[skimage] annotated tag debian/0.9.3-1 created (now 0028723)
Andreas Tille
tille at debian.org
Fri Dec 23 08:22:13 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to annotated tag debian/0.9.3-1
in repository skimage.
at 0028723 (tag)
tagging 9ae0313a31c3825ec9c6a508851fa1dd522530c4 (commit)
replaces debian/0.8.2-1
tagged by Yaroslav Halchenko
on Sun Nov 24 19:07:37 2013 -0500
- Log -----------------------------------------------------------------
skimage Debian release 0.9.3-1
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Adam Wisniewski (4):
support for saving to file-like object in imsave
Merge pull request #1 from tonysyu/pr/613
fix arraypad
adding main to run tests
Alexis Mignon (8):
Modified 'denoise_bilateral':\n1) check that image max value is not zero to avoid segmentation fault.\n2) initialize color_lut after sigma_range has been checked.
Deported variable initialization after the cdef block to allow verifications.
Moved image conversion after the verification of the max_value
Added non rotation invariant local binary patterns
Corrected duplicate variable declarations, variable name change from 'var_index' to 'rot_index' and corrected minor bugs
Finalized changes. Added reference for non rotation-invariant uniform patterns. Added test case. Modified comments to clarify the process, and changed the code to make it more consistent with explanations and actuall encoding
Corrected name in reference [2]
Changed link to the reference [2]
Almar (6):
Create dummy WindowsError that is an actual Exception instead of None. The previous solution prevented installation on py3.3 and OSX 10.6.1.
Add cube selem.
Add ball selem. I verified in 2D that this usage of np.mgrid yields the exact same results as np.meshgrid (np.meshgrid is not available for 3D).
Fix typo in docstring of disk().
Adding octahedron selem (3D equivalent of diamond).
Added test for ball and octahedton selems.
Ankit Agrawal (148):
Deprecating is_rgb()
Reverting the changes
Deprecating is_gray and replacing it with is_gray_2d
Removing is_gray() and is_rgb()
Removing redundant imports used in previous commits
Deprecating is_rgb and is_gray
Added a function for Gamma Correction
Prevented info loss, implemented Log and Sigmoid Correction
Separating the functions
Separating correction methods into different functions
Correcting code quality issues
Added better tests and removed weak ones
Added stronger tests
Corrections and Improvements
Minor improvements in docs, tests
Error handling for images with negative values in Image Correction methods
Adding a utility function to test non-negativity of an image
Renaming rescale_intensity_* as adjust_*
Replacing every occurence of substract* with subtract*
Final stylistic changes in exposure.py
Correcting typo in the reference section of adjust_sigmoid
Correcting typo in the reference section of adjust_sigmoid.
Adding author and name of the paper in reference section of adjust_sigmoid
First quick implementation of BRIEF Feature descriptor
Allowing arbitrary descriptor sizes in BRIEF
Removing hard-coding in BRIEF code
Adding custom sampling seed, Normal sampling mode
Added docs and used numpy trickery to filter keypoints
Changed dtype of hamming dist matrix and added docs
Fixing indentation
Merge branch 'ankit-brief' of https://github.com/ahojnnes/scikit-image into ahojnnes-ankit-brief
Clearing docs and making feature.util
Removing unused import and fixing indentation issue
First implementation of Integer Up/Downsampling
PEP8 corrections
Removing code repetition
Minor refactoring
Downsampling of nD arrays
Padding ndarray with zeros to support downsampling by any integer factor
Added docs, tests for downsample() in skimage.transform._warps
Making code compatible with Python 3
Add _sum_blocks
Cleaning up downsampling for integer factors
Expanding the documentation in transform._warps
Attempt to solve circular import issue
Another attempt at solving circular import issue
Correcting typos
Added an example in skimage.feature._brief
Fixing bug in _remove_border_keypoints
Added more detailed example in docstrings
Adding match_keypoints_brief
Adding docs for match_keypoints_brief
Making hamming_distance more generalized; improving docs
Broadcasting in pairwise_hamming_distance; numpy optimization in match_keypoints_brief
Added _brief_cy.pyx in bento.info
Moving _brief_cy.pyx changes in bento.info to the features section
Adding tests for BRIEF and pairwise_hamming_distance
Fixing bugs and making code compatible with Python 3
Final changes
Replacing np.all by equivalent np.any
Stylistic changes
Added if __name__ == __main__ in new test files
Adding Octagon structural element
Removing circular import
Correcting grammatical typo
Making the doc more explicit
Added star structural element
Minor doc changes
Test for Octagon
Improving the implementation of star
Adding namespace
Adding test for star
Adding tests for smallest selem
Added partial implementation of censure for mode=DoB
Line Suppression of the response
Correcting import for a private function
Adding TODO's
Added mode Octagon using np.convolve
Correcting typo
For loop for mode=DoB in Cython
Commenting out _filter_using_convolve
Removing time() statements and correcting types in censure_cy
Removing hard-coding in censure_keypoints()
Returning keypoints with the scale info
Correcting the expression of response in censure_keypoints()
Correcting the definition of Ratio of Principal Curvatures
Adding _slanted_integral_image. Removed _oct and _filter_using_convolve
Removing unused stuff
Cleaning up the non-Cython version for mode=Octagon
Cythonizing the for loops
Adding the docs for censure_keypoints
Trying to resolve Cython TypeErrors
Trying to Debug the SegFault
Trying to Debug SegFault : 2
Trying to debug the Segfault-3 : Making the arrays C-contiguous
Fixing many bugs; Working Censure for mode=Octagon
Adding doc for the different modes of _slanted_integral_inage_modes
Correcting the docs and making them explicit
Commenting the sigma passed to _suppress_line
Removing unnecessary data-type conversion
Removing unnecessary array pre-allocation
Changing no_of_scales to n_scales
Renaming *_wt to *_weight; correcting the object type of n in _censure_dob_loop
Documenting the code; Removing ascontiguousarray statements
Correcting indentation
Using convolve in _get_filtered_image for mode=Octagon
Removing slanted_integral_image Cython functions for mode=Octagon
Reverting back to non-debugging mode in Cython
Remove all the slanted integral image functions and the vivid graphics from censure.py
Wrapping the long lines
Added a NOTE explaining the preference of convolve over slanted integral image
Adding the STAR mode
Making the weight calculation statements more readable
PEP8 corrections
Replacing threshold by nms_threshold
Returning the keypoints and scales separately
Changing the variable names of constant objects
Correcting a bug in Line Suppression
Putting constant variables outside the definition
Making the docs more explicit
Correcting the imports
Assigning boolean to the feature mask in line suppression
Actively filtering border keypoints on all scales
Adding tests for all the modes in censure
Debugging Travis error
Reverting back to last but one commit
Making the code compatible with Python 3
Actively filtering border keypoints for all the scales part 2
Removing print statements
Returning mask in _remove_border_keypoints
Filtering out border keypoints using masking
Replacing int32 by intp
Changing _remove_border_keypoints to _mask_border_keypoints
Lowercasing variables; removing unused import; replacing _remove by _mask
Replacing censure_keypoints by keypoints_censure, n_scales by max_scale
Documenting the code
Including min_scale as another input parameter
Adding remaining tests
Adding gallery example for plotting censure keypoints
Adding a short description of the algorithm
PEP8 corrections and stylistic changes
Adding Octagon shapes for higher scales
Importing star and octagon from morphplogy.selem
Correcting selem.star for Python 3
Reverting back to changes made by Johannes
Final changes in censure example
Documenting the choice of filter sizes
Correcting bug in SimialarityTransform
Chintak Sheth (34):
Clean, and implemented using horse.jpeg
Added horse.png to skimage/data and added a horse() in the _init_.py in data subpackage
End newline added and removed the .jpeg version
URL formatting
Minor changes
Trailing _
URL
URL
.in to .com
Added convex_hull_object function
Trailing whitespace
Added the note in docstring as suggested by Josh
Update convex_hull.py
Note and relative import
Added unit test for convex_hull_object function in test_convex_hull.py
Unit tests added
Resolve fast forward
Remove trailing whitespace
Remove trailing whitespace
Using labeled_im == i
Blank at the end of docstring
Add convex_hull_object in __init__.py
Minor changes
Ability to choose the type of connectivity and ValueError
Test for the two neighborhood values
Note rewritten
Endline
Added test for checking ValueError
Note re-worded
Whitespaces and note
Space
Add convex_hull_object to __all__
new line
Docstring for _dilate and _erode were interchanged
Chris Beaumont (1):
vectorized transform.integral.integrate
Davin Potts (1):
Modified test_rank.test_compare_autolevels and test_rank.test_compare_8bit_vs_16bit to correct for assumption that data.camera() would always be loaded as ubyte (or ints at least) when using matplotlib as backend (which caused data.camera() to load as float32).
