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08da07b1cd44c6f2d89c3066294f72ccc7b5eff8
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1197 Commits
Author SHA1 Message Date
Tony S Yu 08da07b1cd Merge pull request #377 from jni/jni-segmentation-join 
Add functions to join and relabel segmentations
 2012-12-17 06:44:47 -08:00
Juan Nunez-Iglesias 2ebac38c4d Rename ar to label_field for clarity 2012-12-17 16:37:41 +11:00
Tony S Yu a641ce6a0e BUG: Move import inside deprecated function 
Fixes circular import
 2012-12-15 15:59:14 -05:00
Johannes Schönberger 746d815dfa Fix recursion problem with nose test suite 2012-12-15 20:08:18 +01:00
Johannes Schönberger e0f4cd0978 Fix double space in warning message 2012-12-15 19:35:49 +01:00
Johannes Schönberger 450eaee4d9 Hide functools and imp packages in global skimage namespace 2012-12-15 19:35:17 +01:00
Steven Silvester a8dcb32b60 STY: Replaced indent with original formatting, no need to change. 2012-12-15 09:19:26 -06:00
Steven Silvester 49119524e3 Fixed indent on nose.run, so it will run when verbose is False 2012-12-15 09:17:39 -06:00
Steven Silvester b620c0ade6 STY: Added newline at the end of file 2012-12-15 07:40:04 -06:00
Steven Silvester cb1527bbe8 STY: Fixed indent on docstring. 2012-12-15 07:24:31 -06:00
Steven Silvester 380e27e60d Lazily import nose for testing, makes skimge load in 1/3 time. 2012-12-14 16:38:48 -06:00
Juan Nunez-Iglesias e3951a2a78 Rename ar_relabeled to relabeled for simplicity 2012-12-12 14:31:05 +11:00
Johannes Schönberger 33c58ad854 Fix some doc string formatting issues of random walker 2012-12-09 23:19:42 +01:00
Johannes Schönberger a410f1c47e UmfPack warning is now only raised if random walker is explicitly called 2012-12-09 23:17:06 +01:00
Johannes Schönberger 81c01eac0f Fix confused parameters in doc string of peak_local_max 2012-12-09 17:39:15 +01:00
Stefan van der Walt 95f7177708 Merge pull request #376 from JDWarner/unify_peak_finder_backend 
ENH: Unify peak finder backend.
 2012-12-08 20:36:18 -08:00
Josh Warner (Mac) 5cba69a4fa test: add additional tests for 100% coverage of new peak_local_max 
Also fix minor bug in label reordering.
 2012-12-08 21:12:26 -06:00
Josh Warner (Mac) 4f68f1cd36 doc: fix and clarify peak_local_max docstring 2012-12-03 20:23:01 -06:00
Johannes Schönberger 50c0399aa7 Merge pull request #379 from cpsaltis/fix_rotate 
Fix resize argument handling in rotate.
 2012-12-03 14:48:52 -08:00
Stefan van der Walt 68c2ab205e BUG: WindowsError not defined under Linux. 2012-12-03 08:49:35 -08:00
Christos Psaltis 298abe1ac0 Add test for resize option in rotate 2012-12-03 15:54:26 +02:00
Tony S Yu bf28a38f6e ENH: Make black the default boundary color for mark_boundaries. 
This improves visibility in light-colored image regions. Note also that the new behavior matches the behavior from the 0.7 release.
 2012-12-02 16:02:27 -05:00
Christos Psaltis 22f94d8707 Fix resize argument handling in rotate. 
It used to have exactly the opposite effect that it supposed to.
 2012-12-01 12:30:40 +02:00
Juan Nunez-Iglesias b906082034 Add testing functions for join and relabel 2012-11-28 12:48:13 +11:00
Juan Nunez-Iglesias dc377970f5 Add functions to join and relabel segmentations 
The join of two segmentations is the segmentation in which two voxels
are in the same segment if and only if they are in the same segment in
both input segmentations.
 2012-11-28 12:22:14 +11:00
Josh Warner (Mac) 98ce475113 style: initialize out at beginning of function 
* remove API compatibility comment
* remove unnecessary `del maskim`
 2012-11-25 23:09:06 -06:00
Josh Warner (Mac) 45a91aa9c5 doc: deprecated string and docstring formatting fixes in is_local_maximum 2012-11-25 22:56:45 -06:00
Josh Warner (Mac) d2262227d9 BUG - rank_order now imported. 
