Commit Graph

198 Commits

Author SHA1 Message Date
Juan Nunez-Iglesias 0d3d5f1319 Update See Also to References
"See Also" is apparently reserved by sphinx-numpydoc for pointers to
other code functions, rather than documentation.
2015-03-15 12:21:18 +11:00
Juan Nunez-Iglesias 2f62cf9d2e Clarify 'low-contrast' in docstring 2015-03-15 12:21:18 +11:00
Steven Silvester 0e61374a89 Add a helper function to check for low contrast
Add a helper function to check for low contrast

Add a check for low contrast when using imsave

Use the low contrast helper in imshow and make sure warnings are always shown

Clean up parameter names and add doctests

Remove unnecessary warning context

Remove unnecessary warning context

Add dtype ranges for 64bit types

Update tests with new warnings

Fix doctest logic

Fix doctest logic

Add a low contrast test with multiple dtypes

Fix check for color images

Fix color check again

Add support for int32 types

Relax assertion for 32bit builds

Add a low contrast test with multiple dtypes

Add a low contrast test with multiple dtypes

Fix check for color images

Fix color check again

Add support for int32 types
2015-03-09 21:34:58 -05:00
Johannes Schönberger ee5c6fbeb2 Use relative imports in skimage files 2015-01-22 07:36:48 -05:00
Steven Silvester f898bd0209 Style fixes 2014-12-26 11:26:30 -06:00
Steven Silvester 2e0deb9595 Fix syntax error and missing | operator 2014-12-24 07:47:05 -06:00
Steven Silvester d37ccca598 Fix Py2.7 build errors 2014-12-24 06:54:56 -06:00
Steven Silvester c0a0490eed Fix handling of multiple warnings and update tests
Fix handling of multiple warnings

Update all test __init__ files

Update segmentation pkg

Update the color pkg

Update the exposure pkg

Update the filters pkg

Update the io pkg

Update the measure pkg

Update morphology package

Restructure test setup function

Add expected_warnings to __all__

Update restoration pkg.

Remove explicit filter check since it is done elsewhere

Fix the image test helpers

Update the transform pkg

Fix util pkg

Update viewer pkg
2014-12-23 16:51:06 -06:00
Steven Silvester 4680f30466 Add a test setup helper function
Add a function to set up a skimage test

Switch to new test helper function

Import local packages that raise warnings in test setup function

More fixes to doctests

Fix regionprops doc test

Try and fix the test_rank failure.

Remove no longer needed RectangleSelector shim

Skip more doctests in _regionprops

Try importing another scipy subpackage
2014-12-23 16:49:20 -06:00
Steven Silvester f72882fbd2 Import scipy before turning on warnings 2014-12-23 16:49:19 -06:00
Steven Silvester 874d68ba3f # This is a combination of 7 commits.
# The first commit's message is:
Add a known_warning decorator and suppress warnings in color pkg

# This is the 2nd commit message:

Use the existing all_warnings context manager

# This is the 3rd commit message:

Raise warnings in data

# This is the 4th commit message:

Raise warnings in draw

# This is the 5th commit message:

Raise warnings in exposure

# This is the 6th commit message:

Suppress warnings in exposure tests

# This is the 7th commit message:

Add comments about warning suppressions
2014-12-23 16:46:24 -06:00
Johannes Schönberger 7fe31b280d Merge pull request #1295 from stefanv/doc_build_fixes
Doc build fixes
2014-12-15 10:04:42 +01:00
Juan Nunez-Iglesias b0a822a9ac Use integer bins when histeq'ing int images 2014-12-15 12:54:22 +11:00
Stefan van der Walt a38b1c1257 Fix integer division in CLAHE 2014-12-15 02:20:42 +02:00
Johannes Schönberger 3a1079a180 Misc PEP8 fixes 2014-12-14 02:56:14 +01:00
emmanuelle f9b10c58ad Corrected another bug that made doctest fail 2014-12-04 22:39:42 +01:00
emmanuelle 5553ea44b3 Corrected typos + modified docstring that made doctest fail 2014-12-02 22:10:30 +01:00
emmanuelle 2636abba92 Small additions to some docstrings in exposure module 2014-12-01 23:32:21 +01:00
Juan Nunez-Iglesias 879f8bb8a8 Protect exposure.histogram from integer overflow
Fixes #1228 .

