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ROIanalysis.m
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ROIanalysis.m
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function ROIanalysis(ImageFile, ExperimentFile, ROIFile, varargin)
% ROIANALYSIS Circle ROIs in imaging data as well as and/or create
% presentable data.
%
% ROIANALYSIS(ImageFile), for a string or cell array of strings
% specifying the filenames of the image file(s), the program will
% automatically open the file(s). (Supports ScanImage or Scanbox
% generated images)
%
% ROIANALYSIS(ImageFile,ExperimentFile), for a string specifying the
% filename of an Experiment File, the program will automatically load in
% the file. (Experiment File generated by 'CaImaging' only)
%
% ROIANALYSIS(ImageFile,ExperimentFile,ROIFile), for a string specifying
% the filename of a ROI File, the program will automatically load in the
% file. (ROI File generated by 'ROIanalysis' only)
%
% HotKeys:
% Base State
% Add ROI - 'r'
% Edit ROI - 'e'
% Toggle Viewing ROIs - 'v'
% Toggle Motion Correction - 'm'
% Next Frame - 'd' or right arrow
% Last Frame - 'a' or left arrow
% Play/Pause - spacebar or 'enter'
% ROI being edited
% Save ROI - spacebar, 'enter', or 'r'
% Delete ROI - 'backspace', 'delete', or 'e'
% Move up - 'w' or up arrow
% Move down - 's' or down arrow
% Move right - 'd' or right arrow
% Move left - 'a' or left arrow
% Move deeper - '>'
% Move shallower - '<'
%% Parse input arguments
LoadType = 'Direct';
Frames = [1 inf];
Channels = [1 inf];
index = 1;
while index<=length(varargin)
try
switch varargin{index}
case 'Config'
configFile = varargin{index+1};
index = index + 2;
case 'LoadType'
LoadType = varargin{index+1};
index = index + 2;
case {'Frames', 'frames'}
Frames = varargin{index+1};
index = index + 2;
case {'Channels', 'channels'}
Channels = varargin{index+1};
index = index + 2;
otherwise
warning('Argument ''%s'' not recognized',varargin{index});
index = index + 1;
end
catch
warning('Argument %d not recognized',index);
index = index + 1;
end
end
if exist('ImageFile', 'var') && ~isempty(ImageFile)
if ~iscellstr(ImageFile)
ImageFile = {ImageFile};
end
gd.state.dataAvailable = true;
else
gd.state.dataAvailable = false;
end
if exist('ExperimentFile', 'var') && ~isempty(ExperimentFile)
gd.state.experimentAvailable = true;
else
gd.state.experimentAvailable = false;
end
if exist('ROIFile', 'var') && ~isempty(ROIFile)
gd.state.roisAvailable = true;
else
gd.state.roisAvailable = false;
end
if ~exist('configFile', 'var')
gd.config = initConfig;
else
temp = load(configFile, 'config', '-mat');
gd.config = temp.config;
end
%% Configure Default Display Settings
gd.Internal.directory = '\\128.32.173.33\Imaging\ResonantScope';
gd.Internal.Settings.ROITextSize = 20;
gd.Internal.Settings.ROILineWidth = 2;
gd.Internal.Settings.StimMarkSize = 20;
gd.Internal.Settings.StimMarkColor = [1,0,0];
gd.Internal.Settings.RunSpeedSize = 20;
gd.Internal.Settings.RunSpeedColor = [1,1,1];
gd.Internal.Settings.PlayFrameRate = 15.5;
gd.Internal.Settings.NeuropilDistance = 5;
%% Configure Image settings
gd.Internal.Images.defaultComputations = {'Raw'};
gd.state.UIstate = 'base';
%% Configure ROI settings
gd.Internal.ROIs.n = 0;
gd.ROIs.filename = [];
gd.ROIs.offset = [0,0,0];
gd.ROIs.rois = [];
gd.Internal.ROIs.tagIndex = 0;
gd.Internal.ROIs.current = false;
gd.Internal.ROIs.nlabels = numel(gd.config.ROIs.labels);
gd.Internal.ROIs.labels = [gd.config.ROIs.labels, 'other', 'multiple', 'none'];
gd.Internal.ROIs.colors.labels = [gd.config.ROIs.colors.labels, 'blue', 'white', 'magenta'];
gd.Internal.ROIs.colors.random = ...
[1,0,1;...
0,1,1;...
1,0,0;...
0,1,0;...
0,0,1;...
1,1,1]; % colors to display ROIs in
gd.Internal.ROIs.nColors = size(gd.Internal.ROIs.colors.random, 1);
%% Create & Populate Figure
% Create figure
gd.fig = figure(...
'NumberTitle', 'off',...
'Name', 'ROIanalysis',...
'ToolBar', 'none',...
'Units', 'pixels',...
'Position', gd.config.Figure.pos,...
