Mailman 3 June 2013 - scikit-image

How to get full size image which is transformed by warp function
by Yongda Chen June 19, 2013

June 19, 2013

I am trying to do geometric transformation with warp in scikit-image, but I cannot get the full size transformed image which has different image size to original image. Even after setting up output_shape parameter, it still lost part of image which is transformed to negative coordinates. My question is how to get full size transformed image when doing affine transform, projective transform with warp function? Following is the example code I am working on import matplotlib.pyplot as plt import skimage.transform import * import skimage import data import numpy as np checkboard = data.checkboard() tform = AffineTransform(rotation = np.pi/6) checkborad_transformed = warp(checkboard, tform, output_shape=(400,400)) fig = plt.figure() plt.imshow(checkboard_transformed, cmap = plt.cm.gray) Thanks

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Re: Heap and Eikonal eqn
by Stéfan van der Walt June 19, 2013

June 19, 2013

Hi Chintak On Wed, Jun 19, 2013 at 12:50 PM, Chintak Sheth <chintaksheth(a)gmail.com> wrote: > How should I implement a heap structure in Python? In-built heapq is not > flexible enough. namedtuple seems to be an alternative. Although how should > I add the pointer support for next and prev? I need 2 ints and 1 float for > data. Any thoughts ? We already have some heap structures in skimage--have you had a look at those? Stéfan

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Heap and Eikonal eqn
by Chintak Sheth June 19, 2013

June 19, 2013

Hi guys, I'm implementing image inpainting for my GSoC project. The proposal is scikit-image: Image Inpainting for Restoration<http://www.google-melange.com/gsoc/proposal/review/google/gsoc2013/chintak/1>. I am first wanting to implement it using Fast Marching Method (FMM). For this I need to solve the Eikonal equation and also implement a heap structure. I checked StackOverflow. ODE can be solved using scipy.integrate.odeint. Any other approaches? How should I implement a heap structure in Python? In-built heapq is not flexible enough. namedtuple seems to be an alternative. Although how should I add the pointer support for next and prev? I need 2 ints and 1 float for data. Any thoughts ? Thanks, Chintak

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Re: Feature Detectors and Descriptors in scikit-image
by Anders Boesen Lindbo Larsen June 18, 2013

June 18, 2013

On Friday, June 7, 2013 3:32:25 PM UTC+2, Ankit Agrawal wrote: > Hi all, > > I have some queries about feature Detectors and Descriptors that I > have to implement as a part of my GSoC project<https://github.com/scikit-image/scikit-image/wiki/GSoC-2013-Ankit-Agrawal-I…> > . > > Practically, a descriptor is more useful around feature points that > are more distinctive in nature and hence will then produce a greater > accuracy for the tasks where descriptors are used - Correspondence matching > in two image frames for Stereo, Image Alignment, Object Recognition and > Tracking etc. On the same note, the feature descriptors in OpenCV take > input argument as a Keypoint object which is mainly a vector of > keypoints(extracted using a feature detector). OpenCV thus has classes for > Keypoint<http://docs.opencv.org/modules/features2d/doc/common_interfaces_of_feature_…>, > Feature Detector<http://docs.opencv.org/modules/features2d/doc/common_interfaces_of_feature_…>, > DescriptorExtractor<http://docs.opencv.org/modules/features2d/doc/common_interfaces_of_descript…>etc. This enables the flexibility of using any FeatureDescriptor an > keypoints extracted using any FeatureDetector. > > I took a look at the implementation<https://github.com/scikit-image/scikit-image/blob/master/skimage/feature/_d…>of Daisy feature descriptor in skimage and noticed that it finds > descriptors around points that are spread uniformly with density based on > step argument as the input. For this I checked its paper<http://www.ele.puc-rio.br/~visao/Topicos/Tola%202010%20Efficient%20Dense%20…>(Pg > 3, section 3) and it said it can be used around feature-points as well as > non feature-points. Almost all the Feature Descriptors(that I know of) > including the ones that I am going to implement are calculated about > keypoints. Because of the above reasons, I think an option should be > provided in the functions of feature detectors to return the output as a > vector containing location of feature-points. I would like to know the > views/suggestions of community members experienced in this part of Computer > Vision on this point and to suggest the best possible data-flow between > functions of Feature Detectors and Feature Descriptors. Thank you. > Feature description is a messy business - there is little consensus in the literature and in the implementations available! For an overview of the feature extraction pipeline, I recommend reading until and including section 2.3.2 in http://www.vlfeat.org/~vedaldi/assets/pubs/vedaldi10knowing.pdf Here, different types of interest points are described (disk, oriented disk, ellipse, etc.). Moreover, the feature description pipeline is divided into 3 steps (detection, canonization, description). This means that for each interest point type, you will have to make a canonization method that can bring the underlying image patch can to a form suitable for the description algorithm, e.g. a 64x64 image patch. I recommend this approach because it is more flexible than if the detection and description code is combined as it is done in e.g. SIFT. However, I should mention that the approach is not ideal for 2 reasons: - It requires more computations. In SIFT, the scale-space pyramid generated in the detection step can be reused for description. - The canonization step introduces noise because we typically will have to warp the image. I hope some of it made sense. Returning to your question on the data flow between detectors and descriptors: I would recommend making the detectors return a list of interest points. This list of interest points can then be given to a descriptor function. It is up to the descriptor to canonize the interest points if needed. BTW, some time ago I wrote some code to canonize an affine interest point (ellipse): https://github.com/andersbll/jetdesc/blob/master/util.py#L50 Feel free to copy-paste whatever you might find useful in that repository. :) Cheers, Anders

