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Exporting Dataset with Frame Images sometimes results in stalled progress bar with confusing MemoryError message #1594

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amblypatty opened this issue Nov 14, 2023 · 0 comments
Open
1 of 4 tasks

Exporting Dataset with Frame Images sometimes results in stalled progress bar with confusing MemoryError message #1594

amblypatty opened this issue Nov 14, 2023 · 0 comments
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bug Something isn't working

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@amblypatty
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Bug description

Sometimes, when exporting a dataset for training, the progress bar dialog stops at 271 frame images, an error pops up in the terminal, and the export never finishes. The only way I have gotten around the error is from closing the program and restarting. The error message is confusing because it states that it cannot allocate 23.1Gb of space for a smaller array, however, I am not attempting to allocate nearly that much space, nor are any of my videos that large in size. I am not sure what it means or where the real issue is coming from. The entire size of the pkg.slp file to be created shouldn't be larger than ~2Gb. I have not identified a specific pattern for when the error occurs except for that it has not happened during the first attempt to export a training dataset after a fresh opening of the SLEAP program. It often, but not always has been occurring with the second attempt to export a training dataset. I can still close the windows and shut down the program from the GUI, so the windows are not stalled,

Expected behaviour

I expect that the training export progresses forward and does not produce a numpy MemoryError.

Actual behaviour

Your personal set up

  • OS:
    Windows 10
  • Version(s):

