sessions renamed to trials, function set for 1d and 3d analysis almos…

…t complete

analyzeSessions.m → analyzeTrials.asv

@@ -2,9 +2,11 @@
 
 % This function requires that a video has already been cropped and pawData has already been saved
 % into the sessions folder for each of 3 viewing angles
-function analyzeSessions(frameRate,pxToMm,pelletCoords)
+function analyzeTrials(frameRate,pxToMm,pelletCoords)
     workingDirectory = uigetdir;
-    % load all the .mat sessions created for each video, from each angle
+    workingDirectoryParts = strsplit(workingDirectory,filesep);
+    sessionName = workingDirectoryParts(end);
+    % load all the .mat trials created for each video, from each angle
     leftSessions = dir(fullfile(workingDirectory,'left','sessions','*.mat'));
     centerSessions = dir(fullfile(workingDirectory,'center','sessions','*.mat'));
     rightSessions = dir(fullfile(workingDirectory,'right','sessions','*.mat'));
@@ -42,18 +44,18 @@ function analyzeSessions(frameRate,pxToMm,pelletCoords)
 
         % save data
         mkdir(fullfile(workingDirectory,'_xyzData'));
-        save(fullfile(workingDirectory,'_xyzData','xyzData'),'allAlignedXyzPawCenters','allAlignedXyzDistPawCenters',...
+        save(fullfile(workingDirectory,'_xyzData',sessionName,'_xyzData'),'allAlignedXyzPawCenters','allAlignedXyzDistPawCenters',...
             'allXyzPawCenters','allXyzDistPawCenters');
 
         % create plots and save images/figures
         h1 = plot1dDistance(allAlignedXyzDistPawCenters);
-        saveas(h1,fullfile(workingDirectory,'_xyzData','1dDistancePlot'),'png');
-        saveas(h1,fullfile(workingDirectory,'_xyzData','1dDistancePlot'),'fig');
+        saveas(h1,fullfile(workingDirectory,'_xyzData',sessionName,'_1dDistancePlot'),'png');
+        saveas(h1,fullfile(workingDirectory,'_xyzData',sessionName,'_1dDistancePlot'),'fig');
 
         h2 = plot3dDistance(allAlignedXyzPawCenters);
         % use view() to rotate and save a couple angles
-        saveas(h2,fullfile(workingDirectory,'_xyzData','3dDistancePlot'),'png');
-        saveas(h2,fullfile(workingDirectory,'_xyzData','3dDistancePlot'),'fig');
+        saveas(h2,fullfile(workingDirectory,'_xyzData',sessionName,'_3dDistancePlot'),'png');
+        saveas(h2,fullfile(workingDirectory,'_xyzData',sessionName,'_3dDistancePlot'),'fig');
     else
         disp('The session counts do not match, why not? Fix that and try again');
     end

analyzeSessions.asv → analyzeTrials.m

@@ -1,59 +1,61 @@
-% >> analyzeSessions(150,0.1053,STRUCT(left,center,right))
+% >> analyzeTrials(150,0.1053,STRUCT(left,center,right))
 
 % This function requires that a video has already been cropped and pawData has already been saved
-% into the sessions folder for each of 3 viewing angles
-function analyzeSessions(frameRate,pxToMm,pelletCoords)
+% into the trials folder for each of 3 viewing angles
+function analyzeTrials(frameRate,pxToMm,pelletCoords)
     workingDirectory = uigetdir;
-    % load all the .mat sessions created for each video, from each angle
-    leftSessions = dir(fullfile(workingDirectory,'left','sessions','*.mat'));
-    centerSessions = dir(fullfile(workingDirectory,'center','sessions','*.mat'));
-    rightSessions = dir(fullfile(workingDirectory,'right','sessions','*.mat'));
+    workingDirectoryParts = strsplit(workingDirectory,filesep);
+    sessionName = workingDirectoryParts(end);
+    % load all the .mat trials created for each video, from each angle
+    leftTrials = dir(fullfile(workingDirectory,'left','trials','*.mat'));
+    centerTrials = dir(fullfile(workingDirectory,'center','trials','*.mat'));
+    rightTrials = dir(fullfile(workingDirectory,'right','trials','*.mat'));
 
     % just make sure there are equal session for each angle
-    if(numel(leftSessions) == numel(centerSessions) && numel(leftSessions) == numel(rightSessions))
+    if(numel(leftTrials) == numel(centerTrials) && numel(leftTrials) == numel(rightTrials))
         % load the pawCenter variables from the session files
-        allLeftPawCenters = loadPawCenters(leftSessions,fullfile(workingDirectory,'left','sessions'));
-        allCenterPawCenters = loadPawCenters(centerSessions,fullfile(workingDirectory,'center','sessions'));
-        allRightPawCenters = loadPawCenters(rightSessions,fullfile(workingDirectory,'right','sessions'));
+        allLeftPawCenters = loadPawCenters(leftTrials,fullfile(workingDirectory,'left','trials'));
+        allCenterPawCenters = loadPawCenters(centerTrials,fullfile(workingDirectory,'center','trials'));
+        allRightPawCenters = loadPawCenters(rightTrials,fullfile(workingDirectory,'right','trials'));
 
