Comments (3)
luispedro
commented on June 3, 2024
Sorry, this seems strange: if mahotas imports OK when you run it on the shell, it seems that it should also work on from cellprofiler
Can you run:
import mahotas
mahotas.test()? This may require pytest to be available, so it may fail for that reason.
from mahotas.
bethac07
commented on June 3, 2024
I definitely agree that it's weird! A second 20.04 user has confirmed it though, so whatever the error is, it's reproducible across machines.
Thanks so much for taking a look at all!
From the shell:
ubuntu@ip-XXXXXXXXX:~$ python3
Python 3.8.2 (default, Jul 16 2020, 14:00:26)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import mahotas
>>> mahotas.test()
================================================================================================== test session starts ==================================================================================================
platform linux -- Python 3.8.2, pytest-6.0.1, py-1.9.0, pluggy-0.13.1
rootdir: /home/ubuntu
collected 307 items
.local/lib/python3.8/site-packages/mahotas/tests/test_bbox.py ....... [ 2%]
.local/lib/python3.8/site-packages/mahotas/tests/test_bwperim.py . [ 2%]
.local/lib/python3.8/site-packages/mahotas/tests/test_center_of_mass.py ..... [ 4%]
.local/lib/python3.8/site-packages/mahotas/tests/test_citation.py . [ 4%]
.local/lib/python3.8/site-packages/mahotas/tests/test_close_holes.py . [ 4%]
.local/lib/python3.8/site-packages/mahotas/tests/test_colors.py ... [ 5%]
.local/lib/python3.8/site-packages/mahotas/tests/test_convolve.py ......................... [ 14%]
.local/lib/python3.8/site-packages/mahotas/tests/test_demos.py . [ 14%]
.local/lib/python3.8/site-packages/mahotas/tests/test_dilate_erode.py ........... [ 17%]
.local/lib/python3.8/site-packages/mahotas/tests/test_distance.py ... [ 18%]
.local/lib/python3.8/site-packages/mahotas/tests/test_edge.py ....... [ 21%]
.local/lib/python3.8/site-packages/mahotas/tests/test_euler.py ... [ 22%]
.local/lib/python3.8/site-packages/mahotas/tests/test_features_shape.py .... [ 23%]
.local/lib/python3.8/site-packages/mahotas/tests/test_filters.py ... [ 24%]
.local/lib/python3.8/site-packages/mahotas/tests/test_find.py .. [ 25%]
.local/lib/python3.8/site-packages/mahotas/tests/test_freeimage.py ssssssss [ 27%]
.local/lib/python3.8/site-packages/mahotas/tests/test_gvoronoi.py .. [ 28%]
.local/lib/python3.8/site-packages/mahotas/tests/test_histogram.py ..... [ 29%]
.local/lib/python3.8/site-packages/mahotas/tests/test_hitmiss.py ... [ 30%]
.local/lib/python3.8/site-packages/mahotas/tests/test_imresize.py ... [ 31%]
.local/lib/python3.8/site-packages/mahotas/tests/test_internal.py ............................. [ 41%]
.local/lib/python3.8/site-packages/mahotas/tests/test_interpolate.py ............. [ 45%]
.local/lib/python3.8/site-packages/mahotas/tests/test_io.py .... [ 46%]
.local/lib/python3.8/site-packages/mahotas/tests/test_label.py ... [ 47%]
.local/lib/python3.8/site-packages/mahotas/tests/test_labeled.py ................... [ 54%]
.local/lib/python3.8/site-packages/mahotas/tests/test_lbp.py .......... [ 57%]
.local/lib/python3.8/site-packages/mahotas/tests/test_mahotas.py . [ 57%]
.local/lib/python3.8/site-packages/mahotas/tests/test_majority.py ...... [ 59%]
.local/lib/python3.8/site-packages/mahotas/tests/test_mean_filter.py . [ 59%]
.local/lib/python3.8/site-packages/mahotas/tests/test_median_filter.py .... [ 61%]
.local/lib/python3.8/site-packages/mahotas/tests/test_moments.py ......... [ 64%]
.local/lib/python3.8/site-packages/mahotas/tests/test_morph.py ............. [ 68%]
