Scikit-image: Scikit-image appears to be incompatible with numpy==0.16.0
Description
When installing numpy==0.16.0 and scikit-image==0.14.1 into the same environment, there appears to be an incompatibility that prevents scikit-image from importing successfully.
mattbΒ ξ°Β ~Β ξ°Β conda create -n deleteme python=3 -y
[...]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate deleteme
#
# To deactivate an active environment, use:
# > source deactivate
#
Β mattbΒ ξ°Β ~Β ξ°Β . activate deleteme
Β mattbΒ ξ°Β (e)Β deletemeΒ ξ°Β ~Β ξ°Β pip install scikit-image==
Looking in indexes: https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/simple, https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-snapshot-local/simple
Collecting scikit-image==
Could not find a version that satisfies the requirement scikit-image== (from versions: 0.7.2, 0.8.0, 0.8.1, 0.8.2, 0.9.0, 0.9.1, 0.9.3, 0.10.0, 0.10.1, 0.11.2, 0.11.3, 0.12.0, 0.12.1, 0.12.2, 0.12.3, 0.13.0, 0.13.1, 0.14.0, 0.14.1)
No matching distribution found for scikit-image==
Β mattbΒ ξ°Β (e)Β deletemeΒ ξ°Β ~Β ξ°Β 1Β ξ°Β pip install numpy
Looking in indexes: https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/simple, https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-snapshot-local/simple
Collecting numpy
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/3d/10/62224c551acfd3a3583ad16d1e0f1c9e9c333e74479dc51977c31836119c/numpy-1.16.0-cp37-cp37m-manylinux1_x86_64.whl (17.3MB)
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Installing collected packages: numpy
Successfully installed numpy-1.16.0
Β mattbΒ ξ°Β (e)Β deletemeΒ ξ°Β ~Β ξ°Β pip install scikit-image
Looking in indexes: https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/simple, https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-snapshot-local/simple
Collecting scikit-image
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/bc/b3/d294429adcc4aff0372208494f0f0625f1112428e56070e47bf2cd055579/scikit_image-0.14.1-cp37-cp37m-manylinux1_x86_64.whl (25.3MB)
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Collecting pillow>=4.3.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/ae/2a/0a0ab2833e5270664fb5fae590717f867ac6319b124160c09f1d3291de28/Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0MB)
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Collecting scipy>=0.17.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/80/39/066ecde98f373430bf7a39a02d91c7075b01ef4fc928456e8e31577342d6/scipy-1.2.0-cp37-cp37m-manylinux1_x86_64.whl (26.6MB)
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Collecting six>=1.10.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting PyWavelets>=0.4.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/eb/38/210cf3c704be7f2706ea1397fbe2eeae4f88d791175918455daa65043b21/PyWavelets-1.0.1-cp37-cp37m-manylinux1_x86_64.whl (4.4MB)
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Collecting networkx>=1.8 (from scikit-image)
Collecting cloudpickle>=0.2.1 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/fc/87/7b7ef3038b4783911e3fdecb5c566e3a817ce3e890e164fc174c088edb1e/cloudpickle-0.6.1-py2.py3-none-any.whl
Collecting matplotlib>=2.0.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/e7/f9/5377596cb1c035c102396f5934237a046f80da69974026f90bee5db8b7ba/matplotlib-3.0.2-cp37-cp37m-manylinux1_x86_64.whl (12.9MB)
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Collecting dask[array]>=0.9.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/b4/e5/6407c2349622699eab0881e6bc6e978b8da67872a105e5e20b72ff190c65/dask-1.0.0-py2.py3-none-any.whl (685kB)
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Requirement already satisfied: numpy>=1.8.2 in ./programs/anaconda3/envs/deleteme/lib/python3.7/site-packages (from scipy>=0.17.0->scikit-image) (1.16.0)
Collecting decorator>=4.3.0 (from networkx>=1.8->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib>=2.0.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl (61kB)