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Re: source compilation error: undefined references
by Evan June 13, 2013

June 13, 2013

On Wednesday, June 12, 2013 2:52:10 PM UTC+2, Stefan van der Walt wrote: > > Hi Evan > > On Wed, Jun 12, 2013 at 2:33 PM, Evan <evan...(a)gmail.com <javascript:>> > wrote: > > On the command line, I seem to avoid the errors by adding the math > library, > > -lm, at the end: > > If you modify the setup file as shown here: > > http://docs.cython.org/src/tutorial/external.html#dynamic-linking > > Does that help? If so, a pull request would be welcome. I'm not sure > why the error occurs: I don't see the same problem on my Ubuntu > machine. > > Stéfan > Thanks for your reply. Can you coach me a little on the modification I need to make. I assume the file to edit is: ... /scikit-image-0.8.2/skimage/_shared/setup.py But so far I don't see how to resolve what's needed from http://docs.cython.org/src/tutorial/external.html#dynamic-linking into the setup file. Thanks, Evan

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Re: source compilation error: undefined references
by Josh Warner June 13, 2013

June 13, 2013

Did you use ATLAS/LAPACK installed from your distro's repo, or a personally compiled version? I'm wondering if something in your system environment might not quite be right, especially suspicious about LD_LIBRARY_PATH. On Wednesday, June 12, 2013 7:33:22 AM UTC-5, Evan wrote: > > Hi, I get the below compilation error when compiling from source on a > Linux system. > > Linux marula 2.6.39.4-5.1-server #1 SMP Wed Jan 4 15:15:54 UTC 2012 x86_64 > x86_64 x86_64 GNU/Linux > > @marula scikit-image-0.8.2]$ python setup.py build > non-existing path in 'skimage/_shared': 'tests' > running build > running config_cc > ... > ... > build/temp.linux-x86_64-2.7/skimage/_shared/interpolation.o: In function > `__pyx_f_7skimage_7_shared_13interpolation_bilinear_interpolation': > /opt/python2.7/scikit/scikit-image-0.8.2/skimage/_shared/interpolation.c:559: > undefined reference to `floor' > /opt/python2.7/scikit/scikit-image-0.8.2/skimage/_shared/interpolation.c:568: > undefined reference to `floor' > /opt/python2.7/scikit/scikit-image-0.8.2/skimage/_shared/interpolation.c:577: > undefined reference to `ceil' > /opt/python2.7/scikit/scikit-image-0.8.2/skimage/_shared/interpolation.c:586: > undefined reference to `ceil' > collect2: ld returned 1 exit status > error: Command "gcc -pthread -shared -Wl,--as-needed -Wl,--no-undefined > -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags > build/temp.linux-x86_64-2.7/skimage/_shared/interpolation.o -L/usr/lib64 > -lpython2.7 -o build/lib.linux-x86_64-2.7/skimage/_shared/interpolation.so" > failed with exit status 1 > > On the command line, I seem to avoid the errors by adding the math > library, -lm, at the end: > @marula scikit-image-0.8.2]$ gcc -pthread -shared -Wl,--as-needed > -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id > -Wl,--enable-new-dtags > build/temp.linux-x86_64-2.7/skimage/_shared/interpolation.o -L/usr/lib64 > -lpython2.7 -o build/lib.linux-x86_64-2.7/skimage/_shared/interpolation.so > -lm > @marula scikit-image-0.8.2]$ > > However, i don't know how to introduce this flag into the overall > compilation process. > > I'd be grateful for any help, thanks in advance. > > Evan > > >

