v0.1.8

[v0.1.8, 7/24/2018]
GUI "Replay" window:
  Added "[G]oto frame" keyboard shortcut.
  Added fast frame jump by pressing "Shift" + Left/Right keys.
Debugged "vistrack update" command.
Uploaded sample files (R12A2*).
Removed dependencies for "Statistics and Machine Learning" toolbox.
  Only "Image processing toolbox" is required.
  "Parallel processing toolbox" is optional for faster processing.
GUI "Initialize" button caches previous answers and a movie clip.
New command added: "vistrack download-sample"
  Download a sample video file that is too large to host from Github.com

Author: jamesjun

GUI.fig

@@ -22,7 +22,7 @@
 
 % Edit the above text to modify the response to help GUI
 
-% Last Modified by GUIDE v2.5 23-Jul-2018 16:44:51
+% Last Modified by GUIDE v2.5 24-Jul-2018 11:57:00
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -62,10 +62,7 @@ function GUI_OpeningFcn(hObject, eventdata, handles, varargin)
 
 [vcVer, vcVer_date] = version_();
 set(handles.textVer, 'String', sprintf('%s (%s) James Jun', vcVer, vcVer_date));
-
-if ~exist('.git', 'dir') ~= 7
-    set(handles.btnUpdate, 'Enable', 'off');
-end
+set(handles.btnUpdate, 'Enable', ifeq_(exist_dir_('.git'), 'on', 'off'));
 
 % Update handles structure
 guidata(hObject, handles);
@@ -133,6 +130,7 @@ function btnLoadVideo_Callback(hObject, eventdata, handles)
 end
 handles.vidFname = vidFname;
 buttons_off_(handles);
+clear_cache_();
 
 % Set result field
 vcFile_out = subsFileExt_(vidFname, '_Track.mat');
@@ -158,7 +156,7 @@ function btnLoadVideo_Callback(hObject, eventdata, handles)
 
 try      
     set(handles.edit1, 'String', handles.vidFname);
-    h = msgbox('Loading... (this will close automatically)');
+    h = msgbox('Loading... (this will close automatically)', 'modal');
 %     handles.vidobj = VideoReader(handles.vidFname);
     handles.vidobj = vistrack('VideoReader', vidFname);
     fprintf('Video file info: %s\n', handles.vidFname);
@@ -535,35 +533,11 @@ function btnPreview_Callback(hObject, eventdata, handles)
 [WINPOS, ~] = getBoundingBoxPos(handles.xy_init, size(img0), winlen*[1 1]);
 img = handles.img1(WINPOS(3):WINPOS(4), WINPOS(1):WINPOS(2), :);
 img0c = img0(WINPOS(3):WINPOS(4), WINPOS(1):WINPOS(2), :);
-% img00c = handles.img00(WINPOS(3):WINPOS(4), WINPOS(1):WINPOS(2));
-
-% dimg = uint8(img0c - img);
 dimg = uint8_diff(img0c, img, 0);
-% dimg = uint8(mean(single(img0c) - single(img),3));
-% dimg = uint8(sum(img0c - img, 3));
-% dimg = uint8(mean(single(img) - single(img0c), 3)/3);
-% dimg = uint8(abs(mean(single(img0c) - single(img), 3)/3));
-
-% absimg = imabsdiff(handles.img00, handles.img1);
-% absimg(~handles.MASK) = 0;
-% absimg = absimg(WINPOS(3):WINPOS(4), WINPOS(1):WINPOS(2));
-% figure; subplot 121; imagesc(absimg); title('absdiff');
-% subplot 122; imagesc(dimg); title('diff');
-% return;
-
 BW = imdilate(bwmorph((dimg > IM_THRESH), 'clean', inf), SE);
 BW = imfill(BW, 'holes');
 BW = imclearborder(BW);
 
-% dimg1 = dimg;
-% dimg1(bwperim(BW)) = 256;
-% imgabs = im(handles.img00, handles.img1);
-% imgabs(~handles.MASK) = 0;
-% figure; imagesc(imgabs);
-% figure; imagesc(dimg1);
-% return;
-
-% [BW, AreaTarget] = bwgetlargestblob(BW);
 regions = regionprops(BW, {'Area', 'Centroid', 'Orientation', 'FilledImage', 'BoundingBox'});
 if numel(regions)>1
     L = bwlabel(BW, 8);
@@ -610,7 +584,7 @@ function btnPreview_Callback(hObject, eventdata, handles)
 imagesc(img4, INTENSITY_LIM);  
 axis equal; axis tight;
 set(gca, {'XTick', 'YTick'}, {[],[]});
-title('4. Superimposed');
+title_('4. Superimposed (if incorrect, lower "IM_THRESH")');
 colormap gray;
 
