Installing lastest pycocotools fails on numpy.ufunc size changed error #248

guysoft · 2019-01-16T16:41:37Z

Ran pip3 install pycocotools

Then when I trying to import I get:

>>> from pycocotools.coco import COCO
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/venv/lib/python3.5/site-packages/pycocotools/coco.py", line 55, in <module>
    from . import mask as maskUtils
  File "/venv/lib/python3.5/site-packages/pycocotools/mask.py", line 3, in <module>
    import pycocotools._mask as _mask
  File "__init__.pxd", line 918, in init pycocotools._mask
ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject
>>>

Related:
hooram/ownphotos#56

The text was updated successfully, but these errors were encountered:

joyyang1215 · 2019-01-28T03:45:17Z

The same error!

PrakrutiChandak · 2019-01-28T11:47:07Z

same issue. It would be a great help. Thank you in advance!

learner0903 · 2019-01-29T05:25:39Z

Same error!

PrakrutiChandak · 2019-01-29T06:04:53Z

instead of using pip, try using this:

(pip install git+https://github.com/philferriere/cocoapi.git#subdirectory=PythonAPI)

I guess pip doesn't install everything, and git clone does.
Also, keep your cache clean.

sinter-w · 2019-01-31T08:01:01Z

The same error!!!

LarissaCasteluci · 2019-02-05T13:00:27Z

I tried using older versions of cocoapi as well as older versions of cython. I am really clueless to where the problem is from.

I get this error when the code tries to import pycocotools._mask:

File "__init__.pxd", line 918, in init pycocotools._mask

ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

guysoft · 2019-02-05T13:54:15Z

We switched to install via conda to avoid this. Which is a pretty bad workaround.

guysoft · 2019-02-05T13:55:57Z

@PrakrutiChandak Your solution is to use a different repository, its not a real solution to this current codebase. If there is a fix there it would be a good idea to PR it.

LarissaCasteluci · 2019-02-06T11:57:04Z

I found out what I was doing wrong. I was compiling the pycocotools folder on my host OS, while trying to use it with a docker container. If you are using virtual environments be sure to be consistent with them.

woshisj · 2019-02-27T02:56:11Z

I solve it like #14 (comment)

$ git clone https://github.com/pdollar/coco.git
$ cd coco/PythonAPI
$ make
$python setup.py install

gouthamvgk · 2019-03-03T13:43:49Z

I faced the same problem. Solved it by installing the numpy version 1.15.1

chAwater · 2019-04-27T06:34:07Z

I faced the same problem.

In my case, I think it because the numpy version changed after I installed pycocotools by pip (Both conda and pip might cause that version change).

So, I solved it by clear the Python environment, make sure there is only ONE version of numpy in the environment.

buncybunny · 2021-02-28T11:50:21Z

I found out what I was doing wrong. I was compiling the pycocotools folder on my host OS, while trying to use it with a docker container. If you are using virtual environments be sure to be consistent with them.

can you please give me some specific ways to solve this problem? I think my problem is exactly same as yours...

duffjay · 2021-03-06T01:03:02Z

I faced the same problem - not windows, not a docker situation.
Not sure where I went wrong.
numpy was not the problem
Ubuntu 18.04 (and 20.04)
TF 2.4 (I was following the object detection tutorial install instructions)
Python 3.7 (Ubuntu 18.04), 3.8 (20.04)

error:
File "/home/jay/anaconda3/envs/tf24/lib/python3.7/site-packages/pycocotools/mask.py", line 3, in
import pycocotools._mask as _mask
File "pycocotools/_mask.pyx", line 1, in init pycocotools._mask
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

here's how I flxed it.
go to the env directory, in my case:
/home/jay/anaconda3/envs/tf24/lib/python3.7/site-packages/pycocotools
list the files

git clone the coco project, make per the instructions
you'll have compiled products in (my example):
/project/cocoapi/PythonAPI/pycocotools/

the two lists should be about the same.
delete the files in: /home/jay/anaconda3/envs/tf24/lib/python3.7/site-packages/pycocotools
copy over the files from: /project/cocoapi/PythonAPI/pycocotools/

evidently, the _mask.pyx file has a problem
Not sure why this worked but it worked for me

antedesk · 2021-03-11T11:53:09Z

@duffjay you kinda save my day.

Your solution worked for me.

BTW fun fact:
I didn't experience this issue on Google Colab. Then I moved to GCP using the Deep Learning VM product in order to have an already configured env and I experienced this issue.

jason-su · 2021-03-13T07:32:54Z

I have the same error, and solve it by:

pip uninstall pycocotools
pip install pycocotools

update pycocotools from 2.0 to 2.0.2,

vriez · 2021-04-20T05:52:19Z

pycocotools==2.0.2
numpy==1.20.2

did the trick.

dreamgonsalves · 2021-04-25T10:24:27Z

pycocotools==2.0.2
numpy==1.20.2
did the trick.

