initial adds

elanAnnotationMatches.m

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+% function res=elanAnnotationMatches(tier, matchingString)
+%
+% calculates the occurences of 'matchingString' in the annotations of 'tier' and 
+% returns the number of matches. The match is ignoring the case (e.g.
+% 'Biron' matches 'biron').
+% 
+% arguments: tier:              _one_ tier structure 
+%            matchingString:    the string to search for (if it is a cell
+%                               array, all the values are search for and
+%                               results are reported separately
+%
+% example:
+% s=elanAnnotationStats(e.tiers.SaySrv,'ich');
+%
+% res = 
+%
+%      matchingCount: 99
+%         totalCount: 181
+%    matchingPercent: 0.5470
+%    matchingIndices: [1x99 double]
+%
+% example:
+% res=elanAnnotationMatches(e.tiers.SaySrv,{' ist ' ' ich '})
+%
+% res = 
+%
+%    anno_ist: [1x1 struct]
+%    anno_ich: [1x1 struct]
+%res.anno_ich
+%
+% ans = 
+%
+%      matchingCount: 99
+%         totalCount: 181
+%    matchingPercent: 0.5470
+%    matchingIndices: [1x99 double]
+
+
+function res=elanAnnotationMatches(tier, pattern)
+if (iscell(pattern)) 
+    for i=1:length(pattern);
+        res.(correctStructID(pattern{i}))=elanAnnotationMatches(tier, pattern{i});
+    end;
+else
+
+    % compute for each value
+
+    annos=lower({tier.value});
+
+    matches=[];
+    for i=1:length(annos);
+        if (strfind(annos{i}, lower(pattern)))
+            matches=[matches i];
+        end;
+    end;
+    res.matchingCount = length(matches);
+    res.totalCount= length(annos);
+    res.matchingPercent = res.matchingCount / res.totalCount;
+    res.matchingIndices = matches;
+end;
+
+function structID=correctStructID(in)
+structID=regexprep(strtrim(in),'[^\w]|[äöüßÄÖÜ]','_');
+%     structID = strrep(in, '.', '_');
+%     structID = strrep(structID, '-', '_');
+%     structID = strrep(structID, ' ', '_');
+%     structID = strrep(structID, ',', '_');
+%     structID = strrep(structID, ';', '_');
+%     structID = strrep(structID, ':', '_');
+%     structID = strrep(structID, ':', '_');
+%         structID = strrep(structID, ':', '_');
+%             structID = strrep(structID, ':', '_');
+
+% add 'anno_' before annotation value
+if (~isempty(structID))
+	structID = strcat('anno_',structID);
+	%	 else
+	%		 warning ('empty tierID');
+end