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Qhull error
by Juan Nunez-Iglesias June 13, 2013

June 13, 2013

Hi all. I'm getting the below error when computing regionprops(..., ['Solidity']). Does anyone know what's going on? At first I thought maybe it was passing a singleton array or something, but this array looks like a reasonable thing to compute a convex hull on, no? If I'm not being totally stupid (which is a big if), perhaps we should add a try/except around the convex hull calculation and return a non-value, e.g. -1, when the calculation fails? In [49]: test_im = array([[ 0., 0., 0., 0., 1., 0., 0.], [ 0., 0., 1., 1., 1., 1., 1.], [ 1., 1., 1., 0., 0., 0., 0.]], np.int) In [50]: test_im Out[50]: array([[0, 0, 0, 0, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1], [1, 1, 1, 0, 0, 0, 0]]) In [51]: measure.regionprops(test_im.astype(int), ['Solidity']) QH6228 Qhull internal error (qh_findbestlower): all neighbors of facet 8 are flipped or upper Delaunay. Please report this error to qhull_bug(a)qhull.org with the input and all of the output. ERRONEOUS FACET: - f8 - flags: bottom simplicial upperDelaunay - normal: -0.8366 -0.5167 0.182 - offset: 1.254902 - center: 0.7380952380952381 2.30952380952381 3.054054054054054 - vertices: p30(v6) p56(v3) p28(v0) - neighboring facets: f3 f23 f22 While executing: | qhull d Qz Qbb Qt Options selected for Qhull 2010.1 2010/01/14: run-id 1680623163 delaunay Qz-infinity-point Qbbound-last Qtriangulate _pre-merge _zero-centrum Pgood _max-width 7 Error-roundoff 9.7e-15 _one-merge 6.8e-14 _near-inside 3.4e-13 Visible-distance 1.9e-14 U-coplanar-distance 1.9e-14 Width-outside 3.9e-14 _wide-facet 1.2e-13 Last point added to hull was p33. Last merge was #1. At error exit: Delaunay triangulation by the convex hull of 57 points in 3-d: Number of input sites and at-infinity: 10 Number of nearly incident points: 10 Number of Delaunay regions: 0 Number of non-simplicial Delaunay regions: 1 Statistics for: | qhull d Qz Qbb Qt Number of points processed: 10 Number of hyperplanes created: 27 Number of facets in hull: 15 Number of distance tests for qhull: 512 Number of distance tests for merging: 127 Number of distance tests for checking: 0 Number of merged facets: 1 --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) <ipython-input-51-efe47406d455> in <module>() ----> 1 measure.regionprops(test_im.astype(int), ['Solidity']) /Users/nuneziglesiasj/venv/husc/lib/python2.7/site-packages/scikit_image-0.9dev-py2.7-macosx-10.5-x86_64.egg/skimage/measure/_regionprops.pyc in regionprops(label_image, properties, intensity_image) 363 if 'Solidity' in properties: 364 if _convex_image is None: --> 365 _convex_image = convex_hull_image(array) 366 obj_props['Solidity'] = m[0, 0] / np.sum(_convex_image) 367 /Users/nuneziglesiasj/venv/husc/lib/python2.7/site-packages/scikit_image-0.9dev-py2.7-macosx-10.5-x86_64.egg/skimage/morphology/convex_hull.pyc in convex_hull_image(image) 52 53 # Find the convex hull ---> 54 chull = Delaunay(coords).convex_hull 55 v = coords[np.unique(chull)] 56 /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/scipy/spatial/qhull.so in scipy.spatial.qhull.Delaunay.__init__ (scipy/spatial/qhull.c:4109)() /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/scipy/spatial/qhull.so in scipy.spatial.qhull._construct_delaunay (scipy/spatial/qhull.c:1314)() RuntimeError: Qhull error > /Users/nuneziglesiasj/Data/images-work/qhull.pyx(172)scipy.spatial.qhull._construct_delaunay (scipy/spatial/qhull.c:1314)()