Tried this but now getting different error:
NotImplementedError: Cannot convert a symbolic Tensor (strided_slice:0) to a numpy array.

Please help

### Description Python Package Pipeline failed since there is exception raised in test_smooth_quant (from #16288): ``` File "/home/cloudtest/.local/lib/python3.8/site-packages/onnxruntime/quantization/quantize.py", line 384, in quantize_static importlib.import_module("neural_compressor.adaptor.ox_utils.smooth_quant") File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/__init__.py", line 24, in <module> from .contrib import * File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/contrib/__init__.py", line 19, in <module> from .strategy import * File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/contrib/strategy/__init__.py", line 26, in <module> __import__(basename(f)[:-3], globals(), locals(), level=1) File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/contrib/strategy/sigopt.py", line 22, in <module> from neural_compressor.strategy.strategy import strategy_registry, TuneStrategy File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/strategy/__init__.py", line 20, in <module> from .strategy import STRATEGIES File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/strategy/strategy.py", line 41, in <module> from ..algorithm import AlgorithmScheduler, ALGORITHMS File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/algorithm/__init__.py", line 20, in <module> from .algorithm import ALGORITHMS, Algorithm, AlgorithmScheduler, algorithm_registry File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/algorithm/algorithm.py", line 21, in <module> from neural_compressor.utils.create_obj_from_config import get_algorithm File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/utils/create_obj_from_config.py", line 20, in <module> from neural_compressor.metric import METRICS File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/metric/__init__.py", line 30, in <module> __import__(basename(f)[:-3], globals(), locals(), level=1) File "/home/cloudtest/.local/lib/python3.8/site-packages/neural_compressor/metric/coco_tools.py", line 54, in <module> from pycocotools import coco File "/usr/local/lib/python3.8/dist-packages/pycocotools/coco.py", line 52, in <module> from . import mask as maskUtils File "/usr/local/lib/python3.8/dist-packages/pycocotools/mask.py", line 3, in <module> import pycocotools._mask as _mask File "pycocotools/_mask.pyx", line 1, in init pycocotools._mask ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject ``` The cause is pycocotools package uses "oldest-supported-numpy", which might cause older version numpy in build pycocotools: https://github.com/ppwwyyxx/cocoapi/blob/9e9164f979fe4265c6f387f10e234f8697a15922/PythonAPI/pyproject.toml#L4 Related issue: cocodataset/cocoapi#248 ### Motivation and Context

BertaBescos mentioned this issue Apr 9, 2019

Importing Mask R-CNN Settings... Segmentation fault (core dumped) BertaBescos/DynaSLAM#24

Closed

suniique mentioned this issue Jul 17, 2022

zip to hdf5 error SysCV/shift-dev#10

Closed

tianleiwu mentioned this issue Jul 29, 2023

skip test_smooth_quant to unblock Python Package Pipeline microsoft/onnxruntime#16914

Merged

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Installing lastest pycocotools fails on numpy.ufunc size changed error #248

Installing lastest pycocotools fails on numpy.ufunc size changed error #248

guysoft commented Jan 16, 2019

joyyang1215 commented Jan 28, 2019

PrakrutiChandak commented Jan 28, 2019

learner0903 commented Jan 29, 2019

PrakrutiChandak commented Jan 29, 2019 •

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sinter-w commented Jan 31, 2019

LarissaCasteluci commented Feb 5, 2019 •

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guysoft commented Feb 5, 2019

guysoft commented Feb 5, 2019

LarissaCasteluci commented Feb 6, 2019 •

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woshisj commented Feb 27, 2019 •

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gouthamvgk commented Mar 3, 2019

chAwater commented Apr 27, 2019

buncybunny commented Feb 28, 2021

duffjay commented Mar 6, 2021

antedesk commented Mar 11, 2021

jason-su commented Mar 13, 2021

vriez commented Apr 20, 2021

dreamgonsalves commented Apr 25, 2021

Installing lastest pycocotools fails on numpy.ufunc size changed error #248

Installing lastest pycocotools fails on numpy.ufunc size changed error #248

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guysoft commented Jan 16, 2019

joyyang1215 commented Jan 28, 2019

PrakrutiChandak commented Jan 28, 2019

learner0903 commented Jan 29, 2019

PrakrutiChandak commented Jan 29, 2019 • edited Loading

sinter-w commented Jan 31, 2019

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guysoft commented Feb 5, 2019

guysoft commented Feb 5, 2019

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gouthamvgk commented Mar 3, 2019

chAwater commented Apr 27, 2019

buncybunny commented Feb 28, 2021

duffjay commented Mar 6, 2021

antedesk commented Mar 11, 2021

jason-su commented Mar 13, 2021

vriez commented Apr 20, 2021

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