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hdf5 dataset reader #173

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bendichter opened this issue Jul 8, 2022 · 3 comments · Fixed by #174
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hdf5 dataset reader #173

bendichter opened this issue Jul 8, 2022 · 3 comments · Fixed by #174
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@h-mayorquin

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@bendichter
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roiextractors/src/roiextractors/extractors/hdf5imagingextractor/hdf5imagingextractor.py

Line 103 in 57b5305

frames = self._video.lazy_slice[slice_start:slice_stop, :, :, channel].dsetread()

why use lazy_ops and then read the data? This line should simply be

frames = self._video[:, :, :, channel]
@bendichter
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@h-mayorquin

@bendichter bendichter mentioned this issue Jul 8, 2022
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@h-mayorquin
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That was needed for it to work with nwb conversion tools functionality. Something with the add_two_photon_series functionality required the output of get frames to be a numpy array. I will double check it the week after.

@h-mayorquin h-mayorquin mentioned this issue Jul 19, 2022
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@h-mayorquin
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Ok, I tested the linked branch (#174) against nwb conversion tools and it seems to work but there are some errors there discussed in the pull request.

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Fix HDF5 and NWB get_frames behavior catalystneuro/roiextractors
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@bendichter @h-mayorquin