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Good detections but calibration routine crashes

See original GitHub issue

Hi,

I’m using 5 cameras and the standard charuco board for camera calibration. This results in 100’s of detections per camera and anipose-calibrate makes it to the point where it saves detections.pickle. However, during the actual model estimation step, it crashes with the following

Calibrating...
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/calibration.toml
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-0_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [02:45<00:00, 42.51it/s]
4676 boards detected
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-1_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [03:04<00:00, 38.08it/s]
5149 boards detected
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-2_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [03:12<00:00, 36.55it/s]
5403 boards detected
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-3_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [03:01<00:00, 38.74it/s]
5122 boards detected
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-4_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [03:02<00:00, 38.49it/s]
6628 boards detected
defaultdict(<class 'int'>, {('1', '4'): 4900, ('4', '1'): 4900})
Traceback (most recent call last):
  File "/home/jon/anaconda3/envs/anipose/bin/anipose", line 8, in <module>
    sys.exit(cli())
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/anipose.py", line 314, in run_data
    calibrate_all(config)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/calibrate.py", line 203, in process_session
    verbose=True)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 1563, in calibrate_rows
    rvecs, tvecs = get_initial_extrinsics(rtvecs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/utils.py", line 173, in get_initial_extrinsics
    pairs = find_calibration_pairs(graph, source=0)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/utils.py", line 156, in find_calibration_pairs
    for new in graph[item]:
TypeError: 'NoneType' object is not subscriptable

I’ve attached my detections.pickle in case there is evidence of what corner case I’ve reached here…

detections.zip

Issue Analytics

State:
Created 3 years ago
Comments:28 (4 by maintainers)

Top GitHub Comments

5reactions

kevinyamauchicommented, Nov 9, 2020

Hello everyone! I have been trying to run the tutorial and I have run into this same issue. After running the tutorial as-is, I noticed there were different number of board detections in each video. I then trimmed the video down to the first 1200 frames and there are 1200 board detections in all three calibration videos (per the terminal outputt - see traceback below). I still received the same NoneType error. I have pasted the traceback and my conda environment info below. Also, I’ve attached the detections.pickle file.

traceback

Calibrating...
C:\Users\realtime\Downloads\hand-demo-unfilled-20201109T151316Z-001\hand-demo-unfilled\2019-08-02
C:\Users\realtime\Downloads\hand-demo-unfilled-20201109T151316Z-001\hand-demo-unfilled\2019-08-02\calibration\calibration.toml
C:\Users\realtime\Downloads\hand-demo-unfilled-20201109T151316Z-001\hand-demo-unfilled\2019-08-02\calibration\calib-charuco-trim-camA.mov
100%|█████████████████████████████| 1200/1200 [00:40<00:00, 29.36it/s]
1200 boards detected
C:\Users\realtime\Downloads\hand-demo-unfilled-20201109T151316Z-001\hand-demo-unfilled\2019-08-02\calibration\calib-charuco-trim-camB.mov
100%|█████████████████████████████| 1200/1200 [00:43<00:00, 27.56it/s]
1200 boards detected
C:\Users\realtime\Downloads\hand-demo-unfilled-20201109T151316Z-001\hand-demo-unfilled\2019-08-02\calibration\calib-charuco-trim-camC.mov
100%|█████████████████████████████| 1200/1200 [00:42<00:00, 28.08it/s]
1200 boards detected
defaultdict(<class 'int'>, {('A', 'B'): 1200, ('B', 'A'): 1200})
Traceback (most recent call last):
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\realtime\anaconda3\envs\anipose-dlc\Scripts\anipose.exe\__main__.py", line 7, in <module>
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\click\core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\click\core.py", line 782, in main
    rv = self.invoke(ctx)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\click\core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\click\core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\click\decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\anipose\anipose.py", line 116, in calibrate
    calibrate_all(config)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\anipose\common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\anipose\common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\anipose\calibrate.py", line 203, in process_session
    verbose=True)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\aniposelib\cameras.py", line 1563, in calibrate_rows
    rvecs, tvecs = get_initial_extrinsics(rtvecs)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\aniposelib\utils.py", line 173, in get_initial_extrinsics
    pairs = find_calibration_pairs(graph, source=0)
  File "c:\users\realtime\anaconda3\envs\anipose-dlc\lib\site-packages\aniposelib\utils.py", line 156, in find_calibration_pairs
    for new in graph[item]:
TypeError: 'NoneType' object is not subscriptable

