Hume 1.0a

Hume-1.0a/coreFunctions/importFunctions/convertScores_BrownTASCI.m

@@ -0,0 +1,280 @@
+function [scorer id cond outname outfile stageData] = convertScores_BrownTASCI(file,srate)
+% [scorer id cond outname outfile stageData] = convertScores_BrownTASCI(file,srate)
+%  
+%   Function to convert sleep stage data from VITASCORE TASCI to a stageData
+%   struct for Húmë processing (e.g. a plotSleepStats call)
+%
+%   Inputs (Required)
+%
+%       file (string)   ?  Name of TASCI file
+%
+%   Inputs (Optional)
+%
+%       srate ? Sampling rate of the scored data (default: 200 Hz)
+%
+%   Outputs:
+%
+%       scorer, id, cond, outname, outfile ? meta-information for saving
+%       data.
+%
+%       stageData ? converted stageData .mat file for Húmë processing
+%
+%%   Copyright (c) 2015 Jared M. Saletin, PhD and Stephanie M. Greer, PhD
+%
+%   This file is part of Húmë.
+%   
+%   Húmë is free software: you can redistribute it and/or modify it
+%   under the terms of the GNU General Public License as published by the
+%   Free Software Foundation, either version 3 of the License, or (at your
+%   option) any later version.
+% 
+%   Húmë is distributed in the hope that it will be useful, but
+%   WITHOUT ANY WARRANTY; without even the implied warranty of
+%   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+%   General Public License for more details.
+% 
+%   You should have received a copy of the GNU General Public License along
+%   with Húmë.  If not, see <http://www.gnu.org/licenses/>.
+%
+%   Húmë is intended for research purposes only. Any commercial or medical
+%   use of this software is prohibited. The authors accept no
+%   responsibility for its use in this manner.
+
+%% Check inputs
+
+if nargin == 2
+
+    savename = file(1:end-6);
+
+elseif nargin==1
+
+    srate = 200;
+
+elseif nargin==0
+
+    stageData={'Brown *.TASCI','.TASCI','convertScores_BrownTASCI'};
+
+    scorer=[];
+    id = [];
+    cond = [];
+    outname = [];
+    outfile = [];
+
+    return
+end
+
+%% META DATA
+[path, fileName, fileExt] = fileparts(file);
+
+mkdir([path,'/',fileName]);
+
+if isletter(fileName(3))
+
+        scorer = fileName(1:3);
+        trimmedName = fileName(4:end);
+    else
+        scorer = fileName(1:2);
+        trimmedName = fileName(3:end);
+
+
+end
+
+id = trimmedName(1:min(find(isletter(trimmedName)))-2);
+cond = trimmedName(min(find(isletter(trimmedName))):end);
+
+outname = [path,'/',fileName,'/',fileName];
+outfile = fileName;
+
+savename = [outname,'_scores'];
+
+%% PARSE 11 LINE HEADER
+
+fid = fopen(file);
+header = textscan(fid,'%s\t%s\t%s\t%s',11,'delimiter','|');
+
+scoringFile = file;
+EDFName = header{1,2}{2,1};
+recDate = header{1,2}{3,1};
+recStart = header{1,2}{4,1};
+
+win = str2num(header{1,4}{11,1});
+
+head = [char(header{1})  char(header{2}) char(header{3}) char(header{4})];
+stageData.Notes = head;
+
+%% READ STAGE DATA
+
+data = textscan(fid,'%d\t%d\t%d\t%d\t%s\t%s\t%s\t%s','Delimiter','|','headerlines',6);
+
+%% FIX NEW TASCIS
+
+if strcmp(data{1,7}{2},'')
+    stageString = data{1,7}(1:2:end);
+    times = data{1,5}(1:2:end);
+    eventMarks = data{1,6}(1:2:end);
+else
+    stageString = data{1,7};
+    times = data{1,5};
+    eventMarks = data{1,6};
+end
+
+%% SetUp Events
+
+stageData=eventSetup(stageData,length(stageString));
+LUT = eventLUT;
+lightsOffFound = 0;
+lightsOnFound = 0;
+
+for i = 1:length(eventMarks)
+
+    LOffEv =[];
+    LOnEv = [];
+    BkmkEv = [];
+    %Check if empty
+    if ~isempty(eventMarks{i})
+
+        separated = strsplit(eventMarks{i},', ');
+