 
@@ -861,7 +835,7 @@ function btnMovOut_Callback(hObject, eventdata, handles)
 %colorbar
 plotColorbar(size(handles.img0), vrRateSrt, vrQuantSrt);
 EODR1 = EODR(TEOD > TLIM(1) & TEOD < TLIM(2));
-RLIM = [quantile(EODR1, .001), quantile(EODR1, .999)];
+RLIM = [quantile_(EODR1, .001), quantile_(EODR1, .999)];
 htext = [];
 vhChevron = [];
 for iframe=1:nframes
@@ -1156,7 +1130,7 @@ function btnReplay_Callback(hObject, eventdata, handles)
 %setup fig
 timer1 = timer('Period', 1/15, 'ExecutionMode', 'fixedRate', 'TasksToExecute', inf);
 hFig = figure('NumberTitle', 'off', 'Name', ...
-    '[H]elp; [L/R/U/D]; SPACEBAR:Pause; [F]lip; [C]ut upto here');
+    '[H]elp; (Sft)+[L/R/U/D]; SPACEBAR:Pause; [F]lip; [C]ut upto here; [G]oto Frame');
 hImg = imshow(imadjust(MOV(:,:,1))); hold on;
 iFrame = 1;
 XC = mrXC(iFrame,:);
@@ -1292,7 +1266,7 @@ function btnUpdate_Callback(hObject, eventdata, handles)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
 vistrack('update');
-msgbox('Update successful, please restart');
+msgbox('Update successful, Restart the app');
 
 
 %--------------------------------------------------------------------------
@@ -1396,11 +1370,12 @@ function btnListFiles_Callback(hObject, eventdata, handles)
 end
 
 
-% --- Executes on button press in pushbutton65.
-function pushbutton65_Callback(hObject, eventdata, handles)
-% hObject    handle to pushbutton65 (see GCBO)
+% --- Executes on button press in btnBarPlots.
+function btnBarPlots_Callback(hObject, eventdata, handles)
+% hObject    handle to btnBarPlots (see GCBO)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
+vistrack('trialset-barplots', get_str_(handles.editTrialSet));
 
 
 % --- Executes on button press in pushbutton66.
@@ -1439,7 +1414,13 @@ function pushbutton70_Callback(hObject, eventdata, handles)
 
 
 function [FLIM, TC, img1, img00] = mov_flim_(vidobj, nFrames_load)
+% mov_flim_(): clear cache
+
+persistent csAns1 csAns2 csAns3 mov1
+if nargin==0, [csAns1, csAns2, csAns3] = deal([]); return; end %clear cache
+
 if nargin<2, nFrames_load = 300; end % skip every 10 frames
+
 % if isempty(nFrames_skip), nFrames_skip = 75; end
 warning off;
 nFrames = vidobj.NumberOfFrames;
@@ -1448,39 +1429,49 @@ function pushbutton70_Callback(hObject, eventdata, handles)
 % viF = 1:nFrames_skip:nFrames;
 viF = unique(round(linspace(1, nFrames, nFrames_load)));
 % viF = 1:nFrames_load; % much faster to load
-tmr = read_(vidobj, viF);    
+if isempty(mov1)
+    mov1 = mov_shrink_(read_(vidobj, viF), 2); 
+end
 
 % rough scan
-implay(tmr);
+implay(mov1);
 uiwait(msgbox('Find the first and last frame to track, and close the movie'));
-csAns = inputdlg({'First frame', 'Last frame'}, 'Get frames', 1, ...
-    {'1', sprintf('%d', numel(viF))});
+if isempty(csAns1), csAns1 = {'1', sprintf('%d', numel(viF))}; end
+csAns = inputdlg({'First frame', 'Last frame'}, 'Get frames', 1, csAns1);
+csAns1 = csAns;
 frame_first = viF(str2num(csAns{1}));
 frame_last = viF(str2num(csAns{2}));
+fprintf('#1: First frame: %s; Last frame: %s\n', csAns{1}, csAns{2});
 
