From eb4c5c9ee4baf11b613a6b6613410974a97d7092 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= Date: Mon, 14 Oct 2013 16:14:30 +0200 Subject: [PATCH 1/4] PEP8 --- doc/examples/plot_join_segmentations.py | 1 - doc/examples/plot_marching_cubes.py | 1 - skimage/__init__.py | 1 + skimage/data/__init__.py | 1 - skimage/exposure/exposure.py | 2 +- skimage/filter/__init__.py | 2 +- skimage/filter/_denoise.py | 2 +- skimage/filter/_rank_order.py | 12 ++++++------ skimage/filter/edges.py | 6 +++--- skimage/morphology/convex_hull.py | 2 +- skimage/segmentation/_join.py | 5 ++--- viewer_examples/plugins/watershed_demo.py | 1 + 12 files changed, 17 insertions(+), 19 deletions(-) diff --git a/doc/examples/plot_join_segmentations.py b/doc/examples/plot_join_segmentations.py index 625113e5..8ccc5038 100644 --- a/doc/examples/plot_join_segmentations.py +++ b/doc/examples/plot_join_segmentations.py @@ -60,4 +60,3 @@ for ax in axes: ax.axis('off') plt.subplots_adjust(hspace=0.01, wspace=0.01, top=1, bottom=0, left=0, right=1) plt.show() - diff --git a/doc/examples/plot_marching_cubes.py b/doc/examples/plot_marching_cubes.py index 36685434..5dad1680 100644 --- a/doc/examples/plot_marching_cubes.py +++ b/doc/examples/plot_marching_cubes.py @@ -22,7 +22,6 @@ voxel spacing is not equal for every spatial dimension, through use of the """ import numpy as np import matplotlib.pyplot as plt -from mpl_toolkits.mplot3d import Axes3D from mpl_toolkits.mplot3d.art3d import Poly3DCollection from skimage import measure diff --git a/skimage/__init__.py b/skimage/__init__.py index 53d31eae..c73a79b7 100644 --- a/skimage/__init__.py +++ b/skimage/__init__.py @@ -91,6 +91,7 @@ test_verbose.__doc__ = test.__doc__ class _Log(Warning): pass + class _FakeLog(object): def __init__(self, name): """ diff --git a/skimage/data/__init__.py b/skimage/data/__init__.py index cea2a9f5..ecd261f7 100644 --- a/skimage/data/__init__.py +++ b/skimage/data/__init__.py @@ -200,4 +200,3 @@ def coffee(): """ return load("coffee.png") - diff --git a/skimage/exposure/exposure.py b/skimage/exposure/exposure.py index 9c50ab7d..fd5d53dd 100644 --- a/skimage/exposure/exposure.py +++ b/skimage/exposure/exposure.py @@ -287,7 +287,7 @@ def adjust_log(image, gain=1, inv=False): inv : float If True, it performs inverse logarithmic correction, else correction will be logarithmic. Defaults to False. - + Returns ------- out : ndarray diff --git a/skimage/filter/__init__.py b/skimage/filter/__init__.py index 67088b20..0d1c33bb 100644 --- a/skimage/filter/__init__.py +++ b/skimage/filter/__init__.py @@ -3,7 +3,7 @@ from .ctmf import median_filter from ._gaussian import gaussian_filter from ._canny import canny from .edges import (sobel, hsobel, vsobel, scharr, hscharr, vscharr, prewitt, - hprewitt, vprewitt, roberts , roberts_positive_diagonal, + hprewitt, vprewitt, roberts, roberts_positive_diagonal, roberts_negative_diagonal) from ._denoise import denoise_tv_chambolle, tv_denoise from ._denoise_cy import denoise_bilateral, denoise_tv_bregman diff --git a/skimage/filter/_denoise.py b/skimage/filter/_denoise.py index ff89b78b..5a810336 100644 --- a/skimage/filter/_denoise.py +++ b/skimage/filter/_denoise.py @@ -250,7 +250,7 @@ def denoise_tv_chambolle(im, weight=50, eps=2.e-4, n_iter_max=200, out = np.zeros_like(im) for c in range(im.shape[2]): out[..., c] = _denoise_tv_chambolle_2d(im[..., c], weight, eps, - n_iter_max) + n_iter_max) else: out = _denoise_tv_chambolle_3d(im, weight, eps, n_iter_max) else: diff --git a/skimage/filter/_rank_order.py b/skimage/filter/_rank_order.py index f878702f..cdd992ff 100644 --- a/skimage/filter/_rank_order.py +++ b/skimage/filter/_rank_order.py @@ -8,7 +8,7 @@ Copyright (c) 2009-2011 Broad Institute All rights reserved. Original author: Lee Kamentstky """ -import numpy +import numpy as np def rank_order(image): @@ -47,14 +47,14 @@ def rank_order(image): (array([0, 1, 2, 1], dtype=uint32), array([-1. , 2.5, 3.1])) """ flat_image = image.ravel() - sort_order = flat_image.argsort().astype(numpy.uint32) + sort_order = flat_image.argsort().astype(np.uint32) flat_image = flat_image[sort_order] - sort_rank = numpy.zeros_like(sort_order) + sort_rank = np.zeros_like(sort_order) is_different = flat_image[:-1] != flat_image[1:] - numpy.cumsum(is_different, out=sort_rank[1:]) - original_values = numpy.zeros((sort_rank[-1] + 1,), image.dtype) + np.cumsum(is_different, out=sort_rank[1:]) + original_values = np.zeros((sort_rank[-1] + 1,), image.dtype) original_values[0] = flat_image[0] original_values[1:] = flat_image[1:][is_different] - int_image = numpy.zeros_like(sort_order) + int_image = np.zeros_like(sort_order) int_image[sort_order] = sort_rank return (int_image.reshape(image.shape), original_values) diff --git a/skimage/filter/edges.py b/skimage/filter/edges.py index 7a70f00b..764c7d34 100644 --- a/skimage/filter/edges.py +++ b/skimage/filter/edges.py @@ -31,8 +31,8 @@ HPREWITT_WEIGHTS = np.array([[ 1, 1, 1], [-1,-1,-1]]) / 3.0 VPREWITT_WEIGHTS = HPREWITT_WEIGHTS.T -ROBERTS_PD_WEIGHTS = np.array([[ 1, 0], - [ 0, -1]], dtype=np.double) +ROBERTS_PD_WEIGHTS = np.array([[1, 0], + [0, -1]], dtype=np.double) ROBERTS_ND_WEIGHTS = np.array([[0, 1], [-1, 0]], dtype=np.double) @@ -346,7 +346,7 @@ def roberts(image, mask=None): """Find the edge magnitude using Roberts' cross operator. Parameters - ---------- + ---------- image : 2-D array Image to process. mask : 2-D array, optional diff --git a/skimage/morphology/convex_hull.py b/skimage/morphology/convex_hull.py index 3d592dca..adc63607 100644 --- a/skimage/morphology/convex_hull.py +++ b/skimage/morphology/convex_hull.py @@ -44,7 +44,7 @@ def convex_hull_image(image): (-0.5, 0.5, 0, 0))): coords_corners[i * N:(i + 1) * N] = coords + [x_offset, y_offset] - # repeated coordinates can *sometimes* cause problems in + # repeated coordinates can *sometimes* cause problems in # scipy.spatial.Delaunay, so we remove them. coords = unique_rows(coords_corners) diff --git a/skimage/segmentation/_join.py b/skimage/segmentation/_join.py index 462bb18f..6095382d 100644 --- a/skimage/segmentation/_join.py +++ b/skimage/segmentation/_join.py @@ -94,7 +94,7 @@ def relabel_sequential(label_field, offset=1): Examples -------- >>> from skimage.segmentation import relabel_sequential - >>> label_field = array([1, 1, 5, 5, 8, 99, 42]) + >>> label_field = np.array([1, 1, 5, 5, 8, 99, 42]) >>> relab, fw, inv = relabel_sequential(label_field) >>> relab array([1, 1, 2, 2, 3, 5, 4]) @@ -117,7 +117,7 @@ def