I also removed a min() calculation and prevented an image copy when
offset is 0, which is most of the time.
2014-11-24 23:59:43 +11:00
emmanuelle c8bf2b5d9d Added a short paragraph + see also section in docstring of
exposure.equalize_adapthist
2014-11-23 22:37:27 +01:00
Rebecca 1b217f971e replacing lena in examples and most tests 2014-11-07 16:01:23 +02:00
Steven Silvester 2355c17e3c Add mask option to exposure.equalize_hist with test.
Remove print and fix comparision to None

Update test to make it clear there is a difference

Fix mask logic and `equalize_hist` in `__all__`.

Fix handling of mask and tweak mask test

Another run at travis

Update travis to avoid conflict
2014-08-31 21:15:01 -05:00
blink1073 b6dcf3c336 Update Travis build to use Anaconda.
Update Travis build to use Anaconda

Travis updates and fixes

More travis fixes

Another travis attempt

Revert changes

Use PIL and Pillow

Refactor travis into 4 different builds

Fix activation error

Remove explicit mpl in build_versions.py

Make matplotlib an explicit requirement

Rearrange travis

Make pillow a hard requirement

Try again to make Pillow optional

Fix bash syntax error

Fix bash syntax error

Bump required cython version

More rearrangments

Remove mpl from build_versions, rearrange travis

Fix version check

Make matplotlib explicit again

Conda install into test env

Check for proper install

Allow tests to skip if networkx is not available

Allow tests to skip if networkx is not available

Try swapping pillow for matplotlib

Allow tests to pass when matplotlib is not present

Remove matplotlib from build_versions

Print PIL version

Get pillow from PIP

Allow tests to skip if matplotlib is not present.

Allow tests to skip if networkx is not present.

travis fix

Remove unused mpl import that caused test error

Use nose-cov and do not run doctests without optional libs

Bump required numpy version and fix nose calls

Make overlay test repeatable

bump numpy version again

Move low-end numpy to python 2.7

Play with minimum versions

Add version requirements and use functions

Add version requirements and use functions

Allow require to skip a test

More implementation of require decorator

Update require decorator and clean up tests

Only use requires decorator when needed

Fix python3 error in version_requirements

Fix build errors

Fix handling of require with tests

More fixes for require handler

Use latest miniconda

Fix more build errors

Fix another dict comprehension and travis file.

Fix missing imports

Fix dictionary again

Fix import warning

Fix last failing test on 2.6

Skip doc examples on python2.6

Do not run doctests on python2.6

Fix typo in travis.yml

Make numpy-1.6 compatibility changes

Use numpy-1.6 in travis python2.6

Add tests for version requirements

Fix line noise in PR

Add additional io plugins

Fix simpleitk test.

Fix python 3 error in freeimage_plugin.

Install imread in Travis.

Put matplotlib settings in XDG recommended directory

Fix formatting in travis yml

Fix formatting in travis yml

Make sure to close PIL file atexit

Fix name of apt package xcftools

Fix pil fp closing

Fix matplotlibrc creation

Only download SimpleITK on py2x, run coverage on py27

Fix travis yml syntax error

Run coveralls on py2.7

Install SimpleITK on py3.3 and run coverage on py3.3

Make simpleitk install quiet

Use standard nose and clean up incantation

Fix travis yml syntax error

Put in miniconda workout for libc error.

Fix imread plugin.

Fix travis syntax

Remove unused import

Remove miniconda libpng in favor of system png

Fix imread install and move libm removal to after optional pkg install.

Fix png header copy in travis yml

Another attempt to use png headers

Debug freeimage

Add jpeg library for freeimage and debug imread.

More debug for imread and freeimage

More freeimage and imread debugging

More debugging

Use correct paths for test env

Make sure imread is tied to libpng15

Add a TODO note for simpleitk test causing error.

Fix typo in yml

Cleanup and add more comments to travis yml

Update comment

Try and add 3.2 support.

Docstring formatting

Add more travis comments.

Try numpy 1.6 on python 2.7

Fix travis syntax error

Rename CONDA to ENV for clarity

Alias python on python 3.2

Use python 3.2 as the system python

Clean up libfreeimage install

Fix order on py3.2 pre_install

Move old numpy back to py26

Use the appropriate python calls.

