b5efe5ed94
Merge pull request #1956 from emmanuelle/label_zero
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New handling of background pixels for measure.label
2016-02-23 10:10:56 +11:00
a5a771a8e4
Modified label function so that background pixels are labeled with 0, and
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background=0 by default.
Modified label function so that background pixels are labeled with 0, and
background=0 by default. All tests of _ccomp.pyx pass
Modified a couple of files to be consistent with the new behavior of
measure.label
Modified doctring of label to pass doctest
Modified TODO.txt as well as release notes to mention the new behavior of
label.
Typo in docstring
Typo in docstring
Changed default value of kw argument background in measure.label
Removed unnecessary and outdated comment
2016-02-22 21:19:23 +01:00
44150989ee
WIP
2016-02-21 16:50:21 +01:00
fc70f73064
STY: more tweaks in response to review comments
2016-02-20 17:29:13 +00:00
ba328e7531
MAINT: address review comments
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Use recommended idioms in the .py wrapper
2016-02-20 17:29:13 +00:00
2bc8538f9f
MAINT: address review comments
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* 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
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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
87541b661d
BLD: skel3d: eradicate stray unicode symbols from source files
2016-02-20 17:29:13 +00:00
27b5dbca48
MAINT: skel3d: address review comments
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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
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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
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* 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
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(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
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* 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.
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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.
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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
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(yet another x1.6)
2016-02-20 17:26:12 +00:00
b7889b2c4f
MAINT: avoid doing np.sum in the hot loop
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(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
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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
b710bd21d2
Use a stacklevel of 2 by default for all warnings
2016-01-30 08:57:46 -06:00
d4b3aeeed3
Merge pull request #1846 from arokem/hull-docs
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DOC: Small one. The input to this one needs to be 2D.
2015-12-24 10:34:00 +01:00
9fb5f1333d
TST: Test both functions(!).
2015-12-23 15:36:35 -08:00
436d0e8ca3
TST: Test error handling in convex_hull, convex_hull_object.
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Also, a few PEP8 fixes in both module and tests.
2015-12-23 14:57:44 -08:00
227211fec7
DOC: Small one. The input to this one needs to be 2D.
2015-12-23 14:24:52 -08:00
0b61b8f46f
Removed deprecated label function from morphology module in preparation
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for 0.12 release.
2015-12-23 23:24:22 +01:00
3b525987f5
Merge pull request #1787 from ahojnnes/rpropsfix
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Various fixes and improvements
2015-11-19 15:16:16 +11:00
9d3a7b4ecd
Remove redundant type conversion
2015-11-18 08:58:01 -05:00
a63b746e6c
Move import test to top of function and import outside of function
2015-11-17 10:25:05 -05:00
6e644c4aa6
Remove single author from header, fix typo
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Functions in this file are from multiple authors, the original
author is attributed in the contributors section and the Git history.
2015-11-17 10:22:44 -05:00
Juan Nunez-Iglesias