'KeyPressFcn', @(hObject,eventdata)KeyPressCallback(hObject,eventdata,guidata(hObject)));
% gd.Internal.zoom = zoom;
% gd.Internal.zoom.ButtonDownFilter = @KeyPressCallback;
% IMAGE LOADING
% panel
gd.LoadImages.panel = uipanel(...
'Title', 'Image File',...
'Parent', gd.fig,...
'Units', 'Normalized',...
'Position', [0, .7, .15, .3]);
% load button
gd.LoadImages.load = uicontrol(...
'Style', 'pushbutton',...
'String', 'Load Images',...
'Parent', gd.LoadImages.panel,...
'Units', 'normalized',...
'Position', [.01,.9,.49,.1],...
'Callback', @(hObject,eventdata)LoadImages(hObject,eventdata,guidata(hObject)),...
'BackgroundColor', [.3,.3,.3],...
'ForegroundColor', [1,1,1]);
% load type
gd.LoadImages.type = uicontrol(...
'Style', 'popupmenu',...
'String', {'Direct','MemMap'},...
'Parent', gd.LoadImages.panel,...
'Units', 'normalized',...
'Position', [.5,.9,.49,.1]);
% frames to load
gd.LoadImages.framestext = uicontrol(...
'Style', 'text',...
'String', 'Frames:',...
'Parent', gd.LoadImages.panel,...
'Units', 'normalized',...
'Position', [.01,.8,.24,.1]);
gd.LoadImages.frames = uicontrol(...
'Style', 'edit',...
'String', '1:100',...
'Parent', gd.LoadImages.panel,...
'Units', 'normalized',...
'Position', [.25,.8,.25,.1]);
% channels to load
gd.LoadImages.channelstext = uicontrol(...
'Style', 'text',...
'String', 'Channels:',...
'Parent', gd.LoadImages.panel,...
'Units', 'normalized',...
'Position', [.5,.8,.24,.1]);
gd.LoadImages.channels = uicontrol(...
'Style', 'edit',...
'String', 'all',...
'Parent', gd.LoadImages.panel,...
'Units', 'normalized',...
'Position', [.74,.8,.25,.1]);
% information listbox
gd.LoadImages.info = uicontrol(...
'Style', 'listbox',...
'String', [],...
'Parent', gd.LoadImages.panel,...
'Units', 'normalized',...
'Position', [.01,0,.98,.78]);
% EXPERIMENT LOADING
% panel
gd.LoadExperiment.panel = uipanel(...
'Title', 'Experiment File',...
'Parent', gd.fig,...
'Units', 'Normalized',...
'Position', [0, 0, .15, .3]);
% load button
gd.LoadExperiment.load = uicontrol(...
'Style', 'pushbutton',...
'String', 'Load Experiment',...
'Parent', gd.LoadExperiment.panel,...
'Units', 'normalized',...
'Position', [.1,.9,.8,.1],...
'Callback', @(hObject,eventdata)LoadExperiment(hObject,eventdata,guidata(hObject)),...
'BackgroundColor', [.3,.3,.3],...
'ForegroundColor', [1,1,1]);
% information listbox
gd.LoadExperiment.info = uicontrol(...
'Style', 'listbox',...
'String', [],...
'Parent', gd.LoadExperiment.panel,...
'Units', 'normalized',...
'Position', [.01,.3,.98,.58],...
'Callback', @(hObject,eventdata)ExperimentInfo(hObject,eventdata,guidata(hObject)));
% frame organization pop up menu (temporal, trial type)
gd.LoadExperiment.display = uicontrol(...
'Style', 'popupmenu',...
'String', {'temporal', 'stimulus'},...
'Parent', gd.LoadExperiment.panel,...
'Units', 'normalized',...
'Position', [.01,.2,.48,.1],...
'Callback', @(hObject,eventdata)DisplayTimeline(hObject,eventdata,guidata(hObject)),...
'Enable', 'off');
% correct motion
gd.LoadExperiment.MC = uicontrol(...
'Style', 'checkbox',...
'String', 'Apply Motion Correction',...
'Parent', gd.LoadExperiment.panel,...
'Units', 'normalized',...
'Position', [.01,0,.48,.2],...
'Enable', 'off',...
'Callback', @(hObject,eventdata)plotmainaxes([],[],guidata(hObject)));
% show stimulus mark
gd.LoadExperiment.showStimMark = uicontrol(...
'Style', 'checkbox',...
'String', 'Stimulus Mark',...
'Parent', gd.LoadExperiment.panel,...
'Units', 'normalized',...
'Position', [.5,.15,.49,.1],...
'Enable', 'off',...
'Callback', @(hObject,eventdata)replotaxes(hObject,eventdata,guidata(hObject)));
% show running speed
gd.LoadExperiment.showRunSpeed = uicontrol(...