Debug 3.2 build.

Update comment

Fix syntax error

Another fix for syntax error.

Install scipy after downloading import tools

More debugging for py32

Do not install conda on py3.2 (duh)

Fix typo in travis yml

Fix py32 qt install, separate pyfits and imread to find error

Fix syntax error and front-load option lib check for debug

pyfits is not supported in py3.2, try imread now

imread is also not supported on py3.2

install imread before pyfits to show relationship with libs

Make pip builds quiet

Minor formatting to retrigger build

Allow simpleitk to fail to download without breaking the build

Use travis_retry for SimpleITK

See what breaks when we keep libm in

Now remove libm again
2014-08-02 06:47:09 -05:00
Tony S Yu ee3b9f2d66 Remove orphaned import 2014-07-17 20:50:39 -05:00
Tony S Yu d9a39d44eb Remove cast and rescale and adjust test values to match 2014-07-16 23:24:03 -05:00
Tony S Yu c24adec714 Add adapt_rgb decorator and helpers.
This applies `adapt_rgb` to `equalize_adapthist` and removes the
special-casing of RGB images in that function. Note that tests of
`adapt_rgb` fail because some type conversion and intensity scaling
were added to pass tests for `equalize_adapthist`.
2014-07-16 23:13:04 -05:00
blink1073 94bbb58274 Minor cleanup of adapthist module 2014-07-16 14:06:08 -05:00
blink1073 70a3760bca Remove unused deprecation import. 2014-07-12 19:43:57 -05:00
blink1073 0392299fae Refactor to use np.pad, naming changes, update test. 2014-07-12 19:12:53 -05:00
blink1073 a924e55b52 Fix handling of border pixels and update tests 2014-07-12 19:12:53 -05:00
Tony S Yu 5cafbd95e6 Add tests for intensity_range and rename parameter 2014-07-12 19:12:53 -05:00
blink1073 cc68b0c392 Start removing optional edge pixel handling 2014-07-12 19:10:32 -05:00
blink1073 2bdfcc7d5e Fix failing tests and turn module level testing back ony 2014-07-12 19:10:32 -05:00
blink1073 ba010a3191 Update adapthist tests, add test for alpha channel and rgb mode handling. 2014-07-12 19:10:32 -05:00
blink1073 909f23baab Switch to HSV, refactor equalize_adapthist, fix #757, cleanup docstring 2014-07-12 19:10:31 -05:00
blink1073 95a208eec5 Add test for adapthist modes 2014-07-12 19:10:31 -05:00
blink1073 9f7119b1c0 Change 'trim' to 'crop' 2014-07-12 19:10:31 -05:00
blink1073 9fa39e564a Update docstring 2014-07-12 19:10:31 -05:00
blink1073 61fb831d31 Implement a mode enum 2014-07-12 19:10:31 -05:00
blink1073 196205956e Set the unused portion of the image to 0 2014-07-12 19:10:31 -05:00
Tony S Yu 4c000c4d89 Use normal deprecation warning 2014-07-11 17:01:54 -05:00
Tony S Yu 879c2c7f36 Add tests for intensity_range and rename parameter 2014-07-11 16:30:18 -05:00
Tony S Yu b066a143b9 Clarify docstrings 2014-06-17 23:08:03 -05:00
Tony S Yu 8e539cc12a Clarify docstrings 2014-06-17 23:08:03 -05:00
Tony S Yu ec9198c58e Edit wording of docstrings 2014-06-17 23:08:03 -05:00
Tony S Yu 423207e07c Make intensity_range a public function 2014-06-17 23:08:03 -05:00
Tony S Yu 9b110d6c6e Tweak range definition in rescale_intensity 2014-06-17 23:08:02 -05:00
Josh Warner (Mac) 8663e23f4a FIX: Use //= instead of /= to fix deprecation warnings in adapthist 2014-05-08 20:45:19 -05:00
Johannes Schönberger 8e95ea0ea4 Fix deprecation warnings 2014-04-11 10:49:51 -04:00
Johannes Schönberger 3d50a03c56 Remove deprecated skimage.exposure.exposure 2014-04-11 10:05:50 -04:00