Bugfix in Sources2D save_workspace method and get_data_dimension.m

[bahanonu]

@zhoupc

There is a bug at https://github.com/zhoupc/CNMF_E/blob/master/ca_source_extraction/%40Sources2D/Sources2D.m#L1810.

if ~exist('zip_file_path', 'var') || ~isempty(zip_file_path)

should be changed to

if exist('zip_file_path', 'var') && ~isempty(zip_file_path)

to avoid errors in the default scripts when the method is called without a zip file specified (e.g. neuron.save_workspace();). See https://github.com/zhoupc/CNMF_E/blob/master/demos/demo_large_data_1p.m#L215.

[bahanonu]

@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.

[zhoupc]

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.

[bahanonu]

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.

[bahanonu]

@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.

[bahanonu]

@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');