Emmanuelle Gouillart (15):
median filter outlier
histogram example
Find contours example
Blank lines in reconstruction docstring for nicer display
Mentioned the Neurodebian repo in the install doc
DOC: Comment on the behavior of ``histogram`` for color images.
Merge pull request #584 from josteinbf/iradon-algebraic
Merge pull request #635 from josteinbf/radon-cleanup
Merge pull request #672 from jni/chull-fix
Merge pull request #710 from jni/pyamg-depends
Added a wrapper around ndimage's Gaussian filter
DOC: corrected description of multichannel parameter
[BUG] iterable sigma and multichannel
Gaussian filter function: changed the default value of multichannel
Merge pull request #469 from JDWarner/add_marching_cubes
Ferdinand Deger (3):
Added isotropic TV denoising + comment
minor changes in isortopic tv denoising
eleminate empty line
François Boulogne (141):
Merge branch 'master' of git://github.com/scikit-image/scikit-image
Merge branch 'master' of git://github.com/scikit-image/scikit-image
fix comment
DOC: minor fix ellipse_perim.
Merge branch 'master' of git://github.com/scikit-image/scikit-image
DOC: add docstring for deprecation
Fix mistake in example
Merge branch 'docstring' of github.com:sciunto/scikit-image
add note for distance/angle convention. Thanks to Emre Safak.
replace hough() by hough_line() in doc
remove docstring
be consistant with python implementation
improve unittests
Fix and improve example
Fix docstring
minor doc improv.
doc, minor improv.
big clean-up!
fix names
fix signature
cosmectics (flake8)
fix deprecated variable
Tony's comment on output format
add option full_output to hough_circ
fix travis complaint
readability
implement rotated ellipses
add contribution
remove old line
minor fixes
change bezier_curve definition for consistency
split tests
docstring
rename function bezier_curve to bezier_segment
add unittest
pep8
fix int + pep
use bint
oops
add optional + default in pyx docstring
MIN: use print() instead of print
MIN: fix unused import
fix blank print for python2
cast range to list for python3
minor contrib.
MIN: remove unnecessary brackets
import configparser for python3
fix path import viewers
fix import urllib2 for python3
workaround for itervalues
fix iteritems for python3 compat
use items/values for python2/3 compat
Hough transform for ellipses
use memoryview
s/int/long memory view
delete duplicated import
fix imports
remove commented lines
fix import
delete comment
fix import testing
add spaces for travis (pep8)
fix import testing
pep8
fix missing space
PEP8 + import
activate travis for a fork
erode & dilate -> private functions
DOC: add doctrings
MIN: fix pep8
use previous import
add coffee picture from flickr
add example HT for ellipse
add extra comments
fix title
rename files
fix doctest
PEP8
add original picture
simplify modification image + comment
fix Johannes' comments
use shorter URL
typo
revert, accum is a tuple of lists
detailed procedure
minor modifications
DOC: changes for Marianne's coffee cup
DOC: protect last character in URL
Review the procedure
DOC: this step seems to be useless
DOC: add titles to plots
import Fedor's contribution
TEST: add unittest and check with travis
DOC: update return according to wu's method
TEST: fix returned tuple
TEST: fix unittest
DOC: fix refs
MAINT: put AA method in draw.*_aa
DOC: remove wu in methods
Implement line_aa
Anti-aliasing
MAINT: bezier_segment is private
MAINT: val in [0,1]
DOC: split non-AA/AA
FIX: division for value
PEP8
PEP8
ADD: bezier_curve
DOC: add bezier_curve
MINOR: doctrings + various improvements
FIX: broken test (thanks unittest!)
MINOR: some comments
PEP8
PEP8: comparison
MAINT: unused import
MAINT: matplotlib is in requierements.txt
DOC: no import numpy in doc
DOC: add missing import
PEP8: fix indentation
PEP8
DOC: fix indent
TEST: fix mistake
FIX: fix angle convention
MAINT change HT return API
ENH: use heapq to select the best match
TEST: fix precision
TEST: fix bad subs
TEST: revert precision
MINOR: fix non ascii char
add missing import heapq
FIX: handle correctly main axis def
fix example according to new API
remove heapq
MAINT: np.pi -> M_PI
MINOR: add missing type
FIX: import M_PI
PEP8
PEP8
PEP8 another one
DOC: fix syntax error
DOCTEST: fix
Horea Christian (12):
User-specified output ratio
Corrected indentation and spacing.
Corrected indents (4space instead tab).
Corrected indents Again.
Added usage example.
Refined syntax.
Removed blank lines in between parameters.
Renamed parameter
Syntax and default variable.
Adapted if statement to grid_shape=None
Added test case for grid_shape parameter.
Resolved faulty montage2d import.
JDWarner (2):
move `unpack_unique_verts` to Cython for speed
fix: symmetric ambiguous dual-plane cases require special treatment
Johannes Schönberger (433):
Add gabor filter function
Fix meshgrid bug in gabor kernel and argument passing
Add test cases for gabor filter
Add example script for gabor filter
Remove unnecessary kernel description for filtering
Use char type for circle_perimeter method for speedup
Use same cython directives for whole source file
Fix PEP8 issues
Change deprecated decorator to display warning in doc string
Remove duplicate code for alternative function
Use double instead of single quotes for doc string
Make deprecation warning in doc string bold
Add API documentation to latex docs
Increase list-depth for nested quotes etc.