 % Find first frame to track
 viF_first = trim_(frame_first + (-150:149), 1, nFrames);
 tmr = read_(vidobj, viF_first);
-implay(tmr);
+implay(mov_shrink_(tmr, 2));
 uiwait(msgbox('Find the first frame to track and background, and close the movie'));
-csAns = inputdlg({'First frame', 'Background frame'}, 'Get frames', 1, ...
-    {'1', num2str(numel(viF_first))});
+if isempty(csAns2), csAns2 = {'1', num2str(numel(viF_first))}; end
+csAns = inputdlg({'First frame', 'Background frame'}, 'Get frames', 1, csAns2);
+csAns2 = csAns;
 img1 = tmr(:,:,str2num(csAns{1}));
 img00 = tmr(:,:,str2num(csAns{2}));
 frame_first = viF_first(str2num(csAns{1}));
+fprintf('#2: First frame: %s; Background frame: %s\n', csAns{1}, csAns{2});
 
 % Find last frame to track
 viF_last = trim_(frame_last + (-150:149), 1, nFrames);
 tmr = read_(vidobj, viF_last);
-implay(tmr);
+implay(mov_shrink_(tmr, 2));
 uiwait(msgbox('Find the last frame to track, and close the movie'));
-csAns = inputdlg({'Last frame'}, 'Get frames', 1, ...
-    {'1'});
+iFrame3 = ceil(numel(viF_last)/2);
+if isempty(csAns3), csAns3 = {num2str(iFrame3)}; end
+csAns = inputdlg({'Last frame'}, 'Get frames', 1, csAns3);
+csAns3 = csAns;
 frame_last = viF_last(str2num(csAns{1}));
+fprintf('#3: Last frame: %s\n', csAns{1});
 
 FLIM = [frame_first, frame_last];
 TC = TC(frame_first:frame_last);
 
+
 function close_(h)
 try close(h); catch; end
 
@@ -1572,3 +1563,52 @@ function disp_cs_(cs)
         P.(vcName_) = [];
     end
 end
+
+
+%--------------------------------------------------------------------------
+% 7/24/2018 JJJ: Copied from jrc3.m 
+function flag = exist_dir_(vcDir)
+if isempty(vcDir)
+    flag = 0;
+else
+    flag = exist(vcDir, 'dir') == 7;
+end
+
+
+%--------------------------------------------------------------------------
+% 7/24/2018: Copied from jrc3.m
+function flag = key_modifier_(event, vcKey)
+% Check for shift, alt, ctrl press
+try
+    flag = any(strcmpi(event.Modifier, vcKey));
+catch
+    flag = 0;
+end
+
+
+%--------------------------------------------------------------------------
+% 7/24/2018: Copied from jrc3.m
+function out = ifeq_(if_, true_, false_)
+if (if_)
+    out = true_;
+else
+    out = false_;
+end
+
+
+%--------------------------------------------------------------------------
+% 7/24/2018 JJJ: Clear persistent memories
+function clear_cache_()
+mov_flim_(); % clear cache;
+
+
+%--------------------------------------------------------------------------
+% 7/24/2018 JJJ: resize movie by a scale factor
+function mov = mov_shrink_(mov, nSkip)
+if nSkip==1, return; end
+mov = mov(1:nSkip:end, 1:nSkip:end, :);
+
+
+%--------------------------------------------------------------------------
+function hTItle = title_(vc)
+hTItle = title(vc, 'Interpreter', 'none');

GUI.m

@@ -1,6 +1,19 @@
 Visual Tracker (vistrack) change log
   James Jun, Maler Lab
 
+[v0.1.8, 7/24/2018]
+GUI "Replay" window:
+  Added "[G]oto frame" keyboard shortcut.
+  Added fast frame jump by pressing "Shift" + Left/Right keys.
+Debugged "vistrack update" command.
+Uploaded sample files (R12A2*).
+Removed dependencies for "Statistics and Machine Learning" toolbox.
+  Only "Image processing toolbox" is required. 
+  "Parallel processing toolbox" is optional for faster processing.
+GUI "Initialize" button caches previous answers and a movie clip.
+New command added: "vistrack download-sample"
+  Download a sample video file that is too large to host from Github.com
+
 [v0.1.7, 7/23/2018]
 Added "Summary" button in GUI
 Added "Export" button in GUI

R12A2_Rs.mat

@@ -0,0 +1,8 @@
+pixpercm = 7.238; % run S141106_LearningCurve_Control.m first cell
+angXaxis = -0.946;
+vcFile_settings = 'settings_vistrack.m'; % default settings for vistrack GUI
+
+%# Commit
+vcDir_commit = 'D:\Dropbox\Git\vistrack\';
+csFiles_commit = {'*.m', 'GUI.fig', 'change_log.txt', 'readme.txt', 'example.trialset', 'default.cfg', 'R12A2_Ts.mat', 'R12A2_Rs.mat', 'R12A2_Track.mat'};
+csLink_sample = {'https://www.dropbox.com/s/wamrg6ha2nk2ik3/R12A2.wmv?dl=1'}; % too large to upload via Github.com. Hosting from Dropbox instead.