         % combines the paw centers from each video into an nx3 matrix, where n=numberOfFrames in the
         % video, and 3=[x y z] data in relation to the pellet
-        allXyzPawCenters = cell(1,numel(leftSessions)); % number of videos
-        for i=1:numel(leftSessions)
+        allXyzPawCenters = cell(1,numel(leftTrials)); % number of videos
+        for i=1:numel(leftTrials)
             allXyzPawCenters{i} = createXyzPawCenters(allLeftPawCenters{i},allCenterPawCenters{i},...
                 allRightPawCenters{i},pelletCoords);
             allXyzPawCenters{i} = allXyzPawCenters{i}.*pxToMm; % convert pixels to distance
         end
 
         % takes the [x y z] data just created and calculates a single distance based on all three
         % coordinates in relation to the pellet
-        allXyzDistPawCenters = cell(1,numel(leftSessions));
-        for i=1:numel(leftSessions)
+        allXyzDistPawCenters = cell(1,numel(leftTrials));
+        for i=1:numel(leftTrials)
             allXyzDistPawCenters{i} = createXyzDistPawCenters(allXyzPawCenters{i});
         end
 
         % aligns data based on distance threshold, ultimately compresses the data set slightly (see
         % alignData function for more)
-        allAlignedXyzPawCenters = cell(1,numel(leftSessions));
-        allAlignedXyzDistPawCenters = cell(1,numel(leftSessions));
-        for i=25:numel(leftSessions)
+        allAlignedXyzPawCenters = cell(1,numel(leftTrials));
+        allAlignedXyzDistPawCenters = cell(1,numel(leftTrials));
+        for i=25:numel(leftTrials)
             [allAlignedXyzPawCenters{i},allAlignedXyzDistPawCenters{i}] = alignData(allXyzPawCenters{i},allXyzDistPawCenters{i});
         end
 
         % save data
         mkdir(fullfile(workingDirectory,'_xyzData'));
-        save(fullfile(workingDirectory,'_xyzData','xyzData'),'allAlignedXyzPawCenters','allAlignedXyzDistPawCenters',...
+        save(fullfile(workingDirectory,'_xyzData',sessionName,'_xyzData'),'allAlignedXyzPawCenters','allAlignedXyzDistPawCenters',...
             'allXyzPawCenters','allXyzDistPawCenters');
 
         % create plots and save images/figures
         h1 = plot1dDistance(allAlignedXyzDistPawCenters);
-        saveas(h1,fullfile(workingDirectory,'_xyzData','1dDistancePlot'),'png');
-        saveas(h1,fullfile(workingDirectory,'_xyzData','1dDistancePlot'),'fig');
+        saveas(h1,fullfile(workingDirectory,'_xyzData',sessionName,'_1dDistancePlot'),'png');
+        saveas(h1,fullfile(workingDirectory,'_xyzData',sessionName,'_1dDistancePlot'),'fig');
 
         h2 = plot3dDistance(allAlignedXyzPawCenters);
         % use view() to rotate and save a couple angles
-        saveas(h2,fullfile(workingDirectory,'_xyzData','3dDistancePlot'),'png');
-        saveas(h2,fullfile(workingDirectory,'_xyzData','3dDistancePlot'),'fig');
+        saveas(h2,fullfile(workingDirectory,'_xyzData',sessionName,'_3dDistancePlot'),'png');
+        saveas(h2,fullfile(workingDirectory,'_xyzData',sessionName,'_3dDistancePlot'),'fig');
     else
         disp('The session counts do not match, why not? Fix that and try again');
     end
@@ -99,9 +101,10 @@ function analyzeSessions(frameRate,pxToMm,pelletCoords)
     end
 end
 
-% Creates [x y z] data for a single session/video
+% Creates [x y z] data for a single session/video. Not the most elegant way of handling the logic,
+% but intended to remain readable and workable.
 function xyzPawCenters=createXyzPawCenters(leftPawCenters,centerPawCenters,rightPawCenters,pelletCoords)
-    % x=C, y=mean(L,R), z=mean(L,C,R), *where L, C, and R are 
+    % x=C, y=mean(L,R), z=mean(L,C,R), *where L, C, and R are not NaN
     frameCount = size(leftPawCenters,1);
     xyzPawCenters = NaN(frameCount,3);
     for i=1:frameCount
@@ -125,7 +128,7 @@ function analyzeSessions(frameRate,pxToMm,pelletCoords)
         else
             xyzPawCenters(i,2) = NaN;
         end
-        % calculate z, not the most elegant way, but at least it is readable
+        % calculate z
         if(~isnan(leftPawCenters(i,1)) && ~isnan(centerPawCenters(i,1)) && ~isnan(rightPawCenters(i,1)))
             leftDist = pelletCoords.left(2)-leftPawCenters(i,2); % y-axis
             centerDist = pelletCoords.center(2)-centerPawCenters(i,2); % y-axis
@@ -155,10 +158,11 @@ function analyzeSessions(frameRate,pxToMm,pelletCoords)
     end
 end
 