elanAssignTiersWithCSV.m

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+% function elan = elanAssignTiersWithCSV (elan, tiers, csvid, part)
+%
+% This function assigns tiers with linkedFiles (or parts of them) given in
+% the arguments.
+%
+% NEEDS    :
+% USED BY  :
+%
+% ARGUMENTS: elan: an elan .eaf file loaded with elanReadFile.m
+%            tiers: one or more tiers
+%            csvid: id of one linkedFile (timeseries/csv)
+%            part: columns of csv file that are assigned to tiers
+% RETURNS  : elan: elan .eaf file with assignedTiers struct added            
+%
+% adierker / 2011-03-03
+% USAGE    : [elan] = elanAssignTiersWithCSV(eaffile,{'Kopfgesten_remus','mt9_remus_classification_hg_004'},'csv_1',[2:7]);
+% 
+% Note: If your assigned pairs are erroneous you have to explicitly 
+% reset the assignments to a new value or delete
+% them by using the variable browser in your workspace and choose "delete"
+% on the assignedTiers struct
+function elan = elanAssignTiersWithCSV (elan, tiers, csvid, part)
+
+% check correctness of arguments
+
+% argument one: elan
+if (~isfield(elan,'linkedFiles'))
+	error('there are no timeseries files linked to your elan file');
+end%if
+
+% argument two: tiers
+if (~iscell(tiers))
+	% if 'tiers' is only single tier create cell with one element
+	tiers = {tiers};
+end%if	
+
+% argument three: csvid
+if (nargin < 3)
+	linkedFiles = fieldnames(elan.linkedFiles);
+	csvid = linkedFiles{1};
+	if (length(linkedFiles)>1)
+		warning('please choose _one_ linked File');
+	end
+elseif (iscell(csvid))
+	warning('Elan does not support more than one linked File yet and thus this software toolkit does not support it as well');
+elseif (~isfield(elan.linkedFiles,csvid))
+	warning('csvid "%s" not found in linked Files',csvid);
+end%if
+
+csvlength = size(elan.linkedFiles.(csvid).data,2);
+% argument four: part
+if (nargin < 4)
+	part = [2:csvlength];
+elseif (length(part) > csvlength-1)
+	error('%s has only columns 2 to %s assign',csvid,num2str(csvlength))
+end%if
+
+% which part of the csv shall be assigned?
+%partname = strcat('part_',num2str(1));
+partsize = strcat('part_',regexprep(num2str(part),' ','_'));
+
+% assign csvids (with parts) with tiernames
+% add entries for csvids and all tiernames
+for tiernum = 1:length(tiers)
+	if (~isfield(elan,'assignedTiers'))
+		elan.assignedTiers = struct();
+	end%if
+	tiername = tiers{tiernum};
+	if (isfield(elan.tiers,tiername))
+		if (~isfield(elan.assignedTiers,csvid))
+			elan.assignedTiers.(csvid) = struct();
+		end%if
+		elan.assignedTiers.(csvid).(partsize) = tiers;
+		%elan.assignedTiers.(csvid).(partname).partsize = num2str(part);
+		elan.assignedTiers.(tiername)= struct();
+		elan.assignedTiers.(tiername).(csvid) = num2str(part);
+		%elan.assignedTiers.(tiername).(partname) = part;
+	else
+		warning('tiername "%s" not found',tiername); 
+	end%if
+end%for
+
+end%mainfunction
+% suppress some matlab code warnings for this file (only for use with matlab editor)
+%#ok<*WNTAG>

