Failure to import, merge or open an analysis.h5 file in SLEAP GUI with skeleton edges

[amblypatty]

I exported some analysis.h5 files from the SLEAP GUI from a slp file. Attempts to Import, Merge into Project or Open Project all fail to import the HDF5 file appropriately in the SLEAP GUI. While Import... SLEAP analysis HDF5 file works somewhat, the file has all the information it should need to pull the videos and generate the edges of the skeleton, but the GUI asks for the location of the video file and only keypoint positions are populated once the video is located. The other two options fail with a TypeError without an adaptor.

The expected behavior is for the SLEAP GUI to use the information from the analysis.h5 file to create a new SLEAP project file or to be able to merge into an existing SLEAP project and have a full skeleton set up. The keypoints are populated in each frame with a track but without the rest of the skeleton, even though the analysis.h5 file contains edge_inds and edge_names.

From the image below of the analysis.h5 file open in HDFView, all of the file parts are there that should be able to be used to open the file in SLEAP with the full skeleton intact and without having to locate the video file unless the video_path no longer exists. Additionally, users should be able to Merge into Project from HDF5 files if they contain all the information.

Your personal set up

• OS:

Windows 10

• Version(s): SLEAPv1.3.3, Python 3.7.12

• SLEAP installation method (listed here):

  • [x ] Conda from package

Environment packages

# packages in environment at C:\ProgramData\Anaconda2\envs\sleap133:
#
# Name                    Version                   Build  Channel
absl-py                   1.0.0                    pypi_0    pypi
anyio                     3.7.1                    pypi_0    pypi
argon2-cffi               23.1.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
av                        10.0.0                   pypi_0    pypi
backcall                  0.2.0                    pypi_0    pypi
backports-zoneinfo        0.2.1                    pypi_0    pypi
beautifulsoup4            4.12.2                   pypi_0    pypi
bleach                    6.0.0                    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
cffi                      1.15.1                   pypi_0    pypi
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
colorama                  0.4.6                    pypi_0    pypi
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
debugpy                   1.7.0                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
efficientnet              1.0.0                    pypi_0    pypi
entrypoints               0.4                      pypi_0    pypi
exceptiongroup            1.2.0                    pypi_0    pypi
fastjsonschema            2.19.0                   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
imageio-ffmpeg            0.4.9                    pypi_0    pypi
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
ipykernel                 6.16.2                   pypi_0    pypi
ipython                   7.34.0                   pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
jasper                    2.0.33               hc2e4405_1    conda-forge
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
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
jupyter-client            7.4.9                    pypi_0    pypi
jupyter-core              4.12.0                   pypi_0    pypi
jupyter-server            1.24.0                   pypi_0    pypi
jupyterlab-pygments       0.2.2                    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
markupsafe                2.1.3                    pypi_0    pypi
matplotlib-base           3.5.3            py37hbaab90a_2    conda-forge
matplotlib-inline         0.1.6                    pypi_0    pypi
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2                    pypi_0    pypi
mkl                       2022.1.0           h6a75c08_874    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclassic                 1.0.0                    pypi_0    pypi
nbclient                  0.7.4                    pypi_0    pypi
nbconvert                 7.6.0                    pypi_0    pypi
nbformat                  5.8.0                    pypi_0    pypi
ndx-pose                  0.1.1                    pypi_0    pypi
nest-asyncio              1.5.8                    pypi_0    pypi
networkx                  2.6.3              pyhd8ed1ab_1    conda-forge
nixio                     1.5.3                    pypi_0    pypi
notebook                  6.5.6                    pypi_0    pypi
notebook-shim             0.2.3                    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
pandocfilters             1.5.0                    pypi_0    pypi
parso                     0.8.3                    pypi_0    pypi
partd                     1.4.0              pyhd8ed1ab_1    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                    pypi_0    pypi
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
prometheus-client         0.17.1                   pypi_0    pypi
prompt-toolkit            3.0.41                   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
pycparser                 2.21                     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
pywin32                   306                      pypi_0    pypi
pywinpty                  2.0.10                   pypi_0    pypi
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
send2trash                1.8.2                    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
simplejson                3.19.2                   pypi_0    pypi
six                       1.16.0             pyh6c4a22f_0    conda-forge
sleap                     1.3.3                    pypi_0    pypi
sleap-io                  0.0.13                   pypi_0    pypi
snappy                    1.1.10               hfb803bf_0    conda-forge
sniffio                   1.3.0                    pypi_0    pypi
soupsieve                 2.4.1                    pypi_0    pypi
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
terminado                 0.17.1                   pypi_0    pypi
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tifffile                  2021.11.2          pyhd8ed1ab_0    conda-forge
tinycss2                  1.2.1                    pypi_0    pypi
tk                        8.6.13               hcfcfb64_0    conda-forge
tomli                     2.0.0                    pypi_0    pypi
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2                      pypi_0    pypi
traitlets                 5.9.0                    pypi_0    pypi
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
wcwidth                   0.2.12                   pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
websocket-client          1.6.1                    pypi_0    pypi
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