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Re: failing tests of 0.8.2 with python3.2 and numpy 1.7.1
by Josh Warner June 13, 2013

June 13, 2013

The first three are inplace division casting errors supposedly fixed two years ago, according to the 4th and 5th posts in https://github.com/numpy/numpy/pull/99. Are you sure you're using NumPy 1.7.1, not something older like 1.5.1? An older version might explain the other error as well (harder to pin down without the old/new shape tuples). What does `import numpy; numpy.__version__` return using the same python you tried to build with? On Wednesday, June 12, 2013 3:44:54 AM UTC-5, Stefan van der Walt wrote: > > Does anyone have a moment to look over these? > > ---------- Forwarded message ---------- > From: Yaroslav Halchenko > Date: Tue, Jun 11, 2013 at 5:09 AM > Subject: failing tests of 0.8.2 with python3.2 and numpy 1.7.1 > > any of those look familiar? > > ====================================================================== > ERROR: Test a scalar uint8 image > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest > self.test(*self.arg) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/tests/test_exposure.py", > > line 83, in test_adapthist_scalar > adapted = exposure.equalize_adapthist(img, clip_limit=0.02) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", > > line 82, in equalize_adapthist > out = _clahe(*args) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", > > line 142, in _clahe > aLUT /= bin_size > TypeError: ufunc 'true_divide' output (typecode 'd') could not be > coerced to provided output parameter (typecode 'l') according to the > casting rule ''same_kind'' > > ====================================================================== > ERROR: Test a grayscale float image > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest > self.test(*self.arg) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/tests/test_exposure.py", > > line 103, in test_adapthist_grayscale > nbins=128) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", > > line 74, in equalize_adapthist > new_l = _clahe(*args).astype(float) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", > > line 142, in _clahe > aLUT /= bin_size > TypeError: ufunc 'true_divide' output (typecode 'd') could not be > coerced to provided output parameter (typecode 'l') according to the > casting rule ''same_kind'' > > ====================================================================== > ERROR: Test an RGB color uint16 image > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest > self.test(*self.arg) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/tests/test_exposure.py", > > line 115, in test_adapthist_color > adapted = exposure.equalize_adapthist(img, clip_limit=0.01) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", > > line 74, in equalize_adapthist > new_l = _clahe(*args).astype(float) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", > > line 142, in _clahe > aLUT /= bin_size > TypeError: ufunc 'true_divide' output (typecode 'd') could not be > coerced to provided output parameter (typecode 'l') according to the > casting rule ''same_kind'' > > ====================================================================== > ERROR: test_spath.test_basic > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest > self.test(*self.arg) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/tests/test_spath.py", > > line 11, in test_basic > path, cost = spath.shortest_path(x) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/spath.py", > > line 48, in shortest_path > offsets = np.reshape(offset_indices, (arr.ndim, offset_size), > order='F').T > File "/usr/local/lib/python3.2/dist-packages/numpy/core/fromnumeric.py", > line 172, in reshape > return reshape(newshape, order=order) > ValueError: total size of new array must be unchanged > > ====================================================================== > ERROR: test_spath.test_reach > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest > self.test(*self.arg) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/tests/test_spath.py", > > line 20, in test_reach > path, cost = spath.shortest_path(x, reach=2) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/spath.py", > > line 48, in shortest_path > offsets = np.reshape(offset_indices, (arr.ndim, offset_size), > order='F').T > File "/usr/local/lib/python3.2/dist-packages/numpy/core/fromnumeric.py", > line 172, in reshape > return reshape(newshape, order=order) > ValueError: total size of new array must be unchanged > > ====================================================================== > ERROR: test_spath.test_non_square > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest > self.test(*self.arg) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/tests/test_spath.py", > > line 30, in test_non_square > path, cost = spath.shortest_path(x, reach=2) > File > "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/spath.py", > > line 48, in shortest_path > offsets = np.reshape(offset_indices, (arr.ndim, offset_size), > order='F').T > File "/usr/local/lib/python3.2/dist-packages/numpy/core/fromnumeric.py", > line 172, in reshape > return reshape(newshape, order=order) > ValueError: total size of new array must be unchanged > > ---------------------------------------------------------------------- > Ran 576 tests in 70.458s > > -- > Yaroslav O. Halchenko, Ph.D. > http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org > Senior Research Associate, Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 > WWW: http://www.linkedin.com/in/yarik >

