Commit Graph

194 Commits

Author SHA1 Message Date
Steven Silvester 260e01333d Add a plugin and test for imageio 2015-09-04 08:02:35 -05:00
Connelly Barnes 4ca1f49d20 fix scikit-image bug #1680 (grayscale png round trip fails) and add unit test 2015-08-30 11:51:04 -04:00
Josh Warner cbc851bba6 FIX/STY: Remove magic and enforce PEP8 in plugins. 2015-08-13 19:47:00 -05:00
Juan Nunez-Iglesias c2f8c4ab12 Merge pull request #1599 from blink1073/viridis
Add the viridis colormap and use it for non-standard images
2015-07-22 12:54:07 +10:00
Steven Silvester 5632c9c1a9 Only add colorbar if the cmap is not the default 2015-07-16 21:39:05 -05:00
Steven Silvester 9fb7676c92 Fix relative import 2015-07-16 21:28:37 -05:00
Steven Silvester eaaea690f2 Allow viridis to be used by name 2015-07-16 07:58:14 -05:00
Steven Silvester 3d963649fc Use a less-invasive approach 2015-07-16 07:56:14 -05:00
Steven Silvester a8580f76b3 Always create a colorbar and update tests 2015-07-14 07:47:59 -05:00
Steven Silvester 756b9289c9 Add the viridis colormap and make it the default 2015-07-14 07:47:59 -05:00
Steven Silvester f6653b781f Fix tifffile plugin import 2015-07-14 07:45:41 -05:00
Steven Silvester b67a4e3076 Move the tifffile wrapper to tiff plugin 2015-07-14 07:45:41 -05:00
Steven Silvester 182a6f6904 Fix handling of tiffile handles 2015-07-14 07:45:41 -05:00
Steven Silvester 6d7e0554a4 Use context manager for tif imread as well 2015-07-14 07:45:41 -05:00
Steven Silvester 2fb59b9243 Fix variable name 2015-07-14 07:45:41 -05:00
Steven Silvester 1a27bea7da Allow pil imread to accept file-like objects again 2015-07-14 07:44:34 -05:00
Steven Silvester 3272b85f86 Do not let PIL handle the file handle 2015-07-14 07:44:34 -05:00
Steven Silvester ef9c4d8d19 Fix handling of img_num=0 cases 2015-05-09 09:32:33 -05:00
hawkerpl 9adcd89883 fix more informative error while reading image 2015-05-02 16:09:41 +02:00
Juan Nunez-Iglesias b6f2125e71 Allow keyword arguments to imsave for PIL plugin
Certain formats allow additional arguments, such as `compress=` for
TIFF or `quality=` for JPEG. Without this patch, the plugin simply
does not allow these arguments to be passed.
2015-03-31 00:24:23 +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
Antony Lee 10af2b21ee Use relative imports to plugins.
Otherwise e.g. skivi fails to start.
2015-03-05 16:17:57 -08:00
Tony S Yu 977ec17d8a Fix numpy 1.9 warnings about array.fromstring 2015-02-16 22:41:28 -06:00
Tony S Yu 7da811993a Fix compatibility with PIL 2015-02-16 22:02:52 -06:00
Steven Silvester fa226ad807 Update the README with some warning hints
Update the readme with some warning hints

Tweak README

Tweak README

Fix preferred plugins test

Pep8 fix

Remove imshow from PIL plugin

Fix spelling

Tweak readme
2015-02-07 16:40:54 -06:00
Steven Silvester 5ccdd36bc3 Remove imshow from PIL plugin
Do not provide imshow, show in PIL plugin to prevent conflicts