C:/Users/psych/SLEAP-Data/Analysis_h5s/Runway_experiment_1.analysis.h5 doesn't match ext for json or json.zip
Traceback (most recent call last):
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 289, in openProject
    self.execute(OpenProject, filename=filename, first_open=first_open)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 242, in execute
    command().execute(context=self, params=kwargs)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 138, in execute
    self.do_with_signal(context, params)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 162, in do_with_signal
    cls.do_action(context, params)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 727, in do_action
    context.loadProjectFile(filename)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 274, in loadProjectFile
    self.execute(LoadProjectFile, filename=filename)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 242, in execute
    command().execute(context=self, params=kwargs)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 136, in execute
    okay = self.ask(context, params)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 698, in ask
    labels = Labels.load_file(filename, video_search=gui_video_callback)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\dataset.py", line 1969, in load_file
    filename, for_object="labels", video_search=video_search, *args, **kwargs
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\format\main.py", line 113, in read
    return disp.read(filename, *args, **kwargs)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\format\dispatch.py", line 59, in read
    raise TypeError("No file format adaptor could read this file.")
TypeError: No file format adaptor could read this file.

Open Project... above ^

Merge into Project...

Happy SLEAPing! :)
C:/Users/psych/SLEAP-Data/Analysis_h5s/Runway_experiment_1.analysis.h5 doesn't match ext for json or json.zip
Traceback (most recent call last):
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 606, in mergeProject
    self.execute(MergeProject, filenames=filenames)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 242, in execute
    command().execute(context=self, params=kwargs)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 134, in execute
    self.ask_and_do(context, params)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\gui\commands.py", line 2843, in ask_and_do
    new_labels = Labels.load_file(filename, video_search=gui_video_callback)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\dataset.py", line 1969, in load_file
    filename, for_object="labels", video_search=video_search, *args, **kwargs
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\format\main.py", line 113, in read
    return disp.read(filename, *args, **kwargs)
  File "C:\ProgramData\Anaconda2\envs\sleap133\lib\site-packages\sleap\io\format\dispatch.py", line 59, in read
    raise TypeError("No file format adaptor could read this file.")
TypeError: No file format adaptor could read this file.

Screenshots

Image of the HDF5 file contents:

Image of SLEAP asking to find the video even though the HDF5 file contents has the video_path:

Image of the imported HDF5 file with only keypoints showing. While I cannot screen capture it, the setting for Show Edges is enabled with a check mark:

The skeleton shows no symmetry or edges. But the HDF5 file contains the information needed to create the full skeleton from edge_inds, edge_names, and node_names. Currently, it seems that only node_names is utilized.

How to reproduce

1. Go to 'sleap-label in sleap conda environment...'
2. Click on 'Import...SLEAP analysis HDF5 or Merge Project... or Open Project...'
3. Locate the analysis.h5 file.
4. Either locate the video file from the pop-up GUI prompt or see TypeError traceback in conda-CLI.
5. See partial skeleton without edges if importing works

[roomrys]

The Open and Merge into project have historically not been intended to be used to handle analysis files. In general, the lack of support around loading in analysis files is because these were intended to be used as the last step of working with SLEAP (once analysis was exported, you would not come back and make changes to the analysis). Although, by this issue and the other related issues, it seems there is some interest in modifying the data in the analysis and then piping the modified data back into SLEAP.

[amblypatty]

Indeed, using the analysis files to edit mismatched tracks (at least when there should be only one track, but SLEAP created one for the user-labeled instances and a separate one for the predicted instances) is far easier than using the GUI to go through each video to swap them. Cleaning and retracking did not work either, so editing the analysis files was my workaround.