search

schnitzer-lab / EXTRACT-public

EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon calcium imaging movies.
MIT License
62 stars 16 forks source link

`graphconncomp` issue in Matlab 2022b #34

Closed bahanonu closed 1 year ago

bahanonu commented 1 year ago

@fatihdinc When running the current version of EXTRACT in MATLAB 2022b, the below error occurs. Looks like it might be related to #26 and would require checking availability of graphconncomp.

Error using graphconncomp
GRAPHCONNCOMP has been removed. Use CONNCOMP instead.

Error in find_conncomp (line 30)
        [s, memberships] = graphconncomp(sparse(A));

Error in remove_redundant/find_excess_components (line 167)
            C = find_conncomp(M, corr_threshold, A2);

Error in remove_redundant/get_bad_components (line 134)
            [merge, is_T_duplicate] = find_excess_components(T'*corr(S_smooth),... %*(S'*S_smooth)

Error in remove_redundant (line 48)
    [idx_elim, is_attr_bad, merge] = get_bad_components(metrics, ...

Error in run_extract (line 471)
        [classification, is_bad] = remove_redundant(...

Error in extractor (line 392)
        [S_this, T_this, summary_this] = run_extract(M_small, config_this);
fatihdinc commented 1 year ago

Just asked @approbatory to double check, we can simply use the code suggested in the absence of the bioinformatics toolbox.

fatihdinc commented 1 year ago

It seems this has now been fixed. Closing the issue