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Author SHA1 Message Date
Evgeni Burovski 42d4eb6123 TST: skel3d: add more tests 2016-02-20 17:29:13 +00:00
Evgeni Burovski 304660d287 BLD: bump the cython version to 0.23.4 on Travis 2016-02-20 17:29:13 +00:00
Evgeni Burovski 87541b661d BLD: skel3d: eradicate stray unicode symbols from source files 2016-02-20 17:29:13 +00:00
Evgeni Burovski 27b5dbca48 MAINT: skel3d: address review comments 
Tidy up the python wrapper a little.
 2016-02-20 17:26:12 +00:00
Evgeni Burovski 212c3d15ce BLD: add the extension to bento.info, fix names 2016-02-20 17:26:12 +00:00
Evgeni Burovski 99de44744a ENH: skel3d: unroll and inline index_octants into is_euler_invariant 
13.7/7.3 performance boost on the lobster dataset, huh
 2016-02-20 17:26:12 +00:00
Evgeni Burovski a07dd7cb9e MAINT: skel3d: minor sty/perf fixes 
* remove commented out code
* statically type tuple of ints
 2016-02-20 17:26:12 +00:00
Evgeni Burovski de912c4f7b STY: generate octree_labeling routine via tempita at build time 2016-02-20 17:26:12 +00:00
Evgeni Burovski 3bbb766f4e MAINT: skel3d: rename _skel.pyx to _skel.pyx.in 
(no templating yet)
 2016-02-20 17:26:12 +00:00
Evgeni Burovski c4c95ae4bc STY: reformat the filling-in of the Euler LUT 2016-02-20 17:26:12 +00:00
Evgeni Burovski 85f46c6fe8 MAINT: skel3d: address review comments 
* simplify filling in the neighb_idx LUT
* underscore references
* preserve the color range of the original image
 2016-02-20 17:26:12 +00:00
Evgeni Burovski 456a5252c9 STY: skel3d: clarify the status of module-level LUTs. 
Fill in at the module level, then rebind in compute_thin_image, and pass around
as arguments to relevant functions.
 2016-02-20 17:26:12 +00:00
Evgeni Burovski 5fa50a6765 MAINT: skel3d: prune dead code (eg, is_surface_point) 2016-02-20 17:26:12 +00:00
Evgeni Burovski ecf744542e MAINT: remove decorators which have no effect anyway 2016-02-20 17:26:12 +00:00
Evgeni Burovski dc6cf19fec STY: move main functions to the top of the file 2016-02-20 17:26:12 +00:00
Evgeni Burovski f82dddd475 MAINT: stop slicing memoryviews in is_simple_point. 
Use plain C arrays for neighbors[27] + memcpy when copying the `cube`
for labeling.