Change latex doc settings
Fix some doc strings for latex docs
Re-enable plots in doc strings and generate PDF images for them
Explicitly set latex font size and paper size
Use plot_directive from matplotlib.sphinxext if available
Copy some useful latex settings from NumPy
Fix make.bat
Avoid duplicate python module index
Do not set paper size to allow manual setting through make
Fix parameter list format error of rotate
Replace scipy.ndimage routine with skimage.ndimage.rotate
Use nearest neighbour interpolation to avoid different labels
Remove unused import
Replace rotate function of local binary pattern example with builtin skimage function
Explicitly import local_binary_pattern function
Replace ndimage.zoom function in radon transform example with builtin skimage function
Merge pull request #467 from malcolmreynolds/fix-num-peaks-typo
Fix reference syntax for corner detectors
Merge pull request #475 from sciunto/docstring
Merge pull request #480 from sciunto/hl_review
Make sure non-zero values are treated as True
Add test case for different dtypes of structuring element
Merge pull request #483 from almarklein/windowserror
Merge pull request #482 from thouis/master
Merge pull request #486 from yangzetian/peak-local-max-indices-nd
Update release instructions for new robots.txt file
Rename sigma parameters by adding an underscore as separator
Merge pull request #2 from tonysyu/gabor
Merge pull request #3 from tonysyu/gabor
Merge pull request #493 from ChrisBeaumont/vector_integral
Inline helper functions of label
Add option to return number of labels
Add test case for number of labels
Rename development guidelines, so they are shown when opening a new PR
Make return type of skeletonize function boolean
Reformat code to comply with PEP8
Remove unnecessary conversion step to numpy array
Remove duplicate import statement
Merge pull request #525 from stefanv/felzenwalb_32
Merge pull request #535 from JDWarner/fix_mcp
Pre-build edge filter weights and use views
Remove outdated author in doc string
Fix output array dimensions in doc string
Fix hough line examples
Add short description to edge filter example
Rename mean filter example and improve description
Use numpy dtype rather than string
Fix inconsistencies in examples and many more improvements
Let Travis run all examples
Escape dollar-sign in makefile
Add matplotlib to Travis dependencies
Set matplotlib backend to Agg
Use current matplotlib version Python 3
Escape greather-than symbol
Escape double-colon symbol
Change python version test
Fix wrong escaping
Add missing python version to pip
Remove escaping
Change invalid install order
Move example runner loop to Travis config
Unescape dollar sign
Add better description for example runner
Fix print statement for Python 3
Add missing future import
Add missing trailing space to print statement
Install matplotlib after freeimage
Use png rather than jpg for chelsea image
Use png rather than jpg for ihc image
Fix image filename extension from .jpg to .png
Convert to ubyte dtype explicitly for python 3
Fix dtype bug in color tests for python 3
Convert to ubyte dtype explicitly
Deprecate bresenham function
Replace all occurences of bresenham with line
Pass error return code of example scripts and exit
Add __all__ to color package
Add __all__ to exposure package
Explicitly import color functions
Add __all__ to data package
Add __all__ to draw package
Add __all__ to feature package
Add __all__ to filter package
Add __all__ to rank filter package
Add __all__ to graph package
Add __all__ to measure package
Add __all__ to morphology package
Add __all__ to segmentation package
Add __all__ to transform package
Add __all__ to util package
Fix selem test cases
Fix hough transform test cases
Add line estimation model
Add RANSAC algorithm
Add circle estimator model and fix some other bugs
Fix doc string of ransac function
Add ellipse estimator model
Rename variables for better readability
Add todo comment
Add example to ransac function
Add imports of fit to subpackage
Fix example of ransac
Reduce default number of max trials
Add analytical jacobian for ellipse model for 100x speedup
Reduce number of function calls for speedup
Calculate initial guess for closest point on ellipse for speedup
Replace numpy with math for scalar functions and remove Dfun from ellipse residuals for speedup
Fix typos
Add input data shape test to avoid out of memory Jacobians
Fix bug in predict_x of line model
Return combined xy-coordinate array with arbitrary dimensions in predict_xy
Fix bug in ellipse model estimation due to changed predict_xy output
Add test cases for line model
Add test cases for circle model
Add test case for ransac algorithm
Replace triple-single-quotes with triple-double-quotes for doc strings
Add is_degenerate to geometric transforms
Add residuals method to geometric transforms
Change ransac function to accept multiple input data arrays
Fix is_degenerate function to accept src and dst arrays separately
Add new stop criteria to ransac and improve doc string
Add example for ransac and geometric transforms
Add test case for ransac applied to geometric transform
Remove trailing brackets
Add is_degenerate to description of ransac iteration
Replace is_degenerate with is_model_valid and is_data_valid in ransac
Remove is_degenerate methods from estimation models
Replace is_degenerate tests with is_data_valid and is_model_valid tests
Add reference for RANSAC
Add example matching script
Remove unused shear argument
Remove extra space
Clarify SSD description
Add comment to explain commented out code
Use double quotes for code in doc string
Add missing double colons for equations
Add missing double quotes for equations and code
Update doc string of ransac with new validation functions
Add title of wikipedia reference
Add test case for underdetermined LineModel estimation
Add test cases for residuals
Readd Cellprofiler license notes to edges.py
Fix last remaining PEP8 errors
Use boolean mask for inlier return value of RANSAC
Wrap lines
Add simple RANSAC example script
Set random seed to avoid random test failures
Fix spelling
Add python code checkers to travis build process
Replace pep8 and pyflakes with flake8
Use mirrors for flake8 installation
Add exit-zero directive to flake8 command
Merge pull request #563 from JDWarner/docfix_label
Add short example for transforms to warp function
Fix parameter description of warp function
Fix parameter descriptions of warp functions
Add examples to doc strings of resize, rotate and rescale functions
Fix spelling error
Fix incomplete options for mode of _warp_fast function
Wrap lines
Fix doc string injection of deprecated wrapper
Fix invalid index of reference
Escape latex math symbols
Add filter.rank to __all__ of filter package
Fix indentation of ransac doc string example
Fix styling of math and blockquote
Fix doc string of threshold_adaptive
Remove bold font from dt tags
Fix quick search description
Update installation instructions
Remove unnecessary bscript
Implement faster version of circle and ellipse drawing
Capitalize parameter description
Add example to line drawing function
Add example to polygon drawing function
Add example to circle_perimeter drawing function
Add example to ellipse_perimeter drawing function
Add example to ellipse drawing function
Add example to circle drawing function
Add example to set_color drawing function
Merge pull request #532 from ankit-maverick/deprecate_is_rgb
Merge pull request #510 from sciunto/ellipsev2
Set matplotlib backend globally
Create matplotlib config directory
Set matplotlib qt backend
Avoid import of matplotlib QT lib if QT is not installed
Use None instead of 'none' for qt backend
Fix setting of QT_API environment variable
Fix python 3 print statement in example script
Fix window size of sub-pixel corner detection
Fix matching example script
Merge pull request #572 from sciunto/docandco
Merge pull request #578 from josteinbf/radon-test-refactor
Merge pull request #576 from alexis-mignon/master
Merge pull request #570 from stefanv/bento_hookfile
Merge pull request #583 from josteinbf/radon-example-axes-fix
Merge pull request #505 from ankit-maverick/gammaCorrect
Merge pull request #585 from ankit-maverick/typos
Merge pull request #586 from sciunto/print
Merge pull request #587 from sciunto/import
Merge pull request #589 from sciunto/configparser
Refactor contribution workflow
Change branch name for consistency across guidelines
Fix typo
Add additional advice about rebasing
Use long parameter version --force rather than -f
Merge pull request #4 from tonysyu/rebase-workflow-edits
Merge pull request #598 from sciunto/fix_import
Merge pull request #597 from sciunto/hough_ellipse
Fix division by zero bug in corner detectors
Merge pull request #604 from JDWarner/fix_sitk_tests
Merge pull request #621 from tonysyu/fix/rank-dtype-compatibility
Merge pull request #617 from JDWarner/memview_transform
Merge pull request #625 from JDWarner/random_noise
Outsource inner brief loop into cython file
Outsource inner brief loop into cython file
Merge pull request #511 from ankit-maverick/resample
Refactor local block functions and add additional functionality.
