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displayStack.m
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function displayStack(Images, CLim, CMap)
FrameIndex = 1:500; % loading only
%% Parse input arguments
% Select file
if ~exist('Images', 'var')
[f,p] = uigetfile({'*.tif;*.sbx'}, 'Select image file');
if isnumeric(f)
return
end
Images = fullfile(p,f);
end
% Load images
if ischar(Images)
ImageFile = Images;
[gd.Images, gd.loadObj] = load2P(ImageFile, 'Type', 'Direct', 'Frames', FrameIndex, 'Double');
else
gd.Images = Images;
end
gd.class = class(gd.Images);
% Format images
while ndims(gd.Images) < 5
gd.Images = permute(gd.Images, [1:ndims(gd.Images)-1, ndims(gd.Images)+1, ndims(gd.Images)]);
end
gd.dim = size(gd.Images);
% Determine color limits
if ~exist('CLim', 'var') || isempty(CLim)
% gd.CLim = prctile(Images(linspace(1,numel(Images),512*796*100)), [1,99]);
gd.CLimits = double([min(gd.Images(:)), max(gd.Images(:))]);
else
gd.CLim = CLim;
end
% Determine color map
if ~exist('CMap', 'var')
gd.CMap = [];
% gd.CMap = HiLoColormap(CLim(1), CLim(2));
else
gd.CMap = CMap;
end
%% Code
% Create figure
gd.fig = figure;
% Create axis
gd.axes = axes(...
'Parent', gd.fig,...
'Units', 'normalized',...
'XLimMode', 'manual',...
'YLimMode', 'manual');
if isequal(gd.class, 'logical')
gd.axes.Position = [.1, .1, .8, .7];
else
gd.axes.Position = [.1, .2, .8, .6];
end
% Create indexing sliders
sliderIndex = find(gd.dim(3:end)>1);
ndim = numel(sliderIndex);
for sindex = 1:ndim
maxvalue = gd.dim(sliderIndex(sindex)+2);
minorstep = 1/(maxvalue-1);
yloc = .9+(ndim-sindex)*.1/ndim;
gd.sliders(sindex) = uicontrol(...
'Style', 'slider',...
'Parent', gd.fig,...
'Units', 'normalized',...
'Position', [.1,yloc,.9,.1/ndim],...
'Min', 1,...
'Max', maxvalue,...
'Value', 1,...
'SliderStep', [minorstep,max(2*minorstep,.1)],...
'ToolTipString', sprintf('Dimension %d', sliderIndex(sindex)),...
'UserData', [sindex, sliderIndex(sindex), maxvalue],...
'Callback', @(hObject,eventdata)updateindex(hObject, eventdata, guidata(hObject)));
gd.text(sindex) = uicontrol(...
'Style', 'text',...
'Parent', gd.fig,...
'Units', 'normalized',...
'Position', [0,yloc,.1,.1/ndim],...
'String', sprintf('1/%d', maxvalue),...
'HorizontalAlignment', 'right');
end
gd.Position = ones(1,3);
% Create plot type dropdown
gd.Selection = uicontrol(...
'Style', 'popupmenu',...
'Parent', gd.fig,...
'String', {'imagesc','bar3'},...
'Units', 'normalized',...
'Position', [0,.05,.2,.05],...
'Callback', @(hObject,eventdata)plotmainaxes(guidata(hObject)));
if strcmp(gd.class,'logical')
gd.Selection.Enable = 'off';
end
% Create colormap dropdown
gd.Colormap = uicontrol(...
'Style', 'popupmenu',...
'Parent', gd.fig,...
'String', {'gray','parula'},...
'Units', 'normalized',...
'Position', [0,0,.2,.05],...
'Callback', @(hObject,eventdata)plotmainaxes(guidata(hObject)));
if ~isempty(gd.CMap)
gd.Colormap.String{3} = 'input';
end
% Create colorlimit sliders
for index = 1:2
minorstep = min(1/(gd.CLimits(2)-gd.CLimits(1)),.05);
yloc = (index-1)*.1/2;
gd.CLimSliders(index) = uicontrol(...
'Style', 'slider',...
'Parent', gd.fig,...
'Units', 'normalized',...
