2bc8538f9f
MAINT: address review comments
...
* typos in comments
* handle the corner case of width-1 2D image
* vanity
* change up leftover <= to correct ==
2016-02-20 17:29:13 +00:00
dc702a83ee
TST: skel3d: redo 3D test images
...
Remove ad-hoc images from morphology/tests/data folder.
Add a FIJI generated image to skimage/data.
The image was generated via
>>> img = binary_blobs(32, 0.05, n_dim=3, seed=1234)
>>> img = img.astype(np.uint8)*255
>>> img = img[:-2, ...]
then saved as a sequence of png frames, read into FIJI as an image sequence,
and skeletonized via Plugins -> Skeletonize (2D/3D).
2016-02-20 17:29:13 +00:00
d832739300
TST: skel3d: remove 2D test images
2016-02-20 17:29:13 +00:00
64bb1775be
TST: inline a two-hole image
2016-02-20 17:29:13 +00:00
9648d71360
MAINT: skel3d: do not copy more than necessary
2016-02-20 17:29:13 +00:00
81d47328ea
DOC: spell out the names of [Lee94], add the Notes section
2016-02-20 17:29:13 +00:00
42d4eb6123
TST: skel3d: add more tests
2016-02-20 17:29:13 +00:00
304660d287
BLD: bump the cython version to 0.23.4 on Travis
2016-02-20 17:29:13 +00:00
87541b661d
BLD: skel3d: eradicate stray unicode symbols from source files
2016-02-20 17:29:13 +00:00
27b5dbca48
MAINT: skel3d: address review comments
...
Tidy up the python wrapper a little.
2016-02-20 17:26:12 +00:00
212c3d15ce
BLD: add the extension to bento.info, fix names
2016-02-20 17:26:12 +00:00
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
a07dd7cb9e
MAINT: skel3d: minor sty/perf fixes
...
* remove commented out code
* statically type tuple of ints
2016-02-20 17:26:12 +00:00
de912c4f7b
STY: generate octree_labeling routine via tempita at build time
2016-02-20 17:26:12 +00:00
3bbb766f4e
MAINT: skel3d: rename _skel.pyx to _skel.pyx.in
...
(no templating yet)
2016-02-20 17:26:12 +00:00
c4c95ae4bc
STY: reformat the filling-in of the Euler LUT
2016-02-20 17:26:12 +00:00
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
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
5fa50a6765
MAINT: skel3d: prune dead code (eg, is_surface_point)
2016-02-20 17:26:12 +00:00
ecf744542e
MAINT: remove decorators which have no effect anyway
2016-02-20 17:26:12 +00:00
dc6cf19fec
STY: move main functions to the top of the file
2016-02-20 17:26:12 +00:00
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
42ba24deb3
MAINT: skel3d: don't print stuff
2016-02-20 17:26:12 +00:00
88a9bcc874
DOC: skel3d: add basic docstrings
2016-02-20 17:26:12 +00:00
689980124d
MAINT: skel3d: simplify dealing with 2D images
2016-02-20 17:26:12 +00:00
c60b6b05cf
MAINT: statically type img in toplevel _compute_thin_image
2016-02-20 17:26:12 +00:00
2f0d0cc18c
MAINT: avoid incrurring np.r_ overhead in is_simple_point
...
(yet another x1.6)
2016-02-20 17:26:12 +00:00
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
01e1f04b28
TST: skel3d: add a Bat Cochlea sample from FIJI collections
2016-02-20 17:26:11 +00:00
c9ed06ad92
MAINT: skel3d: statically type Euler LUT
2016-02-20 17:26:11 +00:00
32865d2bd9
MAINT: skel3d: statically type index_octants
2016-02-20 17:26:11 +00:00
53f48cb6c0
MAINT: skel3d: only allocate and type neighborhood once; switch off
...
bounds checking
2016-02-20 17:26:11 +00:00
f1176a5319
MAINT: skel3d: add static typing to obvious places
2016-02-20 17:26:11 +00:00
06d5a91f57
MAINT: skel3d: move computations to cython
2016-02-20 17:26:11 +00:00
a85c9ddd3c
MAINT: move new skeletonize3d files to more appropriate places
2016-02-20 17:26:11 +00:00
e421cea331
ENH: start adding a python version of Skeletonize3D code
2016-02-20 17:26:11 +00:00
6614e1339a
Merge pull request #1924 from ev-br/tempita
...
Handle tempita templed cython files
2016-02-16 23:25:53 +01:00
ad535ac2bd
MAINT: address review comments
2016-02-16 07:10:13 +00:00
dd5a5e5556
Merge pull request #1944 from sciunto/temp_file
...
MAINT: fixes #1652
2016-02-16 17:59:55 +11:00
461b06a517
MAINT: fixes #1652
...
add close()
Stephans solution
close file before
remove comment
2016-02-15 22:01:55 -05:00
2217dfc6f2
Merge pull request #1942 from emmanuelle/trailing_todo
...
TST: 3D test for register_translation
2016-02-13 19:33:16 -07:00
45ff200c31
3D test for register_translation, as required by TODO.txt
2016-02-12 22:40:32 +01:00
a6e07615f4
Merge pull request #1936 from ahojnnes/depr
...
Fix some remaining TODO items
2016-02-09 23:25:42 +11:00
116ef0d649
Remove unit tests for deprecated features
2016-02-09 12:25:55 +01:00
e82849a544
Document API changes
2016-02-09 11:16:49 +01:00
9d9a4b3e0b
Fix some remaining TODO items
2016-02-09 11:11:28 +01:00
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
7014d04327
Remove useless multichannel=True kwarg from tests
2016-02-05 14:38:13 +05:30
b40d028550
Add tests for warnings in denoise_bilateral
2016-02-05 08:05:58 +05:30
00fd6f44ae
Merge pull request #1927 from sciunto/doc_inpaint2
...
DOC: make image smaller for better visu
2016-02-04 16:22:49 -06:00
Evgeni Burovski