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Merge pull request #1 from donaldsonlab/addBORISparser
Add boris parser
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| Original file line number | Diff line number | Diff line change |
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| %% Script to take BORIS .csv output and format it for fiber fluorescence analysis with behavior_driver script | ||
| % Written 9/16/20 by Lisa Hiura | ||
| % Editted 9/16/20 by Anna McTigue | ||
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| %% Imports Data | ||
| % % Import behavior Data | ||
| prompt = 'Enter the BORIS output file name \n'; | ||
| behavior_file_name = input(prompt, 's'); | ||
| behaviorData = readtable(behavior_file_name); | ||
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| %drop the first 10 lines because they are extraneous | ||
| behaviorData(1:10,:) = []; | ||
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| %drop columns for media file, total length, FPS, subject, behavioral | ||
| %category, and comment | ||
| behaviorData(:,[2:5,7:8]) = []; | ||
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| %Assign meaningful column names | ||
| behaviorData.Properties.VariableNames = {'Time_in_Video' 'Behavior' 'Status'}; | ||
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| %drop rows that have 'STOP' as Status to treat all behaviors as point | ||
| %events | ||
| behaviorData(ismember(behaviorData.Status,'STOP'),:)=[]; | ||
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| %transform time in sec to msec | ||
| behaviorData.Time_in_Video = behaviorData.Time_in_Video ./ 1000; | ||
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| %move the Status column over 1 to the right (should now be column 4) | ||
| behaviorData(:,4) = [ behaviorData(:,3)]; | ||
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| %prompt time offset to align behavior data with fluorescence data | ||
| prompt = 'Enter the timestamp file name \n'; | ||
| timestamp_file_name = input(prompt, 's'); | ||
| timestamps = readtable(timestamp_file_name); | ||
| time_offset = timestamps{1,1}; | ||
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| %fix column names | ||
| behaviorData.Properties.VariableNames = {'Time_in_Video' 'Behavior' 'corrected_time' 'Status'}; | ||
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| %add offset to the behavioral timestamps | ||
| %behaviorData.Var9 = behaviorData.ObservationId+time_offset; | ||
| behaviorData.corrected_time = behaviorData.Time_in_Video+time_offset; | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,196 @@ | ||
| %% Script to analze behavior fluorescence data (one fiber) | ||
| % written by Katie Gallagher Edited by Kathleen Murphy & Anna McTigue | ||
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| % UPDATE THIS EACH NEW VERSION (date of update): | ||
| onefiberversion = 'v1.1'; | ||
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| format long | ||
| %% Read Tables | ||
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| fTime = table2array(fData(:,1)); %time column in fluorescent data | ||
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| fRed = table2array(fData(:,3)); %3rd column (red) | ||
| fGreen = table2array(fData(:,4)); %4th column (green) | ||
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| bTime = table2array(behaviorData(:,3)); % time of behavior | ||
| behavior = table2array(behaviorData(:,2)); % actual behavior | ||
| bTime = double(bTime); | ||
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| %% De-interleave | ||
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| % determining which row index is red channel | ||
| offset1 = fRed(1:3:end); | ||
| offset2 = fRed(2:3:end); | ||
| offset3 = fRed(3:3:end); | ||
| meanoffsets = [mean(offset1), mean(offset2), mean(offset3)]; | ||
| redIdx = find(meanoffsets == max(meanoffsets(:))); | ||
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| % assigning correct rows to colors | ||
| fGreenisosbestic = fGreen(redIdx+2:3:end); %iso | ||
| fGreenred = fGreen(redIdx:3:end); %red | ||
| fGreengreen = fGreen(redIdx+1:3:end);%green | ||
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| fRedisosbestic = fRed(redIdx+2:3:end); | ||
| fRedred = fRed(redIdx:3:end); | ||
| fRedgreen = fRed(redIdx+1:3:end); | ||
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| fTimeIsosbestic = fTime(redIdx+2:3:end); | ||
| fTimeRed = fTime(redIdx:3:end); | ||
| fTimeGreen = fTime(redIdx+1:3:end); | ||
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| %% Minimize behavior data | ||
| %pull out index and time for every time behavior occurs | ||
| %initialize matrices to hold indices and corresponding times | ||
| behaviorIdx = {}; %will be populated with behavior indices | ||