Also changed (peak.py):
  * Standardized documentation as requested.
  * Removed `threshold` as an optional kwarg.
  * Removed extra line break incorrect by PEP8 standards.

Also changed (watershed.py):
  * Added @deprecated decorator and import statement
 2012-11-24 17:24:14 -06:00
Luis Pedro Coelho 38f699471e TST Remove unneeded test 
Per stefanv's comment on github, this was testing functionality higher
up in skimage.io
 2012-11-24 19:04:55 +00:00
Luis Pedro Coelho 10ce9b89ab RFCT Use skimage.utils.convert for type conversion 2012-11-24 19:04:16 +00:00
Luis Pedro Coelho 6ebc43bad8 ENH Add imread io plugin 
This relies on imread (https://github.com/luispedro/imread) which
supports a few microscopy formats otherwise hard to read (LSM and
MetaMorph STK) as well as basic ones.
 2012-11-24 19:04:01 +00:00
Josh Warner (Mac) e7288f9140 BUG - Dtype conversion to Boolean in a new code path not included in current tests. 2012-11-20 01:17:42 -06:00
Josh Warner (Mac) da5a2a8221 BUG - Now parsing all unique labels != 0 properly, and set threshold_rel=0 in is_local_maximum() wrapper. 2012-11-20 01:11:31 -06:00
Josh Warner (Mac) 233b368195 BUG - Fixed a bug where the image was not properly masked for each unique label. 2012-11-20 00:45:01 -06:00
Josh Warner (Mac) 33c9514062 BUG - Fixed a bug where, when indices = False, output was not Boolean. 2012-11-20 00:36:12 -06:00
Josh Warner (Mac) 226eaaff92 FEAT - Unified peak finder backend 
Detailed changelist:
  * Fully documented new API for peak_local_max()
  * Removed commented-out old code for is_local_maximum()
  * Added "See also" and "Notes" to is_local_maximum() redirecting to peak_local_max()
 2012-11-20 00:12:47 -06:00
Josh Warner (Mac) 63b5c5a4a0 FEAT - combined API from is_local_maximum() into peak_local_max() 
is_local_maximum() is a wrapper function for peak_local_max()
is_local_maximum() runs much faster (~20% of prior runtime, nearly = to peak_local_max())
All tests in .feature and .morphology subpackages pass as written with these changes.

Todo:
  * Fully document API
  * remove commented-out old algorithm in is_local_maximum()
  * add new tests for full coverage of new, more complex peak_local_max()
 2012-11-19 23:38:58 -06:00
Tony S Yu 13c61b9694 Merge pull request #361 from ahojnnes/hough-peaks 
Add hough transform peak detection
 2012-11-17 07:30:08 -08:00
Johannes Schönberger 80a9a5aba5 Apply numpy reference style to rank filter descriptions 2012-11-14 08:33:27 +01:00
Olivier Debeir 70f2b67ef7 fix: ref and test_otsu doc 2012-11-14 08:00:59 +01:00
Olivier Debeir 698d6ae13f fix:< Py_ssize_t > 0 and & pop 2012-11-13 17:07:21 +01:00
Olivier Debeir 411d4686d5 fix:wrap lines in tests 2012-11-13 17:02:08 +01:00
Olivier Debeir f133158792 autopep8 for plot_* and rank sources 2012-11-13 09:37:58 +01:00
Johannes Schönberger 4a0b22aff5 Use common spelling for greylevel 2012-11-12 20:07:02 +01:00
Johannes Schönberger eaf48a71e9 Use numpy reference style 2012-11-12 19:31:06 +01:00
Johannes Schönberger a376a07c3b PEP8 fixes in doc string examples 2012-11-12 19:29:00 +01:00
Johannes Schönberger fce2ae3f5f Fix spelling of X-bit 2012-11-12 19:25:46 +01:00
Johannes Schönberger f724b97f90 Fix typos and spelling of readme 2012-11-12 19:24:02 +01:00
Olivier Debeir da391089cb add: local Otsu synthetic example 2012-11-12 14:48:38 +01:00
Olivier Debeir db2e066f4c add: test otsu 2012-11-12 14:40:49 +01:00