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NEWS
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New in Version 0.1.25
=====================
* rotational_minctracc.py handles source and target masking correctly
New in Version 0.1.24
=====================
* rotational_minctracc.py uses minccmp instead of Pyminc to avoid memory leakage.
* remove minc-scripts submodule and include vtk_meshconvert.py directly.
New in Version 0.1.23
=====================
* Added compute_determinants.py
New in Version 0.1.22
=====================
* Added object_volume_dot_product program from unrelease mouse-thickness package
New in Version 0.1.21
=====================
* TFCE rewritten to use numpy instead of weave, which doesn't support Python 3
New in Version 0.1.20
=====================
* rotational_minctracc.py does not keep any intermediate files anymore; everything is deleted
during the process, and the final transformation is re-created at the end.
* rotational_minctracc.py now can also handle ctrl-c (SIGINT) in its cleanup.
* rotational_minctracc.py can be used for lsq12 instead of lsq6 brute force alignment
New in Version 0.1.19
=====================
* added script: make_xfm_for_grid.pl which creates an xfm file for a provided deformation grid
(vector file)
New in Version 0.1.18
=====================
* 2to3 fixes
* fix `install_requires` in setup.py
New in Version 0.1.17
=====================
* fix bug in TFCE implementation
* fix linking on OS X
New in Version 0.1.16
=====================
* fix compilation against static HDF5 libs
New in Version 0.1.15
=====================
* fairly big overhaul of rotational_minctracc.py: it turns out that the centre of gravity (cog)
of the two input files to rotational_minctracc.py do not always reflect the same part of the
object. In those cases, the alignment most likely will fail because a mask is used, and
representative areas of the input files might not even be compared. For this reason
rotation_minctracc.py now also runs a "translational" part. Multiple centers of gravity
are determined which serve as seeds for the initial translational alignment. All possible
pairs of seeds are tried and by default the best 3 pairs are used for the rotational part
of the code.
* some more Python3 compatibility related fixes
* added options for minc_label_ops
New in Version 0.1.14
=====================
* completely remove the multiprocessing machinery from pmincaverage since this caused extra processes
to be spawned even when running single-threaded, causing large memory usage to be attributed to
running pmincaverage instances. If necessary, this machinery could be reinstated
behind some conditional logic.
* small upgrades to voxel_vote: better help messages and argument parsing,
ability to vote on a single file, small code improvements, --(no-)clobber respected
* sge_batch has been removed; use pipetone/qbatch instead
* atlas_to_atlas.pl has been added, though use of Pydpiper's MAGeT.py is recommended in general
* tagtoxfm and some supporting code have been added to allow their use in environments without
a build of the visual tools from minc-toolkit
New in Version 0.1.13
=====================
* code changes to ensure python3 compatibility
New in Version 0.1.12
=====================
* added the option -flip-images to ray_trace_crosshair in case you are working with a version of
MINC that flips images when using ray_trace
* fixed bug in minc_label_ops; the binarize option now works
* rotational_minctracc uses subprocess instead of system to ensure you get a non-zero return when
the program fails. Also added the --simplex option. By default the simplex value that was used
was only appropriate for human brains. For mouse brains you can set this to 1 (mm) for instance.
New in Version 0.1.11
=====================
* turned off multiprocessing in pmincaverage, because it sometimes crashes on compressed MINC files
New in Version 0.1.10
=====================
* more updates to smooth_vector: exists with a non-zero return (1) if the output file can not be created
New in Version 0.1.9
====================
* smooth_vector: provide useful output when the input does not exist, or is broken
* minc_displacement: if the output file can not be written to disk, exit with 1 (instead of 0...)
New in Version 0.1.8
====================
* clobber option in pmincaverage is activated
New in Version 0.1.7
====================
* added vtk_meshconvert.py a program that can be used to convert between BIC obj, stl and vtk meshes
* added bayes_intensity_update a program that updates an image based on prior knowledge coming from a population (and its stdev)
New in Version 0.1.6
====================
* fixes egg-info file issues. The minc-stuffs version information will be produced correctly now
New in Version 0.1.5
====================
* fixes cython/numpy compilation issues with anaconda-2.1.0
New in Version 0.1.4
====================
* added rotational_minctracc.py
New in Version 0.1.3
====================
* compute_values_across_segmentation, volumes_from_labels_only, and voxel_vote now accepts label files with up to 65536 labels (instead of 256)
* voxel_vote now properly writes out label files (integer values)
New in Version 0.1.2
====================
* minc-stuffs can now be compiled against the minc-toolkit