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Author: rcafoley

ConversionScriptMUEdittoOTBFormatforOpenHDEMGversion2.m

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+%Code for converting MUEdit exports to OTB style exports for use in
+%openHDEMG and analyze HDEMG decompositions.
+% 
+%In openHDEMG open the new file as an OTB format and ensure
+%you select the same extension factor that was chosen in MUEdit as this
+%will not be hardcoded anywhere. 
+
+%Note that this is designed for a very specific export. you need to change
+%the descriptions dection to match your export or the torque data to pull
+%your correct aux channel info. Further, this only imports the first
+%channel of aux data as 'aquired force' if you wish to use some other
+%channel as the reference signal then that must be changed to select the
+%proper column of data from signal.auxillary on line 83
+
+%Last edit April 4 2024
+
+%Copyright Ryan C. A. Foley 2024
+%Github: rcafoley
+%Twitter: foleyneuromech
+%LinkedIn: ryancafoley
+
+%% Clear all variables from the workspace, clear the Command Window, and print the current directory
+clear all; % Clears all variables from the workspace
+clc;       % Clears the Command Window
+disp(['Current working directory: ', pwd]); % Prints the current directory
+
+%Variables to change to accomodate different experimental setups
+%TypeofArray(s)
+emgArray = 'GR04MM1305'
+%muscle
+muscle = 'Tibialis Anterior'
+%MVC value & offset
+mvc = 0.466 %in mV
+offset = 0.13 %inmV
+
+% List all .mat files in the current directory
+files = dir('*.mat');
+
+for i = 1:length(files)
+    originalFileName = files(i).name;
+    fprintf('Processing %s\n', originalFileName);
+    
+    % Load the .mat file
+    loadedData = load(originalFileName);
+    % Assume 'edition' and 'signal' are variables within 'loadedData'
+    % Adjust the following lines if they're nested within another structure
+    edition = loadedData.edition; % Or the appropriate field if nested differently
+    signal = loadedData.signal;   % Adjust based on your data structure
+    
+
+    %% Data Conversion here
+
+    %define the number of units from the decomp - this may need to the "clean"
+    %versions if a unit is deleted
+    
+    numRawChannels = size(signal.data, 1);
+    numMUs = size(edition.Dischargetimes, 2);
+
+    %define the total channels to be created Array size (monopolar + 1
+    %force + number of MUs x2 decomp and source)
+
+    totalChannels = numRawChannels + 1 + numMUs + numMUs; 
+
+    %FileType
+    OTBFile = 'unknown';
+    %SamplingRate
+    SamplingFrequency = signal.fsamp;
+
+    %Time Vector
+    % Initialize the cell array
+    Time = cell(1,1); % Creates a 1x1 cell array
+    % Insert the array 'edition.time' into the {1,1} location of the cell array 'Time'
+    Time{1,1} = edition.time';
+
+    %Convert the HDEMG Array Data Arrays
+    %first 64 are the raw data from the grid
+    Data = cell(1,1); % Creates a 1x1 cell array
+    Data{1,1} = signal.data';
+
+    % Extract the specific torque data from 'signal.auxillary' - ours is in
+    % row 1 but you may have more or want a different row for other aux or
+    % the target path
+   torqueColumnData = signal.auxiliary(10, :).'; % Transpose it to match the orientation (rows, not columns)
+    
+    % Check to ensure dimensions match for concatenation
+    if size(Data{1,1}, 1) == length(torqueColumnData)
+        % Add the new column to the array in 'Data{1,1}'
+        Data{1,1} = [Data{1,1}, torqueColumnData];
+    else
+        disp('Error: Dimension mismatch. Cannot concatenate torque to the new column.');
+    end
+
+    %Extract the decomposition aka discharge times
+    maxSamples = length(edition.time);
+
+    % Initialize the array to hold all converted data. Rows represent samples, columns represent scenarios.
+    allDecompositionConvertedData = zeros(maxSamples, numMUs);
+    
+    % Loop through each scenario and fill in the allConvertedData array
+    for i = 1:numMUs
+        % Extract the event data for the current scenario
+        spikeData = edition.Dischargetimes{1, i};
+        
+        % Create a temporary array of zeros for the current scenario
+        otbSpikeData = zeros(maxSamples, 1);
+        
+        % Mark the events in the tempData
+        otbSpikeData(spikeData) = 1;
+        
+        % Assign the converted data to the corresponding column in allConvertedData
+        allDecompositionConvertedData(:, i) = otbSpikeData;
+    end
+
+        % Check to ensure dimensions match for concatenation
+    if size(Data{1,1}, 1) == length(allDecompositionConvertedData)
+        % Add the new column to the array in 'Data{1,1}'
+        Data{1,1} = [Data{1,1}, allDecompositionConvertedData];
+    else
+        disp('Error: Dimension mismatch. Cannot concatenate spike decomposition to the new column.');
+    end
+
+        %Extract the source data for the decomposition aka individual optimised
+    %EMG channels for that MU **** NOTE: this may have to be changed to
+    %PulseTrainCLEAN as that may be the edited data - same for decomp
+    sourceEMGColumnData = edition.Pulsetrain{1,1}.'; % Transpose it to match the orientation (rows, not columns)
+    
+    % Check to ensure dimensions match for concatenation
+    if size(Data{1,1}, 1) == length(sourceEMGColumnData)
+        % Add the new column to the array in 'Data{1,1}'
+        Data{1,1} = [Data{1,1}, sourceEMGColumnData];
+    else
+        disp('Error: Dimension mismatch. Cannot concatenate sourceEMG to the new column.');
+    end
+
+    %Reconstruct the needed Descriptions for each channel
+    %these cannot be extracted from the MUedit export easily so we will
+    %reconstruct them. If your setup is different you will need to adjust
+    %these to have the coorect info. this can be found 
+
+    % Initialize the Descriptions cell array
+    Description = cell(totalChannels, 1); % Adjust the size based on the total number of descriptions
+    
+    % Fill the array with descriptions using dynamic components
+    for i = 1:numRawChannels % For the repetitive part with numbers 1 to 64
+        Description{i} = sprintf('%s - MULTIPLE IN 1 (Channel 1->64) - %s (%d)[mV]', muscle, emgArray, i);
+    end
+    
+    % Add unique descriptions after the loop with dynamic MVC and Offset values
+    Description{numRawChannels+1} = sprintf('acquired data MVC=%.3f Offset=%.2f[mV]', mvc, offset);
+    
+    % For Decomposition and Source for decomposition descriptions using dynamic components
+    for i = 1:numMUs
+        Description{(numRawChannels+1) + i} = sprintf('Decomposition of %s - MULTIPLE IN 1 (Channel 1->64) - %s (%d)[a.u]', muscle, emgArray, i);
+        Description{(numRawChannels+1+numMUs) + i} = sprintf('Source for decomposition of %s - MULTIPLE IN 1 (Channel 1->64) - %s (%d)[a.u]', muscle, emgArray, i);
+    end
+    
+    % Display the Descriptions cell array to verify
+    %disp(Description);
+
+    %% Output here
+    %% Output here
+    % Save the original data with a new name (_MUEditExport appended)
+    originalFileNewName = [originalFileName(1:end-4), '_MUEditExport.mat'];
+    save(originalFileNewName, '-struct', 'loadedData');
+    
+    % Save the variables into the new MAT file
+    newFileName = [originalFileName(1:end-4), '_ConvertedToOTBExportFormat.mat'];
+    save(newFileName, 'Time', 'Data', 'Description', 'SamplingFrequency', 'OTBFile');
+end