From c48302d70ba84853aaa3b38993fc0a213f7228e5 Mon Sep 17 00:00:00 2001 From: Stefan van der Walt Date: Sun, 6 Mar 2016 22:56:47 -0800 Subject: [PATCH 1/4] Bring release notes and API changes in sync --- doc/release/release_0.12.txt | 8 ++++++++ doc/source/api_changes.txt | 2 ++ 2 files changed, 10 insertions(+) diff --git a/doc/release/release_0.12.txt b/doc/release/release_0.12.txt index fbf2deac..470abb65 100644 --- a/doc/release/release_0.12.txt +++ b/doc/release/release_0.12.txt @@ -67,6 +67,14 @@ API Changes float arrays instead of integer arrays. - ``transform.integrate`` now takes lists of tuples instead of integers to define the window over which to integrate. +- `reverse_map` parameter in `skimage.transform.warp` has been removed. +- `enforce_connectivity` in `skimage.segmentation.slic` defaults to ``True``. +- `skimage.measure.fit.BaseModel._params`, + `skimage.transform.ProjectiveTransform._matrix`, + `skimage.transform.PolynomialTransform._params`, + `skimage.transform.PiecewiseAffineTransform.affines_*` attributes + have been removed. +- `skimage.filters.denoise_*` have moved to `skimage.restoration.denoise_*`. Deprecations ------------ diff --git a/doc/source/api_changes.txt b/doc/source/api_changes.txt index cdf82eca..61e13f5d 100644 --- a/doc/source/api_changes.txt +++ b/doc/source/api_changes.txt @@ -4,6 +4,8 @@ Version 0.12 the ``ntiles_*`` arguments. - The functions ``blob_dog``, ``blob_log`` and ``blob_doh`` now return float arrays instead of integer arrays. +- ``transform.integrate`` now takes lists of tuples instead of integers + to define the window over which to integrate. - `reverse_map` parameter in `skimage.transform.warp` has been removed. - `enforce_connectivity` in `skimage.segmentation.slic` defaults to ``True``. - `skimage.measure.fit.BaseModel._params`, From b91bb168eba39be50c512d40f6703195a454d73a Mon Sep 17 00:00:00 2001 From: Stefan van der Walt Date: Mon, 7 Mar 2016 01:41:42 -0800 Subject: [PATCH 2/4] Add .in files to source distribution --- .gitignore | 1 + MANIFEST.in | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index e0463700..f6c49609 100644 --- a/.gitignore +++ b/.gitignore @@ -30,3 +30,4 @@ doc/source/_static/random.js doc/release/_release_notes_for_docs.txt doc/gh-pages wheels +skimage/morphology/_skeletonize_3d_cy.pyx diff --git a/MANIFEST.in b/MANIFEST.in index 1a059991..553b55d8 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -3,7 +3,7 @@ include setup*.py include MANIFEST.in include *.txt include Makefile -recursive-include skimage *.pyx *.pxd *.pxi *.py *.c *.h *.ini *.md5 *.npy *.txt +recursive-include skimage *.pyx *.pxd *.pxi *.py *.c *.h *.ini *.md5 *.npy *.txt *.in recursive-include skimage/data * include doc/Makefile From dfffc55c36c529f4aadde152e7ab7e5f1d696471 Mon Sep 17 00:00:00 2001 From: Egor Panfilov Date: Mon, 7 Mar 2016 23:36:26 +0300 Subject: [PATCH 3/4] Added inpaint to module init --- skimage/restoration/__init__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/skimage/restoration/__init__.py b/skimage/restoration/__init__.py index c69ae2dc..424f9939 100644 --- a/skimage/restoration/__init__.py +++ b/skimage/restoration/__init__.py @@ -23,6 +23,7 @@ from .unwrap import unwrap_phase from ._denoise import denoise_tv_chambolle, denoise_tv_bregman, \ denoise_bilateral from .non_local_means import denoise_nl_means +from .inpaint import inpaint_biharmonic from .._shared.utils import copy_func, deprecated nl_means_denoising = copy_func(denoise_nl_means, name='nl_means_denoising') @@ -37,6 +38,7 @@ __all__ = ['wiener', 'denoise_tv_chambolle', 'denoise_bilateral', 'denoise_nl_means', - 'nl_means_denoising'] + 'nl_means_denoising', + 'inpaint_biharmonic'] del copy_func, deprecated From caa2d220b60eeeb2e9462bd389c297a05922a415 Mon Sep 17 00:00:00 2001 From: Egor Panfilov Date: Tue, 8 Mar 2016 01:35:48 +0300 Subject: [PATCH 4/4] Changed docsting sections order --- skimage/restoration/inpaint.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/skimage/restoration/inpaint.py b/skimage/restoration/inpaint.py index 5ecd28c7..cd5b9335 100644 --- a/skimage/restoration/inpaint.py +++ b/skimage/restoration/inpaint.py @@ -92,6 +92,12 @@ def inpaint_biharmonic(img, mask, multichannel=False): out : (M[, N[, ..., P]][, C]) ndarray Input image with masked pixels inpainted. + References + ---------- + .. [1] N.S.Hoang, S.B.Damelin, "On surface completion and image inpainting + by biharmonic functions: numerical aspects", + http://www.ima.umn.edu/~damelin/biharmonic + Examples -------- >>> img = np.tile(np.square(np.linspace(0, 1, 5)), (5, 1)) @@ -100,13 +106,6 @@ def inpaint_biharmonic(img, mask, multichannel=False): >>> mask[1, 3:] = 1 >>> mask[0, 4:] = 1 >>> out = inpaint_biharmonic(img, mask) - - References - ---------- - Algorithm is based on: - .. [1] N.S.Hoang, S.B.Damelin, "On surface completion and image inpainting - by biharmonic functions: numerical aspects", - http://www.ima.umn.edu/~damelin/biharmonic """ if img.ndim < 1: