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giving the KS main file a more rational name
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139 changes: 139 additions & 0 deletions
139
ecephys_spike_sorting/modules/kilosort_helper/main_kilosort_multiversion.m
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,139 @@ | ||
| function main_KS2_KS25( KSver, remDup, finalSplits, labelGood, saveRez ) | ||
| % paths will get set by the pipeline | ||
| % config file created by pipeline and saved in directory with master | ||
| % channel map created by pipeline, path specified in config | ||
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| rP.KSver = KSver; | ||
| rP.remDup = remDup; | ||
| rP.finalSplits = finalSplits; | ||
| rP.labelGood = labelGood; | ||
| rP.saveRez = saveRez; | ||
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| fprintf( 'main_KS2_KS25_KS3 params: \n'); | ||
| disp(rP) | ||
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| if ~(strcmp(rP.KSver, '2.5') | strcmp(rP.KSver, '2.0') | strcmp(rP.KSver, '3.0') ) | ||
| fprintf('unsupported kilosort version\n'); | ||
| return; | ||
| end | ||
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| run('kilosort2_config_file.m') | ||
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| if strcmp(rP.KSver, '2.5') | ||
| % main parameter changes from Kilosort2 to v2.5 | ||
| ops.sig = 20; % spatial smoothness constant for registration | ||
| ops.fshigh = 300; % high-pass more aggresively | ||
| ops.nblocks = 5; % blocks for registration. 0 turns it off, 1 does rigid registration. Replaces "datashift" option.; | ||
| % random number generator is used in datashift and to set order of batches | ||
| % set seed and initialize here. | ||
| iseed = 1; | ||
| rng(iseed); | ||
| elseif strcmp(rP.KSver, '3.0') | ||
| % main parameter changes from Kilosort2 to v2.5 | ||
| ops.sig = 20; % spatial smoothness constant for registration | ||
| ops.fshigh = 300; % high-pass more aggresively | ||
| ops.nblocks = 5; % blocks for registration. 0 turns it off, 1 does rigid registration. Replaces "datashift" option. | ||
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| % main parameter changes from Kilosort2.5 to v3.0 | ||
| % if using KS3, set ops.Th appropriately from the calling program | ||
| % ops.Th = [9, 9]; | ||
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| end | ||
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| % find the binary file | ||
| rootZ = ops.rootZ; | ||
| ops.fbinary = fullfile(ops.datafile); | ||
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| % print out ops | ||
| ops | ||
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| % preprocess data to create temp_wh.dat | ||
| rez = preprocessDataSub(ops); | ||
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| if ~strcmp(rP.KSver, '3.0') | ||
| % That is for KS2.0 and KS 2.5 | ||
| if strcmp(rP.KSver, '2.5') | ||
| % data registration step | ||
| rez = datashift2(rez, 1); % last input is for shifting data | ||
| % main tracking and template matching algorithm | ||
| rez = learnAndSolve8b(rez, iseed); | ||
| elseif strcmp(KSver, '2.0') | ||
| % time-reordering as a function of drift | ||
| rez = clusterSingleBatches(rez); | ||
| rez = learnAndSolve8b(rez); | ||
| end | ||
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| % OPTIONAL: remove double-counted spikes - solves issue in which individual spikes are assigned to multiple templates. | ||
| % See issue 29: https://github.com/MouseLand/Kilosort/issues/29 | ||
| if rP.remDup | ||
| rez = remove_ks2_duplicate_spikes(rez); | ||
| end | ||
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| % final merges | ||
| rez = find_merges(rez, 1); | ||
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| % final splits by SVD | ||
| if rP.finalSplits | ||
| rez = splitAllClusters(rez, 1); | ||
| end | ||
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| % decide on cutoff | ||
| rez = set_cutoff(rez); | ||
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| % eliminate widely spread waveforms (likely noise); only implemented in KS2.5 release | ||
| if ( rP.labelGood & strcmp(rP.KSver, '2.5')) | ||
| rez.good = get_good_units(rez); | ||
| end | ||
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| fprintf('found %d good units \n', sum(rez.good>0)) | ||
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| else | ||
| % For KS 3.0 | ||
| rez = datashift2(rez, 1); | ||
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| [rez, st3, tF] = extract_spikes(rez); | ||
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| rez = template_learning(rez, tF, st3); | ||
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| [rez, st3, tF] = trackAndSort(rez); | ||
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| rez = final_clustering(rez, tF, st3); | ||
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| rez = find_merges(rez, 1); | ||
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| rezToPhy2(rez, rootZ); | ||
| end | ||
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| % write to Phy | ||
| fprintf('Saving results to Phy \n') | ||
| rezToPhy(rez, rootZ); | ||
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| if rP.saveRez | ||
| %% if you want to save the results to a Matlab file... | ||
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| % discard features in final rez file (too slow to save) | ||
| rez.cProj = []; | ||
| rez.cProjPC = []; | ||
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| % final time sorting of spikes, for apps that use st3 directly | ||
| [~, isort] = sortrows(rez.st3); | ||
| rez.st3 = rez.st3(isort, :); | ||
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| % Ensure all GPU arrays are transferred to CPU side before saving to .mat | ||
| rez_fields = fieldnames(rez); | ||
| for i = 1:numel(rez_fields) | ||
| field_name = rez_fields{i}; | ||
| if(isa(rez.(field_name), 'gpuArray')) | ||
| rez.(field_name) = gather(rez.(field_name)); | ||
| end | ||
| end | ||
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| % save final results as rez2 | ||
| fprintf('Saving final results in rez2 \n') | ||
| fname = fullfile(rootZ, 'rez2.mat'); | ||
| save(fname, 'rez', '-v7.3'); | ||
| end | ||
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| end |
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