Fix import namespace
Fix doc string examples
Update test cases for block functions
Update doc string for new functionality
Rename block_* functions to local_*
Fix deprecated function name referneces in doc strings
Use pad function and add option to define cval
Merge pull request #643 from stefanv/bento_fixes
Let travis-ci check bento.info
Merge pull request #648 from stefanv/ransac_faulty_cast
Merge pull request #652 from josteinbf/local-binary-pattern-example
Refactor rank filter package for consistent naming
Use typed memoryviews in rank filter package
Improve code layout and styling
Use typed memoryviews for diff array
Fix styling of some comments
Fix wrong module name
Capitalize parameter description in doc string
Extend bitdepth from 12bit to full 16bit
Fix attack-release border initialization
Fix test cases for full 16bit support
Fix README for full 16bit support
Use missing memoryviews for bilateral kernels
Improve description of bilateral filter
Add test case for bilateral filters
Improve indentation
Cast to int for python 3
Update bento.info for refactored rank package
Log warning when bitdepth > 10
Refactor rank filter package as combined implementation for 8- and 16-bit
Update bento config
Improve entropy example
Improve mean example
Update entropy example with improved matplotlib usage
Improve long rank filter example
Update bitdepth warning
Replace log warning with UserWarning
Rename mean_subtraction, morph_contr_enh to subtract_mean and enhance_contrast
Use consistent description of output image
Append percentile, bilateral function name part
Add TODO.txt
Add note about TODO.txt to release instructions
Deprecate old rank filter functions
Replace deprecated function calls in examples
Add option to return double output image for rank filters
Replace all float dtypes with double
Add test for output dtype of entropy
Merge pull request #546 from jni/3d-slic
Rename and combine local_* functions to block_reduce
Add short doc string example
Merge pull request #591 from ankit-maverick/brief
Merge pull request #660 from RONNCC/add_to_depends
Merge pull request #561 from RONNCC/fix_filter_doc_gaussian
Merge pull request #659 from RONNCC/add_bento_to_docs
Replace deprecated import of _local_func with block_reduce
Merge pull request #653 from iNand/master
Fix typo in doc string
Wrap line
Add missing space in parameter defintion in doc string
Add missing p1 parameter to percentile and threshold functions
Add specific branch for the percentile p0 = 0 case
Fix accidential variable naming confusion
Integrate new test cases from @odebeir and fix old function names of dilate and erode
Fix invalid previous fix for percentile edge case
Fix loop ranges of rank filter kernel functions
Fix Otsu rank filter kernel loop range
Let travis also run long example scripts
Add short comment for travis flake8
Fix image data type issues in rank filter example
Merge pull request #641 from sciunto/example_ht
Add cached_property decorator
Refactor regionprops
Remove cached_property class from shared utils
Add note about backwards compatibility to TODO.txt
Remove legacy doc strings
Use asbolute import for Cython lib
Remove unused cached_property from _shared.utils namespace
Improve fromatting of regionprops doc string
Hide cached_property and caching flag
Merge pull request #669 from ankit-maverick/octagon
Fix radon example script
Merge pull request #684 from sciunto/doc_fix_url
Fix missing label property description and backwards compatibility
Fix bugs in censure keypoint detector and improve code
Fix several bugs in DoB method and improve overall code quality
Fix censure example and fix some minor issues
Merge pull request #668 from ankit-maverick/censure
Improve moments code and use typed memoryviews
Make moments functions public, rename, add tests
Sort functions in alphabetical order
Add test cases for moments functions
Fix PEP8 issues and typos
Use typed memoryviews in draw package
Use typed memoryviews in feature package
Use typed memoryviews in filter package
Fix reference of corner_foerstner
Fix missing conversion of typed memoryview to numpy array
Fix missing conversion of typed memoryview to numpy array
Improve tests of graph package
Use typed memoryviews in measure package
Use typed memoryviews in morphology package
Use typed memoryviews in transform package
Fix bugs in usage of typed memoryviews
Convert to int for Py_ssize_t
Merge pull request #700 from stefanv/remove_logger
Merge pull request #702 from stefanv/remove_image_wrap
Merge pull request #720 from michaelaye/patch-1
Remove unnecessary mirror option
Improve SLIC
Reduce memory footprint
Remove unnecessary parameters and update doc string
Remove legacy comment
Fix dtype bug
Fix bug in window extent determination
Reorder variable declarations
Improve documentation of sigma
Revert multichannel magic and improve parameter docs
Use absolute imports
Add missing rgb2lab import
Merge pull request #722 from stefanv/shape_step
Make image C-contiguous
Rename clusters to segments
Add optional description to parameters
Fix indentation
Change default value of sigma
Merge pull request #686 from radioxoma/yen-threshold
Merge pull request #704 from alexis-mignon/master
Merge pull request #630 from JDWarner/improve_noise
Merge pull request #727 from jni/fix-small
Revert default value of maximum iterations
Merge pull request #5 from jni/slic-speed-fix-dims
Raise warning for sigma parameter and add to TODO for next release
Merge pull request #6 from jni/slic-speed-spacing
Merge pull request #731 from ankit-maverick/SimilarityTransform
Document default value API change
Merge pull request #7 from jni/slic-cython-docstring
Merge pull request #733 from riaanvddool/contribution-riaanvddool
Define 1d arrays as contiguous
Scale sigma only in scalar case
Fix doc string of warp functions
Fix various doc strings using the warp function
Merge pull request #746 from luispedro/master
Some improvements for perimeter
Add support for unsigned integer label images
Raise error for non 2-D images
Fix dtype bug in perimeter
Hide experimental GSoC functions for 0.9 release
Remove call to deprecated is_gray function
Misc doc string fixes
Only clip for ndimage.map_coordinates case
Add note about internal usage of transformation matrix
Add support for matrix as inverse_map
Improve example of warp function to show all available options
Fix deprecated function name in example
Temporarily remove censure keypoints example
Merge pull request #752 from sciunto/pep
Merge pull request #755 from jni/rename-relabel
Merge pull request #709 from sciunto/wu
Merge pull request #762 from jni/update-slic-example
Merge pull request #764 from jni/example-py3
Merge pull request #767 from cgohlke/patch-1
Merge pull request #771 from cgohlke/patch-4
Fix euler number bug for scipy-0.13
Add missing perimeter function to __all__
Merge pull request #768 from cgohlke/patch-2
Fix numpy 1.8 bug
Split grey and binary erosion tests in two files
Fix overflow error
Reduce number of specializations
Remove unused import
Add support older numpy versions
Deprecate out parameter
Improve shape plot
Use libc.math.atan2
Miscellaneous fixes and improvements
Merge pull request #776 from tonysyu/update-api-doc
Merge pull request #772 from JDWarner/fix_poisson_noise
Merge pull request #775 from JDWarner/spacing_random_walker
Add logger deprecation to todo list
Merge pull request #780 from JDWarner/spacing_marching_cubes
Merge pull request #781 from stefanv/gh_stable_doc_versions
Merge pull request #782 from sciunto/pep8
Merge pull request #778 from stefanv/binary_morph_out
Remove duplicate set_color function
Add test case for set_color function
Re-add missing parts
Merge pull request #624 from mkcor/filter_median_dtypes
Remove deprecated is_local_maximum function
Add deprecated is_rgb and is_gray functions to todo list
Remove deprecated tv_denoise function
Remove deprecated hough_* functions
Re-add tests
Remove print statement
Rename weighted central moments property
Fix dtype error on 32bit systems as convolve is only implemented for 32bit integers
Change data type of convolution to more general uint
Speed up memory views in local_binary_pattern
Speed up memory views in line drawing function
Speed up memory views in skeletonize function
Speed up memory views in watershed function
Set version to 0.9.3
Josh Warner (19):
Merge pull request #526 from sciunto/fixtravis
Merge pull request #545 from odebeir/master
Merge pull request #551 from tonysyu/pyside
Merge pull request #558 from chintak/convex_hull
Merge pull request #571 from ahojnnes/travis-fix
Merge pull request #588 from sciunto/range
Merge pull request #575 from tonysyu/feature/viewer-linking
Merge pull request #634 from josteinbf/arraypad-zeros
Merge pull request #640 from sciunto/missingdoc
Merge pull request #637 from sciunto/minorfix
Merge pull request #656 from josteinbf/doc-makefile
Merge pull request #603 from TheChymera/master
Merge pull request #632 from ahojnnes/local-blocks
Merge pull request #682 from jni/slic-type-hotfix
Merge pull request #692 from angelatlarge/fix_hog_orient_bins_rounding
Merge pull request #770 from cgohlke/patch-3
Merge pull request #789 from ahojnnes/binary
Merge pull request #787 from cgohlke/patch-2
Merge pull request #788 from ahojnnes/patch-1
Josh Warner (Mac) (59):
workaround: convert `dtype(image)` to `image.astype(dtype)`
FIX use specific structuring element in Canny
fix to preserve input image shape upon executing `random_walker`
PEP8 fixes; remove unneeded pyamg import; add `data` shape check
Use `force_copy` argument of `img_as_float`
fix: remove unnecessary forced copy
add assertion checks to ensure `data` shape is unchanged
temporarily use Cython 0.18 to restore normal Travis builds
Fix Cython 0.19 build error due to global wraparound=False
DOCFIX: "\" in `label` docstring now escaped
FEAT: Generalized n-dimensional array padding
FIX: prepend `np.testing.` to assert_* statements
Use memoryviews in skimage.transform
FEAT: Automatically switch between RGB / grayscale lineprofile
DOC: Add viewer example for RGB line profile
FIX: refactor code, fix linewidth calculation
FIX: lineprofile no longer flips on left half and cardinals work
FIX: remove blit, fix 0-length error on grayscale images
FIX: only reset axes when gray <-> rgb, not every update
FIX: No longer reset for each update
FEAT: generator to add various types of random noise to images
ENH: Improve random_noise with better param names & docfixes
FEAT: Full 3d anisotropic implementation of marching cubes
import `marching_cubes` and `mesh_surface_area`
add _marching_cubes.pyx to list of Cython modules to build
fix import of _marching_cubes
fix: bug in second `_append_tris` call in case 125
rename files to conform with naming conventions
fix import error from `_marching_cubes_cy`
fix error in triangulation of case 120
FIX: dimension ordering now correct (x, y, z)
FIX: volume now directly cast, docfixes, C-contiguous ordering
FIX: use memoryviews, docfix, and change tri_list to face_list
FIX: incorrect name for `unpack_unique_verts`, revert axis ordering
DOCFIX: clarify docstrings and output vertex dimension ordering
FEAT: add tests for marching cubes and mesh surface area
DOC: Minor documentation formatting fixes in marching cubes
MAINT: Refactor ellipsoid generator into skimage.draw
DOC: Add concise marching cubes example to gallery using Matplotlib
TEST: Add test suite for draw3d (ellipsoid/ellipsoid_stats)
FIX: Add _marching_cubes_cy.pyx to bento.info
FIX: Errors in unit tests
STYLE: Use `np.array` instead of `np.r_` and import Poly3DCollection
Credit myself for Marching Cubes
DOC: Further improvements to naming conventions.