'Style', 'checkbox',...
'String', 'Running Speed',...
'Parent', gd.LoadExperiment.panel,...
'Units', 'normalized',...
'Position', [.5,.05,.49,.1],...
'Enable', 'off',...
'Callback', @(hObject,eventdata)replotaxes(hObject,eventdata,guidata(hObject)));
% DATA SELECTION
% panel
gd.DataSelection.panel = uipanel(...
'Title', 'Display',...
'Parent', gd.fig,...
'Units', 'Normalized',...
'Position', [0, .3, .15, .4]);
% channel selection table
gd.DataSelection.channel = uitable(...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [.01,.75,.98,.25],...
'ColumnName', {'View','Color'},...
'ColumnEditable', [true, false],...
'ColumnFormat', {'logical','char'},...
'ColumnWidth', {50,50,70},...
'CellEditCallback', @(hObject,eventdata)DataSelection(hObject,eventdata,guidata(hObject)));
% lower limit slider
gd.DataSelection.climMin = uicontrol(...
'Style', 'slider',...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [.2,.625,.78,.125],...
'Callback', @(hObject,eventdata)ClimMinimum(hObject,eventdata,guidata(hObject)),...
'Enable', 'off');
gd.DataSelection.climMinText = uicontrol(...
'Style', 'text',...
'String', '',...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [0,.625,.2,.125],...
'FontSize', 10);
% upper limit slider
gd.DataSelection.climMax = uicontrol(...
'Style', 'slider',...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [.2,.5,.78,.125],...
'Callback', @(hObject,eventdata)ClimMaximum(hObject,eventdata,guidata(hObject)),...
'Enable', 'off');
gd.DataSelection.climMaxText = uicontrol(...
'Style', 'text',...
'String', '',...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [0,.5,.2,.125],...
'FontSize', 10);
% computation selection listbox
gd.DataSelection.computation = uicontrol(...
'Style', 'listbox',...
'String', [],...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [.01,.2,.98,.3],...
'Callback', @(hObject,eventdata)ViewSelection(hObject,eventdata,guidata(hObject)));
% histogram equalizer
gd.DataSelection.histeq = uicontrol(...
'Style', 'radio',...
'String', 'Histogram Equalization',...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [.01,.1,.98,.1],...
'Callback', @(hObject,eventdata)plotmainaxes([],[],guidata(hObject)));
% built-in computations
gd.DataSelection.computationAvail = uicontrol(...
'Style', 'popupmenu',...
'String', {'Average'},...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [.01,0,.69,.1]);
% built-in compute computation
gd.DataSelection.computationCompute = uicontrol(...
'Style', 'pushbutton',...
'String', 'Compute',...
'Parent', gd.DataSelection.panel,...
'Units', 'normalized',...
'Position', [.7,0,.29,.1],...
'Callback', @(hObject,eventdata)ComputeComputation(hObject,eventdata,guidata(hObject)));
% DATA VIEW
% panel
gd.View.panel = uipanel(...
'Title', 'Display',...
'Parent', gd.fig,...
'Units', 'Normalized',...
'Position', [.15, 0, .6, 1]);
% axes
gd.View.axes = axes(...
'Parent', gd.View.panel,...
'Units', 'normalized',...
'Position', [0,0,1,.9]);
axis off;
% frame selection slider
gd.View.frameSlider = uicontrol(...
'Style', 'slider',...
'Parent', gd.View.panel,...
'Units', 'normalized',...
'Position', [0,.925,1,.025],...
'Enable', 'off',...
'Callback', @(hObject,eventdata)FrameSelection(hObject,eventdata,guidata(hObject)));
% depth selection slider
gd.View.depthSlider = uicontrol(...
'Style', 'slider',...
'Parent', gd.View.panel,...
'Units', 'normalized',...
'Position', [0,.9,1,.025],...
'Enable', 'off',...
'Callback', @(hObject,eventdata)DepthSelection(hObject,eventdata,guidata(hObject)));
% frame count
gd.View.currentFrame = uicontrol(...
'Style', 'text',...
'String', '',...
'Parent', gd.View.panel,...
'Units', 'normalized',...
'Position', [.2,.96,.2,.04],...
'FontSize', 20);
% depth count
gd.View.currentDepth = uicontrol(...
'Style', 'text',...
'String', '',...
'Parent', gd.View.panel,...
'Units', 'normalized',...
'Position', [.4,.96,.2,.04],...
'FontSize', 20);
% play button
gd.View.playPause = uicontrol(...
'Style', 'togglebutton',...
'String', 'Play',...
'Parent', gd.View.panel,...
'Units', 'normalized',...
'Position', [0,.96,.2,.04],...
'Callback', @(hObject,eventdata)PlayPause(hObject,eventdata,guidata(hObject)));
% save image button
gd.View.saveImage = uicontrol(...
