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5047 Commits
Author SHA1 Message Date
Sergey Karayev 5108d8c346 Fixed RGB<->XYZ conversion. 
Now correctly follows the algorithm from EasyRGB.
Also fixed a XYZ<->Lab conversion issue by adding
a .copy().
 2012-11-29 12:06:01 -08:00
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
Tony S Yu 9d653fec78 BUG: Clean up imports 2012-11-15 23:53:47 -05:00
Tony S Yu 0d411e21dc STY: Refactor parts of LineTool to CanvasToolBase 2012-11-15 22:04:02 -05:00
Tony S Yu d219a76f58 BUG: Fix blitting behavior in canvastools 2012-11-15 21:56:51 -05:00
Tony S Yu 5be5813070 STY: Reuse ThickLineTool in LineProfile 2012-11-15 00:16:19 -05:00
Tony S Yu 2ff3e78c52 BUG: Move callback connection to parent class 2012-11-15 00:16:19 -05:00
Tony S Yu 4f6f25efe9 ENH: Add canvastools subpckages with base class and line tools 2012-11-15 00:16:19 -05:00
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
Olivier Debeir add437a9f2 add: test entropy 8- & 16-bit 2012-11-12 10:39:12 +01:00
Olivier Debeir c9f1b67c7b fix: check pop==0 for some kernels 2012-11-12 10:05:52 +01:00
Olivier Debeir fd82ac9959 add new tests 2012-11-12 09:54:10 +01:00
Olivier Debeir a09ec78977 remove local demo from git 2012-11-12 09:34:33 +01:00
odebeir 08b748c379 local Otsu returns now the threshold values 2012-11-11 14:39:09 +01:00
Johannes Schönberger 8fea5d15d1 Change data type of pop variable to float 2012-11-10 13:49:52 +01:00
Johannes Schönberger f5ad204aca Use single file for test cases and rename file 2012-11-10 11:23:43 +01:00
Johannes Schönberger c9f95db67f Fix, improve and extend test cases 2012-11-10 11:21:55 +01:00
Johannes Schönberger 8c55640d60 Do not ignore exceptions in core functions 2012-11-10 11:20:56 +01:00
Johannes Schönberger c00fedde6c Fix, improve and extend histogram test cases 2012-11-10 09:43:15 +01:00
Johannes Schönberger 7ea3a754e0 Remove duplicate contiguous conversion 2012-11-10 08:59:48 +01:00
Johannes Schönberger 2bb139fb03 Wrap lines 2012-11-10 08:39:27 +01:00
Johannes Schönberger 804b426787 Clean Readme 2012-11-10 08:35:23 +01:00
Johannes Schönberger 045eb88e9f Change type of pop variable from float to Py_ssize_t 2012-11-10 08:31:20 +01:00
Johannes Schönberger 28e7b19c93 Improve code layout of kernel functions 2012-11-10 08:24:44 +01:00
Johannes Schönberger 4a14a217b9 Improve overall code style 2012-11-09 19:39:30 +01:00