FIX: Fix and improve Poisson random noise generator
ENH: More concise next-power-of-2 calculation
ENH: Add optional `clip` kwarg, docs, & handling of signed inputs.
ENH: Tighten tests, all noise types now support signed I/O
FIX: Better handling of skimage.data.camera for Python3 compatibility
FEAT: Add 'localvar' mode to random_noise
REBASE: Resolve first conflict
ENH: `spacing` kwarg for random_walker and improved tests
FIX: roll back incorrect testing change of gradient order
DOC: Add removal of `depth` from random_walker in 0.10
DOC: Fix minor typo in docstring
DOC: Change sampling kwarg name to spacing in marching_cubes
DOC: Change sampling to spacing in skimage.draw.ellipsoid and tests
DOC: Fix capitalization in ellipsoid docstring.
Jostein Bø Fløystad (90):
Add reconstruction circle option to transform.radon.
Tests for reconstruction circle option for transform.radon.
Add reconstruction circle option to transform.iradon.
Tests for reconstruction circle mode in transform.iradon.
Correct documentation and string formatting.
PEP8 style changes for transform.radon_transform and its tests
Style improvements in docstrings in transform.radon_transform
Update contributors
Reduce code duplication in test_radon_transform
PEP8 fixes for test_radon_transform
Radon transform example: Correct axis labels
Radon transform example: Remove semicolons.
transform.radon: Add test to verify the projection center.
transform.radon: Add testcases for rectangular input arrays.
transform.iradon: Add tests for center of projection.
transform.radon: Remove unneccesary matrix inverse.
transform.radon: Use correct padding for rectangular images.
transform.radon: Consistent definition of center of array.
radon tests: Refactor test for circle reconstructions.
transform.iradon: Redefine slice and projection center.
test_radon_transform: Add helper functions.
transform.iradon: Refactoring for shorter functions.
test_radon_transform: Test sinogram conversions.
test_radon_transform: Refactor and improve test_radon_iradon.
test_radon_transform: debug option for test_iradon_minimal.
radon_transform: Stylistic changes.
test_radon_transform: Refactor tests and make them stricter.
test_radon_transform: Change test criterion for iradon_minimal.
test_radon_transform: Change test criterion for sinogram_circle.
transform.radon: Robust determination of center of projection.
transform.iradon: Correct determination of center of projection.
test_radon_transform: Clean up imports.
test_radon_transform: Style fixes, PEP8.
Add SART tomography reconstruction to radon_transform.
Make iradon_sart visible in the transform package.
Add tests for transform.iradon_sart.
Implement projection shifts.
Tests for the projection_shifts functionality of iradon_sart.
Fix docstrings for transform.iradon_sart with subroutines.
transform.iradon_sart: Clean up code for ordering projections.
iradon_sart: Add wikipedia reference to Kaczmarz method.
iradon_sart: Clarify how constants are chosen.
Tests for iradon_sart: Robust path handling.
iradon_sart: Clean up cython code to minimize python calls.
iradon_sart: Improve argument checking.
iradon_sart's cython exts: Use typed memoryviews, not ndarrays.
iradon_sart: Reduce code duplication in interpolation.
iradon_sart: Remove needless memoryview/ndarray conversion.
iradon_sart: Add Kaczmarz reference and reformat citations.
radon_transform: Declare encoding.
iradon_sart: Order angles using a golden ratio approach.
iradon_sart: Add test for order_angles_golden_ratio.
iradon_sart: Also test accuracy with a missing wedge.
iradon_sart: Style fixes.
test_radon_transform: Style fixes.
Rewrite Radon example; include SART.
iradon_sart: Test clip functionality and add a test for it.
radon example: Display plots when run from command line.
Improve the text in and add references to the Radon example.
Radon example: Style fixes.
Radon example: print RMS errors of the reconstructions.
Radon example: Declare UTF-8 encoding.
Radon tests: Check the correct error metric.
iradon_sart: redefine projection center.
iradon_sart: fix comment spelling.
iradon_sart: flip signs to reflect changes to radon.
Add SART to contributors.
arraypad: allow padding with zero entries (i.e. no padding).
radon: Use util.pad for array padding.
iradon: Use util.pad for array padding.
iradon: Reduce code duplication.
radon: Use numpy.interp/scipy.interpolate.
iradon: Only allow interpolation methods working well.
iradon: Add test for cubic interpolation.
iradon: Cleanup by locating related code in one place.
iradon: use util.pad for sinogram padding.
iradon_sart: Format docs correctly.
iradon_sart: Reformat references.
iradon_sart: Fix docstring typo.
examples: Avoid python3-specific syntax.
Radon transform: Redefine projection center for sinograms.
Radon transform: Document rotation axis location.
radon: Reduce duplication; simplifications.
radon: Correct docstring of order_angles_golden_ratio.
Radon transform: Include boundary in reconstruction circle.
Radon transform: PEP8 fixes.
iradon: Clean up filter code.
iradon: Do not suppress 0 frequency for filter=None.
docs: Makefile respects variables from environment.
doc: Allow specifying python binary.
