First commit of a starting GRIDlab codebase

Author: davidjuliancaldwell

.gitignore

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+##---------------------------------------------------
+## Remove autosaves generated by the Matlab editor
+## We have git for backups!
+## from https://github.com/github/gitignore/blob/master/Global/Matlab.gitignore ## We have git for backups!
+
+##---------------------------------------------------
+
+# images
+*.png
+*.jpg
+*.jpeg
+*.svg
+*.fig
+
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Simulink Code Generation
+slprj/
+
+# Session info
+octave-workspace
+
+# Simulink autosave extension
+.autosave

README.md

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+# CodeBase
+This is the github repository for the GRIDlab code base. The first existing code (circa JDW, 2.10.2015), has been pushed to a "StartingCodeRepo" folder. Variations or substantial deviations should be based off of this in other subfolders under the master Codebase folder

StartingCodeRepo/DataPrep/AnonymizeCodes.m

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+function AnonymizeCodes(subjID, dirToStartIn)
+
+    if dirToStartIn(end) ~= '\'
+        dirToStartIn(end+1) = '\';
+    end
+
+    patientDir = [dirToStartIn subjID '\'];
+
+    ProcessDir(patientDir, subjID)
+%     ProcessDir(dirToStartIn, subjID);
+    
+    fprintf('DONE\n');
+end
+
+function ProcessDir(directory, subjID)
+
+    subDirs = dir(directory);
+    subDirs = subDirs([subDirs.isdir]);
+    subDirs = {subDirs.name};
+    
+    subFiles = dir(directory);
+    subFiles = subFiles(~[subFiles.isdir]);
+    subFiles = {subFiles.name};
+
+    
+    for next = subFiles
+        fullFile = [directory next{:}];
+        locs = regexp(next{:},['(?i)' subjID], 'once');
+        if ~isempty(locs)
+            fprintf('Converting file %s...\n', fullFile);
+            oldFile = fullFile;
+            newFile = [directory strrep(next{:},subjID,genPID(subjID))];
+            cmd = sprintf('movefile(''%s'', ''%s'');', oldFile, newFile);
+            eval(cmd);
+        end
+    end
+    
+
+
+    
+    for target=subDirs
+        if strcmp(target{:},'..') == 1 || strcmp(target{:},'.') == 1
+            continue
+        end
+        ProcessDir([directory target{:} '\'], subjID);
+    end
+    
+    slashies = find(directory == '\',2,'last');
+    if isempty(slashies)
+        return;
+    end
+    subDirHasSubjID = regexp(directory(slashies(1):slashies(2)),['(?i)' subjID], 'once');
+    if isempty(subDirHasSubjID)
+        return
+    end
+    fprintf('Converting directory %s...\n', directory);
+    oldDir = directory;
+    newDir = [directory(1:slashies(1)) strrep(directory(slashies(1)+1:slashies(2)),subjID,genPID(subjID))];
+    cmd = sprintf('movefile(''%s'', ''%s'');', oldDir, newDir);
+    eval(cmd);
+end

StartingCodeRepo/DataPrep/CleanBCI2000ParamStruct.m

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+function params = CleanBCI2000ParamStruct(parms)
+
+flds = fieldnames(parms);
+    for i=flds';
+        try
+            tempField = parms.(i{1});
+        %         fprintf('%s ',tempField.Type);
+            switch tempField.Type
+                case 'string'
+                    eval(sprintf('params.%s = tempField.Value;',i{1}));
+                case 'matrix'
+                    eval(sprintf('params.%s = tempField.Value;',i{1}));
+                otherwise
+                    numVal = double(tempField.NumericValue);
+                    eval(sprintf('params.%s = numVal;',i{1}));
+            end
+        catch
+            bad = cell2mat(i);
+            fprintf('  ignoring params.%s, not numerical\n', bad);
+        end
+    end