| behaviorT = {}; | ||
| j=1; | ||
| for i = 1:length(behavior) | ||
| if string(behavior(i)) == behavior_name | ||
| behaviorIdx{j} = i; | ||
| behaviorT{j} = bTime(i); | ||
| j=j+1; | ||
| end | ||
| end | ||
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| behaviorT = cell2mat(behaviorT); | ||
| behaviorIdx = cell2mat(behaviorIdx); | ||
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| % if time between behaviors sis greater than threshold seconds then count as | ||
| % one bout | ||
| Thres=200; | ||
| startbout = {}; %start of first bout is the first time it licks | ||
| startboutIdx = {}; %index of start bout | ||
| finbout = {}; | ||
| finboutIdx = {}; %index of end bout | ||
| % i=1; | ||
| % startbout{i}=behaviorT(i); | ||
| % startboutIdx{i} = behaviorIdx(i); | ||
| % j=1; | ||
| % % seeing if diff in time btwn licks is great enough to consider it as | ||
| % % about5 | ||
| % while i < length(behaviorT) | ||
| % if abs(behaviorT(i+1)-behaviorT(i))>=Thres | ||
| % endTime=behaviorT(i); | ||
| % endTimeIdx = behaviorIdx(i); | ||
| % startTime=behaviorT(i+1); | ||
| % startTimeIdx = behaviorIdx(i+1); | ||
| % finbout{j} = endTime; | ||
| % finboutIdx{j} = endTimeIdx; | ||
| % startbout{j+1} = startTime; | ||
| % startboutIdx{j+1} = startTimeIdx; | ||
| % | ||
| % j=j+1; | ||
| % end | ||
| % i=i+1; | ||
| % end | ||
| % finbout{j} = behaviorT(end); | ||
| % finboutIdx{j}=behaviorIdx(end); | ||
| % finbout{length(startbout)} = behaviorT(length(behaviorT)); | ||
| % finbout = cell2mat(finbout); | ||
| % startbout = cell2mat(startbout); | ||
| % finboutIdx = cell2mat(finboutIdx); | ||
| % startboutIdx = cell2mat(startboutIdx); | ||
| % %seeing if number of licks within each bout is great enough to consider it | ||
| % %as a bout | ||
| % % threshold on how many licks constitute a bout | ||
| % numLicksThres = 0; %must have 10 licks in order to be considered a bout | ||
| % i=1; | ||
| % j=1; | ||
| % while i < length(startbout) | ||
| % if (finboutIdx(i) - startboutIdx(i)) < numLicksThres | ||
| % finbout(i) = []; | ||
| % startbout(i) = []; | ||
| % j=j+1; | ||
| % end | ||
| % i=i+1; | ||
| % end | ||
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| %% Plot behavior times on raw data plot as tick marks | ||
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| %Green Plot | ||
| gplot_title = string(behavior_name) + ' Green Plot ' + ' Animal no. '+ ... | ||
| animal_num + ' ' + onefiberversion; | ||
| figure('Name', gplot_title) | ||
| subplot(3,1,1) | ||
| plot(fTimeIsosbestic,fGreenisosbestic) | ||
| xlabel('Time (ms)') | ||
| ylabel('Isosbestic') | ||
| for i = 1:length(behaviorT) | ||
| xline(behaviorT(i),'k') | ||
| end | ||
| for i = 1:length(startbout) | ||
| xline(startbout(i),'g'); | ||
| end | ||
| for i = 1:length(finbout) | ||
| xline(finbout(i),'r'); | ||
| end | ||
| subplot(3,1,2) | ||
| plot(fTimeRed,fGreenred) | ||
| xlabel('Time (ms)') | ||
| ylabel('Red') | ||
| for i = 1:length(behaviorT) | ||
| xline(behaviorT(i),'k') | ||
| end | ||
| for i = 1:length(startbout) | ||
| xline(startbout(i),'g'); | ||
| end | ||
| for i = 1:length(finbout) | ||
| xline(finbout(i),'r'); | ||
| end | ||
| subplot(3,1,3) | ||
| plot(fTimeGreen,fGreengreen) | ||
| xlabel('Time (ms)') | ||
| ylabel('Green') | ||
| for i = 1:length(behaviorT) | ||
| xline(behaviorT(i),'k') | ||
| end | ||
| for i = 1:length(startbout) | ||
| xline(startbout(i),'g'); | ||
| end | ||
| for i = 1:length(finbout) | ||
| xline(finbout(i),'r'); | ||
| end | ||
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| %Red PLot | ||
| rplot_title = string(behavior_name) + ' Red Plot' + ' Animal no. '+ ... | ||
| animal_num + ' ' + onefiberversion; | ||
| figure('Name', rplot_title) | ||
| subplot(3,1,1) | ||
| plot(fTimeIsosbestic,fRedisosbestic) | ||
| xlabel('Time (ms)') | ||
| ylabel('Isosbestic') | ||
| for i = 1:length(behaviorT) | ||
| xline(behaviorT(i),'k') | ||
| end | ||
| for i = 1:length(startbout) | ||
| xline(startbout(i),'g'); | ||
| end | ||
| for i = 1:length(finbout) | ||
| xline(finbout(i),'r'); | ||
| end | ||
| subplot(3,1,2) | ||
| plot(fTimeRed,fRedred) | ||
| xlabel('Time (ms)') | ||
| ylabel('Red') | ||
| for i = 1:length(behaviorT) | ||
| xline(behaviorT(i),'k') | ||
| end | ||
| for i = 1:length(startbout) | ||
| xline(startbout(i),'g'); | ||
| end | ||
| for i = 1:length(finbout) | ||
| xline(finbout(i),'r'); | ||
| end | ||
| subplot(3,1,3) | ||
| plot(fTimeGreen,fRedgreen) | ||
| xlabel('Time (ms)') | ||
| ylabel('Green') | ||
| for i = 1:length(behaviorT) | ||
| xline(behaviorT(i),'k') | ||
| end | ||
| for i = 1:length(startbout) | ||
| xline(startbout(i),'g'); | ||
| end | ||
| for i = 1:length(finbout) | ||
| xline(finbout(i),'r'); | ||
| end |
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