+        % FIND LIGHTS OFF
+        if sum(ismember(separated,'Lights Off'))>0;
+            if lightsOffFound==1
+                 warning('Found Duplicate Lights Off. Last is used, Check Scored File to Confirm');
+            end
+
+           LOffEv = find(ismember(separated,'Lights Off')); 
+           lightsOffFound = 1;
+            epLightsOff = i;
+
+         % FIND LIGHTS ON   
+         elseif sum(ismember(separated,'Lights On'))>0;
+           if lightsOnFound==1
+                 warning('Found Duplicate Lights On. Last Is Used, Check Scored File to Confirm');
+           end
+
+            LOnEv = find(ismember(separated,'Lights On')); 
+            lightsOnFound = 1;
+            epLightsOn = i;
+
+        end
+
+        % FIND OTHER EVENTS
+
+        for ev = 1:size(LUT,1);
+            if sum(ismember(separated,LUT{ev,1}))>=1
+                stageData.eventMat(i,ev)=sum(ismember(separated,LUT{ev,1}));
+            end
+        end
+    end
+end
+
+
+%% SetUp Stage Data
+
+stages = NaN(length(stageString),1);
+
+% Set Stages from Staged Array
+
+for Ep = 1:length(stages)
+
+    Str = stageString{Ep};
+
+    switch Str
+        case 'Undefined'
+            stages(Ep)=7;
+        case 'Awake'
+            stages(Ep)=0;
+        case 'Wake'
+            stages(Ep)=0;
+        case '1'
+            stages(Ep)=1;
+        case 'N1'
+            stages(Ep)=1;
+        case '2'
+            stages(Ep)=2;
+        case 'N2'
+            stages(Ep)=2;
+        case '3'
+            stages(Ep)=3;
+        case 'N3'
+            stages(Ep)=3;
+        case '4' 
+            stages(Ep)=4;
+        case 'REM'
+            stages(Ep)=5;
+        case 'MVT'
+            stages(Ep)=6;
+    end         
+end
+
+stageData.stages = stages;
+
+stageData.win = win; % PULL FROM HEADER
+
+stageData.recStart = datenum(recStart,'HH:MM:SS'); % PULL FROM HEADER
+
+
+%epLightsOff = find(ismember(eventMarks, 'Lights Off')==1);
+stageData.lightsOFF = datenum(times(epLightsOff),'HH:MM:SS');
+%epLightsOn = find(ismember(eventMarks, 'Lights On')==1);
+stageData.lightsON = datenum(times(epLightsOn),'HH:MM:SS');
+
+%Add a day to the time if it looks like lights on happened before the
+%record start.
+if(~(stageData.recStart < stageData.lightsON))
+    stageData.lightsON = stageData.lightsON + 1;
+end
+%Add a day to the time if it looks like lights off happened before the
+%record start.
+if(~(stageData.recStart < stageData.lightsOFF))
+    stageData.lightsOFF = stageData.lightsOFF + 1;
+end
+
+stageData.srate = srate;
+
+stageData.stageTime = (0:(size(stageData.stages, 1) - 1))./(60/stageData.win);
+
+% stageData.onsets
+
+scoredEps = find(stageData.stages ~=7); 
+firstScoredEp = scoredEps(1);
+lastScoredEp = scoredEps(end);
+
+stageData.onsets = zeros(length(stageData.stages), 1);
+
+for i = firstScoredEp:lastScoredEp
+
+    stageData.onsets(i) = ((i-1)*stageData.win*stageData.srate)+1;
+
+end
+
+%% Save
+
+save(savename,'stageData');
+
+end
+
+
+% %get only the data that is scored
+% 
+% for i = 1:6
+%     inds = find(stages(:, 1) == i);
+%     totalTime(i) = sum((onsets(inds)/stageData.srate + stageData.win));
+% end
+% 
+% perTime = totalTime(1:5)./sum(totalTime(1:5));
+% 
+% figure;
+% 
+% subplot(1, 2, 1)
+% bar(totalTime/60)
+% title('Total Time')
+% set(gca, 'XTick', 1:6, 'XTickLabel', {'1'; '2'; '3'; '4'; 'REM'; 'Wake'})
+% ylabel('Minutes')
+% xlim([.5, 6.5])
+% 
+% subplot(1, 2, 2)
+% bar(perTime)
+% title('Percentage of Sleep')
+% set(gca, 'XTick', 1:5, 'XTickLabel', {'1'; '2'; '3'; '4'; 'REM'})
+% ylabel('% of sleep')
+% xlim([.5, 5.5])