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talmolab
Failure to import, merge or open an analysis.h5 file in SLEAP GUI with skeleton edges
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
- Go to '
sleap-labelin sleap conda environment...' - Click on 'Import...SLEAP analysis HDF5 or Merge Project... or Open Project...'
- Locate the analysis.h5 file.
- Either locate the video file from the pop-up GUI prompt or see
TypeErrortraceback in conda-CLI. - See partial skeleton without edges if importing works
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.
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.