Add initial hdsort_compiled.m

Author: chyumin

hdsort-compiled/hdsort_compiled.m

@@ -0,0 +1,55 @@
+function hdsort_compiled(outputFolder)
+    try
+
+        %% Load sorter configs and params
+        load(fullfile(outputFolder, 'configsParams.mat'))
+
+        if (strcmp(fileFormat, 'maxwell'))
+            RAW = hdsort.file.MaxWellFile(rawFile);
+        elseif (strcmp(fileFormat, 'mea1k'))
+            RAW = hdsort.file.BELMEAFile(rawFile);
+        end
+
+        RAW.restrictToConnectedChannels(); % This line is very important to not sort empty electrodes!
+
+        %% Create the object that performs the sorting:
+        mainFolder = '.';
+        HDSorting = hdsort.Sorting(RAW, mainFolder, sortingName)
+
+        %% Preprocess:
+        % The preprocessor loads data from the file in chunks, filters it, and saves
+        % the filtered data into a new hdf5 file that is standardized for all types
+        % of input data.
+        % It further performs a couple of operations for each local electrode group
+        % (LEG) such as spike detection, spike waveform cutting and noise
+        % estimation. The result is a folder named group000x for each LEG that
+        % contains the data necessary to perform the parallel parts of the sorting.
+        % This implementation minimizes the number of time-consuming file access
+        % operations and thus speeds up the parallel processes significantly, even
+        % allowing the parallel processes to be run on a small desktop computer or
+        % laptop.
+
+        chunkSize = chunkSize; % This number depends a lot on the available RAM
+        HDSorting.preprocess('chunkSize', chunkSize, 'forceFileDeletionIfExists', true);
+
+        %% Sort each LEG independently:
+        HDSorting.sort('sortingMode', loopMode); % (default)
+        % Alternative sorting modes are:
+        % HDSorting.sort('sortingMode', 'local'); % for loop over each LEG
+        % HDSorting.sort('sortingMode', 'grid'); % requires a computer grid architecture
+
+        %% Combine the results of each LEG in the postprocessing step:
+        HDSorting.postprocess()
+
+        %% Export the results in an easy to read format:
+        [sortedPopulation, sortedPopulation_discarded] = HDSorting.createSortedPopulation(mainFolder);
+
+        %% When the sorting has already been run before, open the results from a file with:
+        % sortedPopulation = hdsort.results.Population(HDSorting.files.results);
+    catch
+        fprintf('----------------------------------------');
+        fprintf(lasterr());
+        quit(1);
+    end
+    quit(0);
+end