.local/lib/python3.8/site-packages/mahotas/tests/test_polygon.py ......... [ 71%]
.local/lib/python3.8/site-packages/mahotas/tests/test_segmentation.py . [ 71%]
.local/lib/python3.8/site-packages/mahotas/tests/test_stretch.py ......... [ 74%]
.local/lib/python3.8/site-packages/mahotas/tests/test_surf.py .............. [ 79%]
.local/lib/python3.8/site-packages/mahotas/tests/test_surf_regression.py .. [ 79%]
.local/lib/python3.8/site-packages/mahotas/tests/test_tas.py ..... [ 81%]
.local/lib/python3.8/site-packages/mahotas/tests/test_template_match.py . [ 81%]
.local/lib/python3.8/site-packages/mahotas/tests/test_texture.py .................... [ 88%]
.local/lib/python3.8/site-packages/mahotas/tests/test_thin.py ..... [ 89%]
.local/lib/python3.8/site-packages/mahotas/tests/test_thresholding.py .......... [ 93%]
.local/lib/python3.8/site-packages/mahotas/tests/test_watershed.py .................. [ 99%]
.local/lib/python3.8/site-packages/mahotas/tests/test_zernike.py ... [100%]
=================================================================================================== warnings summary ====================================================================================================
.local/lib/python3.8/site-packages/mahotas/tests/test_convolve.py::test_center_decenter
.local/lib/python3.8/site-packages/mahotas/tests/test_convolve.py::test_center_border
.local/lib/python3.8/site-packages/mahotas/tests/test_convolve.py::test_center_wavelet_iwavelet_decenter
/home/ubuntu/.local/lib/python3.8/site-packages/mahotas/convolve.py:479: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
nimage[position] = f
.local/lib/python3.8/site-packages/mahotas/tests/test_convolve.py::test_center_decenter
.local/lib/python3.8/site-packages/mahotas/tests/test_convolve.py::test_center_wavelet_iwavelet_decenter
/home/ubuntu/.local/lib/python3.8/site-packages/mahotas/convolve.py:510: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
return w[position]
-- Docs: https://docs.pytest.org/en/stable/warnings.html
====================================================================================== 299 passed, 8 skipped, 5 warnings in 14.20s ======================================================================================
<ExitCode.OK: 0>
from mahotas.
luispedro
commented on June 3, 2024
Thanks for the test outputs. I think from mahotas' POV, everything is working so I am closing here
from mahotas.
Related Issues (20)
- Proposing a PR to fix a few small typos
- "Input data has unexpected types" - Bug in mahotas.features.lbp.lbp HOT 1
- Publish wheels for python 3.9 HOT 3
- Error in using the Zernike moments. HOT 6
- Add support to release linux aarch64 wheels
- freeimage tests fail due to use of `tmpdir` HOT 1
- Latest version (1.4.12) is without a source distribution HOT 2
- make fill_polygon accept floats HOT 2
- Pip install error HOT 3
- Make dilate and erode accept floats HOT 5
- Python 3.11 wheels HOT 1
- Is it possible to *not* release the GIL? HOT 4
- RuntimeError: module compiled against API version 0x10 but this version of numpy is 0xf HOT 1
- Online documentation outdated HOT 2
- Mahotas.features.haralick takes too long to compute when distance increases is greater than 100.
- Texture Correlation Calculation HOT 1
- Segmentation fault: test_negative_values_haralick crashes Python on linux-aarch64 HOT 1
- Failure on pip install mahotas HOT 15
- How to return classification? After training the model HOT 2
- `std::random_shuffle` deprecated in C++14 and removed in C++17 HOT 4
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from mahotas.