diff --git a/skimage/color/__init__.py b/skimage/color/__init__.py index 08b5f739..52d6e760 100644 --- a/skimage/color/__init__.py +++ b/skimage/color/__init__.py @@ -1 +1,85 @@ -from .colorconv import * +from .colorconv import (convert_colorspace, + rgb2hsv, + hsv2rgb, + rgb2xyz, + xyz2rgb, + rgb2rgbcie, + rgbcie2rgb, + rgb2grey, + rgb2gray, + gray2rgb, + xyz2lab, + lab2xyz, + lab2rgb, + rgb2lab, + rgb2hed, + hed2rgb, + separate_stains, + combine_stains, + rgb_from_hed, + hed_from_rgb, + rgb_from_hdx, + hdx_from_rgb, + rgb_from_fgx, + fgx_from_rgb, + rgb_from_bex, + bex_from_rgb, + rgb_from_rbd, + rbd_from_rgb, + rgb_from_gdx, + gdx_from_rgb, + rgb_from_hax, + hax_from_rgb, + rgb_from_bro, + bro_from_rgb, + rgb_from_bpx, + bpx_from_rgb, + rgb_from_ahx, + ahx_from_rgb, + rgb_from_hpx, + hpx_from_rgb, + is_rgb, + is_gray) + +__all__ = ['convert_colorspace', + 'rgb2hsv', + 'hsv2rgb', + 'rgb2xyz', + 'xyz2rgb', + 'rgb2rgbcie', + 'rgbcie2rgb', + 'rgb2grey', + 'rgb2gray', + 'gray2rgb', + 'xyz2lab', + 'lab2xyz', + 'lab2rgb', + 'rgb2lab', + 'rgb2hed', + 'hed2rgb', + 'separate_stains', + 'combine_stains', + 'rgb_from_hed', + 'hed_from_rgb', + 'rgb_from_hdx', + 'hdx_from_rgb', + 'rgb_from_fgx', + 'fgx_from_rgb', + 'rgb_from_bex', + 'bex_from_rgb', + 'rgb_from_rbd', + 'rbd_from_rgb', + 'rgb_from_gdx', + 'gdx_from_rgb', + 'rgb_from_hax', + 'hax_from_rgb', + 'rgb_from_bro', + 'bro_from_rgb', + 'rgb_from_bpx', + 'bpx_from_rgb', + 'rgb_from_ahx', + 'ahx_from_rgb', + 'rgb_from_hpx', + 'hpx_from_rgb', + 'is_rgb', + 'is_gray'] diff --git a/skimage/color/colorconv.py b/skimage/color/colorconv.py index fc9ab342..11f11630 100644 --- a/skimage/color/colorconv.py +++ b/skimage/color/colorconv.py @@ -43,20 +43,6 @@ References from __future__ import division -__all__ = ['convert_colorspace', 'rgb2hsv', 'hsv2rgb', 'rgb2xyz', 'xyz2rgb', - 'rgb2rgbcie', 'rgbcie2rgb', 'rgb2grey', 'rgb2gray', 'gray2rgb', - 'xyz2lab', 'lab2xyz', 'lab2rgb', 'rgb2lab', 'rgb2hed', 'hed2rgb', - 'separate_stains', 'combine_stains', 'rgb_from_hed', 'hed_from_rgb', - 'rgb_from_hdx', 'hdx_from_rgb', 'rgb_from_fgx', 'fgx_from_rgb', - 'rgb_from_bex', 'bex_from_rgb', 'rgb_from_rbd', 'rbd_from_rgb', - 'rgb_from_gdx', 'gdx_from_rgb', 'rgb_from_hax', 'hax_from_rgb', - 'rgb_from_bro', 'bro_from_rgb', 'rgb_from_bpx', 'bpx_from_rgb', - 'rgb_from_ahx', 'ahx_from_rgb', 'rgb_from_hpx', 'hpx_from_rgb', - 'is_rgb', 'is_gray' - ] - -__docformat__ = "restructuredtext en" - import numpy as np from scipy import linalg from ..util import dtype diff --git a/skimage/data/__init__.py b/skimage/data/__init__.py index ac55557f..07d2688d 100644 --- a/skimage/data/__init__.py +++ b/skimage/data/__init__.py @@ -12,6 +12,20 @@ from ..io import imread from skimage import data_dir +__all__ = ['load', + 'camera', + 'lena', + 'text', + 'checkerboard', + 'coins', + 'moon', + 'page', + 'horse', + 'clock', + 'immunohistochemistry', + 'chelsea'] + + def load(f): """Load an image file located in the data directory. diff --git a/skimage/draw/__init__.py b/skimage/draw/__init__.py index 0cb0b72a..a5ba8869 100644 --- a/skimage/draw/__init__.py +++ b/skimage/draw/__init__.py @@ -1,2 +1,11 @@ from ._draw import line, polygon, ellipse, ellipse_perimeter, \ circle, circle_perimeter, set_color, bresenham + +__all__ = ['line', + 'polygon', + 'ellipse', + 'ellipse_perimeter', + 'circle', + 'circle_perimeter', + 'set_color', + 'bresenham'] diff --git a/skimage/exposure/__init__.py b/skimage/exposure/__init__.py index 3d1aebe4..aba05dae 100644 --- a/skimage/exposure/__init__.py +++ b/skimage/exposure/__init__.py @@ -1,3 +1,10 @@ from .exposure import histogram, equalize, equalize_hist, \ rescale_intensity, cumulative_distribution from ._adapthist import equalize_adapthist + +__all__ = ['histogram', + 'equalize', + 'equalize_hist', + 'equalize_adapthist', + 'rescale_intensity', + 'cumulative_distribution'] diff --git a/skimage/feature/__init__.py b/skimage/feature/__init__.py index 9f1e5f92..09ac4540 100644 --- a/skimage/feature/__init__.py +++ b/skimage/feature/__init__.py @@ -6,3 +6,19 @@ from .corner import (corner_kitchen_rosenfeld, corner_harris, corner_shi_tomasi, corner_foerstner, corner_subpix, corner_peaks) from .corner_cy import corner_moravec from .template import match_template + + +__all__ = ['daisy', + 'hog', + 'greycomatrix', + 'greycoprops', + 'local_binary_pattern', + 'peak_local_max', + 'corner_kitchen_rosenfeld', + 'corner_harris', + 'corner_shi_tomasi', + 'corner_foerstner', + 'corner_subpix', + 'corner_peaks', + 'corner_moravec', + 'match_template'] diff --git a/skimage/filter/__init__.py b/skimage/filter/__init__.py index 5479af5d..ef8460a5 100644 --- a/skimage/filter/__init__.py +++ b/skimage/filter/__init__.py @@ -1,4 +1,4 @@ -from .lpi_filter import * +from .lpi_filter import inverse, wiener, LPIFilter2D from .ctmf import median_filter from ._canny import canny from .edges import (sobel, hsobel, vsobel, scharr, hscharr, vscharr, prewitt, @@ -9,3 +9,31 @@ from ._denoise_cy import denoise_bilateral, denoise_tv_bregman from ._rank_order import rank_order from ._gabor import gabor_kernel, gabor_filter from .thresholding import threshold_otsu, threshold_adaptive + + +__all__ = ['inverse', + 'wiener', + 'LPIFilter2D', + 'median_filter', + 'canny', + 'sobel', + 'hsobel', + 'vsobel', + 'scharr', + 'hscharr', + 'vscharr', + 'prewitt', + 'hprewitt', + 'vprewitt', + 'roberts', + 'roberts_positive_diagonal', + 'roberts_negative_diagonal', + 'denoise_tv_chambolle', + 'tv_denoise', + 'denoise_bilateral', + 'denoise_tv_bregman', + 'rank_order', + 'gabor_kernel', + 'gabor_filter', + 'threshold_otsu', + 'threshold_adaptive'] diff --git a/skimage/filter/lpi_filter.py b/skimage/filter/lpi_filter.py index 2af74d7a..b3755a8b 100644 --- a/skimage/filter/lpi_filter.py +++ b/skimage/filter/lpi_filter.py @@ -3,9 +3,6 @@ :license: modified BSD """ -__all__ = ['inverse', 'wiener', 'LPIFilter2D'] -__docformat__ = 'restructuredtext en' - import numpy as np from scipy.fftpack import ifftshift diff --git a/skimage/filter/rank/__init__.py b/skimage/filter/rank/__init__.py index 30d936db..8f632469 100644 --- a/skimage/filter/rank/__init__.py +++ b/skimage/filter/rank/__init__.py @@ -1,3 +1,37 @@ -from .rank import * -from .percentile_rank import * -from .bilateral_rank import * +from .rank import (autolevel, bottomhat, equalize, gradient, maximum, mean, + meansubstraction, median, minimum, modal, morph_contr_enh, + pop, threshold, tophat, noise_filter, entropy, otsu) +from .percentile_rank import (percentile_autolevel, percentile_gradient, + percentile_mean, percentile_mean_substraction, + percentile_morph_contr_enh, percentile, + percentile_pop, percentile_threshold) +from .bilateral_rank import bilateral_mean, bilateral_pop + + +__all__ = ['autolevel', + 'bottomhat', + 'equalize', + 'gradient', + 'maximum', + 'mean', + 'meansubstraction', + 'median', + 'minimum', + 'modal', + 'morph_contr_enh', + 'pop', + 'threshold', + 'tophat', + 'noise_filter', + 'entropy', + 'otsu', + 'percentile_autolevel', + 'percentile_gradient', + 'percentile_mean', + 'percentile_mean_substraction', + 'percentile_morph_contr_enh', + 'percentile', + 'percentile_pop', + 'percentile_threshold', + 'bilateral_mean', + 'bilateral_pop'] diff --git a/skimage/graph/__init__.py b/skimage/graph/__init__.py index 9e2ac4e0..eb817c77 100644 --- a/skimage/graph/__init__.py +++ b/skimage/graph/__init__.py @@ -1,10 +1,7 @@ -try: - from .spath import shortest_path - from .mcp import MCP, MCP_Geometric, route_through_array -except ImportError: - print """*** The cython extensions have not been compiled. Run +from .spath import shortest_path +from .mcp import MCP, MCP_Geometric, route_through_array -python setup.py build_ext -i - -in the source directory to build in-place. Please refer to INSTALL.txt -for further detail.""" +__all__ = ['shortest_path', + 'MCP', + 'MCP_Geometric', + 'route_through_array'] \ No newline at end of file diff --git a/skimage/measure/__init__.py b/skimage/measure/__init__.py index 1c92d9ee..226c4235 100755 --- a/skimage/measure/__init__.py +++ b/skimage/measure/__init__.py @@ -1,4 +1,11 @@ from .find_contours import find_contours from ._regionprops import regionprops, perimeter from ._structural_similarity import structural_similarity -from ._polygon import approximate_polygon, subdivide_polygon \ No newline at end of file +from ._polygon import approximate_polygon, subdivide_polygon + +__all__ = ['find_contours', + 'regionprops', + 'perimeter', + 'structural_similarity', + 'approximate_polygon', + 'subdivide_polygon'] diff --git a/skimage/morphology/__init__.py b/skimage/morphology/__init__.py index 044fcf89..2cbfcd37 100644 --- a/skimage/morphology/__init__.py +++ b/skimage/morphology/__init__.py @@ -1,10 +1,46 @@ from .binary import (binary_erosion, binary_dilation, binary_opening, binary_closing) -from .grey import * -from .selem import * +from .grey import (erosion, dilation, opening, closing, white_tophat, + black_tophat, greyscale_erode, greyscale_dilate, + greyscale_open, greyscale_close, greyscale_white_top_hat, + greyscale_black_top_hat) +from .selem import square, rectangle, diamond, disk, cube, octahedron, ball from .ccomp import label from .watershed import watershed, is_local_maximum from ._skeletonize import skeletonize, medial_axis from .convex_hull import convex_hull_image from .greyreconstruct import reconstruction from .misc import remove_small_objects + + +__all__ = ['binary_erosion', + 'binary_dilation', + 'binary_opening', + 'binary_closing', + 'erosion', + 'dilation', + 'opening', + 'closing', + 'white_tophat', + 'black_tophat', + 'greyscale_erode', + 'greyscale_dilate', + 'greyscale_open', + 'greyscale_close', + 'greyscale_white_top_hat', + 'greyscale_black_top_hat', + 'square', + 'rectangle', + 'diamond', + 'disk', + 'cube', + 'octahedron', + 'ball', + 'label', + 'watershed', + 'is_local_maximum', + 'skeletonize', + 'medial_axis', + 'convex_hull_image', + 'reconstruction', + 'remove_small_objects'] diff --git a/skimage/morphology/tests/test_selem.py b/skimage/morphology/tests/test_selem.py index ccaf43a0..9a8ca895 100644 --- a/skimage/morphology/tests/test_selem.py +++ b/skimage/morphology/tests/test_selem.py @@ -8,7 +8,7 @@ from numpy.testing import * from skimage import data_dir from skimage.io import * from skimage import data_dir -from skimage.morphology import * +from skimage.morphology import selem class TestSElem(): @@ -36,7 +36,7 @@ class TestSElem(): expected_mask = expected_mask[:, np.newaxis] assert_equal(expected_mask, actual_mask) k = k + 1 - + def strel_worker_3d(self, fn, func): matlab_masks = np.load(os.path.join(data_dir, fn)) k = 0 @@ -48,20 +48,24 @@ class TestSElem(): # Test center slice for each dimension. This gives a good # indication of validity without the need for a 3D reference # mask. - c = int(expected_mask.shape[0]/2) + c = int(expected_mask.shape[0]/2) assert_equal(expected_mask, actual_mask[c,:,:]) assert_equal(expected_mask, actual_mask[:,c,:]) assert_equal(expected_mask, actual_mask[:,:,c]) k = k + 1 - + def test_selem_disk(self): self.strel_worker("disk-matlab-output.npz", selem.disk) def test_selem_diamond(self): self.strel_worker("diamond-matlab-output.npz", selem.diamond) - + def