diff --git a/TODO.txt b/TODO.txt index 67429880a8d..b1a92607326 100644 --- a/TODO.txt +++ b/TODO.txt @@ -41,14 +41,5 @@ Version 0.12 ------------ * Change `label` to mark background as 0, not -1, which is consistent with SciPy's labelling. -* Remove deprecated `reverse_map` parameter of `skimage.transform.warp` -* Change deprecated `enforce_connectivity=False` on skimage.segmentation.slic - and set it to True as default -* Remove deprecated `skimage.measure.fit.BaseModel._params` attribute -* Remove deprecated `skimage.measure.fit.BaseModel._params`, - `skimage.transform.ProjectiveTransform._matrix`, - `skimage.transform.PolynomialTransform._params`, - `skimage.transform.PiecewiseAffineTransform.affines_*` attributes -* Remove deprecated functions `skimage.filters.denoise_*` * Add 3D phantom in `skimage.data` * Add 3D test case of `skimage.feature.phase_correlate` diff --git a/doc/source/api_changes.txt b/doc/source/api_changes.txt index e87445b3e4e..dc023149c3b 100644 --- a/doc/source/api_changes.txt +++ b/doc/source/api_changes.txt @@ -4,6 +4,14 @@ Version 0.12 the ``ntiles_*`` arguments. - The functions ``blob_dog``, ``blob_log`` and ``blob_doh`` now return float arrays instead of integer arrays. +- `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_*`. Version 0.11 ------------ diff --git a/skimage/filters/__init__.py b/skimage/filters/__init__.py index 708f5d5346c..30e7dcd3007 100644 --- a/skimage/filters/__init__.py +++ b/skimage/filters/__init__.py @@ -15,12 +15,7 @@ from .._shared.utils import deprecated, copy_func from .. import restoration -denoise_bilateral = deprecated('skimage.restoration.denoise_bilateral')\ - (restoration.denoise_bilateral) -denoise_tv_bregman = deprecated('skimage.restoration.denoise_tv_bregman')\ - (restoration.denoise_tv_bregman) -denoise_tv_chambolle = deprecated('skimage.restoration.denoise_tv_chambolle')\ - (restoration.denoise_tv_chambolle) + gaussian_filter = copy_func(gaussian, name='gaussian_filter') gaussian_filter = deprecated('skimage.filters.gaussian')(gaussian_filter) gabor_filter = copy_func(gabor, name='gabor_filter') diff --git a/skimage/measure/fit.py b/skimage/measure/fit.py index 360a5d6d99e..37de27217c8 100644 --- a/skimage/measure/fit.py +++ b/skimage/measure/fit.py @@ -24,11 +24,6 @@ class BaseModel(object): def __init__(self): self.params = None - @property - def _params(self): - warn('`_params` attribute is deprecated, use `params` instead.') - return self.params - class LineModel(BaseModel): diff --git a/skimage/measure/tests/test_fit.py b/skimage/measure/tests/test_fit.py index 794d173ea68..6bb8c7b44ae 100644 --- a/skimage/measure/tests/test_fit.py +++ b/skimage/measure/tests/test_fit.py @@ -301,14 +301,5 @@ def test_ransac_invalid_input(): residual_threshold=0, stop_probability=1.01) -def test_deprecated_params_attribute(): - model = LineModelND() - model.params = ((0, 0), (1, 1)) - x = np.arange(-10, 10) - y = model.predict_y(x) - with expected_warnings(['`_params`']): - assert_equal(model.params, model._params) - - if __name__ == "__main__": np.testing.run_module_suite() diff --git a/skimage/segmentation/slic_superpixels.py b/skimage/segmentation/slic_superpixels.py index b558f78ac54..64506de0c91 100644 --- a/skimage/segmentation/slic_superpixels.py +++ b/skimage/segmentation/slic_superpixels.py @@ -13,7 +13,7 @@ def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=0, spacing=None, multichannel=True, convert2lab=None, - enforce_connectivity=False, min_size_factor=0.5, max_size_factor=3, + enforce_connectivity=True, min_size_factor=0.5, max_size_factor=3, slic_zero=False): """Segments image using k-means clustering in Color-(x,y,z) space. @@ -53,7 +53,7 @@ def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=0, segmentation. The input image *must* be RGB. Highly recommended. This option defaults to ``True`` when ``multichannel=True`` *and* ``image.shape[-1] == 3``. - enforce_connectivity: bool, optional (default False) + enforce_connectivity: bool, optional Whether the generated segments are connected or not min_size_factor: float, optional Proportion of the minimum segment size to be removed with respect @@ -110,10 +110,6 @@ def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=0, >>> segments = slic(img, n_segments=100, compactness=20) """ - if enforce_connectivity is None: - warn('Deprecation: enforce_connectivity will default to' - ' True in future versions.') - enforce_connectivity = False image = img_as_float(image) is_2d = False diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py index 1e06e8b5d90..1cd5621f733 100644 --- a/skimage/transform/_geometric.py +++ b/skimage/transform/_geometric.py @@ -181,11 +181,6 @@ def __init__(self, matrix=None): raise ValueError("invalid shape of transformation matrix") self.params = matrix - @property - def _matrix(self): - warn('`_matrix` attribute is deprecated, use `params` instead.') - return self.params - @property def _inv_matrix(self): return np.linalg.inv(self.params) @@ -778,11 +773,6 @@ def __init__(self, params=None): raise ValueError("invalid shape of transformation parameters") self.params = params - @property - def _params(self): - warn('`_params` attribute is deprecated, use `params` instead.') - return self.params - def estimate(self, src, dst, order=2): """Set the transformation matrix with the explicit transformation parameters. diff --git a/skimage/transform/tests/test_geometric.py b/skimage/transform/tests/test_geometric.py index d34e5e8fd80..a12eb50b2fc 100644 --- a/skimage/transform/tests/test_geometric.py +++ b/skimage/transform/tests/test_geometric.py @@ -249,17 +249,6 @@ def test_invalid_input(): assert_raises(ValueError, PolynomialTransform, np.zeros((3, 3))) -def test_deprecated_params_attributes(): - for t in ('projective', 'affine', 'similarity'): - tform = estimate_transform(t, SRC, DST) - with expected_warnings(['`_matrix`.*deprecated']): - assert_equal(tform._matrix, tform.params) - - tform = estimate_transform('polynomial', SRC, DST, order=3) - with expected_warnings(['`_params`.*deprecated']): - assert_equal(tform._params, tform.params) - - def test_degenerate(): src = dst = np.zeros((10, 2))