-function allPawCenters=loadPawCenters(sessions,sessionsPath)
-    allPawCenters = cell(1,numel(sessions));
-    for i=1:numel(sessions)
-        load(fullfile(sessionsPath,sessions(i).name));
+% Load and return the pawCenters variable from a session file (one video).
+function allPawCenters=loadPawCenters(trials,trialsPath)
+    allPawCenters = cell(1,numel(trials));
+    for i=1:numel(trials)
+        load(fullfile(trialsPath,trials(i).name));
         allPawCenters{i} = pawCenters; % "pawCenters" variable is loaded via .mat file
     end
 end

runFolder.m → createTrialData.m

@@ -1,13 +1,13 @@
 % pixelBounds is a struct with 3 fields, hsvBounds is an array
-function runFolder(pixelBounds,hsvBounds)
+function createTrialData(pixelBounds,hsvBounds)
     workingDirectory = uigetdir;
 
     % crop videos
-%     originalVideos = dir(fullfile(workingDirectory,'*.avi'));
-%     for i=1:size(originalVideos,1)
-%        videoFile = fullfile(workingDirectory,originalVideos(i).name);
-%        cropVideo(videoFile,pixelBounds); 
-%     end
+    originalVideos = dir(fullfile(workingDirectory,'*.avi'));
+    for i=1:size(originalVideos,1)
+       videoFile = fullfile(workingDirectory,originalVideos(i).name);
+       cropVideo(videoFile,pixelBounds); 
+    end
 
     % get data from all crops
     fields = fieldnames(pixelBounds);

createVideo.m

@@ -2,7 +2,6 @@
 function [pawCenters,pawHulls] = createVideo(videoFile,hsvBounds)
 
     [pawCenters,pawHulls] = getDataFromVideo(videoFile,hsvBounds);
-    %pawCenters = cleanCentroids(pawCenters); %cant do this here, only after session save
     [pathstr,name,ext] = fileparts(videoFile);
 
     video = VideoReader(videoFile);
@@ -35,6 +34,6 @@
     end
 
     close(newVideo);
-    mkdir(fullfile(pathstr,'sessions'));
-    save(fullfile(pathstr,'sessions',name),'pawCenters','pawHulls','hsvBounds');
+    mkdir(fullfile(pathstr,'trials'));
+    save(fullfile(pathstr,'trials',name),'pawCenters','pawHulls','hsvBounds');
 end

getPelletCoords.m

@@ -1,10 +1,15 @@
-function coords=getPelletCoords()
-    [videoName,videoPath] = uigetfile('*.avi');
-    videoFile = fullfile(videoPath,videoName);
-    video = VideoReader(videoFile);
-    imshow(read(video,50));
-    disp('Identify pellet, press ENTER when done...');
-    [x,y] = ginput;
-    close;
-    coords=[x,y];
+function pelletCoords=getPelletCoords(boundNames)
+    pelletCoords = {};
+    for i=1:size(boundNames,2)
+        disp(['Navigate to video for "',boundNames{i},'"...']);
+        [videoName,videoPath] = uigetfile('*.avi');
+        videoFile = fullfile(videoPath,videoName);
+        video = VideoReader(videoFile);
+        figure;
+        imshow(read(video,1));
+        disp('Identify pellet, press ENTER when done...');
+        [x,y] = ginput;
+        close;
+        pelletCoords.(boundNames{i}) = [x,y];
+    end
 end

getPixelBounds.m

@@ -1,11 +1,13 @@
 % >> pixelBounds = getPixelBounds({'left','center','right'});
 function pixelBounds=getPixelBounds(boundNames)
+    disp('Select one of your videos...');
     [videoName,videoPath] = uigetfile('*.avi');
     videoFile = fullfile(videoPath,videoName);
     video = VideoReader(videoFile);
     pixelBounds = {};
     im = read(video,1);
-
+    figure;
+
     for i=1:size(boundNames,2)
        disp(['Create ROI for "',boundNames{i},'"...']);
        h_im = imshow(im);

px2mm.m → getPx2mm.m

@@ -1,4 +1,4 @@
-function pxToMm=px2mm(knownDistMm)
+function pxToMm=getPx2mm(knownDistMm)
     [videoName,videoPath] = uigetfile('*.avi');
     videoFile = fullfile(videoPath,videoName);
     video = VideoReader(videoFile);