relabel_sequential(label_field, offset=1): labels = np.unique(label_field) labels0 = labels[labels != 0] m = labels.max() - if m == len(labels0): # nothing to do, already 1...n labels + if m == len(labels0): # nothing to do, already 1...n labels return label_field, labels, labels forward_map = np.zeros(m+1, int) forward_map[labels0] = np.arange(offset, offset + len(labels0) + 1) @@ -127,4 +127,3 @@ def relabel_sequential(label_field, offset=1): inverse_map[(offset - 1):] = labels relabeled = forward_map[label_field] return relabeled, forward_map, inverse_map - diff --git a/viewer_examples/plugins/watershed_demo.py b/viewer_examples/plugins/watershed_demo.py index 683e8a30..612ec6c9 100644 --- a/viewer_examples/plugins/watershed_demo.py +++ b/viewer_examples/plugins/watershed_demo.py @@ -7,6 +7,7 @@ from skimage.viewer import ImageViewer from skimage.viewer.widgets import history from skimage.viewer.plugins.labelplugin import LabelPainter + class OKCancelButtons(history.OKCancelButtons): def update_original_image(self): From 69bdfe0339416cc5063bbb17ba4d7380075a235a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= Date: Mon, 14 Oct 2013 16:22:29 +0200 Subject: [PATCH 2/4] PEP8 another one --- skimage/util/shape.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/skimage/util/shape.py b/skimage/util/shape.py index 5fe27a36..f91286c3 100644 --- a/skimage/util/shape.py +++ b/skimage/util/shape.py @@ -233,9 +233,7 @@ def view_as_windows(arr_in, window_shape, step=1): tuple(window_shape) arr_strides = np.array(arr_in.strides) - new_strides = np.concatenate( - (arr_strides * step, arr_strides) - ) + new_strides = np.concatenate((arr_strides * step, arr_strides)) arr_out = as_strided(arr_in, shape=new_shape, strides=new_strides) From 65f73ee17123b13488c97a17cba661f394f284c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= Date: Mon, 14 Oct 2013 16:25:29 +0200 Subject: [PATCH 3/4] DOC: fix syntax error --- skimage/util/unique.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/skimage/util/unique.py b/skimage/util/unique.py index 16a83f6b..635f6e89 100644 --- a/skimage/util/unique.py +++ b/skimage/util/unique.py @@ -30,9 +30,9 @@ def unique_rows(ar): Examples -------- >>> ar = np.array([[1, 0, 1], - [0, 1, 0], - [1, 0, 1]], np.uint8) - >>> aru = unique_rows(ar) + ... [0, 1, 0], + ... [1, 0, 1]], np.uint8) + >>> unique_rows(ar) array([[0, 1, 0], [1, 0, 1]], dtype=uint8) """ From ca6ecf08e6bdc5b02f186e6efbf0f04d88c8564a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= Date: Mon, 14 Oct 2013 16:28:53 +0200 Subject: [PATCH 4/4] DOCTEST: fix --- skimage/measure/_marching_cubes.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/skimage/measure/_marching_cubes.py b/skimage/measure/_marching_cubes.py index 37dab1c0..41bafd90 100644 --- a/skimage/measure/_marching_cubes.py +++ b/skimage/measure/_marching_cubes.py @@ -77,9 +77,9 @@ def marching_cubes(volume, level, spacing=(1., 1., 1.)): >>> from mayavi import mlab >>> verts, tris = marching_cubes(myvolume, 0.0, (1., 1., 2.)) >>> mlab.triangular_mesh([vert[0] for vert in verts], - [vert[1] for vert in verts], - [vert[2] for vert in verts], - tris) + ... [vert[1] for vert in verts], + ... [vert[2] for vert in verts], + ... tris) >>> mlab.show() References