'Style', 'pushbutton',...
'String', 'Save Frame',...
'Parent', gd.View.panel,...
'Units', 'normalized',...
'Position', [.8,.975,.2,.024],...
'Callback', @(hObject,eventdata)SaveImage(hObject,eventdata,guidata(hObject)),...
'BackgroundColor', [.8,.8,.8]);
% save video button (save from current or beggining to input value)
gd.View.saveVideo = uicontrol(...
'Style', 'pushbutton',...
'String', 'Save Video',...
'Parent', gd.View.panel,...
'Units', 'normalized',...
'Position', [.8,.951,.2,.024],...
'Callback', @(hObject,eventdata)SaveVideo(hObject,eventdata,guidata(hObject)),...
'BackgroundColor', [.8,.8,.8]);
% ROI MANAGEMENT
% panel
gd.ROI.panel = uipanel(...
'Title', 'ROIs',...
'Parent', gd.fig,...
'Units', 'Normalized',...
'Position', [.75, .05, .25, .95]);
% load button
gd.ROI.load = uicontrol(...
'Style', 'pushbutton',...
'String', 'Load ROIs',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.95,.2,.05],...
'Callback', @(hObject,eventdata)LoadROIs(hObject,eventdata,guidata(hObject)),...
'BackgroundColor', [.3,.3,.3],...
'ForegroundColor', [1,1,1]);
% save button
gd.ROI.saveFile = uicontrol(...
'Style', 'pushbutton',...
'String', 'Save ROIs',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.9,.2,.05],...
'Callback', @(hObject,eventdata)SaveROIs(hObject,eventdata,guidata(hObject)),...
'Enable', 'off',...
'BackgroundColor', [.8,.8,.8]);
% show ROIs toggle
gd.ROI.show = uicontrol(...
'Style', 'checkbox',...
'String', 'Show ROIs',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.8,.25,.025],...
'Value', true,...
'ToolTipString', 'Show ROIs: ''v''',...
'Callback', @(hObject,eventdata)replotaxes(hObject,eventdata,guidata(hObject)));
% show ID numbers toggle
gd.ROI.showIDs = uicontrol(...
'Style', 'checkbox',...
'String', 'Show ID #s',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.775,.25,.025],...
'Value', true,...
'Callback', @(hObject,eventdata)replotaxes(hObject,eventdata,guidata(hObject)));
% show on depth toggle
gd.ROI.showDepth = uicontrol(...
'Style', 'checkbox',...
'String', 'Specific depth',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.26,.8,.25,.025],...
'Value', false,...
'Callback', @(hObject,eventdata)replotaxes(hObject,eventdata,guidata(hObject)),...
'Enable', 'off');
% show ID numbers toggle
gd.ROI.editAll = uicontrol(...
'Style', 'pushbutton',...
'String', 'Edit All',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.8625,.2,.025],...
'Value', false,...
'Callback', @(hObject,eventdata)EditAllROIs(hObject,eventdata,guidata(hObject)),...
'Enable', 'off',...
'BackgroundColor', [1,1,.7]);
% delete all button
gd.ROI.deleteAll = uicontrol(...
'Style', 'pushbutton',...
'String', 'Delete All',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.8375,.2,.025],...
'Callback', @(hObject,eventdata)DeleteAllROIs(hObject,eventdata,guidata(hObject)),...
'Enable', 'off',...
'BackgroundColor', [1,.7,.7]);
% color popupmenu
gd.ROI.color = uicontrol(...
'Style', 'popupmenu',...
'String', {'random', 'labels'},...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.59,.8,.2,.025],...
'Callback', @(hObject,eventdata)replotaxes(hObject,eventdata,guidata(hObject)));
% type of ROI pop up menu
gd.ROI.type = uicontrol(...
'Style', 'popupmenu',...
'String', {'ellipse', 'polygon'},...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.75,.2,.025]); %[.01,.775,.25,.025]
% add ROI button
gd.ROI.add = uicontrol(...
'Style', 'pushbutton',...
'String', 'Add',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.7,.2,.05],...
'Callback', @(hObject,eventdata)AddROI(hObject,eventdata,guidata(hObject)),...
'Enable', 'off',...
'BackgroundColor', [.7,.7,1],...
'ToolTipString', 'Add ROI: ''r''');
% edit ROI button
gd.ROI.edit = uicontrol(...
'Style', 'pushbutton',...
'String', 'Edit',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.65,.2,.05],...
'Callback', @(hObject,eventdata)EditROI(hObject,eventdata,guidata(hObject)),...
'Enable', 'off',...
'BackgroundColor', [1,1,.7],...
'ToolTipString', 'Edit ROI: ''e''');
% info listbox
gd.ROI.info = uicontrol(...
'Style', 'listbox',...
