Bugfix in Sources2D save_workspace method and get_data_dimension.m about cnmf_e HOT 5 OPEN

@zhoupc

get_data_dimension.m throws an error for a 3D ([x y frames]) HDF5 movie saved using Matlab's H5 IO functions at line https://github.com/zhoupc/CNMF_E/blob/master/ca_source_extraction/endoscope/get_data_dimension.m#L35.

If I change dims = temp([2, 3, 5]); to dims = temp; CNMF-E runs fine on all the movies I've tested on. Might want to add a check for cases in which people have HDF5s saved as I do.

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thanks, good catch. the first bug is fixed.

as for the second bug, i don't have a good solution yet. it seems that different groups have different format of saving hdf5 files. i guess the hdf5 file i have was saved as [channel, x, y, z, frames].

you can use use your current solution to solve the problem. in the meanwhile, i will also think about a robust solution to this issue.

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Sounds good, thanks.

re: second issue, could potentially have users input a vector as an option indicating the 3 relevant dimensions to make 3D [x y frames] matrix for CNMF-E to analyze. e.g hdf5Dims = [2 3 5];' for [channel, x, y, z, frames]saved files orhdf5Dims = [1 2 3];' for [x y frames] saved files.

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@zhoupc
The bug for
https://github.com/zhoupc/CNMF_E/blob/master/ca_source_extraction/endoscope/get_data_dimension.m#L35
is still not fixed. Makes it hard to integrate into other pipelines when users need to clone from your repository.

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@zhoupc
In line: https://github.com/zhoupc/CNMF_E/blob/master/ca_source_extraction/%40Sources2D/set_parameters.m#L99

I assume should say min_corr instead of min_pnr? e.g. fprintf('\tmin_corr stands for minimum local correlation. \n');

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