'Position', [.35,yloc,.45,.1/2],...
'Min', gd.CLimits(1),...
'Max', gd.CLimits(2),...
'Value', gd.CLimits(index),...
'SliderStep', [minorstep,max(2*minorstep,.1)],...
'UserData', index,...
'Callback', @(hObject,eventdata)updateCLim(hObject, eventdata, guidata(hObject)));
gd.CLimText(index) = uicontrol(...
'Style', 'text',...
'Parent', gd.fig,...
'Units', 'normalized',...
'Position', [.2,yloc,.15,.1/2],...
'String', sprintf('%d', gd.CLimits(index)),...
'HorizontalAlignment', 'right');
end
gd.CLim = gd.CLimits;
% Create colorlimit individual toggle
gd.CLimIndiv = uicontrol(...
'Style', 'radiobutton',...
'Parent', gd.fig,...
'Units', 'normalized',...
'Position', [.8,.05,.2,.05],...
'Value', 0,...
'String', 'CLim each',...
'Callback', @(hObject,eventdata)CLimIndiv(hObject, eventdata, guidata(hObject)));
% Create histeq toggle
gd.histeq = uicontrol(...
'Style', 'radiobutton',...
'Parent', gd.fig,...
'Units', 'normalized',...
'Position', [.8,0,.2,.05],...
'Value', 0,...
'String', 'hist eq',...
'Callback', @(hObject,eventdata)plotmainaxes(guidata(hObject)));
guidata(gd.fig, gd);
% Plot first image
plotmainaxes(gd);
% If output: wait for figure to be closed
% waitfor(gd.fig);
function updateindex(hObject, ~, gd)
% update index
gd.Position(hObject.UserData(2)) = round(hObject.Value);
guidata(hObject, gd);
% update text
gd.text(hObject.UserData(1)).String = sprintf('%d/%d', gd.Position(hObject.UserData(2)), hObject.UserData(3));
% plot new image
plotmainaxes(gd)
function updateCLim(hObject, ~, gd)
% update CLim
value = hObject.Value;
if hObject.UserData==1
if value >= gd.CLim(2)
hObject.Value = hObject.Min;
return
end
elseif hObject.UserData==2
if value <= gd.CLim(1)
hObject.Value = hObject.Max;
return
end
end
gd.CLim(hObject.UserData) = value;
guidata(hObject, gd);
% update text
gd.CLimText(hObject.UserData).String = sprintf('%d', gd.CLim(hObject.UserData));
% plot new image
plotmainaxes(gd);
function CLimIndiv(hObject, ~, gd)
% disable clim sliders
if hObject.Value
set([gd.CLimSliders,gd.CLimText], 'Enable', 'off');
else
set([gd.CLimSliders,gd.CLimText], 'Enable', 'on');
end
% plot new image
plotmainaxes(gd);
function plotmainaxes(gd)
axes(gd.axes)
% Lim = get(gca,{'XLim','YLim'});
img = gd.Images(:,:, gd.Position(1), gd.Position(2), gd.Position(3));
if gd.Selection.Value==1 % imagesc
gd.histeq.Enable = 'on';
if gd.histeq.Value
img = adapthisteq(img, 'NumTiles', [16 16], 'Distribution', 'Exponential');
end
switch gd.class
case 'logical'
imshow(img);
otherwise
if gd.CLimIndiv.Value
imagesc(img);
else
imagesc(img, gd.CLim);
end
end
axis tight %equal
elseif gd.Selection.Value==2 % bar3
gd.histeq.Enable = 'off';
temp = bar3(img);
for index=1:numel(temp)
temp(index).CData = temp(index).ZData;
temp(index).FaceColor = 'interp';
end
if gd.CLimIndiv.Value
zlim([min(img(:)),max(img(:))]);
else
gd.axes.CLim = gd.CLim;
zlim(gd.CLimits);
end
end
% Set colormap
if gd.Colormap.Value==1
colormap('gray')
elseif gd.Colormap.Value==2
colormap('parula')
elseif gd.Colormap.Value==3
colormap(gd.CMap)
end
% set(gca, 'XLim', Lim{1}, 'YLim', Lim{2});
% axis off
% xlabel(sprintf('Frame %d', Index));