Moriel

bento/data_builder/util/loadAnnotFileObserver.m

@@ -1,5 +1,6 @@
 function [annot, maxTime] = loadAnnotFileObserver(cleantext, fr)
 
+
 cleantext = cellfun(@(x) regexprep(x,{'\"','(',')'},''), cleantext, 'uniformoutput',false);
 
 headers = split(cleantext{1},';');
@@ -24,7 +25,7 @@
         flag = 1;
     elseif strcmpi(event,'state stop')
         flag = 2;
-    elseif strcmpi(event,'state point') % not sure what this means.
+    elseif strcmpi(event,'state point') % start==stop
         continue
     else % does this ever happen??
         flag = 0;

bento/data_builder/util/loadAnnotFileXls.m

@@ -0,0 +1,41 @@
+function [annot,maxTime,hotkeys,FR] = loadAnnotFileXls(fname,defaultFR, tmin,tmax)
+%
+% (C) Ann Kennedy, 2019
+% California Institute of Technology
+% Licensing: https://github.com/annkennedy/bento/blob/master/LICENSE.txt
+
+if(nargin<2)
+    defaultFR = 1000;
+elseif(nargin<3)
+    tmin = 1;
+    tmax = inf;
+elseif(isstr(tmin))
+    tmin = str2num(tmin);
+    tmax = str2num(tmax);
+end
+FR = nan; %framerate not usually specified in these kinds of files, return nan to let the gui decide.
+
+fid = fopen(fname);
+if(fid==-1)
+    keyboard
+end
+
+[~,sheetlist]   = xlsfinfo(fname);
+fid = sheetlist{1};  % let's assume there's just one sheet for now- go back and fix this later
+[~,~,M]      = xlsread(fname,fid);
+
+hotkeys=struct();
+
+if(any(strcmpi(M(1,:),'Event_type'))) % it's probably an Ethovision Observer log
+    [annot,maxTime]  = loadAnnotSheetObserver(M, defaultFR);  % need to add tmin/tmax support
+    FR = defaultFR;
+elseif(any(strcmpi(M(1,:), 'Sinuosity')))  % it's probably DeepSqueak
+    if defaultFR<1024
+        defaultFR = 1024;
+    end
+    [annot,maxTime]  = loadAnnotSheetDeepSqueak(M, defaultFR);  % need to add tmin/tmax support
+    FR = defaultFR;
+else
+    annot=[];maxTime=[];hotkeys=struct();
+end
+end

bento/data_builder/util/loadAnnotSheetDeepSqueak.m

@@ -0,0 +1,47 @@
+function [annot, maxTime] = loadAnnotSheetDeepSqueak(M, defaultFR)
+
+headers = M(1,:);
+label_index = find(strcmpi(headers,'Label'));
+accepted_index = find(strcmpi(headers,'Accepted'));
+time_start = find(strcmpi(headers,'Begin Time (s)')|strcmpi(headers,'BeginTime_s_'));
+time_stop = find(strcmpi(headers,'End Time (s)')|strcmpi(headers,'EndTime_s_'));
+cluster_index = find(strcmpi(headers,'cluster'));
+
+if length([label_index accepted_index time_start time_stop])~=4
+    disp('something went wrong- I couldn''t find fields Label, Accepted, Begin Time, and/or End Time.');
+    return
+end
+
+annot.Ch1 = [];
+tstop = 0;
+for i=2:length(M)
+    if (isstr(M{i,accepted_index}) && ~strcmpi(M{i,accepted_index},'TRUE')) || ~M{i,accepted_index}
+        continue;
+    end
+
+    if isempty(cluster_index)
+        beh = strrep(M{i, label_index},' ','_');
+    else
+        beh = strrep(M{i, label_index},' ','_');
+        beh = [beh '_' num2str(M{i,cluster_index})];
+    end
+    beh = regexprep(beh, '[^\w]', ''); % remove bad characters
+    if ~isfield(annot.Ch1,beh)
+        annot.Ch1.(beh) = [];
+    end
+    tstart = ceil(M{i, time_start}*defaultFR);
+    tstop = ceil(M{i, time_stop}*defaultFR);
+    annot.Ch1.(beh)(end+1,:) = [tstart tstop];
+end
+maxTime = tstop;
+
+
+
+
+
+
+
+
+
+
+

bento/data_builder/util/loadAnnotSheetObserver.m

@@ -0,0 +1,54 @@
+function [annot, maxTime] = loadAnnotSheetObserver(M, defaultFR)
+
+headers = M(1,:);
+behavior_name_index = find(strcmpi(headers,'behavior'));
+event_type_index = find(strcmpi(headers,'event_type'));
+timestamp_index = find(strcmpi(headers,'Time_Relative_sf'));
+
+if length([behavior_name_index event_type_index timestamp_index])~=3
+    disp('something went wrong- I couldn''t find fields Behavior, Event_Type, and/or Time_Relative_sf.');
+    return
+end
+
+annot.Ch1 = [];
+counts=[];
+for i=2:length(M)
+    event = M{i,event_type_index};
+    if isnan(event)
+        continue;
+    end
+    if strcmpi(event,'state start')
+        flag = 1;
+    elseif strcmpi(event,'state stop')
+        flag = 2;
+    elseif strcmpi(event,'state point') % start==stop
+        continue
+    else % does this ever happen??
+        flag = 0;
+        keyboard
+    end
+
+    beh = strrep(M{i, behavior_name_index},' ','_');
+    beh = regexprep(beh, '[^\w]', ''); % remove bad characters
+    time = ceil(M{i, timestamp_index}*defaultFR);
+    if ~isfield(annot.Ch1,beh)
+        annot.Ch1.(beh) = [];
+        counts.(beh) = 0;
+    end
+    if flag==1
+        counts.(beh) = counts.(beh)+1;
+    end
+    annot.Ch1.(beh)(counts.(beh),flag) = time;
+end
+maxTime = time;
+
+
+
+
+
+
+
+
+
+
+

bento/data_builder/util/loadAnnotSheetTxt.m

@@ -108,7 +108,7 @@
                 end
             end
             if((vals(2)+tmin)>=winStart && (vals(1)+tmax)<=winStop) %if this annotation is within the range we're loading
-                annot.(ch).(beh)(end+1,:) = min(max(vals(1:2)-winStart,1),winStop-winStart+1);
+                annot.(ch).(beh)(end+1,:) = min(max(vals(1:2)-winStart+1-tmin+1,0),winStop-winStart+1);
                 if(vals(2)-tmin+1 > tmax)
                     tmax = vals(2)-tmin+2;
                 end