StartingCodeRepo/DataPrep/CreateSmoothGloveTrace.m

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+function gloveTrace = CreateSmoothGloveTrace(states, parameters, method)
+% function [gloveTrace] = CreateSmoothGloveTrace(states, parameters, method)
+%
+% Changelog
+%   8/11/11 - tmb - originally written
+%   6/16/21 - jdw - changed to accept multiple cyberglove states naming
+%   conventions
+%
+% Simple function to take in the states and parameter structure from
+% BCI2000 and use a spline to interpolate the stairstepped glove trace.
+%
+% states - the bci2k state struct
+% parameters - the bci2k parameters structure
+% method - 'spline' or 'pchip', which is the piecewise cubic Hermite
+% interpolation. Slightly less organic than the spline, but avoids the
+% flat-step-flat artifacts that occur with splines
+
+if isstruct(parameters.SamplingRate) == 1
+    params = CleanBCI2000ParamStruct(parameters);
+else
+    params = parameters;
+end
+
+if (isfield(states, 'rCyber1'))
+    prefix = 'r';
+elseif (isfield(states, 'lCyber1'))
+    prefix = 'l';
+else
+    prefix = '';
+end
+
+for i=1:22
+    eval(sprintf('gloveTrace(:,i) = double(states.%sCyber%i);',prefix,i));
+    zeroPeriod = find(gloveTrace(:,i) > 0, 1, 'first')-1;
+    gloveTrace(1:zeroPeriod,i) = gloveTrace(zeroPeriod+1,i);
+
+%     gloveTrace(:,i) =
+%     spline(1:params.SampleBlockSize:length(gloveTrace(:,i)),gloveTrace(1:params.SampleBlockSize:end,i),1:length(gloveTrace(:,i)));
+    gloveTrace(:,i) = interp1(1:params.SampleBlockSize:length(gloveTrace(:,i)),gloveTrace(1:params.SampleBlockSize:end,i),1:length(gloveTrace(:,i)),method);
+end