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Collecting python-dateutil>=2.1 (from matplotlib>=2.0.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl (225kB)
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Collecting kiwisolver>=1.0.1 (from matplotlib>=2.0.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/5c/7e/d6cae2f241ba474a2665f24b480bf4e247036d63939dda2bbc4d2ee5069d/kiwisolver-1.0.1-cp37-cp37m-manylinux1_x86_64.whl (89kB)
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Collecting cycler>=0.10 (from matplotlib>=2.0.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting toolz>=0.7.3; extra == "array" (from dask[array]>=0.9.0->scikit-image)
Requirement already satisfied: setuptools in ./programs/anaconda3/envs/deleteme/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=2.0.0->scikit-image) (40.6.3)
Installing collected packages: pillow, scipy, six, PyWavelets, decorator, networkx, cloudpickle, pyparsing, python-dateutil, kiwisolver, cycler, matplotlib, toolz, dask, scikit-image
Successfully installed PyWavelets-1.0.1 cloudpickle-0.6.1 cycler-0.10.0 dask-1.0.0 decorator-4.3.0 kiwisolver-1.0.1 matplotlib-3.0.2 networkx-2.2 pillow-5.4.1 pyparsing-2.3.1 python-dateutil-2.7.5 scikit-image-0.14.1 scipy-1.2.0 six-1.12.0 toolz-0.9.0
Β mattbΒ ξ°Β (e)Β deletemeΒ ξ°Β ~Β ξ°Β python -c "import skimage"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/mattb/programs/anaconda3/envs/deleteme/lib/python3.7/site-packages/skimage/__init__.py", line 167, in <module>
from .util.dtype import (img_as_float32,
File "/home/mattb/programs/anaconda3/envs/deleteme/lib/python3.7/site-packages/skimage/util/__init__.py", line 8, in <module>
from .arraycrop import crop
File "/home/mattb/programs/anaconda3/envs/deleteme/lib/python3.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name '_validate_lengths' from 'numpy.lib.arraypad' (/home/mattb/programs/anaconda3/envs/deleteme/lib/python3.7/site-packages/numpy/lib/arraypad.py)
Way to reproduce
- [X] Code example
- [ ] Relevant images (if any)
- [X] Operating system and version - Ubuntu 16.04
- [X] Python version - 3.7.2
- [ ] scikit-image version (run
skimage.__version__) 0.14.1
AetherUnbound
All 34 comments
This also occurs just by installing scikit-image alone:
Β mattbΒ ξ°Β ~Β ξ°Β conda create -n deleteme python=3 -y
Solving environment: done
## Package Plan ##
environment location: /home/mattb/programs/anaconda3/envs/deleteme
added / updated specs:
- python=3
The following NEW packages will be INSTALLED:
ca-certificates: 2018.03.07-0
certifi: 2018.11.29-py37_0
libedit: 3.1.20170329-h6b74fdf_2
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 8.2.0-hdf63c60_1
libstdcxx-ng: 8.2.0-hdf63c60_1
ncurses: 6.1-he6710b0_1
openssl: 1.1.1a-h7b6447c_0
pip: 18.1-py37_0
python: 3.7.2-h0371630_0
readline: 7.0-h7b6447c_5
setuptools: 40.6.3-py37_0
sqlite: 3.26.0-h7b6447c_0
tk: 8.6.8-hbc83047_0
wheel: 0.32.3-py37_0
xz: 5.2.4-h14c3975_4
zlib: 1.2.11-h7b6447c_3
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate deleteme
#
# To deactivate an active environment, use
#
# $ conda deactivate
Β mattbΒ ξ°Β ~Β ξ°Β . activate deleteme
Β mattbΒ ξ°Β (e)Β deletemeΒ ξ°Β ~Β ξ°Β pip install scikit-image
Looking in indexes: https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/simple, https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-snapshot-local/simple
Collecting scikit-image
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/bc/b3/d294429adcc4aff0372208494f0f0625f1112428e56070e47bf2cd055579/scikit_image-0.14.1-cp37-cp37m-manylinux1_x86_64.whl (25.3MB)
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Collecting scipy>=0.17.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/80/39/066ecde98f373430bf7a39a02d91c7075b01ef4fc928456e8e31577342d6/scipy-1.2.0-cp37-cp37m-manylinux1_x86_64.whl (26.6MB)
100% |ββββββββββββββββββββββββββββββββ| 26.6MB 1.8MB/s
Collecting six>=1.10.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting networkx>=1.8 (from scikit-image)