'String', [],...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.21,.55,.5,.2]);
% add label button
gd.ROI.addLabel = uicontrol(...
'Style', 'pushbutton',...
'String', 'Add Label',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.79,.8,.2,.025],...
'Callback', @(hObject,eventdata)AddROILabel(hObject,eventdata,guidata(hObject)));
% labels table
gd.ROI.labels = uitable(...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.23,.825,.76,.175],...
'RowName', [],...
'ColumnWidth', {70,70,50,50,40},...
'ColumnName', {'Label','Color','Up','Down','Delete'},...
'ColumnEditable', [true, true, true, true, true],...
'ColumnFormat', {'char','char','logical','logical','logical'},...
'CellEditCallback', @(hObject,eventdata)EditLabelsTable(hObject,eventdata,guidata(hObject)));
data = cell(numel(gd.Internal.ROIs.labels),3);
data(:,1) = gd.Internal.ROIs.labels;
data(:,2) = gd.Internal.ROIs.colors.labels;
data(:,3:5) = {false};
set(gd.ROI.labels, 'Data', data);
% current: save
gd.ROI.save = uicontrol(...
'Style', 'pushbutton',...
'String', 'Save',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.6,.2,.05],...
'Callback', @(hObject,eventdata)SaveROI(hObject,eventdata,guidata(hObject)),...
'Enable', 'off',...
'BackgroundColor', [.7,1,.7],...
'ToolTipString', 'Save ROI: ''space'', ''r'', or ''enter''');
% current: delete
gd.ROI.delete = uicontrol(...
'Style', 'pushbutton',...
'String', 'Delete',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,.55,.2,.05],...
'Callback', @(hObject,eventdata)DeleteROI(hObject,eventdata,guidata(hObject)),...
'Enable', 'off',...
'BackgroundColor', [1,.7,.7],...
'ToolTipString', 'Delete ROI: ''backspace'' or ''delete''');
% current: labels
gd.ROI.currentLabels = uicontrol(...
'Style', 'listbox',...
'String', '',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.71,.55,.28,.2],...
'Callback', @(hObject,eventdata)ROIcurrentLabels(hObject,eventdata,guidata(hObject)),...
'KeyPressFcn', @(hObject,eventdata)ROIcurrentLabelKeyPress(hObject,eventdata,guidata(hObject)));
% current: tag
gd.ROI.currentTag = uicontrol(...
'Style', 'edit',...
'String', 'tag',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.21,.75,.78,.025],...
'Callback', @(hObject,eventdata)ROIcurrentTag(hObject,eventdata,guidata(hObject)));
% tabs
% gd.ROI.tabgroup = uitabgroup(...
% 'Parent', gd.ROI.panel,...
% 'Units', 'normalized',...
% 'Position', [0,0,1,.7]);
% current ROI tab
% gd.ROI.currentTab = uitab(...
% 'Title', 'Current ROI',...
% 'Parent', gd.ROI.tabgroup);
% current: activity axes
% h.ROI.currentInfo = axes(...
% 'Parent', h.ROI.currentTab,...
% 'Units', 'normalized',...
% 'Position', [.01,.7,.98,.2]);
% xray tab
% gd.ROI.xrayTab = uitab(...
% 'Title', 'X-Ray',...
% 'Parent', gd.ROI.tabgroup);
% xray: axes
% EXPORT
gd.ExportData.panel = uipanel(...
'Title', 'Export data',...
'Parent', gd.fig,...
'Units', 'Normalized',...
'Position', [.75, 0, .25, .05]);
% export button
gd.ExportData.export = uicontrol(...
'Style', 'pushbutton',...
'String', 'Export',...
'Parent', gd.ExportData.panel,...
'Units', 'normalized',...
'Position', [.79,0.1,.2,.98],...
'Callback', @(hObject,eventdata)ExportData(hObject,eventdata,guidata(hObject)),...
'BackgroundColor', [.8,.8,.8]);
% selection popup menu
gd.ExportData.selection = uicontrol(...
'Style', 'popupmenu',...
'String', {},...
'Parent', gd.ExportData.panel,...
'Units', 'normalized',...
'Position', [.01,.1,.78,.98]);
% load button
gd.Holo.send = uicontrol(...
'Style', 'pushbutton',...
'String', 'Send to HoloStim',...
'Parent', gd.ROI.panel,...
'Units', 'normalized',...
'Position', [.01,0,.98,.3],...
'Callback', @(hObject,eventdata)sendToHolostim(hObject,eventdata,guidata(hObject)),...
'BackgroundColor', [.3,.3,.3],...
'ForegroundColor', [1,1,1]);
%% Context Menus
% Right click ROI
gd.ROIcontextmenu.handle = uicontextmenu(...
