[med-svn] [relion] branch upstream updated (c062815 -> a366454)

[Roland Fehrenbacher]

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rfehren-guest pushed a change to branch upstream
in repository relion.

      from  c062815   Imported Upstream version 1.3+dfsg
       new  a366454   Imported Upstream version 1.4+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 INSTALL.sh                       |   23 +-
 Makefile.am                      |   34 +-
 Makefile.in                      |   60 +-
 autogen.sh                       |    4 +-
 config.h.in                      |    6 +
 configure                        |  268 +-
 configure.ac                     |   50 +-
 scripts/qsub.csh                 |    5 +-
 src/apps/autopick_mpi.cpp        |    5 +-
 src/apps/find_tiltpairs.cpp      |   74 +-
 src/apps/image_handler.cpp       |  605 ++--
 src/apps/maingui.cpp             |   13 +-
 src/apps/mask_create.cpp         |    4 +-
 src/apps/particle_polish_mpi.cpp |    5 +-
 src/apps/particle_sort_mpi.cpp   |    5 +-
 src/apps/preprocess_mpi.cpp      |    2 +-
 src/apps/project.cpp             |  131 +-
 src/apps/reconstruct.cpp         |  122 +-
 src/apps/refine_mpi.cpp          |    7 +-
 src/apps/run_ctffind_mpi.cpp     |    5 +-
 src/apps/stack_create.cpp        |   14 +-
 src/apps/star_compare.cpp        |  109 +
 src/apps/tiltpair_plot.cpp       |  329 +++
 src/assembly.cpp                 |    6 +-
 src/assembly.h                   |   12 +-
 src/autopicker.cpp               |  104 +-
 src/autopicker.h                 |   32 +-
 src/backprojector.cpp            |  375 ++-
 src/backprojector.h              |  100 +-
 src/complex.cpp                  |   34 +-
 src/complex.h                    |   33 +-
 src/ctf.cpp                      |   28 +-
 src/ctf.h                        |   78 +-
 src/ctffind_runner.cpp           |   50 +-
 src/ctffind_runner.h             |   36 +-
 src/ctffind_runner_mpi.cpp       |    4 +-
 src/displayer.cpp                |  113 +-
 src/displayer.h                  |   56 +-
 src/euler.cpp                    |  101 +-
 src/euler.h                      |  106 +-
 src/exp_model.cpp                |  852 +++---
 src/exp_model.h                  |  115 +-
 src/fftw.cpp                     |  424 +--
 src/fftw.h                       |  106 +-
 src/filename.cpp                 |   29 +-
 src/funcs.cpp                    |  273 +-
 src/funcs.h                      |  129 +-
 src/gcc_version.h                |    1 -
 src/gui_entries.h                |    8 +-
 src/gui_jobwindow.cpp            |  165 +-
 src/gui_jobwindow.h              |   39 +-
 src/gui_mainwindow.cpp           |   39 +-
 src/healpix_sampling.cpp         |  928 +++---
 src/healpix_sampling.h           |  139 +-
 src/image.cpp                    |   89 +-
 src/image.h                      |   42 +-
 src/macros.h                     |   71 +-
 src/manualpicker.cpp             |   29 +-
 src/mask.cpp                     |   42 +-
 src/mask.h                       |   10 +-
 src/matrix1d.cpp                 |   16 +-
 src/matrix1d.h                   |  105 +-
 src/matrix2d.cpp                 |    4 +-
 src/matrix2d.h                   |  168 +-
 src/metadata_container.cpp       |  120 +-
 src/metadata_container.h         |   27 +-
 src/metadata_label.cpp           |    2 +-
 src/metadata_label.h             |   10 +-
 src/metadata_table.cpp           |  263 +-
 src/metadata_table.h             |   22 +-
 src/ml_model.cpp                 |  136 +-
 src/ml_model.h                   |   77 +-
 src/ml_optimiser.cpp             | 5730 ++++++++++++++++++++------------------
 src/ml_optimiser.h               |  235 +-
 src/ml_optimiser_mpi.cpp         |  362 ++-
 src/ml_optimiser_mpi.h           |    5 +-
 src/mpi.cpp                      |  216 +-
 src/mpi.h                        |   10 +-
 src/multidim_array.h             |  241 +-
 src/numerical_recipes.cpp        |  265 +-
 src/numerical_recipes.h          |   53 +-
 src/parallel.cpp                 |    1 +
 src/particle_polisher.cpp        |  389 ++-
 src/particle_polisher.h          |   41 +-
 src/particle_polisher_mpi.cpp    |   42 +-
 src/particle_sorter.cpp          |   96 +-
 src/particle_sorter.h            |   18 +-
 src/particle_sorter_mpi.cpp      |    4 +-
 src/postprocessing.cpp           |   96 +-
 src/postprocessing.h             |   26 +-
 src/preprocessing.cpp            |   77 +-
 src/preprocessing.h              |   13 +-
 src/projector.cpp                |  220 +-
 src/projector.h                  |   52 +-
 src/rwIMAGIC.h                   |   22 +-
 src/rwMRC.h                      |   42 +-
 src/rwSPIDER.h                   |   22 +-
 src/strings.cpp                  |   10 +-
 src/strings.h                    |    9 +-
 src/symmetries.cpp               |   38 +-
 src/symmetries.h                 |   12 +-
 src/tabfuncs.cpp                 |   30 +-
 src/tabfuncs.h                   |   24 +-
 src/transformations.cpp          |   29 +-
 src/transformations.h            |   98 +-
 105 files changed, 9013 insertions(+), 7143 deletions(-)
 create mode 100644 src/apps/star_compare.cpp
 create mode 100644 src/apps/tiltpair_plot.cpp

-- 
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