R12A2_Track.mat

@@ -26,8 +26,9 @@
 end
 
 h=msgbox('Loading... (this will close automatically)', 'detect LED blink'); drawnow;    
-trImg = read(handles.vidobj, FLIM1);
-trImg = squeeze(trImg(:,:,1,:));
+% trImg = read(handles.vidobj, FLIM1);
+% trImg = squeeze(trImg(:,:,1,:));
+trImg = vid_read(handles.vidobj, FLIM1(1):FLIM1(2));
 try close(h); catch, end;
 
 if isempty(xyLED), xyLED = find_mov_max_(trImg); end

R12A2_Ts.mat

@@ -13,24 +13,38 @@ function keyFcnPreview(hFig, event)
 [iFrame, hObject] = deal(S.iFrame, S.hObject);
 switch lower(event.Key)
     case 'h' %help
-        csHelp = {'SPACE: start and stop', 'LEFT/RIGHT: backward/forward', ...
-            'HOME/END: start/end', 'F: Flip head/tail', ...
-            'UP/DOWN: Speed up/down', 'C: Trim video'};
+        csHelp = { ...
+            '----Playback----', 
+            '[SPACE]: start and stop video', 
+            '(Shift) + LEFT/RIGHT: backward/forward (Shift: 4x)', 
+            '[UP/DOWN]: Speed up/down', 
+            '[HOME/END]: Go to start/end',
+            '[G]oto: Go to a specific frame}', 
+            '----EDIT----',
+            '[F]lip head/tail', 
+            '[C]ut: Trim video up to the current frame'};
         msgbox(csHelp);
 
     case 'space'  % toggle start and stop  
         if fRunning, stop(timer1);
         else start(timer1); end
 
-    case {'leftarrow', 'rightarrow', 'f', 'home', 'end'}
+    case {'leftarrow', 'rightarrow', 'f', 'home', 'end', 'g'}
     %'f' for flip, 'left' for back, 'right' for forward
         if fRunning, stop(timer1); end
         switch event.Key
-            case 'leftarrow', S.iFrame = max(1, S.iFrame-S.REPLAY_STEP);
-            case 'rightarrow', S.iFrame = min(nFrames, S.iFrame+S.REPLAY_STEP);
+            case {'leftarrow', 'rightarrow'}
+                nStep = S.REPLAY_STEP * ifeq_(key_modifier_(event, 'shift'), 4, 1);
+                nStep = nStep * ifeq_(strcmpi(event.Key, 'leftarrow'), -1, 1);
+                S.iFrame = min(max(1, S.iFrame + nStep), nFrames);
             case 'home', S.iFrame = 1;
             case 'end', S.iFrame = nFrames;
             case 'f', GUI_FLIP; %flip orientation
+            case 'g' % go to frame
+                S.iFrame = uigetnum(sprintf('Go to Frame (choose from 1-%d)', nFrames), S.iFrame);
+                if isempty(S.iFrame), return; end
+                if (S.iFrame < 1 || S.iFrame > nFrames), S.iFrame = nan; end
+                if isnan(S.iFrame), msgbox('Cancelled'); return; end
         end  
         set(S.hImg, 'CData', imadjust(handles.MOV(:,:,S.iFrame)));
 
@@ -50,6 +64,7 @@ function keyFcnPreview(hFig, event)
 
     case 'uparrow' %speed up
         S.REPLAY_STEP = min(S.REPLAY_STEP+1, 30);
+        
 
     case 'downarrow' %speed up
         S.REPLAY_STEP = max(S.REPLAY_STEP-1, 1);  
@@ -64,4 +79,28 @@ function keyFcnPreview(hFig, event)
     sprintf('F1: %d; T1: %0.3f s, Step: %d (%s)', ...
     S.iFrame, S.TC1(S.iFrame), S.REPLAY_STEP, vcDataID));
 
-set(timer1, 'UserData', S);
+set(timer1, 'UserData', S);
+end %func
+
+
+%--------------------------------------------------------------------------
+% 7/24/2018: Copied from jrc3.m
+function flag = key_modifier_(event, vcKey)
+% Check for shift, alt, ctrl press
+try
+    flag = any(strcmpi(event.Modifier, vcKey));
+catch
+    flag = 0;
+end
+end %func
+
+
+%--------------------------------------------------------------------------
+% 7/24/2018: Copied from jrc3.m
+function out = ifeq_(if_, true_, false_)
+if (if_)
+    out = true_;
+else
+    out = false_;
+end
+end %func