0800 (Tue, 01 Mar 2005) | 2 lines
Changed paths:
   M /trunk/SConscript
   M /trunk/array_family/boost_python/SConscript
   M /trunk/detectors/boost_python/SConscript
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/dptbx/boost_python/SConscript
   M /trunk/labelit/command_line/default_param.py
   M /trunk/libtbx_config
   M /trunk/symmetry/boost_python/SConscript

major libtbx.config overhaul to introduce --repository support

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r641 | sauter | 2005-01-27 13:45:12 -0800 (Thu, 27 Jan 2005) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

Hard code the LABELIT default; able to change this in the preferences file.

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r630 | sauter | 2005-01-25 15:54:49 -0800 (Tue, 25 Jan 2005) | 4 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

Add a new passthru parameter -d1 for specifying the minimum signal-to-
background level for identifying local maxima on the image.  Necessary
if weaker candidate Bragg peaks are to be identified.

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r566 | sauter | 2004-11-18 18:08:48 -0800 (Thu, 18 Nov 2004) | 8 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/labelit/tnear2.py

New procedures for handling close spots.  This eliminates much of the
need for the overlapping_spot_criterion previously used.  If there are
a lot of close spots on an image, they are scrutinized to see if the
inter-spot vectors are all similar, indicating the spot-separation is
truly a unit cell vector.  These spots are then accepted.  Also, a check is
run to make sure there are no large spots that are really multiple
closely-spaced spots stuck together.

------------------------------------------------------------------------
r564 | sauter | 2004-11-18 17:54:09 -0800 (Thu, 18 Nov 2004) | 6 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/array_family/boost_python/flex_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h

Supporting C++ code for new close-spot heuristics.  For cases where
candidate Bragg spots are close to each other on the image, cache a list
of xy vectors connecting a spot to its nearest neighbor.  This list
will then be analyzed to see if separation vectors are the same, indicating
a candidate cell vector.

------------------------------------------------------------------------
r474 | sauter | 2004-08-19 13:03:36 -0700 (Thu, 19 Aug 2004) | 2 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/array_family/boost_python/flex_labelit_arrays.cpp
   M /trunk/detectors/detectors.cpp
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/dptbx/dptbx.cpp
   M /trunk/include/labelit/basis_refine.h
   M /trunk/include/labelit/beamplotter.h
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/command_line/scala_symmetry.py
   M /trunk/labelit/command_line/test2_harker.py
   M /trunk/labelit/diffraction/limits.py
   M /trunk/labelit/dptbx/__init__.py
   M /trunk/labelit/dptbx/tools.py

clean the whitespace clutter

------------------------------------------------------------------------
r437 | sauter | 2004-06-18 14:29:47 -0700 (Fri, 18 Jun 2004) | 5 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/command_line/runprinter.py
   M /trunk/labelit/tnear2.py

In the event that there are too few spots for parameter refinement, make extra
effort to make a very detailed inspection of the border pixels of each spot
so that more non-overlapping spot candidates can be included in the calculation.
This is the only way to index Bart Hazes' low resolution image.

------------------------------------------------------------------------
r322 | rwgk | 2003-12-19 12:43:32 -0800 (Fri, 19 Dec 2003) | 2 lines
Changed paths:
   M /trunk/SConscript
   M /trunk/array_family/boost_python/SConscript
   A /trunk/array_family/boost_python/flex_ext.cpp
   D /trunk/array_family/boost_python/flex_labelit_ext.cpp
   M /trunk/detectors/boost_python/SConscript
   A /trunk/detectors/boost_python/detectors_ext.cpp
   D /trunk/detectors/boost_python/detectorsmodule.cpp
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/dptbx/boost_python/SConscript
   M /trunk/dptbx/boost_python/dptbx_ext.cpp
   M /trunk/labelit/array_family/flex.py
   M /trunk/labelit/detectors/__init__.py
   M /trunk/labelit/distltbx/__init__.py
   M /trunk/labelit/dptbx/__init__.py

adjust to latest cctbx changes: all extensions moved to top level #libtbx in build directory (e.g. labelit_deterctors_ext.so); use boost.python.import_ext