environment

# packages in environment at C:\Users\realtime\anaconda3\envs\anipose-dlc:
#
# Name                    Version                   Build  Channel
_tflow_select             2.1.0                       gpu
absl-py                   0.11.0           py37haa95532_0
anipose                   0.9.0                    pypi_0    pypi
aniposelib                0.4.1                    pypi_0    pypi
apptools                  4.5.0                      py_0
argon2-cffi               20.1.0           py37he774522_1
astor                     0.8.1                    py37_0
async_generator           1.10             py37h28b3542_0
attrs                     20.3.0             pyhd3eb1b0_0
backcall                  0.2.0                      py_0
blas                      1.0                         mkl
bleach                    3.2.1                      py_0
bzip2                     1.0.8                he774522_0
ca-certificates           2020.10.14                    0
certifi                   2020.6.20          pyhd3eb1b0_3
cffi                      1.14.3           py37h7a1dbc1_0
chardet                   3.0.4                    pypi_0    pypi
click                     7.1.2                    pypi_0    pypi
colorama                  0.4.4                      py_0
configobj                 5.0.6                    py37_1
cudatoolkit               10.0.130                      0
cudnn                     7.6.5                cuda10.0_0
curl                      7.71.1               h2a8f88b_1
cycler                    0.10.0                   pypi_0    pypi
decorator                 4.4.2                      py_0
deeplabcut                2.1.8.2                  pypi_0    pypi
defusedxml                0.6.0                      py_0
easydict                  1.9                      pypi_0    pypi
entrypoints               0.3                      py37_0
envisage                  4.9.2                      py_0
expat                     2.2.10               h33f27b4_2
ffmpeg                    4.2.2                he774522_0
freetype                  2.10.4               hd328e21_0
future                    0.18.2                   py37_1
gast                      0.4.0                      py_0
geos                      3.8.0                h33f27b4_0
grpcio                    1.31.0           py37he7da953_0
h5py                      2.10.0           py37h5e291fa_0
hdf4                      4.2.13               h712560f_2
hdf5                      1.10.4               h7ebc959_0
icc_rt                    2019.0.0             h0cc432a_1
icu                       58.2                 ha925a31_3
idna                      2.10                     pypi_0    pypi
imageio                   2.9.0                    pypi_0    pypi
imageio-ffmpeg            0.4.2                    pypi_0    pypi
imgaug                    0.4.0                    pypi_0    pypi
importlib-metadata        2.0.0                      py_1
importlib_metadata        2.0.0                         1
intel-openmp              2019.0                   pypi_0    pypi
ipykernel                 5.3.4            py37h5ca1d4c_0
ipython                   7.19.0           py37hd4e2768_0
ipython_genutils          0.2.0                    py37_0
ipywidgets                7.5.1                      py_1
jedi                      0.17.2                   py37_0
jinja2                    2.11.2                     py_0
joblib                    0.17.0                   pypi_0    pypi
jpeg                      9b                   hb83a4c4_2
jsoncpp                   1.8.4                h74a9793_0
jsonschema                3.2.0                      py_2
jupyter                   1.0.0                    py37_7
jupyter_client            6.1.7                      py_0
jupyter_console           6.2.0                      py_0
jupyter_core              4.6.3                    py37_0
jupyterlab_pygments       0.1.2                      py_0
keras-applications        1.0.8                      py_1
keras-preprocessing       1.1.0                      py_1
kiwisolver                1.3.1                    pypi_0    pypi
krb5                      1.18.2               hc04afaa_0
libcurl                   7.71.1               h2a8f88b_1
libiconv                  1.15                 h1df5818_7
libnetcdf                 4.6.1                h411e497_2
libpng                    1.6.37               h2a8f88b_0
libprotobuf               3.13.0.1             h200bbdf_0
libsodium                 1.0.18               h62dcd97_0
libssh2                   1.9.0                h7a1dbc1_1
libtiff                   4.1.0                h56a325e_0
libxml2                   2.9.10               hb89e7f3_3
llvmlite                  0.33.0                   pypi_0    pypi
lz4-c                     1.8.1.2              h2fa13f4_0
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gmp                 6.1.0                         2
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
markdown                  3.3.2                    py37_0
markupsafe                1.1.1            py37hfa6e2cd_1
matplotlib                3.0.3                    pypi_0    pypi
mayavi                    4.7.1            py37h11817fe_2
mistune                   0.8.4           py37hfa6e2cd_1001
mkl                       2020.2                      256
mkl-service               2.3.0            py37hb782905_0
mkl_fft                   1.2.0            py37h45dec08_0
mkl_random                1.1.1            py37h47e9c7a_0
mock                      4.0.2                      py_0
moviepy                   1.0.1                    pypi_0    pypi
msgpack                   1.0.0                    pypi_0    pypi
msgpack-numpy             0.4.7.1                  pypi_0    pypi
msys2-conda-epoch         20160418                      1
nb_conda                  2.2.1                    py37_0
nb_conda_kernels          2.3.0                    py37_0
nbclient                  0.5.1                      py_0
nbconvert                 6.0.7                    py37_0