Juan Nunez-Iglesias (100):
Revert remove_small_objects to raise TypeError
Make `exclude_borders` option in peak_local_max nD
Use range instead of xrange
Make color functions used by SLIC 3D-aware
Make more colorconv functions 3D aware
Add initial 3D modifications (not working)
Add function to calculate regularly-spaced grid in nD
Modify SLIC to allow uneven step sizes
Add more descriptive error message to _prepare_colorarray
Separate inner loop of SLIC computation
Bug fixes: concatenation order and shape assignments
Bug fix: don't add singleton dimension to 3D gray images
Bug fix: remove unnecessary __get__ in test_slic
Add 3D slic tests (gray not working yet)
bug fix: 3d test working
Improve PEP8 and Python 3 compliance
PEP8
Always convert image to float in [0, 1]
Rename slic.py to avoid name conflicts
Use educated guesses for presence of color channels in SLIC
Add function to guesstimate number of spatial dimensions
Revert change to is_rgb
Bug fix: add z dimension regardless of multichannel
Bug fix: spatial vs image dimension comparison reversed
Make means array contiguous for numpy <= 1.6.1
Add UTF8 coding declaration to slic_superpixels.py
Suppress warning of ambiguous array dim in test
Initial attempt at updating SLIC for memoryviews
Fix build errors with memoryviews
Improve _slic.pyx doc, bug fixes, debug print
Remove diagnostic print
Bug fix: correctly initialize distance in slic
Speed up initialising 'distance' in SLIC
Fix automerge bug
Bug fix: map returns iterator in Py3k
Remove old commented-out code
Improve doc for regular_grid.py
Add tests for 'regular_grid()'
Rename regular_grid.py
Add test coverage for guess_spatial_dimensions()
Complete test_regular_grid coverage
Fix typo using assert_raises in test_colorconv.py
Fix ratio scaling in SLIC
Merge pull request #662 from stefanv/bento_installation
Remove unused 'ratio' argument from _slic_cython
Precision issues appear to have vanished
Replace 'ratio' kwarg with 'compactness' in SLIC
Do not use 'ratio' in test_slic.py either
Add unique_rows function
Add test for unique_rows
Add unique_rows to util/__init__.py
Remove repeated coordinates before computing convex hull
Unique rows after getting the pixel corners
Move code comment to appropriate line
Add (previously) pathological qhull test case
Add test to unique_rows for discontiguous arrays
Ensure array input to unique_rows is contiguous
Use Py_ssize_t instead of int in _slic_cython
Change 'long' to 'int' in Cython docs
Merge pull request #689 from mkcor/coffeepic-credits
Merge pull request #665 from mrterry/deltae
Add note describing array copy if discontiguous
Add docstring note explaining coord use case
Add PyAMG to the optional dependencies list
Update PyAMG URL (no longer in Google Code)
Merge pull request #712 from emmanuelle/gaussian_filter
Fix errors in relabel_from_one docs; PEP8
Fix type hierarchy check in remove_small_objects
Fix image dimension sanitizing at function start
Update SLIC docstring to remove deprecated example
Ignore `convert2lab` keyword if not multichannel
Add support for list sigma input in SLIC
Add spacing support for new, speeded-up SLIC
Add `spacing` descriptions; use np.double
Bug fix: typo: wrote spacing instead of sigma
Add note about (z, y, x) order in slic cython doc
Update snippets in notes to use double backticks
Merge pull request #719 from ahojnnes/slic
Merge pull request #740 from ahojnnes/warp-fix
Merge pull request #748 from ahojnnes/regionprops-dtype
Add relabel_sequential, deprecate relabel_from_one
Add relabel_sequential to __init__ import
Add new tests for relabel_sequential
Remove deprecated use of relabel_from_one
Rename deprecated relabel_from_one in docstring example
Only raise umfpack warning if cg mode is used
Monkey-patch UmfpackContext __del__
Remove unused imports in random_walker source
Add comment and links explaining Umfpack import
Deprecate default mode 'bf' in random_walker
Add change in random_walker default mode to TODO
Update SLIC in example to most recent interface
Merge pull request #761 from kemaleren/optimized_colorlabel
Fix join_segmentations example using img_as_float
Merge pull request #774 from ahojnnes/shape-plot
Merge pull request #769 from tonysyu/consistent-color-labels
Merge pull request #753 from stefanv/pr_plots
Merge pull request #779 from ahojnnes/log-depr
Merge pull request #791 from stefanv/regionprops_as_dict
Merge pull request #794 from ahojnnes/lbp-memview
Julian Taylor (5):
add autopkgtests
update packaging to use dh_sphinxdoc and dh_python2
fix navbar links in documentation
wrap-and-sort debian/
add python3 packages
K.-Michael Aye (1):
removing some unused selem declarations
Kemal Eren (3):
ENH: optimized label2rgb()
fixed error in label2rgb() when label is a binary array
handle case when there are no labels
Kirill Shklovsky (1):
Changed the 180 constant in bin calculation to avoid rounding errors
Luis Pedro Coelho (2):
ENH Faster perimeter computation
RFCT Simpler code for initializing array
Malcolm Reynolds (4):
FIX: number of peaks returned from feature.corner_peaks
TEST: added test for num_peaks kwarg in peak_local_max.
FIX: move corner detection outside loop in test_num_peaks.
FIX: changed xrange to range so Python 3 works.
Marianne Corvellec (21):
Used instead of deprecated function.
Documented another easy way to build scikit-image for virtualenv users.
Edited after Stefan's comments.
Okay, I think I got the rst syntax this time...
Improving docstring + style/convention edits
Added some warnings for transparency.
PEP8 compliance!
One line.
Clarified that you can pass images of any type into Canny filter.
Fixed relative threshold: you consider 10% and 20% of the max for range of
Improved style.
Always follow the style guide :)
Included Tony's edits.
Changed variable names so they actually make sense (followed Tony's
Added elements to the coffee picture docstring.
Edited docstring according to comments.
Tiny formatting edits
Added deprecation decorator according to discussion.
Merge branch 'master' of git://github.com/scikit-image/scikit-image into filter_median_dtypes
Added item to to-do list for version 0.10
Oops! Typed one instead of the other again! Fixed.
Matt Terry (38):
add color distance functions, ciede2000 tests
docs
better cmc implementation
don't need lab2lch
add tests. cmc stops naning
cleaner lch implementations
fix path
set testing tolerance
make naming consistent
add references
references
references
expose lab/lch conversion
docs
pep8 math operators
use np.rollaxis
reference formatting
copy editing docs
test for rgb2lch roundtrip
deg2rad > DEG
skimage attribution convention
run_module_suite
docs for deltaE_ciede2000 length scales
copy editing
lab2lch/lch2lab for N-D images (w/tests)
last round of copy-edits
code cleanup
tuples are valid inputs
cleanup
unneeded asarray
doc cleanup
fix table formatting
spell ciede correctly
better roundoff handing of dH
more consistency in naming, better docstring
r is confusing, use ab instead
doc quickfix
comma usage
Nicolas Pinto (1):
DOC: "gabors from lena" isn't under construction
Olivier Debeir (4):
fix:doctring rank/percentile
typo
remove long lines
fix:remove unused parameters in rank.percentile
Riaan van den Dool (1):
Forgotten contribution by riaanvddool: skimage.io plugin - GDAL
Stefan van der Walt (143):
Merge pull request #412 from ahojnnes/draw-cython-directives
STY: PEP8 for logo.
Merge pull request #457 from tonysyu/logo_refactor
Merge pull request #390 from tonysyu/canvastools
Merge pull request #460 from jni/raise-type
Merge pull request #462 from ahojnnes/deprecated-doc-string
Merge pull request #463 from ahojnnes/pdf-docs
Merge pull request #441 from spotter/color_deconv
Merge pull request #473 from ahojnnes/feature-refs
Merge pull request #501 from ahojnnes/skeletonize
Merge pull request #500 from JDWarner/fix_preserve_rw_input_shape
Merge pull request #503 from ahojnnes/exposure
Merge pull request #494 from ahojnnes/release-instr
Merge pull request #496 from ahojnnes/label-performance
Merge pull request #488 from sciunto/minor_docfix
Fix Emmanuelle Gouillart's name in the contributors list.
Refresh contribution guidelines.
Add upstream / username remotes. Illustrate rebase.
ENH: Add `chelsea` to dataset.
BUG: Fix integer type in Felzenwalb cython.
Merge pull request #515 from tonysyu/fix/imread-url-bug
Merge pull request #527 from JDWarner/tempfix_use_old_cython
Merge pull request #530 from npinto/patch-2
Merge pull request #540 from ahojnnes/namespace
Merge pull request #440 from ahojnnes/fitting
Merge pull request #550 from ahojnnes/matching-spelling
Merge pull request #566 from ahojnnes/bscript
Merge pull request #565 from ahojnnes/doc-fix
Merge pull request #564 from ahojnnes/warp-example
Merge pull request #568 from ahojnnes/circle
Merge pull request #567 from josteinbf/radon-reconstruction-circle
Merge pull request #538 from ahojnnes/examples-travis
Remove reference to Bento hookfile.