------------------------------------------------------------------------
r296 | rwgk | 2003-11-20 09:56:02 -0800 (Thu, 20 Nov 2003) | 2 lines
Changed paths:
   M /trunk/SConscript
   M /trunk/array_family/boost_python/SConscript
   M /trunk/detectors/boost_python/SConscript
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/dptbx/boost_python/SConscript
   M /trunk/libtbx_config

adjustments to facilitate inclusion in auto_build

------------------------------------------------------------------------
r293 | ttleese | 2003-11-04 13:31:22 -0800 (Tue, 04 Nov 2003) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp
   M /trunk/dptbx/beamplotter.cpp
   M /trunk/dptbx/dptbx.cpp
   M /trunk/include/labelit/distl.h

*** empty log message ***

------------------------------------------------------------------------
r232 | sauter | 2003-09-08 22:19:55 -0700 (Mon, 08 Sep 2003) | 2 lines
Changed paths:
   M /trunk/LICENSE.txt
   M /trunk/SConscript
   M /trunk/array_family/boost_python/SConscript
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/array_family/boost_python/flex_labelit_ext.cpp
   M /trunk/detectors/boost_python/SConscript
   M /trunk/detectors/boost_python/detectorsmodule.cpp
   M /trunk/detectors/detectors.cpp
   M /trunk/detectors/detectorsquick.cpp
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/dptbx/beamplotter.cpp
   M /trunk/dptbx/boost_python/SConscript
   M /trunk/dptbx/boost_python/dptbx_ext.cpp
   M /trunk/dptbx/dptbx.cpp
   M /trunk/include/labelit/beamplotter.h
   M /trunk/include/labelit/detectors.h
   M /trunk/include/labelit/distl.h
   M /trunk/include/labelit/dptbx.h
   M /trunk/labelit/array_family/flex.py
   M /trunk/labelit/command_line/runprinter.py
   M /trunk/labelit/command_line/screen.py
   M /trunk/labelit/detectors/__init__.py
   M /trunk/labelit/detectors/jpeg.py
   M /trunk/labelit/diffraction/limits.py
   M /trunk/labelit/distltbx/__init__.py
   M /trunk/labelit/dps.py
   M /trunk/labelit/dptbx/__init__.py
   M /trunk/labelit/dptbx/autoindex.py
   M /trunk/labelit/dptbx/character.py
   M /trunk/labelit/dptbx/graphics_procedure.py
   M /trunk/labelit/dptbx/graphics_support.py
   M /trunk/labelit/dptbx/status.py
   M /trunk/labelit/dptbx/tools.py
   M /trunk/labelit/dptbx/zuoreduction.py
   M /trunk/labelit/interface.py
   M /trunk/labelit/procedure.py
   M /trunk/labelit/tnear.py
   M /trunk/labelit/tnear2.py

First pass converting pipeline references to labelit references

------------------------------------------------------------------------
r228 | sauter | 2003-09-01 21:07:30 -0700 (Mon, 01 Sep 2003) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

Trying to debug failure on gcc2.96

------------------------------------------------------------------------
r199 | sauter | 2003-07-29 17:08:31 -0700 (Tue, 29 Jul 2003) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h

Zepu's resolution determination is now run automatically every time.

------------------------------------------------------------------------
r182 | sauter | 2003-07-21 14:48:24 -0700 (Mon, 21 Jul 2003) | 2 lines
Changed paths:
   M /trunk/SConscript

Add DISTL support to the pipeline package.
------------------------------------------------------------------------
r181 | sauter | 2003-07-21 14:47:29 -0700 (Mon, 21 Jul 2003) | 2 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/array_family/boost_python/flex_labelit_ext.cpp

Add the icering list to boost python wrapper.

------------------------------------------------------------------------
r180 | sauter | 2003-07-21 14:46:32 -0700 (Mon, 21 Jul 2003) | 2 lines
Changed paths:
   M /trunk/include/labelit/distl.h

depracate ngoodspots; use size method of flex.spot instead.

------------------------------------------------------------------------
r172 | sauter | 2003-07-21 14:16:32 -0700 (Mon, 21 Jul 2003) | 3 lines
Changed paths:
   M /trunk/labelit/distltbx/__init__.py

The beamxy passed to spotfinder must be the same locale-specific beamxy in
the pd dictionary; otherwise ice ring finder has the wrong beam center.