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Re: source compilation error: undefined references
by Stéfan van der Walt June 12, 2013

June 12, 2013

Hi Evan On Wed, Jun 12, 2013 at 2:33 PM, Evan <evanmason(a)gmail.com> wrote: > On the command line, I seem to avoid the errors by adding the math library, > -lm, at the end: If you modify the setup file as shown here: http://docs.cython.org/src/tutorial/external.html#dynamic-linking Does that help? If so, a pull request would be welcome. I'm not sure why the error occurs: I don't see the same problem on my Ubuntu machine. Stéfan

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Fwd: failing tests of 0.8.2 with python3.2 and numpy 1.7.1
by Stéfan van der Walt June 12, 2013

June 12, 2013

Does anyone have a moment to look over these? ---------- Forwarded message ---------- From: Yaroslav Halchenko Date: Tue, Jun 11, 2013 at 5:09 AM Subject: failing tests of 0.8.2 with python3.2 and numpy 1.7.1 any of those look familiar? ====================================================================== ERROR: Test a scalar uint8 image ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/tests/test_exposure.py", line 83, in test_adapthist_scalar adapted = exposure.equalize_adapthist(img, clip_limit=0.02) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", line 82, in equalize_adapthist out = _clahe(*args) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", line 142, in _clahe aLUT /= bin_size TypeError: ufunc 'true_divide' output (typecode 'd') could not be coerced to provided output parameter (typecode 'l') according to the casting rule ''same_kind'' ====================================================================== ERROR: Test a grayscale float image ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/tests/test_exposure.py", line 103, in test_adapthist_grayscale nbins=128) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", line 74, in equalize_adapthist new_l = _clahe(*args).astype(float) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", line 142, in _clahe aLUT /= bin_size TypeError: ufunc 'true_divide' output (typecode 'd') could not be coerced to provided output parameter (typecode 'l') according to the casting rule ''same_kind'' ====================================================================== ERROR: Test an RGB color uint16 image ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/tests/test_exposure.py", line 115, in test_adapthist_color adapted = exposure.equalize_adapthist(img, clip_limit=0.01) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", line 74, in equalize_adapthist new_l = _clahe(*args).astype(float) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/exposure/_adapthist.py", line 142, in _clahe aLUT /= bin_size TypeError: ufunc 'true_divide' output (typecode 'd') could not be coerced to provided output parameter (typecode 'l') according to the casting rule ''same_kind'' ====================================================================== ERROR: test_spath.test_basic ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/tests/test_spath.py", line 11, in test_basic path, cost = spath.shortest_path(x) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/spath.py", line 48, in shortest_path offsets = np.reshape(offset_indices, (arr.ndim, offset_size), order='F').T File "/usr/local/lib/python3.2/dist-packages/numpy/core/fromnumeric.py", line 172, in reshape return reshape(newshape, order=order) ValueError: total size of new array must be unchanged ====================================================================== ERROR: test_spath.test_reach ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/tests/test_spath.py", line 20, in test_reach path, cost = spath.shortest_path(x, reach=2) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/spath.py", line 48, in shortest_path offsets = np.reshape(offset_indices, (arr.ndim, offset_size), order='F').T File "/usr/local/lib/python3.2/dist-packages/numpy/core/fromnumeric.py", line 172, in reshape return reshape(newshape, order=order) ValueError: total size of new array must be unchanged ====================================================================== ERROR: test_spath.test_non_square ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/tests/test_spath.py", line 30, in test_non_square path, cost = spath.shortest_path(x, reach=2) File "/home/yoh/deb/gits/build-area/skimage-0.8.2/debian/tmp/usr/lib/python3/dist-packages/skimage/graph/spath.py", line 48, in shortest_path offsets = np.reshape(offset_indices, (arr.ndim, offset_size), order='F').T File "/usr/local/lib/python3.2/dist-packages/numpy/core/fromnumeric.py", line 172, in reshape return reshape(newshape, order=order) ValueError: total size of new array must be unchanged ---------------------------------------------------------------------- Ran 576 tests in 70.458s -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik

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