'Callback', @(hObject,eventdata)ROIcontextmenu(hObject,eventdata,guidata(hObject)));
for l = 1:numel(gd.Internal.ROIs.labels)
if ~strcmp(gd.Internal.ROIs.labels(l), {'other', 'multiple', 'none'})
gd.ROIcontextmenu.menus(l).label = gd.Internal.ROIs.labels{l};
gd.ROIcontextmenu.menus(l).handle = uimenu(...
'Parent', gd.ROIcontextmenu.handle,...
'Label', gd.ROIcontextmenu.menus(l).label,...
'Tag', num2str(l),...
'Callback', @(hObject,eventdata)ROIlabel(hObject,eventdata,guidata(hObject)));
end
end
gd.ROIcontextmenu.other = uimenu(...
'Parent', gd.ROIcontextmenu.handle,...
'Label', 'other',...
'Callback', @(hObject,eventdata)ROIlabelOther(hObject,eventdata,guidata(hObject)));
gd.ROIcontextmenu.color = uimenu(...
'Parent', gd.ROIcontextmenu.handle,...
'Label', 'Change Color',...
'Separator', 'on',...
'Callback', @(hObject,eventdata)ROIchangeColor(hObject,eventdata,guidata(hObject)));
% Right click text
gd.Textcontextmenu.handle = uicontextmenu(...
'Callback', @(hObject,eventdata)Textcontextmenu(hObject,eventdata,guidata(hObject)));
gd.Textcontextmenu.size = uimenu(...
'Parent', gd.Textcontextmenu.handle,...
'Label', 'Change Font Size',...
'Callback', @(hObject,eventdata)Textchangesize(hObject,eventdata,guidata(hObject)));
gd.Textcontextmenu.color = uimenu(...
'Parent', gd.Textcontextmenu.handle,...
'Label', 'Change Color',...
'Callback', @(hObject,eventdata)Textchangecolor(hObject,eventdata,guidata(hObject)));
%% Save guidata
guidata(gd.fig, gd);
%% Load passed in arguments
if gd.state.dataAvailable
LoadImages(gd.LoadImages.load, {ImageFile, LoadType, Frames, Channels}, guidata(gd.fig));
end
if gd.state.experimentAvailable
LoadExperiment(gd.LoadExperiment.load, ExperimentFile, guidata(gd.fig));
end
if gd.state.roisAvailable
LoadROIs(gd.ROI.load, ROIFile, guidata(gd.fig));
end
%% KEYPRESS CALLBACKS
function KeyPressCallback(hObject,eventData,gd)
% if strcmp(gd.state.UIstate, 'zoom')
% zoom off
% gd.state.UIstate = 'ready';
% elseif strcmp(gd.state.UIstate, 'pan')
% pan off
% gd.state.UIstate = 'ready';
% end
% Pre Data Loaded
if gd.state.dataAvailable==false %nothing loaded
switch eventData.Key
case 'l' %load Imgs
LoadImages(gd.LoadImages.load, [], gd);
end
else % Post Data Loaded
switch gd.state.UIstate
% ROI not being edited
case 'ready' %base state
if ~isempty(eventData.Modifier)
switch eventData.Modifier{1}
case 'shift'
step = 10;
end
else
step = 1;
end
switch eventData.Key
case {'uparrow','w'} %move up one depth
nextimg = gd.state.currentDepth + step;
if nextimg > get(gd.View.depthSlider,'Max');
nextimg = 1;
end
set(gd.View.depthSlider,'value',nextimg);
plotmainaxes([],nextimg,gd);
case {'downarrow','s'} %move down one depth
nextimg = gd.state.currentDepth - step;
if nextimg < get(gd.View.depthSlider,'Min');
nextimg = get(gd.View.depthSlider, 'Max');
end
set(gd.View.depthSlider,'value',nextimg);
plotmainaxes([],nextimg,gd);
case {'rightarrow','d'} %move right one frame
currentimg = round(get(gd.View.frameSlider,'Value'));
nextimg = currentimg + step;
if nextimg > get(gd.View.frameSlider,'Max');
nextimg = 1;
end
set(gd.View.frameSlider,'value',nextimg);
plotmainaxes(nextimg,[],gd);
case {'leftarrow','a'} %move left one frame
currentimg = round(get(gd.View.frameSlider,'Value'));
nextimg = currentimg - step;
if nextimg < get(gd.View.frameSlider,'Min');
nextimg = get(gd.View.frameSlider,'Max');
end
set(gd.View.frameSlider,'value',nextimg);
plotmainaxes(nextimg,[],gd);
case {'return','space'} %play/pause movie
set(gd.View.playPause,'Value',abs(get(gd.View.playPause,'Value')-1)); %toggle button
PlayPause(gd.View.playPause, [], gd);
case 'r' %add ROI
AddROI(gd.ROI.add, [], gd);