Apparently, slicing memoryviews *is* expensive (cf Jake vdP'2012).
 2016-02-20 17:26:12 +00:00
Evgeni Burovski 42ba24deb3 MAINT: skel3d: don't print stuff 2016-02-20 17:26:12 +00:00
Evgeni Burovski 88a9bcc874 DOC: skel3d: add basic docstrings 2016-02-20 17:26:12 +00:00
Evgeni Burovski 689980124d MAINT: skel3d: simplify dealing with 2D images 2016-02-20 17:26:12 +00:00
Evgeni Burovski c60b6b05cf MAINT: statically type img in toplevel _compute_thin_image 2016-02-20 17:26:12 +00:00
Evgeni Burovski 2f0d0cc18c MAINT: avoid incrurring np.r_ overhead in is_simple_point 
(yet another x1.6)
 2016-02-20 17:26:12 +00:00
Evgeni Burovski b7889b2c4f MAINT: avoid doing np.sum in the hot loop 
(you gotta be kidding me, x2 speed-up)
 2016-02-20 17:26:11 +00:00
Evgeni Burovski 01e1f04b28 TST: skel3d: add a Bat Cochlea sample from FIJI collections 2016-02-20 17:26:11 +00:00
Evgeni Burovski c9ed06ad92 MAINT: skel3d: statically type Euler LUT 2016-02-20 17:26:11 +00:00
Evgeni Burovski 32865d2bd9 MAINT: skel3d: statically type index_octants 2016-02-20 17:26:11 +00:00
Evgeni Burovski 53f48cb6c0 MAINT: skel3d: only allocate and type neighborhood once; switch off 
bounds checking
 2016-02-20 17:26:11 +00:00
Evgeni Burovski f1176a5319 MAINT: skel3d: add static typing to obvious places 2016-02-20 17:26:11 +00:00
Evgeni Burovski 06d5a91f57 MAINT: skel3d: move computations to cython 2016-02-20 17:26:11 +00:00
Evgeni Burovski a85c9ddd3c MAINT: move new skeletonize3d files to more appropriate places 2016-02-20 17:26:11 +00:00
Evgeni Burovski e421cea331 ENH: start adding a python version of Skeletonize3D code 2016-02-20 17:26:11 +00:00
Emmanuelle Gouillart 6614e1339a Merge pull request #1924 from ev-br/tempita 
Handle tempita templed cython files
 2016-02-16 23:25:53 +01:00
Evgeni Burovski ad535ac2bd MAINT: address review comments 2016-02-16 07:10:13 +00:00
Juan Nunez-Iglesias dd5a5e5556 Merge pull request #1944 from sciunto/temp_file 
MAINT: fixes #1652
 2016-02-16 17:59:55 +11:00
François Boulogne 461b06a517 MAINT: fixes #1652 
add close()

Stephans solution

close file before

remove comment
 2016-02-15 22:01:55 -05:00
Josh Warner 2217dfc6f2 Merge pull request #1942 from emmanuelle/trailing_todo 
TST: 3D test for register_translation
 2016-02-13 19:33:16 -07:00
emmanuelle 45ff200c31 3D test for register_translation, as required by TODO.txt 2016-02-12 22:40:32 +01:00
Juan Nunez-Iglesias a6e07615f4 Merge pull request #1936 from ahojnnes/depr 
Fix some remaining TODO items
 2016-02-09 23:25:42 +11:00
Johannes Schönberger 116ef0d649 Remove unit tests for deprecated features 2016-02-09 12:25:55 +01:00
Johannes Schönberger e82849a544 Document API changes 2016-02-09 11:16:49 +01:00
Johannes Schönberger 9d9a4b3e0b Fix some remaining TODO items 2016-02-09 11:11:28 +01:00
Egor Panfilov 66102ad91a Merge pull request #1895 from OrkoHunter/denoise_bilateral 
Raise warning for 3D images in denoise_bilateral
 2016-02-05 17:22:04 +03:00
Himanshu Mishra 7014d04327 Remove useless multichannel=True kwarg from tests 2016-02-05 14:38:13 +05:30
Himanshu Mishra b40d028550 Add tests for warnings in denoise_bilateral 2016-02-05 08:05:58 +05:30
Steven Silvester 00fd6f44ae Merge pull request #1927 from sciunto/doc_inpaint2 
DOC: make image smaller for better visu
 2016-02-04 16:22:49 -06:00
Steven Silvester da89e26289 Merge pull request #1930 from emmanuelle/release_notes 
First version of release notes for 0.12
 2016-02-04 16:11:25 -06:00
emmanuelle 17b43daa56 Correction in release notes (wrong section) 2016-02-04 23:05:28 +01:00
emmanuelle 5bf67460af Minor change in order of contributors 2016-02-04 23:04:13 +01:00
emmanuelle f6f0f7eec4 First version of release notes for 0.12 2016-02-04 22:54:29 +01:00
Evgeni Burovski f4cbcf29f3 BLD: use default encoding 2016-02-04 08:38:52 +00:00
Johannes Schönberger 8890ff8ba0 Merge pull request #1925 from sciunto/test_naming 
MAINT: fix test name
 2016-02-04 08:32:09 +01:00