SLEAP v1.3.3, python 3.7.12

Environment packages 
# packages in environment at C:\ProgramData\Anaconda2\envs\sleap133:
#
# Name                    Version                   Build  Channel
absl-py                   1.0.0                    pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
backports-zoneinfo        0.2.1                    pypi_0    pypi
blosc                     1.21.5               hdccc3a2_0    conda-forge
brotli                    1.0.9                hcfcfb64_9    conda-forge
brotli-bin                1.0.9                hcfcfb64_9    conda-forge
bzip2                     1.0.8                h8ffe710_4    conda-forge
c-blosc2                  2.10.2               h183a6f4_0    conda-forge
ca-certificates           2023.7.22            h56e8100_0    conda-forge
cached-property           1.5.2                    pypi_0    pypi
cachetools                4.2.4                    pypi_0    pypi
cattrs                    1.1.1              pyhd8ed1ab_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cfitsio                   4.0.0                hd67004f_0    conda-forge
charls                    2.3.4                h39d44d4_0    conda-forge
charset-normalizer        2.0.9                    pypi_0    pypi
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
cuda-nvcc                 11.3.58              hb8d16a4_0    nvidia
cudatoolkit               11.3.1              hf2f0253_12    conda-forge
cudnn                     8.2.1.32             h754d62a_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py37hcc03f2d_0    conda-forge
dask-core                 2022.2.0           pyhd8ed1ab_0    conda-forge
efficientnet              1.0.0                    pypi_0    pypi
flatbuffers               2.0                      pypi_0    pypi
fonttools                 4.38.0           py37h51bd9d9_0    conda-forge
freeglut                  3.2.2                h63175ca_2    conda-forge
freetype                  2.12.1               hdaf720e_2    conda-forge
fsspec                    2023.1.0           pyhd8ed1ab_0    conda-forge
gast                      0.4.0                    pypi_0    pypi
geos                      3.11.0               h39d44d4_0    conda-forge
giflib                    5.2.1                h64bf75a_3    conda-forge
google-auth               2.3.3                    pypi_0    pypi
google-auth-oauthlib      0.4.6                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
grpcio                    1.43.0                   pypi_0    pypi
h5py                      3.1.0                    pypi_0    pypi
hdmf                      3.6.1                    pypi_0    pypi
icu                       69.1                 h0e60522_0    conda-forge
idna                      3.3                      pypi_0    pypi
image-classifiers         1.0.0                    pypi_0    pypi
imagecodecs               2021.11.20       py37hfea8715_2    conda-forge
imageio                   2.31.1             pyh24c5eb1_0    conda-forge
imgaug                    0.4.0              pyhd8ed1ab_1    conda-forge
imgstore                  0.2.9                    pypi_0    pypi
importlib-metadata        4.2.0                    pypi_0    pypi
importlib-resources       5.12.0                   pypi_0    pypi
intel-openmp              2023.2.0         h57928b3_49503    conda-forge
jasper                    2.0.33               hc2e4405_1    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   hcfcfb64_3    conda-forge
jsmin                     3.0.1              pyhd8ed1ab_0    conda-forge
jsonpickle                1.2                        py_0    conda-forge
jsonschema                4.17.3                   pypi_0    pypi
jxrlib                    1.1                  h8ffe710_2    conda-forge
keras                     2.7.0                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kiwisolver                1.4.4            py37h8c56517_0    conda-forge
krb5                      1.20.1               h6609f42_0    conda-forge
lcms2                     2.14                 h90d422f_0    conda-forge
lerc                      3.0                  h0e60522_0    conda-forge
libaec                    1.0.6                h63175ca_1    conda-forge
libblas                   3.9.0              18_win64_mkl    conda-forge
libbrotlicommon           1.0.9                hcfcfb64_9    conda-forge
libbrotlidec              1.0.9                hcfcfb64_9    conda-forge
libbrotlienc              1.0.9                hcfcfb64_9    conda-forge
libcblas                  3.9.0              18_win64_mkl    conda-forge
libclang                  12.0.0                   pypi_0    pypi
libcurl                   8.1.2                h68f0423_0    conda-forge
libdeflate                1.10                 h8ffe710_0    conda-forge
libhwloc                  2.9.1                h51c2c0f_0    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
liblapack                 3.9.0              18_win64_mkl    conda-forge
liblapacke                3.9.0              18_win64_mkl    conda-forge
libopencv                 4.5.1            py37ha0199f4_0    conda-forge
libpng                    1.6.39               h19919ed_0    conda-forge
libprotobuf               3.21.8               h12be248_0    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.43.0               hcfcfb64_0    conda-forge
libssh2                   1.10.0               h680486a_3    conda-forge
libtiff                   4.4.0                hc4061b1_0    conda-forge
libwebp-base              1.3.2                hcfcfb64_0    conda-forge
libxcb                    1.13              hcd874cb_1004    conda-forge
libxml2                   2.10.4               hc3477c8_0    conda-forge
libxslt                   1.1.37               h0192164_0    conda-forge
libzlib                   1.2.13               hcfcfb64_5    conda-forge
libzopfli                 1.0.3                h0e60522_0    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lz4-c                     1.9.3                h8ffe710_1    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
markdown                  3.3.6                    pypi_0    pypi
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
matplotlib-base           3.5.3            py37hbaab90a_2    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mkl                       2022.1.0           h6a75c08_874    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ndx-pose                  0.1.1                    pypi_0    pypi
networkx                  2.6.3              pyhd8ed1ab_1    conda-forge
nixio                     1.5.3                    pypi_0    pypi
numpy                     1.19.5                   pypi_0    pypi
oauthlib                  3.1.1                    pypi_0    pypi
opencv                    4.5.1            py37h03978a9_0    conda-forge
opencv-python-headless    4.2.0.34                 pypi_0    pypi
openjpeg                  2.5.0                hc9384bd_1    conda-forge
openssl                   1.1.1w               hcfcfb64_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 21.3                     pypi_0    pypi
pandas                    1.3.5            py37h9386db6_0    conda-forge