nbformat                  5.0.8                      py_0
nest-asyncio              1.4.1                      py_0
networkx                  2.5                      pypi_0    pypi
notebook                  6.1.4                    py37_0
numba                     0.50.1                   pypi_0    pypi
numexpr                   2.7.1                    pypi_0    pypi
numpy                     1.16.4                   pypi_0    pypi
numpy-base                1.19.2           py37ha3acd2a_0
opencv-contrib-python     3.4.11.45                pypi_0    pypi
openssl                   1.1.1h               he774522_0
packaging                 20.4                       py_0
pandas                    1.1.4                    pypi_0    pypi
pandoc                    2.11                 h9490d1a_0
pandocfilters             1.4.2                    py37_1
parso                     0.7.0                      py_0
patsy                     0.5.1                    pypi_0    pypi
pickleshare               0.7.5                 py37_1001
pillow                    8.0.1                    pypi_0    pypi
pip                       20.2.4           py37haa95532_0
proglog                   0.1.9                    pypi_0    pypi
prometheus_client         0.8.0                      py_0
prompt-toolkit            3.0.8                      py_0
prompt_toolkit            3.0.8                         0
protobuf                  3.13.0.1         py37ha925a31_1
psutil                    5.7.3                    pypi_0    pypi
pycparser                 2.20                       py_2
pyface                    7.1.0                    py37_1
pygments                  2.7.2              pyhd3eb1b0_0
pyparsing                 2.4.7                      py_0
pyqt                      5.9.2            py37h6538335_2
pyreadline                2.1                      py37_1
pyrsistent                0.17.3           py37he774522_0
python                    3.7.9                h60c2a47_0
python-dateutil           2.8.1                      py_0
pytz                      2020.4                   pypi_0    pypi
pywavelets                1.1.1                    pypi_0    pypi
pywin32                   227              py37he774522_1
pywinpty                  0.5.7                    py37_0
pyyaml                    5.3.1                    pypi_0    pypi
pyzmq                     19.0.2           py37ha925a31_1
qt                        5.9.7            vc14h73c81de_0
qtconsole                 4.7.7                      py_0
qtpy                      1.9.0                      py_0
requests                  2.24.0                   pypi_0    pypi
ruamel-yaml               0.16.12                  pypi_0    pypi
ruamel-yaml-clib          0.2.2                    pypi_0    pypi
scikit-image              0.17.2                   pypi_0    pypi
scikit-learn              0.23.2                   pypi_0    pypi
scikit-video              1.1.11                   pypi_0    pypi
scipy                     1.5.2            py37h9439919_0
send2trash                1.5.0                    py37_0
setuptools                50.3.1           py37haa95532_1
shapely                   1.7.1            py37h210f175_0
sip                       4.19.8           py37h6538335_0
six                       1.15.0                     py_0
sqlite                    3.33.0               h2a8f88b_0
statsmodels               0.12.1                   pypi_0    pypi
tables                    3.6.1                    pypi_0    pypi
tabulate                  0.8.7                    pypi_0    pypi
tbb                       2020.3               h74a9793_0
tensorboard               1.13.1           py37h33f27b4_0
tensorflow                1.13.1          gpu_py37h83e5d6a_0
tensorflow-base           1.13.1          gpu_py37h871c8ca_0
tensorflow-estimator      1.13.0                     py_0
tensorflow-gpu            1.13.1               h0d30ee6_0
tensorpack                0.10.1                   pypi_0    pypi
termcolor                 1.1.0                    py37_1
terminado                 0.9.1                    py37_0
testpath                  0.4.4                      py_0
threadpoolctl             2.1.0                    pypi_0    pypi
tifffile                  2020.10.1                pypi_0    pypi
toml                      0.10.2                   pypi_0    pypi
tornado                   6.0.4            py37he774522_1
tqdm                      4.51.0                   pypi_0    pypi
traitlets                 5.0.5                      py_0
traits                    6.1.1            py37he774522_0
traitsui                  7.1.0                      py_0
urllib3                   1.25.11                  pypi_0    pypi
vc                        14.1                 h0510ff6_4
vs2015_runtime            14.16.27012          hf0eaf9b_3
vtk                       8.2.0           py37h1e53df8_200
wcwidth                   0.2.5                      py_0
webencodings              0.5.1                    py37_1
werkzeug                  1.0.1                      py_0
wheel                     0.35.1                     py_0
widgetsnbextension        3.5.1                    py37_0
wincertstore              0.2                      py37_0
winpty                    0.4.3                         4
wxpython                  4.0.4            py37ha925a31_0
xz                        5.2.5                h62dcd97_0
zeromq                    4.3.2                ha925a31_3
zipp                      3.4.0              pyhd3eb1b0_0
zlib                      1.2.11               h62dcd97_4
zstd                      1.3.7                h508b16e_0

detections.zip

Quick update: I rolled back to anipose==0.8.1 and aniposelib==0.3.7 and the calibration runs (I haven’t had a chance to evaluate the results)

1reaction

KonradDanielewskicommented, Mar 22, 2021

Ye, had the same issue, it makes detections worse. Rolling back 0.8.1 and 0.3.7 + upgrade calligator, for some reason, was the only way I got everything working fine and reproducible.

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