Collecting PyWavelets>=0.4.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/eb/38/210cf3c704be7f2706ea1397fbe2eeae4f88d791175918455daa65043b21/PyWavelets-1.0.1-cp37-cp37m-manylinux1_x86_64.whl (4.4MB)
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Collecting dask[array]>=0.9.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/b4/e5/6407c2349622699eab0881e6bc6e978b8da67872a105e5e20b72ff190c65/dask-1.0.0-py2.py3-none-any.whl (685kB)
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Collecting matplotlib>=2.0.0 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/e7/f9/5377596cb1c035c102396f5934237a046f80da69974026f90bee5db8b7ba/matplotlib-3.0.2-cp37-cp37m-manylinux1_x86_64.whl (12.9MB)
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Collecting pillow>=4.3.0 (from scikit-image)
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Collecting cloudpickle>=0.2.1 (from scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/fc/87/7b7ef3038b4783911e3fdecb5c566e3a817ce3e890e164fc174c088edb1e/cloudpickle-0.6.1-py2.py3-none-any.whl
Collecting numpy>=1.8.2 (from scipy>=0.17.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/3d/10/62224c551acfd3a3583ad16d1e0f1c9e9c333e74479dc51977c31836119c/numpy-1.16.0-cp37-cp37m-manylinux1_x86_64.whl (17.3MB)
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Collecting decorator>=4.3.0 (from networkx>=1.8->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting toolz>=0.7.3; extra == "array" (from dask[array]>=0.9.0->scikit-image)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib>=2.0.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl (61kB)
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Collecting python-dateutil>=2.1 (from matplotlib>=2.0.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl (225kB)
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Collecting cycler>=0.10 (from matplotlib>=2.0.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib>=2.0.0->scikit-image)
Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/5c/7e/d6cae2f241ba474a2665f24b480bf4e247036d63939dda2bbc4d2ee5069d/kiwisolver-1.0.1-cp37-cp37m-manylinux1_x86_64.whl (89kB)
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Requirement already satisfied: setuptools in ./programs/anaconda3/envs/deleteme/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=2.0.0->scikit-image) (40.6.3)
Installing collected packages: numpy, scipy, six, decorator, networkx, PyWavelets, toolz, dask, pyparsing, python-dateutil, cycler, kiwisolver, matplotlib, pillow, cloudpickle, scikit-image
Successfully installed PyWavelets-1.0.1 cloudpickle-0.6.1 cycler-0.10.0 dask-1.0.0 decorator-4.3.0 kiwisolver-1.0.1 matplotlib-3.0.2 networkx-2.2 numpy-1.16.0 pillow-5.4.1 pyparsing-2.3.1 python-dateutil-2.7.5 scikit-image-0.14.1 scipy-1.2.0 six-1.12.0 toolz-0.9.0
Β mattbΒ ξ°Β (e)Β deletemeΒ ξ°Β ~Β ξ°Β python -c "import skimage"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/mattb/programs/anaconda3/envs/deleteme/lib/python3.7/site-packages/skimage/__init__.py", line 167, in <module>
from .util.dtype import (img_as_float32,
File "/home/mattb/programs/anaconda3/envs/deleteme/lib/python3.7/site-packages/skimage/util/__init__.py", line 8, in <module>
from .arraycrop import crop
File "/home/mattb/programs/anaconda3/envs/deleteme/lib/python3.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name '_validate_lengths' from 'numpy.lib.arraypad' (/home/mattb/programs/anaconda3/envs/deleteme/lib/python3.7/site-packages/numpy/lib/arraypad.py)
It looks like the _validate_lengths function was removed in this commit: https://github.com/numpy/numpy/commit/a4b96ad7649281de2c3a41292fcbab4c77c0743d#diff-4fcddc9140fbe901655b3e1bd484205c
AetherUnbound
on 14 Jan 2019
This has been fixed on master. I'll leave this issue open until a release of 0.14.2 has been made.
stefanv
on 14 Jan 2019
stefanv
on 14 Jan 2019
Ha, I just found #3551 as well. Thanks @stefanv!