------------------------------------------------------------------------
r171 | sauter | 2003-07-21 14:14:09 -0700 (Mon, 21 Jul 2003) | 2 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

add the icering class

------------------------------------------------------------------------
r170 | sauter | 2003-07-21 14:13:17 -0700 (Mon, 21 Jul 2003) | 2 lines
Changed paths:
   M /trunk/distltbx/boost_python/distltbx_ext.cpp

Add the icering class to boost wrapper

------------------------------------------------------------------------
r169 | sauter | 2003-07-16 17:43:38 -0700 (Wed, 16 Jul 2003) | 2 lines
Changed paths:
   M /trunk/labelit/distltbx/__init__.py

nit file for reference implementation of DISTL wrapper.

------------------------------------------------------------------------
r168 | sauter | 2003-07-16 17:42:30 -0700 (Wed, 16 Jul 2003) | 4 lines
Changed paths:
   M /trunk/array_family/boost_python/flex_distl_spot.cpp
   M /trunk/array_family/boost_python/flex_labelit_ext.cpp
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h

An initial implementation of a wrapper for the May 28 DISTL from Zepu.
This compiles, runs and gives apparently reasonable results, but probably
needs some fine-tuning.

------------------------------------------------------------------------
r123 | sauter | 2003-06-10 14:48:26 -0700 (Tue, 10 Jun 2003) | 3 lines
Changed paths:
   M /trunk/SConscript
   M /trunk/include/labelit/distl.h

distltbx is dead code until further notice; need to examine Zepu's latest code
before migrating from spotfinder to distltbx.

------------------------------------------------------------------------
r95 | sauter | 2003-05-26 17:19:51 -0700 (Mon, 26 May 2003) | 3 lines
Changed paths:
   M /trunk/distltbx/distl.cpp

Code that does not compile on tru64 was commented out.  Ultimately this should
either go away, or else malloc should be used to create a new array of char*.

------------------------------------------------------------------------
r80 | sauter | 2003-05-02 21:41:09 -0700 (Fri, 02 May 2003) | 3 lines
Changed paths:
   M /trunk/SConscript
   M /trunk/distltbx/boost_python/SConscript
   M /trunk/distltbx/boost_python/distltbx_ext.cpp
   M /trunk/distltbx/distl.cpp
   M /trunk/include/labelit/distl.h
   M /trunk/labelit/distltbx/__init__.py

Further support for Ashley Deacon's Mar 20 version of DISTL.  However,
things are still not completely working.

------------------------------------------------------------------------
r79 | sauter | 2003-05-02 21:39:25 -0700 (Fri, 02 May 2003) | 2 lines
Changed paths:
   A /trunk/labelit/array_family
   A /trunk/labelit/array_family/__init__.py
   A /trunk/labelit/array_family/flex.py

Python support for flex arrays of distl::w_spot and distl::point

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r78 | sauter | 2003-05-02 21:37:08 -0700 (Fri, 02 May 2003) | 2 lines
Changed paths:
   A /trunk/array_family
   A /trunk/array_family/boost_python
   A /trunk/array_family/boost_python/SConscript
   A /trunk/array_family/boost_python/flex_distl_spot.cpp
   A /trunk/array_family/boost_python/flex_labelit_ext.cpp

Add pipeline flex types for af::shared<w_spot> and af::shared<point>

------------------------------------------------------------------------
r77 | sauter | 2003-05-01 22:55:58 -0700 (Thu, 01 May 2003) | 3 lines
Changed paths:
   M /trunk/SConscript
   A /trunk/distltbx
   A /trunk/distltbx/boost_python
   A /trunk/distltbx/boost_python/SConscript
   A /trunk/distltbx/boost_python/distltbx_ext.cpp
   A /trunk/distltbx/distl.cpp
   A /trunk/include/labelit/distl.h
   A /trunk/labelit/distltbx
   A /trunk/labelit/distltbx/__init__.py

First version of support wrapper for Ashley Deacon's new DISTL version
as of March 20, 2003.  This doesn't fully work yet.

------------------------------------------------------------------------