Merge pull request #581 from ankit-maverick/subtract
Merge pull request #485 from tonysyu/image_label2rgb
Merge pull request #577 from JDWarner/add_pad
Merge pull request #601 from ahojnnes/corner-eps
Merge pull request #612 from applio/master
Remove 2to3.
Add six compatibility module.
Remove is_str and replace by isinstance(..., six.string_types).
Correctly check for string type.
Fix zip.
Fix function code.
Fix iterator.
Fix label casting for numpy 1.7.
Fix im_class access in Python 3.
Fix im_self access in Python 3.
Fix imports under Python 3.
Use int32 for labelling.
Add to public API.
Space code more readably in transform.
Ensure PIL tests run with PIL.
Do not run flakes on test files -- we have too many custom formatted array.
Merge pull request #596 from josteinbf/radon-projection-center
Merge pull request #642 from sciunto/convex_hull_ex
Fix Bento build.
Merge pull request #614 from tonysyu/doc/local-binary-pattern
Merge pull request #646 from ahojnnes/travis-bento
Fix casting in ransac example.
Merge pull request #645 from josteinbf/iradon-sart-docstring
Merge pull request #611 from mkcor/install_pip-requirements
Add javascript for locating latest stable version.
Highlight current doc version.
Shorten Bento installation instructions and fix broken links.
Environment variable is called WAFDIR.
Properly fix WAF environment directory. Tell users to download source (not binary).
Merge pull request #626 from ahojnnes/rank-fixes
Merge pull request #627 from ahojnnes/travis-examples
Merge pull request #666 from jni/slic-scaling
Merge pull request #654 from josteinbf/radon-square-center
Merge pull request #674 from ahojnnes/region-props
Merge pull request #677 from ahojnnes/radon-example
Merge pull request #676 from ahojnnes/regionprops-fixes
Merge pull request #688 from ahojnnes/regionprops-bugfix
Merge pull request #694 from ahojnnes/moments
Merge pull request #696 from ahojnnes/foerstner-ref-fix
Merge pull request #695 from ahojnnes/memoryviews
Merge pull request #698 from mrterry/deltae_docs
Remove logger in favor of warnings.
Remove unnecessary import of Warning.
Merge pull request #697 from ahojnnes/memoryviews
Remove leftover debug statement.
Remove Image wrapper from io. Improve tags handling.
Add tests for image tags.
Merge pull request #638 from sciunto/contribute
Merge pull request #711 from sciunto/minordoc
Merge pull request #721 from ahojnnes/travis
Add skip parameter to view_as_windows.
Merge pull request #750 from ahojnnes/misc
Update PR plotter.
Correctly plot cumulative sum.
Merge branch 'master' into debian
New upstream release.
Replace mentions of old package name.
Development guidelines moved.
Test whether labels are left alone in label2rgb.
Merge pull request #773 from ahojnnes/scipy-0.13rc
Merge pull request #759 from jni/supress-umf
Add labels to releases.
Merge pull request #7 from tonysyu/pr_plots
Merge pull request #675 from sciunto/ellipseht_heapq_fix
Merge pull request #756 from ahojnnes/morph
Simplify output handling for binary morphology.
Merge pull request #749 from ahojnnes/gsoc-experimental
Fix overflow in NumPy 1.7 as suggested by Julian Taylor.
Restore @ahojnnes's overflow test. Correctly assign out argument.
Test that output argument is utilized.
Test that output argument is correct.
Revert to >0 for determining binary values. Document that input should be binary.
Pre-allocate memory for convolution and re-use for output, if no user-override specified.
Allocate less memory, if possible.
Update docs to match output.
Tweak markup of docstring.
Provide stable doc version by naming docs directory 0.9.x, e.g.
Always use uint8 for binary view.
Merge pull request #783 from ahojnnes/draw
Merge pull request #784 from ahojnnes/deprecations
Update TODO.txt after deprecations.
Note deprecations under API changes.
Rewrite contributor lister in Python.
Add contributors to 0.9.
Update author order for 0.9 release notes.
Dictionary interface to preserve backward compatibility for RegionProps.
Fix Python 3 list handling.
Fix Py3 exception in GTK plugin.
Merge pull request #792 from stefanv/gtk_py3
Update contributors script to count by date.
Contrib script now shows PRs and merges.
Update 0.9 release notes with new features.
Update versions for 0.9.0 release.
Update version in docs.
Correctly determine version number from module.
Fix markup error in marching cubes docs.
Update gh-pages instructions in RELEASE.txt.
Mark BRIEF and Censure as experimental in release notes.
Update docversions correctly for 0.9.x.
Get rid of that inherited 's' once and for all.
Update manifest not to include gh-pages in docs.
Add missing files to MANIFEST for sdist upload.
Set version to 0.9.1.
Set version to 0.9.2 for second try at PyPi upload.
Merge pull request #796 from ahojnnes/warp-fix
Steven Silvester (3):
BUG: Remove focus from buttons which caused unintential clicking.
BUG: Added required QtCore import
ENH: Adjusted save_to_file to create a proper composite image
Thouis (Ray) Jones (2):
fix rank filters for float structuring element
Merge pull request #1 from ahojnnes/thouis-master
Tony S Yu (148):
ENH: Add canvastools subpckages with base class and line tools
BUG: Move callback connection to parent class
STY: Reuse ThickLineTool in LineProfile
BUG: Fix blitting behavior in canvastools
STY: Refactor parts of LineTool to CanvasToolBase
BUG: Clean up imports
Fix figure canvas creation.
BUG: Allow slider to accept key press events
ENH: Default to blitting
BUG: Fix background update when canvas resized
STY: Remove commented out code
BUG: Fix blitting behavior
STY: Clean up unused blitting-related code
STY: Minor code clean up
ENH: Draw new line when click is far from handle
STY: Remove reset functionality in line tool
ENH: Increase default selection threshold for ease of use
STY: Rename line_tool module to linetool
ENH: Add measure tool plugin
STY: Refactors general parts of line tool to base tool
ENH: Add rectangle tool and crop plugin example
ENH: Overhaul callback system.
BUG: Fix image viewer for RGB images
BUG: Fix matplotlib import for compatibility
STY: Switch order of callback parameters
BUG: Fix line visibility
STY: Rename parameters for clarity
BUG: Fix renamed parameter
Fix typo
ENH: Add color histogram plugin
ENH: Handle redraw edge case.
Remove x, y parameters from line tool to simplify API
STY: Rename end_pts to end_points
STY: Remove linewidth parameter to simplify API
DOC: Add parameters to docstring
BUG: Fix LineTool example after change to call signature
BUG: Fix line thickness change call back
STY: Simplify imports
ENH: Add setter for extents property
ENH: Improve end_points setter
BUG: Update measure for change in line_tool API
BUG: Fix error when matplotlib is not available
BUG: Fix MRO bug when matplotlib not installed
BUG: fix end_points setter when given a tuple
BUG: Validate mouse interaction
ENH: Allow Save buttons to save overlay
ENH: Let CannyPlugin adapt to input image
Merge pull request #2 from blink1073/canvastools
ENH: Warn if using OverlayPlugin w/ matplotlib < 1.2
BUG: Fix save to stack so it saves filtered image
ENH: Add open and save menu actions
BUG: Fix clean up of canvastools
ENH: Remove unnecessary clean up functions.
ENH: Add PaintTool and LabelPlugin
ENH: Add demo of LabelPlugin
Use print function for python 3 compatibility
Merge pull request #3 from blink1073/canvastools
ENH: Cast arrays for numpy compatibility.
ENH: Improve usability of watershed_demo.
Fix alpha handling for image saving.
Add save buttons to viewer example.
Change `dtype_limits` clipping behavior.
Refactor code that generates scikit-image logo.