AetherUnbound
on 14 Jan 2019
Note to self: improve the release process to where a point release can happen at the push of a button, so that we can synchronize near-seamlessly with NumPy releases.
stefanv
on 14 Jan 2019
Perhaps there should be a note in https://scikit-image.org/ to state that skimage<=0.14.1 is incompatible with numpy>=1.16?
pllim
on 17 Jan 2019
Also, is there a solid time line for 0.14.2 release?
pllim
on 17 Jan 2019
This should be a pinned issue:
- Pip releases are imminent. Though as always there are challenges with release process as it is rather tedious for pypi and Cython
- you can use conda-forge if you want to. I've already patched up 0.14.1 to work with newer numpy
- dask 1.0.0 is broken with numpy 1.16, so even if scikit-image is fixed immediately, your install it will still be broken.
hmaarrfk
on 17 Jan 2019
@pllim Timeline is as soon as possible, likely today still.
stefanv
on 17 Jan 2019
v0.14.2 has been released: https://github.com/scikit-image/scikit-image/blob/master/doc/release/release_0.14.rst
stefanv
on 18 Jan 2019
@stefanv : still failing with Python 2.7
Collecting numpy<1.17,>=1.14 (from -r requirements-travis.txt (line 1))
Downloading https://files.pythonhosted.org/packages/9f/85/163127d3fb0573deb9eca947cfc73aa3618eaaf8656501460574471d114a/numpy-1.16.0-cp27-cp27mu-manylinux1_x86_64.whl (17.0MB)
Collecting scikit-image<0.15,>=0.14 (from tensorlayer<1.12,>=1.9->-r requirements-travis.txt (line 3))
Downloading https://files.pythonhosted.org/packages/6a/04/f726af6b2e39a4dad0e5502670c4b33d5c915880a54a98aeb33b95150531/scikit_image-0.14.2-cp27-cp27mu-manylinux1_x86_64.whl (25.5MB)
Collecting dask[array]>=1.0.0 (from scikit-image<0.15,>=0.14->tensorlayer<1.12,>=1.9->-r requirements-travis.txt (line 3))
Downloading https://files.pythonhosted.org/packages/b4/e5/6407c2349622699eab0881e6bc6e978b8da67872a105e5e20b72ff190c65/dask-1.0.0-py2.py3-none-any.whl (685kB)
main.py:14: in <module>
from skimage.transform import resize
../../../virtualenv/python2.7.14/lib/python2.7/site-packages/skimage/__init__.py:167: in <module>
from .util.dtype import (img_as_float32,
../../../virtualenv/python2.7.14/lib/python2.7/site-packages/skimage/util/__init__.py:6: in <module>
from .apply_parallel import apply_parallel
../../../virtualenv/python2.7.14/lib/python2.7/site-packages/skimage/util/apply_parallel.py:8: in <module>
import dask.array as da
../../../virtualenv/python2.7.14/lib/python2.7/site-packages/dask/array/__init__.py:9: in <module>
from .routines import (take, choose, argwhere, where, coarsen, insert,
../../../virtualenv/python2.7.14/lib/python2.7/site-packages/dask/array/routines.py:256: in <module>
@wraps(np.matmul)
/opt/python/2.7.14/lib/python2.7/functools.py:33: in update_wrapper
setattr(wrapper, attr, getattr(wrapped, attr))
E AttributeError: 'numpy.ufunc' object has no attribute '__module__'
Seems like the error is on dask side, right ?
DEKHTIARJonathan
on 18 Jan 2019
yeah, this is a dask bug. they should have a release to fix this today or later this week.
hmaarrfk
on 18 Jan 2019
Hello all,
I came across the same issue. It took my few days but couldn't solve.
I restricted pip3 install numpy==1.15.4
but how do I restrict scikit-learn to upgrade the numpy?
can it use the numpy I have installed?
komalpharate
on 24 Jan 2019
@komalpharate if you install numpy==1.15.4 and then scikit-learn/scikit-image, it should use that version and not upgrade to numpy==1.16.
AetherUnbound
on 24 Jan 2019
I just tried with a fresh py27 env, and seems to work fine.
stefanv
on 25 Jan 2019
Hi - I'm getting this error to on the latest version.
If I downgrade to 1.15.4 I then get this error:
ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject
Any other thoughts on how to go about solving for this?