StartingCodeRepo/DataPrep/GetBciClinicalData.m

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+%% TODO, needs to cross validate recording DATE for BCI2k File and EDF.
+%% Doesn't currently happen and this can lead to false results.
+
+curDir = pwd;
+
+%% select files of interest and get output filename
+cd (myGetenv('subject_dir'));
+
+fprintf('select an edf file: \n');
+[filename, directory] = uigetfile('*.rec;*.edf','MultiSelect', 'off');
+edfFilename = [directory filename];
+
+fprintf('select a bci2k file: \n');
+[filename, directory] = uigetfile('*.dat','MultiSelect', 'off');
+bci2kFilename = [directory filename];
+
+subjid = extractSubjid(bci2kFilename);
+
+%% load bci2kdata
+[sig, sta, par] = load_bcidat(bci2kFilename);
+defMaxChanNum = size(sig,2);
+
+
+%% get channel montages for comparison
+bChans = input(sprintf('channels from the BCI2K file to compare (default is [1:%d]): ', defMaxChanNum));
+
+if (isempty(bChans))
+    bChans = 1:defMaxChanNum;
+end
+
+cChans = input(sprintf('channels from the Clinical file to compare (default is [2:%d]): ', defMaxChanNum+1));
+
+if (isempty(cChans))
+    cChans = 2:defMaxChanNum+1;
+end
+
+[clinicalMontage, channelConfig] = getMontageFromEDF(edfFilename);
+
+fprintf(' here is the clinical montage: \n\n');
+
+for c = 1:length(clinicalMontage)
+    fprintf('  %d) %s\n', c, clinicalMontage{c});
+end
+
+selectedMontage = input(sprintf('select the components of the clinical montage to extract (typical matlab vector format [a b:c]): '));
+sChans = find(ismember(channelConfig, selectedMontage));
+
+%% match bcidata to clinical data
+
+% [signals, offsets] = matchClinicalData(edfFilename, bci2kFilename, true, 2:chans+1);
+[signals, offsets] = matchClinicalData(edfFilename, bci2kFilename, true, cChans, bChans, sChans);
+
+
+%% save result
+
+% massage the offsets a little bit to account for synch errors either on
+% our side or the clinical side
+offsets = round(offsets/100)*100;
+
+offsets
+mode(offsets)
+
+fprintf('clinical data matched, %f percent of channels correlated gave the same offset (%d of %d) \n', sum(offsets == mode(offsets)) / length(offsets) * 100, sum(offsets == mode(offsets)), length(offsets));
+result = input('  is this sufficient to save the clinical data? ([Y]\\n): ', 's');
+
+trodesFilename = [myGetenv('subject_dir') subjid '\trodes.mat'];
+if (exist(trodesFilename, 'file'))
+    load(trodesFilename);
+end % otherwise all the trodes will be 0,0,0
+
+if (isempty(result) || strcmp(lower(result), 'y') == 1)
+    defOutputFilename = strrep(bci2kFilename, '.dat', '_clinical.mat');
+    outputFilename = input(sprintf('filename to save [%s]: ', strrep(defOutputFilename,'\','\\')), 's');
+
+    if (isempty(outputFilename))
+        outputFilename = defOutputFilename;
+    end    
+    
+    mOutputFilename = strrep(outputFilename, '.mat', '_montage.mat');
+    
+    bci2kFs = par.SamplingRate.NumericValue;
+
+    EDF = sdfopen(edfFilename, 'r', 2);
+    fs = round(mode(EDF.SampleRate));
+    sdfclose(EDF);
+
+%     feedback = resampleBci2kDiscreteState(sta.Feedback, bci2kFs, fs);
+%     targetCode = resampleBci2kDiscreteState(sta.TargetCode, bci2kFs, fs);
+%     resultCode = resampleBci2kDiscreteState(sta.ResultCode, bci2kFs, fs);
+% 
+%     fprintf('saving %s\n', outputFilename);
+%     save(outputFilename, 'signals', 'feedback', 'targetCode', 'resultCode', 'fs');
+
+    stimulusCode = resampleBci2kDiscreteState(sta.StimulusCode, bci2kFs, fs);
+    
+    fprintf('saving %s\n', outputFilename);
+    save(outputFilename, 'signals', 'stimulusCode', 'fs');
+    
+    for c = 1:length(selectedMontage)
+        Montage.Montage(c) = sum(channelConfig == selectedMontage(c));
+    end
+    
+    Montage.MontageTokenized = {clinicalMontage{selectedMontage}};
+
+    Montage.MontageTrodes = [];
+    
+    for c = 1:length(Montage.MontageTokenized)
+        % build montage string
+        if (c == 1)
+            Montage.MontageString = Montage.MontageTokenized{c};
+        else
+            Montage.MontageString = [Montage.MontageString ' ' Montage.MontageTokenized{c}];
+        end
+        
+        % build electrodes
+        mElt = regexpi(Montage.MontageTokenized{c}, '([a-z]+).+', 'tokens', 'once');
+        mElt = mElt{1};
+        
+        if (exist(mElt, 'var'))
+            eval(sprintf('Montage.MontageTrodes = cat(1, Montage.MontageTrodes, %s);', mElt));
+        else
+            warning ('could not find electrode locations for %s, these will need to be set manually in the montage file', mElt);
+            Montage.MontageTrodes = cat(1, Montage.MontageTrodes, zeros(Montage.Montage(c), 3));
+        end
+    end
+
+    fprintf('Bad channels must be updated manually in the montage.\n');
+
+    fprintf('saving %s\n', mOutputFilename);
+    save(mOutputFilename, 'Montage');
+    
+end
+
+cd (curDir);
+    
+
+% %% create the appropriate variables in the .mat file
+% % signals, feedback, targetCode, resultCode, fs, Montage
+% bci2kFs = par.SamplingRate.NumericValue;
+% 
+% EDF = sdfopen(edfFilename, 'r', 2);
+% fs = round(mode(EDF.SampleRate));
+% sdfclose(EDF);
+% 
+% feedback = resampleBci2kDiscreteState(sta.Feedback, bci2kFs, fs);
+% targetCode = resampleBci2kDiscreteState(sta.TargetCode, bci2kFs, fs);
+% resultCode = resampleBci2kDiscreteState(sta.ResultCode, bci2kFs, fs);
+% 
+% montageFilename = strrep(bci2kFilename, '.dat', '_montage.mat');
+% if (exist(montageFilename, 'file'))
+%     load(montageFilename);
+% else
+%     Montage.Montage = size(signals, 2);
+%     Montage.BadChannels = [];
+% end
+% 
+% save(outputFilename, 'signals', 'feedback', 'targetCode', 'resultCode', 'fs');
+% 
+% cd (curDir);
+%