Merge pull request #4 from stefanv/tonysyu_logo_refactor
Merge pull request #468 from ahojnnes/rotate-doc
Merge pull request #470 from ahojnnes/regionprops-example
Merge pull request #477 from JDWarner/convert_dtype_to_astype
Fix kernel-size calculation for non-zero theta.
Add `bandwidth` parameter to `gabor_kernel`
DOC: Tweak docstrings for Gabor filter
Update gabor example.
Add better test of gabor filter
Merge pull request #371 from ahojnnes/gabor
Merge pull request #498 from JDWarner/fix_canny_strel
Merge pull request #497 from ahojnnes/guidelines
Merge pull request #484 from almarklein/3d-selem
Fix imread from urls on some backends.
Merge pull request #512 from mkcor/doc_fix-deprecationwarning
Merge pull request #509 from stefanv/contributor_guidelines
Merge pull request #524 from stefanv/chelsea
Minor cleanups
Merge branch 'pr/517'
Fixes to make doctests pass.
Merge branch 'pr/531'
Merge pull request #528 from chintak/doc_morphology
Merge pull request #537 from ahojnnes/examples-fix
Merge pull request #539 from ahojnnes/bresenham-deprecate
Add `image_label2rgb`
Fix: Add setup.py which adds data file to the build
ENH: Add some checks on the inputs.
TST: Add tests for image_label2rgb
DOC: Change more examples to use `image_label2rgb`
API Change: `image_label2rgb` changed to `label2rgb`.
Merge pull request #536 from ahojnnes/edge-weights
Add skimage.viewer.qt wrapper.
Add PySide compatibility for save dialogs
Fix file open dialog for PySide
Remove `alignment` kwarg for compatibility with older PyQt4
Merge pull request #541 from emmanuelle/doc
Remove `alignment` kwarg (left out from previous commit).
Fix `RequiredAttrs` definition.
Fix parameter name in docstring
Add infrastructure for conneting plugin output to a viewer.
Add example of connected viewers/plugins
Dock plugins to image viewer.
Fix sizing of PlotPlugin
Display title in docked plugins
Add smart window-layout for multi-viewer display
Add mock pyqtSignal to try to get Travis to build
Second attempt to get Travis to pass
Third attempt at getting Travis to build
Accidental deletion
Add attributes to Mock object to fix Travis build
Fix PySide compatibility for signal defs
Fix plugin interaction with CollectionViewer
Add example of connecting plugins to CollectionViewer
Fix display of overlay plugin when original image is updated
Fix docstring for CollectionViewer slider.
Change color definitions from ini file to python module
Tweak Sphinx rendering of contribution page
Merge pull request #593 from ahojnnes/rebase-workflow
Merge pull request #590 from sciunto/python3fix
Fix execution in IPython with qt backend.
Fix PyQt4 segfault caused by PySide fix.
Make histogram threshold adjustable
Change QApp default to previous behavior.
Raise ImageViewer to front on start.
Change default Slider update_on value to 'release'
Add explanation to LBP example
Clean up test.
Merge pull request #613 from adamw523/master
Minor fixes
Merge pull request #620 from scikit-image/2013
Change rank.pyx to _rank.py
Add support for all data types.
Fix build script
Merge pull request #615 from JDWarner/fix_lineprofile
Merge pull request #618 from mkcor/filter_canny_passingtype
Fix naming bug
Fix Python 3 incompatibility (also, some wording tweaks)
Merge pull request #657 from chintak/doc_fix_cmorph
Merge pull request #667 from ahojnnes/denoise-fixes
Merge pull request #726 from jni/fix-relabel-doc
Add support for consistent color labels for sparse labels.
Merge pull request #6 from stefanv/tonysyu-consistent-color-labels
Plot cleanup and tweak to total PRs line.
Add hough_circles change to API doc
Label dates every 3 months instead of every month
Umesh (3):
Updated Implementation of Roberts Algorithm
Upadated Version with test added(/filter/tests/test_edge.py
updated tests for Roberts Edge Detector
Xavier Moles Lopez (8):
FIX: Ran autopep8 on colorconv.py FIX: modified color.data.ihc function FIX: smaller ihc.jpg image
FIX: modified color.data.ihc docstring.
FIX: import rgb2hed and hed2rgb in the test_colorconv script.
FIX: Fixed test_hed_rgb_roundtrip.
FIX: Link to Ruifrok reference
ENH: Updated stain separation function docstrings and added matrices to __all__
FIX: Example in combine_stains docstring.
FIX: Added myself in CONTRIBUTORS.txt
Yaroslav Halchenko (13):
adjusted changelog + releasing into unstable
we never released -2
Merge commit '8a06a2277366d01c5e7e25d3ded0f04ba9aa0b85' into debian
Adding a copyright/license info for skimage/_shared/six.py
Merge tag 'v0.9.3' into debian
debian/changelog: adjusting version for 0.9.3
debian/patches - changeset_0eea2a48fe2dca7bbb3681fcd5b511579cad6347.diff and up_correct_version removed (upstreamed)
debian/rules - added export http(s)_proxy to point to non-existing localhost proxy, so we could guarantee no network is used at pkg build time
appantly python-imaging is now python-pil, thus adding alternative depends and recommends
python3-scipy was missing from build-depends
BF: forgotten build-depends on python3-matplotlib (making it optional if no python3 build for them yet)
we should not build docs in -a and dh_sphinxdoc should not give us problem either
Ignore failed attempts to remove .so from original arch all pkgs (in -a (arch-only) mode those directories are absent)
Zach Pincus (2):
Fix 64-bit multipage tiff writing segfault
Add multipage TIFF unittest
cgohlke (7):
BUG: basestring not defined on PY3
TST: use BytesIO to save images into file-like object
BUG: Fix ValueError: Buffer dtype mismatch, expected 'long' but got 'long long'
TST: Fix ValueError: Buffer dtype mismatch, expected 'intp_t' but got 'long'
TST: Fix test_weighted_moments is defined twice
TST: Fix AttributeError: '_RegionProperties' object has no attribute 'weighted_moments_central'
TST: Fix RuntimeError: data type not supported on Python 2.6
radioxoma (6):
Add Yen threshold method
Codestyle improvement
Yen PEP8 and docstrings
Added Yen tests, typo fixed
Logarithm optimisation
Fix import list sequence
root (1):
Updated function names[Robert's Edge Detection]
sg (6):
add bento to build docs
added revisions by @stefanv and @ahojnnes
updated gaussian doc
added testing dependencies and standardized use of bullets
remove extra :'s
added ahojnnes revisions
spotter (17):
ENH: Adding color deconvolution method to convert to an Haematoxylin-Eosin-DAB colorspace
ENH: Added an Immunohistochemical image example
FIX: the rgb2hed function. Legal issues regarding the ihc image. ENH: added the hed2rgb function.
ENH: Added rgb2hed and hed2rgb to __all__ list
FIX: Simplified deconvolution equations
ENH: Added a short test to validate rgb2hed and hed2rgb conversion
FIX: Removed unused dependency
FIX: Testing for ubyte and float images. Input dtypes are converted beforehand.
FIX: img_as_ubyte function threw ValueError due to floating point errors in hed2rgb function.
ENH: Added example to the gallery for ihc staining separation
FIX: Replaced non-ascii double quotes in Ruifrok reference.
FIX: rgb2hed and hed2rgb can work with both signed and unsigned image.
FIX: fixed docstrings. ENH: Added new stain separation matrices.
ENH: Adding tests for new stain separation functions.
FIX: using the new stain separation functions for the special case of hed.
FIX: combine_stains docstring.
FIX: changed unicode dash in docstrings.
umesh (2):
Final Roberts Edge Detector
Updated Test Case
yangzetian (4):
Fix peak_local_max's output for ndarray when indices is set to False
change doc for indices and remove the unnecessarily tolist() operation
Merge pull request #1 from jni/peak-local-max-indices-nd
Add test for nD `exclude_border` option
zachrahan (2):
Merge pull request #507 from zachrahan/freeimage-multipage-64
Merge pull request #508 from zachrahan/freeimage-multipage-64
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