SoCohesive
on 1 Feb 2019
how did you go about installing scikit-image?
hmaarrfk
on 1 Feb 2019
@stefanv I'm getting the same error
from numpy.lib.arraypad import _validate_lengths
ImportError Traceback (most recent call last)
<ipython-input-6-30d1a12bd26c> in <module>
----> 1 from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name '_validate_lengths'
even after force-reinstalling scikit-image and numpy:
pip install scikit-image --force-reinstall
Successfully installed PyWavelets-1.0.2 cloudpickle-0.8.0 cycler-0.10.0 dask-1.1.3 decorator-4.3.2 kiwisolver-1.0.1 matplotlib-3.0.3 networkx-2.2 numpy-1.16.2 pillow-5.4.1 pyparsing-2.3.1 python-dateutil-2.8.0 scikit-image-0.14.2 scipy-1.2.1 setuptools-40.8.0 six-1.12.0 toolz-0.9.0
pip install numpy --force-reinstall
Successfully installed numpy-1.16.2
aopisco
on 6 Mar 2019
@aopisco Please file a new issue and fill out the provided template. Thanks.
stefanv
on 6 Mar 2019
Ran into the same problem yesterday. I don't see any open issue on this currently, I'll consider filing one.
python2.7, scikit-image 0.14.2, numpy 1.16.2
edrozenberg
on 27 Mar 2019
@edrozenberg hmm, given those versions, things should be working. I suspect you somehow have multiple scikit-image or NumPy versions installed.
jni
on 27 Mar 2019
Locking this issue to encourage users to file a new one. 0.14.2 should be compatible with numpy 1.16
hmaarrfk
on 28 Mar 2019
Tried installing previous versions of numpy as well. Still can't resolve it
abhay2706
on 11 Jul 2019
Update scikit-image? Sometimes multiple versions of numpy can be installed simultaneously... scikit-image 0.14.3 and 0.15.0 both resolve these problems.
jni
on 11 Jul 2019
If what @jni says doesn't work, can you open the anaconda prompt (open the start menu and type anaconda prompt) and type conda list and enter and give us that entire output
hmaarrfk
on 11 Jul 2019
Run this version together to solve this problem
pip install scikit-image==0.14.2
pip install numpy==1.16
02akshay
on 3 Jan 2020
Run this version together to solve this problem
pip install scikit-image==0.14.2
pip install numpy==1.16
thank u so much!
BotMichael
on 9 Feb 2020
Run this version together to solve this problem
pip install scikit-image==0.14.2
pip install numpy==1.16
I like unambiguous instructions that help me get on with my day. Cheers to you, sir
neonb88
on 21 May 2020
I am having similar issue on arm64 (Nvidia Jetson). Unfortunately cannot install with pip, instead use apt-get install python3-
numpy==1.18.3
scikit-image==0.14.0
ImportError: cannot import name '_validate_lengths
Any ideas for working around?
dkatsios
on 3 Jun 2020
You will need scikit-image 0.14.1, which fixed the problem. Or you can patch your installation, or you can compile from scratch.
Note that 0.14 is pretty old by now!
stefanv
on 3 Jun 2020
@dkatsios @stefanv there is another option, installing numpy==1.15
jni
on 3 Jun 2020
@jni would you know how this can be done for arm64 architecture? running pip3 install numpy==1.15 wouldn't work. Instead I have to run apt-get install python3-numpy. the only available version I get for this is 1.13.1 which corresponds to numpy 1.18.3.
dkatsios
on 3 Jun 2020
Oh I didn't realise that apt wouldn't let you install older versions. Um... If there is really no later version of skimage available for ARM, you might be down to @stefanv's solution, patching your install. If your distro ships the uncompiled Python code, you can do:
python3 -c "import skimage; print(skimage)"
to find out where the skimage code tree is. It'll be something like [....]/skimage/__init__.py.
Then, open the file (you'll need root) [....]/skimage/util/arraycrop.py, remove the line from numpy.lib.arraypad import _validate_lengths, and then uncomment all of the commented code.
Hope this helps!!!
jni
on 3 Jun 2020
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Most helpful comment
Run this version together to solve this problem
pip install scikit-image==0.14.2
pip install numpy==1.16