Make the sphinx install quiet

Fix local linka

Fix literal blocks

Fix another local link

Fix richardson-lucy link

Assert world dominance
2015-02-07 16:40:44 -06:00
Steven Silvester d8f6a6697b Do not add alpha channel to CMYK images 2015-02-01 10:05:40 -06:00
Steven Silvester a188380ba8 Add handling of CMYK images 2015-01-30 19:53:26 -06:00
Johannes Schönberger ee5c6fbeb2 Use relative imports in skimage files 2015-01-22 07:36:48 -05:00
Steven Silvester 87998d6518 Update docstring and create test module setup function 2015-01-15 18:57:18 -06:00
Juan Nunez-Iglesias 61d9812cd8 Don't create superfluous ip variable 2015-01-15 23:31:51 +11:00
Juan Nunez-Iglesias 7b2dbcb15b Expand the docstring for imshow 2015-01-15 22:39:50 +11:00
Juan Nunez-Iglesias c6dff6942d Don't create new plot automatically
This behavior is a bit too magical and may interfere with creation of
interactive ImageCollection browsers, for example.
2015-01-15 22:26:55 +11:00
Juan Nunez-Iglesias 2bdd239496 Overhaul imshow to clarify flow 2015-01-15 22:25:41 +11:00
Juan Nunez-Iglesias 30c522e706 Use different colormaps depending on input image 2015-01-15 20:16:24 +11:00
Juan Nunez-Iglesias 400c3fd202 Rename ax to ax_im in mpl imshow plugin 2015-01-15 15:44:55 +11:00
Juan Nunez-Iglesias 9fe4f33793 Add tests for nonstandard images 2015-01-14 20:29:15 +11:00
Juan Nunez-Iglesias 984e22b47a Replace Axes with AxesImage where relevant 2015-01-14 20:13:32 +11:00
Juan Nunez-Iglesias fab4ff2305 Fix incorrect call to colorbar 2015-01-14 20:13:32 +11:00
Juan Nunez-Iglesias c68c8e5468 Improve mpl imshow plugin docstring 2015-01-14 20:13:32 +11:00
Juan Nunez-Iglesias fac8fde9dc Overhaul matplotlib imshow plugin
- images are displayed within their native dtype range,
- unless they are outside of their range (e.g. a float image with
  values greater than 1) or they are of an unsupported dtype (e.g.
  a uint64 image), in which case the dynamic range of the display
  corresponds to the image range,
- which is also done for images with extremely low contrast for their
  native range (e.g. float images in [1e-7, 5e-7].

In the latter two cases, a colorbar is also displayed and a warning is
raised.

Finally, we return the axes object on which the image is plotted, to
enable further plotting in the matplotlib new OO style.
2015-01-14 20:13:32 +11:00
Juan Nunez-Iglesias 8f4d0247b5 Add docstring to matplotlib imshow plugin
The image is now named as an argument, and the axes are returned, in
keeping with matplotlib convention.
2015-01-14 20:13:32 +11:00
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 1b905d4cef More cleanup and updating of tests
Clean up setup_test and add a teardown_test method

Implement new setup/teardown in novice tests

Fix warning handling in pil_plugin

Update rank tests
2014-12-23 16:50:50 -06:00
Steven Silvester 782ba46a4c Handle more warnings
Punt on the issue of warnings with the minimum build

Handle warnings in measure pkg

Fix the rank filter test by forcing a random seed in the function

Compare as boolean in imread test

Import loadmat in test_setup to avoid warning

Use a setup method for imread plugin test

Revoke unintended changes

Fix indentation to appease jni

More indentation fixes

Fix unintentional comment out
2014-12-23 16:49:59 -06:00
Steven Silvester 6db92d387b More doctest and pil_plugin fixes
Fix Python2 imread in pil_plugin.

Load from data

Use all_warnings when importing the other packages

More fixes for regionprops doctest
2014-12-23 16:49:38 -06:00
Steven Silvester 2756358f3c Clean up PIL plugin and handle more warnings
Use the pil plugin to load data files

Fix install_requires string formatting

Dead end commit

Make all tools executable

Remove debug print

Suppress PIL resourcewarnings

Handle a few more warnings
2014-12-23 16:48:38 -06:00
Steven Silvester 9e8f91930e Handle warnings in several packages
Start handling warnings in data, exposure, and draw

Add a known_warning decorator and suppress warnings in color pkg

Use the existing all_warnings context manager

Raise warnings in data

Raise warnings in draw

Raise warnings in exposure

Suppress warnings in exposure tests

Add comments about warning suppressions

Raise warnings in feature

Fix warnings in filter package

Add warning handling to graph

Handle warnings in io package
2014-12-23 16:47:41 -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
Steven Silvester bc78bf8544 Create a new figure for imshow if there is already data 2014-12-13 08:57:14 -06:00