partd                     1.4.0              pyhd8ed1ab_1    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pillow                    9.2.0            py37h42a8222_2    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10                   pypi_0    pypi
protobuf                  3.19.1                   pypi_0    pypi
psutil                    5.9.3            py37h51bd9d9_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
py-opencv                 4.5.1            py37heaed05f_0    conda-forge
pyasn1                    0.4.8                    pypi_0    pypi
pyasn1-modules            0.2.8                    pypi_0    pypi
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pykalman                  0.9.5                      py_1    conda-forge
pynwb                     2.3.3                    pypi_0    pypi
pyparsing                 3.0.6                    pypi_0    pypi
pyrsistent                0.19.3                   pypi_0    pypi
pyside2                   5.13.2           py37h760f651_8    conda-forge
python                    3.7.12          h7840368_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-rapidjson          1.9              py37h7f67f24_0    conda-forge
python_abi                3.7                     4_cp37m    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pywavelets                1.3.0            py37h3a130e4_1    conda-forge
pyyaml                    6.0              py37hcc03f2d_4    conda-forge
pyzmq                     24.0.1           py37h7347f05_0    conda-forge
qimage2ndarray            1.10.0                   pypi_0    pypi
qt                        5.12.9               h556501e_6    conda-forge
qtpy                      2.4.0              pyhd8ed1ab_0    conda-forge
requests                  2.26.0                   pypi_0    pypi
requests-oauthlib         1.3.0                    pypi_0    pypi
rich                      13.5.3             pyhd8ed1ab_0    conda-forge
ruamel-yaml               0.17.32                  pypi_0    pypi
ruamel-yaml-clib          0.2.7                    pypi_0    pypi
scikit-image              0.19.3           py37h3182a2c_1    conda-forge
scikit-learn              1.0              py37ha78be43_1    conda-forge
scikit-video              1.1.11             pyh24bf2e0_0    conda-forge
scipy                     1.7.3            py37hb6553fb_0    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
segmentation-models       1.0.1                    pypi_0    pypi
setuptools                59.8.0           py37h03978a9_1    conda-forge
setuptools-scm            6.3.2                    pypi_0    pypi
shapely                   1.8.5            py37h475e9a0_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sleap                     1.3.3                    pypi_0    pypi
snappy                    1.1.10               hfb803bf_0    conda-forge
sqlite                    3.43.0               hcfcfb64_0    conda-forge
statsmodels               0.13.2           py37h3a130e4_0    conda-forge
tbb                       2021.9.0             h91493d7_0    conda-forge
tensorboard               2.7.0                    pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-wit    1.8.0                    pypi_0    pypi
tensorflow                2.7.0                    pypi_0    pypi
tensorflow-estimator      2.7.0                    pypi_0    pypi
tensorflow-hub            0.12.0             pyhca92ed8_0    conda-forge
tensorflow-io-gcs-filesystem 0.23.1                   pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tifffile                  2021.11.2          pyhd8ed1ab_0    conda-forge
tk                        8.6.13               hcfcfb64_0    conda-forge
tomli                     2.0.0                    pypi_0    pypi
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
typing-extensions         4.0.1                    pypi_0    pypi
typing_extensions         4.7.1              pyha770c72_0    conda-forge
tzdata                    2023.3                   pypi_0    pypi
tzlocal                   5.0.1                    pypi_0    pypi
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
unicodedata2              14.0.0           py37hcc03f2d_1    conda-forge
urllib3                   1.26.7                   pypi_0    pypi
vc                        14.3                h64f974e_17    conda-forge
vc14_runtime              14.36.32532         hdcecf7f_17    conda-forge
vs2015_runtime            14.36.32532         h05e6639_17    conda-forge
werkzeug                  2.0.2                    pypi_0    pypi
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
wrapt                     1.13.3                   pypi_0    pypi
xorg-libxau               1.0.11               hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
zeromq                    4.3.4                h0e60522_1    conda-forge
zfp                       0.5.5                h0e60522_8    conda-forge
zipp                      3.15.0                   pypi_0    pypi
zlib                      1.2.13               hcfcfb64_5    conda-forge
zlib-ng                   2.0.7                hcfcfb64_0    conda-forge
zstd                      1.5.5                h12be248_0    conda-forge
Logs 
Traceback (most recent call last):
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\learning\dialog.py", line 814, in export_package
    suggested=include_suggestions,
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 1432, in export_dataset_gui
    progress_callback=update_progress if verbose else None,
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\dataset.py", line 1997, in save_file
    write(filename, labels, *args, **kwargs)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\format\main.py", line 162, in write
    return disp.write(filename, source_object, *args, **kwargs)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\format\dispatch.py", line 79, in write
    return adaptor.write(filename, source_object, *args, **kwargs)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\format\hdf5.py", line 253, in write
    progress_callback=progress_callback,
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\dataset.py", line 2373, in save_frame_data_hdf5
    frame_numbers=frame_nums,
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\video.py", line 1433, in to_hdf5
    frame_data = self.get_frames(frame_numbers)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\video.py", line 1117, in get_frames
    return np.stack([self.get_frame(idx) for idx in idxs], axis=0)
  File "<__array_function__ internals>", line 6, in stack
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\numpy\core\shape_base.py", line 433, in stack
    return _nx.concatenate(expanded_arrays, axis=axis, out=out)
  File "<__array_function__ internals>", line 6, in concatenate
numpy.core._exceptions.MemoryError: Unable to allocate 23.1 GiB for an array with shape (3982, 1080, 1920, 3) and data type uint8

Screenshots

Training_export_dialog_issue

How to reproduce

  1. Go to '...'
  2. Click on '....'
  3. Scroll down to '....'
  4. See error
@amblypatty amblypatty added the bug Something isn't working label Nov 14, 2023
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