case 'e' %edit ROI
if gd.Internal.ROIs.n > 0 %only if ROIs exist
EditROI(gd.ROI.edit, [], gd);
end
case 'v'
if gd.Internal.ROIs.n > 0 %only if ROIs exist
set(gd.ROI.show, 'Value', abs(get(gd.ROI.show, 'Value')-1));
plotmainaxes([],[],gd);
end
case 'm'
if strcmp(gd.LoadExperiment.MC.Enable, 'on')
gd.LoadExperiment.MC.Value = abs(gd.LoadExperiment.MC.Value-1);
plotmainaxes([],[],gd);
end
case 'z'
if ~isempty(eventData.Modifier) && strcmp(eventData.Modifier, 'shift')
gd.View.axes.XLim = [0,gd.Images.Width+0.5];
gd.View.axes.YLim = [0,gd.Images.Height+0.5];
else
% gd.Internal.zoom.Enable = 'on';
% gd.state.UIstate = 'zoom';
end
% guidata(hObject, gd);
% case 'p'
% pan on
% gd.state.UIstate = 'pan';
% guidata(hObject, gd);
end %switch E.Key, state='ready'
case 'ROIedit' %ROI being edited or added
editIndex = find([gd.ROIs.rois(:).beingEdited]);
editAll = all([gd.ROIs.rois(:).beingEdited]) && numel(gd.ROIs.rois)>1;
if ~isempty(eventData.Modifier)
step = 10;
else
step = .5;
end
switch eventData.Key
case {'uparrow','w'} %translate ROI up
for rindex = editIndex
switch gd.ROIs.rois(rindex).type % save ROI
case 'ellipse'
position = getPosition(gd.ROIs.rois(rindex).handle);
if position(2) >= step+.5 %constrain to image boundary
position(2) = position(2) - step; %translate up
setPosition(gd.ROIs.rois(rindex).handle, position);
gd.ROIs.rois(rindex).position = position;
gd.ROIs.rois(rindex).vertices = getVertices(gd.ROIs.rois(rindex).handle);
end
case 'polygon'
vertices = getPosition(gd.ROIs.rois(rindex).handle);
if vertices(:,2) >= step + .5; %constrain to image boundary
vertices(:,2) = vertices(:,2) - step; %translate up
setPosition(gd.ROIs.rois(rindex).handle, vertices);
gd.ROIs.rois(rindex).vertices = [vertices;vertices(1,:)];
end
end
end
if editAll
gd.ROIs.offset(1) = gd.ROIs.offset(1) + step;
end
guidata(hObject, gd);
case {'downarrow','s'} %translate ROI down
for rindex = editIndex
switch gd.ROIs.rois(rindex).type % save ROI
case 'ellipse'
position = getPosition(gd.ROIs.rois(rindex).handle);
Y = get(gca,'YLim');
if position(2)+position(4) <= Y(2)-step; %constrain to image boundary
position(2) = position(2) + step; %translate down
setPosition(gd.ROIs.rois(rindex).handle,position);
gd.ROIs.rois(rindex).position = position;
gd.ROIs.rois(rindex).vertices = getVertices(gd.ROIs.rois(rindex).handle);
end
case 'polygon'
vertices = getPosition(gd.ROIs.rois(rindex).handle);
Y = get(gca,'YLim');
if vertices(:,2) <= Y(2)-step; %constrain to image boundary
vertices(:,2) = vertices(:,2) + step; %translate down
setPosition(gd.ROIs.rois(rindex).handle,vertices);
gd.ROIs.rois(rindex).vertices = [vertices;vertices(1,:)];
end
end
end
if editAll
gd.ROIs.offset(1) = gd.ROIs.offset(1) - step;
end
guidata(hObject, gd);
case {'rightarrow','d'} %translate ROI right
for rindex = editIndex
switch gd.ROIs.rois(rindex).type % save ROI
case 'ellipse'
position = getPosition(gd.ROIs.rois(rindex).handle);
X = get(gca,'XLim');
if position(1)+position(3) <= X(2)-step; %constrain to image boundary
position(1) = position(1) + step; %translate right
setPosition(gd.ROIs.rois(rindex).handle,position);
gd.ROIs.rois(rindex).position = position;
gd.ROIs.rois(rindex).vertices = getVertices(gd.ROIs.rois(rindex).handle);
end
case 'polygon'
vertices = getPosition(gd.ROIs.rois(rindex).handle);
X = get(gca,'XLim');
if vertices(:,1) <= X(2)-step; %constrain to image boundary
vertices(:,1) = vertices(:,1) + step; %translate right
setPosition(gd.ROIs.rois(rindex).handle,vertices);
gd.ROIs.rois(rindex).vertices = [vertices;vertices(1,:)];
end
end
end
if editAll
gd.ROIs.offset(2) = gd.ROIs.offset(2) + step;
end