test_selem_ball(self): self.strel_worker_3d("disk-matlab-output.npz", selem.ball) def test_selem_octahedron(self): self.strel_worker_3d("diamond-matlab-output.npz", selem.octahedron) + + +if __name__ == '__main__': + np.testing.run_module_suite() diff --git a/skimage/segmentation/__init__.py b/skimage/segmentation/__init__.py index a0fab77a..c3aa1afc 100644 --- a/skimage/segmentation/__init__.py +++ b/skimage/segmentation/__init__.py @@ -5,3 +5,15 @@ from ._quickshift import quickshift from .boundaries import find_boundaries, visualize_boundaries, mark_boundaries from ._clear_border import clear_border from ._join import join_segmentations, relabel_from_one + + +__all__ = ['random_walker', + 'felzenszwalb', + 'slic', + 'quickshift', + 'find_boundaries', + 'visualize_boundaries', + 'mark_boundaries', + 'clear_border', + 'join_segmentations', + 'relabel_from_one'] diff --git a/skimage/transform/__init__.py b/skimage/transform/__init__.py index 92858010..859c7515 100644 --- a/skimage/transform/__init__.py +++ b/skimage/transform/__init__.py @@ -1,10 +1,10 @@ -from ._hough_transform import (hough_circle, - hough_line, - probabilistic_hough_line) -from .hough_transform import * -from .radon_transform import * -from .finite_radon_transform import * -from .integral import * +from ._hough_transform import (hough_circle, hough_line, + probabilistic_hough_line) +from .hough_transform import (hough, probabilistic_hough, hough_peaks, + hough_line_peaks) +from .radon_transform import radon, iradon +from .finite_radon_transform import frt2, ifrt2 +from .integral import integral_image, integrate from ._geometric import (warp, warp_coords, estimate_transform, SimilarityTransform, AffineTransform, ProjectiveTransform, PolynomialTransform, @@ -12,3 +12,34 @@ from ._geometric import (warp, warp_coords, estimate_transform, from ._warps import swirl, resize, rotate, rescale from .pyramids import (pyramid_reduce, pyramid_expand, pyramid_gaussian, pyramid_laplacian) + + +__all__ = ['hough_circle', + 'hough_line', + 'probabilistic_hough_line', + 'hough', + 'probabilistic_hough', + 'hough_peaks', + 'hough_line_peaks', + 'radon', + 'iradon', + 'frt2', + 'ifrt2', + 'integral_image', + 'integrate', + 'warp', + 'warp_coords', + 'estimate_transform', + 'SimilarityTransform', + 'AffineTransform', + 'ProjectiveTransform', + 'PolynomialTransform', + 'PiecewiseAffineTransform', + 'swirl', + 'resize', + 'rotate', + 'rescale', + 'pyramid_reduce', + 'pyramid_expand', + 'pyramid_gaussian', + 'pyramid_laplacian'] diff --git a/skimage/transform/finite_radon_transform.py b/skimage/transform/finite_radon_transform.py index c107546f..dd3bad33 100644 --- a/skimage/transform/finite_radon_transform.py +++ b/skimage/transform/finite_radon_transform.py @@ -4,7 +4,6 @@ """ __all__ = ["frt2", "ifrt2"] -__docformat__ = "restructuredtext en" import numpy as np from numpy import roll, newaxis diff --git a/skimage/transform/hough_transform.py b/skimage/transform/hough_transform.py index a3c010cd..15968fd8 100644 --- a/skimage/transform/hough_transform.py +++ b/skimage/transform/hough_transform.py @@ -1,5 +1,3 @@ -__all__ = ['hough_line_peaks'] - import numpy as np from scipy import ndimage from skimage import measure, morphology diff --git a/skimage/util/__init__.py b/skimage/util/__init__.py index 8daaa60d..7e41627b 100644 --- a/skimage/util/__init__.py +++ b/skimage/util/__init__.py @@ -1,2 +1,13 @@ -from .dtype import * -from .shape import * +from .dtype import (img_as_float, img_as_int, img_as_uint, img_as_ubyte, + img_as_bool, dtype_limits) +from .shape import view_as_blocks, view_as_windows + + +__all__ = ['img_as_float', + 'img_as_int', + 'img_as_uint', + 'img_as_ubyte', + 'img_as_bool', + 'dtype_limits', + 'view_as_blocks', + 'view_as_windows']