elanComputeOverlap.m

@@ -0,0 +1,126 @@
+% function [newCompTier,overlaps,redundantCompTier]=elanComputeOverlap(compTier,refStartTS,refStopTS,refTierValues,numOverlap)
+% 
+% compare compTier with arrays of timestamps (e.g. from refTier): [refStartTS] and [refStopTS];
+% compute overlap cases (CCCCC is the compTier/annotation, RRR is the
+% refTier that actually is sliced)
+% case 1: "extend" (overlapCase 3)
+% CCCCCCCCCCCCCC
+%    RRRRRRR
+% case 2: "end extends" (overlapCase 5)
+%       CCCCCCCC
+%    RRRRRRR
+% case 3: "begin extends" (overlapCase 9)
+%  CCCCCC
+%    RRRRRRR
+% case 4: "include" (overlapCase 17)
+%     CCCC
+%   RRRRRRRRR
+% feature request: function argument that specifies a min number frames to
+% overlap that leads to an overlap situation
+function [newCompTier,overlaps,redundantCompTier]=elanComputeOverlap(compTier,refStartTS,refStopTS,refTierName,compTierName,refTierValues,minOverlap)
+
+% create four grids (one for each start/stop value list)
+% e.g. refStartMat: width=length(refStartTS) length=length(compTier) with refStartTS values
+% e.g. compStartMat: width=length(refStartTS) length=length(compTier) with compTier.start values
+[refStartMat, compStartMat] = meshgrid(refStartTS,[compTier.start]);
+[refStopMat, compStopMat] = meshgrid(refStopTS,[compTier.stop]);
+
+% identify all annotations that at least touch somehow
+overlaps=double((compStartMat < refStopMat) & (compStopMat > refStartMat));
+
+[compIndex, refIndex]=find(overlaps); %[row, col] = find(X)
+
+% set all overlapSeconds to zero
+for i=1:length(refIndex)
+	compTier(compIndex(i)).overlapSeconds=0;
+end;
+
+
+
+% check all overlaps for their overlapCase and plot them
+for i=1:length(refIndex)
+	rStart=refStartTS(refIndex(i));
+	rStop=refStopTS(refIndex(i));
+	rDur=rStop-rStart;
+
+	if nargin > 3 % for plotting of overlaps: RefTier
+		gcf;
+		clf;
+		% plot this annotation
+		annoval = strcat(' "',refTierValues{refIndex(i)},'" id: ',num2str(refIndex(i)));
+		lineval = strcat(' ',refTierName,' (refTier)');
+		z = 2;
+		x=rStart; %start point for annotation
+		w=rDur; %width for annotation
+		y=z-0.4;% 'line' in plot where tier will be plotted
+		h=0.6; % height for tiers in plot
+		grey = [.7 .7 .7];
+		rectangle('Position',[x y w h],'EdgeColor','none','FaceColor',grey);%,'Curvature',0.2);
+		text(x,z,annoval,'Color',[0 0 0],'Interpreter','none');
+		text(x,z-0.25,lineval,'Color',[0 0 0],'Interpreter','none');
+		hold on;
+	end
+
+	cStart=compTier(compIndex(i)).start;
+	cStop=compTier(compIndex(i)).stop;
+	cDur=cStop-cStart;
+	overDur=0;
+
+
+
+	% case 1:
+	% CCCCCCCCCCCCCC
+	%    RRRRRRR
+	if (cStart < rStart && cStop > rStop)
+		overlaps(compIndex(i), refIndex(i)) = bitor(overlaps(compIndex(i), refIndex(i)), 2);
+		overDur=rDur; % duration of overlap
+		% case 2:
+		%       CCCCCCCC
+		%    RRRRRRR
+	elseif (cStart >= rStart && cStop > rStop)
+		overlaps(compIndex(i), refIndex(i)) = bitor(overlaps(compIndex(i), refIndex(i)), 4);
+		overDur=rStop-cStart;
+		% case 3:
+		%  CCCCCC
+		%    RRRRRRR
+	elseif (cStart < rStart && cStop <= rStop)
+		overlaps(compIndex(i), refIndex(i)) = bitor(overlaps(compIndex(i), refIndex(i)), 8);
+		overDur=cStop-rStart;
+		% case 4:
+		%     CCCC
+		%   RRRRRRRRR
+	elseif (cStart >= rStart && cStop <= rStop)
+		overlaps(compIndex(i), refIndex(i)) = bitor(overlaps(compIndex(i), refIndex(i)), 16);
+		overDur=cDur;
+	else
+		warning('unmodeled case');
+	end;
+	compTier(compIndex(i)).overlapCase=overlaps(compIndex(i), refIndex(i));
+	compTier(compIndex(i)).overlapSeconds=compTier(compIndex(i)).overlapSeconds+overDur;
+
+
+	if nargin > 3 % for plotting of overlaps: CompTier
+		% plot overlap case
+		blue = [0.30 0.40 0.6];
+		text(x,1.4,strcat('OverlapCase:  ',num2str(overlaps(compIndex(i)), refIndex(i))),'Color',[0 0 0],'BackgroundColor',blue,'FontWeight','bold','FontSize',14,'EdgeColor','none','Interpreter','none');
+		% plot this annotation
+		annoval = strcat(' "',compTier(compIndex(i)).value,'" id: ',num2str(compIndex(i)));
+		lineval = strcat(' ',compTierName,' (compTier)');
+		z = 1;
+		x=cStart; %start point for annotation
+		w=cDur; %width for annotation
+		y=z-0.4;% 'line' in plot where tier will be plotted
+		h=0.6; % height for tiers in plot
+		grey = [.7 .7 .7];
+		rectangle('Position',[x y w h],'FaceColor',grey,'EdgeColor','none');%,'Curvature',0.2); 
+		text(x,z,annoval,'Color',[0 0 0],'Interpreter','none');
+		text(x,z-0.25,lineval,'Color',[0 0 0],'Interpreter','none');
+		hold off;
+		pause(2.5);
+	end
+end;
+
+% prepare return variables redundantCompTier and newCompTier
+selectedCompInd=unique(compIndex); 
+newCompTier=compTier(selectedCompInd);  % single elements (for slicing)
+redundantCompTier = compTier(compIndex); % repeated elements (only important for elanCorrelateTiers)