guidata(hObject, gd);
case {'leftarrow','a'} %translate ROI left
for rindex = editIndex
switch gd.ROIs.rois(rindex).type % save ROI
case 'ellipse'
position = getPosition(gd.ROIs.rois(rindex).handle);
if position(1) >= step + .5 %constrain to image boundary
position(1) = position(1) - step; %translate left
setPosition(gd.ROIs.rois(rindex).handle,position);
gd.ROIs.rois(rindex).position = position;
gd.ROIs.rois(rindex).vertices = getVertices(gd.ROIs.rois(rindex).handle);
end
case 'polygon'
vertices = getPosition(gd.ROIs.rois(rindex).handle);
if vertices(:,1) >= step + .5 %constrain to image boundary
vertices(:,1) = vertices(:,1) - step; %translate left
setPosition(gd.ROIs.rois(rindex).handle,vertices);
gd.ROIs.rois(rindex).vertices = [vertices;vertices(1,:)];
end
end
end
if editAll
gd.ROIs.offset(2) = gd.ROIs.offset(2) - step;
end
guidata(hObject, gd);
case 'comma' %up depth
for rindex = editIndex
if gd.ROIs.rois(rindex).depth ~= 1
gd.ROIs.rois(rindex).depth = gd.ROIs.rois(rindex).depth - 1;
end
end
if editAll
gd.ROIs.offset(3) = gd.ROIs.offset(3) - step;
end
guidata(hObject, gd);
if gd.state.currentDepth ~= 1
plotmainaxes([],gd.state.currentDepth-1,gd);
end
case 'period' %down depth
for rindex = editIndex
if gd.ROIs.rois(rindex).depth ~= gd.Images.Depth
gd.ROIs.rois(rindex).depth = gd.ROIs.rois(rindex).depth + 1;
end
end
if editAll
gd.ROIs.offset(3) = gd.ROIs.offset(3) + step;
end
guidata(hObject, gd);
if gd.state.currentDepth ~= gd.Images.Depth
plotmainaxes([],gd.state.currentDepth+1,gd);
end
case 'e' %edit ROI
if ~all([gd.ROIs.rois(:).beingEdited]) %only if ROIs exist
EditROI(gd.ROI.edit, [], gd);
end
case {'r','return','space'} %save ROI
SaveROI(gd.ROI.save, [], gd);
case {'backspace','delete'} %delete ROI
DeleteROI(gd.ROI.delete, [], gd);
end %switch E.Key, state='ROIedit'
end %switch h.state.UIstate
end
function ROIcurrentLabelKeyPress(hObject,eventdata,gd)
if any(strcmp(eventdata.Key, {'delete', 'backspace'}))
gd.ROIs.rois(gd.Internal.ROIs.current).label(get(hObject, 'Value')) = [];
set(hObject,...
'String', gd.ROIs.rois(gd.Internal.ROIs.current).label,...
'Value', 1);
guidata(hObject, gd);
plotmainaxes([],[],gd);
end
%% CLICK CALLBACKS
function ROIClickCallback(hObject,eventdata,gd)
if eventdata.Button == 1
switch get(hObject, 'Type')
case 'patch'
index = get(hObject,'UserData');
gd.Internal.ROIs.current = index;
set(gd.ROI.currentLabels, 'String', gd.ROIs.rois(index).label, 'Value', 1);
set(gd.ROI.currentTag, 'String', gd.ROIs.rois(index).tag);
% set(gd.ROI.info, 'String', struct2string(gd.ROIs.rois(index),{'pixels','mask','neuropilmask','rawdata','rawneuropil'}), 'Value', 1);
case 'image'
gd.Internal.ROIs.current = false;
set([gd.ROI.currentLabels,gd.ROI.info], 'String', '');
set(gd.ROI.currentTag, 'String', 'tag');
end
guidata(hObject, gd);
plotmainaxes([],[],gd);
end
%% CONTEXT MENU CALLBACKS
% Right click stimulus mark or running speed
function Textcontextmenu(hObject,eventdata,gd)
% change text size
function Textchangesize(hObject,eventdata,gd)
answer = inputdlg('Font size:', 'Adjust text', 1, {num2str(get(gco, 'FontSize'))});
answer = str2num(answer{1});
set(gco, 'FontSize', answer);
switch get(gco, 'UserData')
case 'StimMark'
gd.Internal.Settings.StimMarkSize = answer;
case 'RunningSpeed'
gd.Internal.Settings.RunningSpeedSize = answer;
end
guidata(hObject, gd);
% change color
function Textchangecolor(hObject,eventdata,gd)
answer = inputdlg('Color:', 'Adjust text', 1, {num2str(get(gco, 'Color'))});
testnum = str2num(answer{1});
if ~isempty(testnum) && numel(testnum) == 3 % input is 'numeric'
if any(testnum>1) || any(testnum<0) % validate input
return
end