<div dir="ltr"><div>I'm running into some issues after upgrading scikit-image, so I tried uninstalling and reinstalling, and it just doesn't seem to work.</div><div><br></div><div><br></div><div>When I try to import skimage.feature, I run into the following issue:</div><br><div><br></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><p style="font-family: Monaco; color: rgb(255, 127, 114); background-color: rgb(0, 0, 0);">---------------------------------------------------------------------------</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72">ImportError</span> Traceback (most recent call last)</p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);"><ipython-input-3-9ed3c50fda3e><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #d1d0ff"><module></span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">()</span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">----> 1</span><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> skimage <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> feature</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0); min-height: 17px;"><br></p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);">/usr/local/lib/python2.7/dist-packages/skimage/feature/__init__.py<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #d1d0ff"><module></span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">()</span></p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);"> 1<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span>from<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee">_canny </span>import<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> canny</span></p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);">----> 2<span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72"> </span>from<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee">_daisy </span>import<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> daisy</span></p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);"> 3<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span>from<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee">_hog </span>import<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> hog</span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 4</span> from .texture import (greycomatrix, greycoprops,</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 5</span> local_binary_pattern<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0); min-height: 17px;"><br></p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);">/usr/local/lib/python2.7/dist-packages/skimage/feature/_daisy.py<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #d1d0ff"><module></span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">()</span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 2</span> <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> scipy <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> sqrt<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> pi<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> arctan2<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> cos<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> sin<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> exp</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 3</span> <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> scipy<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span>ndimage <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> gaussian_filter</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">----> 4</span><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> <span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">..</span> <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> img_as_float<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> draw</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 5</span> <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> <span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">..</span>color <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> gray2rgb</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 6</span> <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> <span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">..</span>_shared<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span>utils <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> assert_nD</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0); min-height: 17px;"><br></p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);">/usr/local/lib/python2.7/dist-packages/skimage/draw/__init__.py<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #d1d0ff"><module></span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">()</span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">----> 1</span><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> <span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span>draw <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> circle<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> ellipse<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> set_color</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 2</span> <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> <span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span>draw3d <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> ellipsoid<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> ellipsoid_stats</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 3</span> from ._draw import (line, line_aa, polygon, ellipse_perimeter,</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 4</span> circle_perimeter<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span> circle_perimeter_aa<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">,</span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 5</span> _bezier_segment, bezier_curve)</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0); min-height: 17px;"><br></p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);">/usr/local/lib/python2.7/dist-packages/skimage/draw/draw.py<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #d1d0ff"><module></span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">()</span></p><p style="font-family: Monaco; color: rgb(255, 127, 114); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 1</span><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span># coding: utf-8</p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);"> 2<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span>import<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> numpy </span>as<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> np</span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">----> 3</span><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">from</span> <span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span>_draw <span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> _coords_inside_image</p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);"> 4<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span></p><p style="font-family: Monaco; color: rgb(173, 251, 100); background-color: rgb(0, 0, 0);"> 5<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0); min-height: 17px;"><br></p><p style="font-family: Monaco; color: rgb(209, 208, 255); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">/scratch/repo/_draw.pyx</span><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> in </span>init skimage.draw._draw (skimage/draw/_draw.c:23752)<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">()</span></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0); min-height: 17px;"><br></p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);">
</p><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72">ImportError</span>: No module named _shared.geometry</p></blockquote><div><br></div><div>Same thing happens with filters and filter</div><div><br></div><div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">---------------------------------------------------------------------------<br><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72">ImportError</span> Traceback (most recent call last)<br><ipython-input-9-6bd277fca327><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #d1d0ff"><module></span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">()<br></span><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">----> 1</span><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64">import</span> skimage<span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span>filters<br>/usr/local/lib/python2.7/dist-packages/skimage/filters/__init__.py<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> in </span><span style="font-variant-ligatures: no-common-ligatures; color: #d1d0ff"><module></span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">()<br></span><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 11</span> from .thresholding import (threshold_adaptive, threshold_otsu, threshold_yen,<br><span style="font-variant-ligatures: no-common-ligatures; color: #adfb64"> 12</span> threshold_isodata, threshold_li)<br>---> 13<span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72"> </span>from<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span>import<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> rank<br></span> 14<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span>from<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span><span style="font-variant-ligatures: no-common-ligatures; color: #a2d6ff">.</span><span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee">rank </span>import<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> median<br></span> 15<span style="font-variant-ligatures: no-common-ligatures; color: #eeeeee"> </span><br><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72">ImportError</span>: cannot import name rank</blockquote>
</div><div><br></div><div>Importing skimage.viewer gives me:</div><div><br></div><div><p style="font-family: Monaco; color: rgb(238, 238, 238); background-color: rgb(0, 0, 0);"><span style="font-variant-ligatures: no-common-ligatures; color: #ff7f72">ImportError</span>: cannot import name _coords_inside_image</p></div><div><br></div><div>Those are all that I have tried. skimage.utils works fine.</div><br><div>I'm running the numpy and scipy packages provided by Ubuntu, and have tried both installing scikit-image using the pip packages as well as downloading from github then installing pip.</div><div><br></div><div>Would be great if someone could shed some light on this.</div></div>