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Added latent plot to PCA, added overlay interface,
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@AlanRace
AlanRace committed Jul 12, 2018
1 parent a2c542d commit 33a4168
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Showing 6 changed files with 315 additions and 8 deletions.
2 changes: 1 addition & 1 deletion src/SpectralAnalysis.m
View file
Expand Up @@ -17,7 +17,7 @@

% Launch spectral analysis interface
try
SpectralAnalysisInterface();
spectralAnalysis = SpectralAnalysisInterface();
catch err
if((strcmp(err.identifier, 'MATLAB:class:undefinedMethod') || strcmp(err.identifier, 'MATLAB:class:InvalidSuperClass')) ...
&& ~isempty(strfind(err.message, 'Figure')))
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8 changes: 5 additions & 3 deletions src/gui/DataViewer.m
View file
Expand Up @@ -33,6 +33,8 @@
spectrumList;

dataRepresentation;

title;
end

% Options
Expand Down Expand Up @@ -139,12 +141,12 @@
obj.dataRepresentation = dataRepresentation;

if(~isempty(obj.dataRepresentation.parser))
title = obj.dataRepresentation.parser.getShortFilename();
obj.title = obj.dataRepresentation.parser.getShortFilename();
else
title = obj.dataRepresentation.name;
obj.title = obj.dataRepresentation.name;
end

obj.setTitle(['DataViewer: ' title]);
obj.setTitle(['DataViewer: ' obj.title]);

% obj.sizeChanged();

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280 changes: 280 additions & 0 deletions src/gui/OverlayFigure.m
View file
@@ -0,0 +1,280 @@
classdef OverlayFigure < Figure
properties
dataViewList;

rImageDisplay;
gImageDisplay;
bImageDisplay;
rgbImageDisplay;

rDataSelectionBox;
gDataSelectionBox;
bDataSelectionBox;

rImageSelectionBox;
gImageSelectionBox;
bImageSelectionBox;

rHisteqCheckbox;
gHisteqCheckbox;
bHisteqCheckbox;

rMinLabel;
rMinEditbox;
rMaxLabel;
rMaxEditbox;

gMinLabel;
gMinEditbox;
gMaxLabel;
gMaxEditbox;

bMinLabel;
bMinEditbox;
bMaxLabel;
bMaxEditbox;
end

methods
function this = OverlayFigure(dataViewList)
this.dataViewList = dataViewList;

this.updateLists();
end

function updateLists(this)
dataViews = this.dataViewList.getObjects();
titles = {};

for i = 1:length(dataViews)
titles{i} = dataViews{i}.title;
end

set(this.rDataSelectionBox, 'String', titles)
set(this.gDataSelectionBox, 'String', titles)
set(this.bDataSelectionBox, 'String', titles)
end

function dataSelected(this, src, event, imageSelectionBox)
dataViewer = this.dataViewList.get(get(src, 'Value'));

set(imageSelectionBox, 'String', {dataViewer.imageList.description});

end

function imageSelected(this, src, event, dataSelectionBox, imageDisplay, minEditbox, maxEditbox)
dataViewer = this.dataViewList.get(get(dataSelectionBox, 'Value'));
image = dataViewer.imageList(get(src, 'Value'));

set(minEditbox, 'String', num2str(min(image.imageData(:))))
set(maxEditbox, 'String', num2str(max(image.imageData(:))))

imageDisplay.setData(image);

this.updateRGBImage();
end

function editMinValue(this, src, event, imageDisplay)
imageDisplay.setMinValueToDisplay(str2double(get(src, 'String')));

this.updateRGBImage();
end

function editMaxValue(this, src, event, imageDisplay)
imageDisplay.setMaxValueToDisplay(str2double(get(src, 'String')));

this.updateRGBImage();
end

function toggleHistogramEqualisation(this, src, event, imageView)
imageView.setEqualiseHistogram(get(src, 'Value'));

this.updateRGBImage();
end

function updateRGBImage(this)
rImageData = this.rImageDisplay.getVisualisedData();
gImageData = this.gImageDisplay.getVisualisedData();
bImageData = this.bImageDisplay.getVisualisedData();

rgbImageData = [];

if(~isequal(size(rImageData), [1 1]))
rgbImageData(:, :, 1) = rImageData;
end
if(~isequal(size(gImageData), [1 1]))
rgbImageData(:, :, 2) = gImageData;
end
if(~isequal(size(bImageData), [1 1]))
rgbImageData(:, :, 3) = bImageData;
end

if(~isempty(rgbImageData))
if(size(rgbImageData, 3) ~= 3)
rgbImageData(1, 1, 3) = 0;
end

rgbImageData(:, :, 1) = rgbImageData(:, :, 1) ./ max(max(rgbImageData(:, :, 1)));
rgbImageData(:, :, 2) = rgbImageData(:, :, 2) ./ max(max(rgbImageData(:, :, 2)));
rgbImageData(:, :, 3) = rgbImageData(:, :, 3) ./ max(max(rgbImageData(:, :, 3)));

this.rgbImageDisplay.setData(Image(rgbImageData));
end
end
end

methods (Access = protected)
function sizeChanged(this)

if(this.handle ~= 0)
newPosition = Figure.getPositionInPixels(this.handle);

margin = 5;

colourBarSize = 80;
leftPanelSize = newPosition(3) / 6;
buttonHeight = 25;

widthForImage = newPosition(3) - leftPanelSize - margin*3 - colourBarSize;

individualImageHeights = newPosition(4)/3 - buttonHeight*2 - margin*5;

Figure.setObjectPositionInPixels(this.rDataSelectionBox, [margin, newPosition(4)-buttonHeight-margin, leftPanelSize*2, buttonHeight]);
Figure.setObjectPositionInPixels(this.rImageSelectionBox, [margin, newPosition(4)-buttonHeight*2-margin, leftPanelSize, buttonHeight]);
Figure.setObjectPositionInPixels(this.rHisteqCheckbox, [margin + leftPanelSize, newPosition(4)-buttonHeight*3-margin, leftPanelSize, buttonHeight]);

Figure.setObjectPositionInPixels(this.rMinLabel, [margin + leftPanelSize, newPosition(4)*2/3, 30, buttonHeight]);
Figure.setObjectPositionInPixels(this.rMinEditbox, [margin*2 + leftPanelSize + 30, newPosition(4)*2/3+margin, 60, buttonHeight]);

Figure.setObjectPositionInPixels(this.rMaxLabel, [margin + leftPanelSize + 100, newPosition(4)*2/3, 30, buttonHeight]);
Figure.setObjectPositionInPixels(this.rMaxEditbox, [margin*2 + leftPanelSize + 130, newPosition(4)*2/3+margin, 60, buttonHeight]);

Figure.setObjectPositionInPixels(this.rImageDisplay.axisHandle, [margin, newPosition(4)*2/3+margin, leftPanelSize - colourBarSize, individualImageHeights]);

Figure.setObjectPositionInPixels(this.gDataSelectionBox, [margin, newPosition(4)*2/3-buttonHeight-margin, leftPanelSize*2, buttonHeight]);
Figure.setObjectPositionInPixels(this.gImageSelectionBox, [margin, newPosition(4)*2/3-buttonHeight*2-margin, leftPanelSize, buttonHeight]);
Figure.setObjectPositionInPixels(this.gHisteqCheckbox, [margin + leftPanelSize, newPosition(4)*2/3-buttonHeight*3-margin, leftPanelSize, buttonHeight]);

Figure.setObjectPositionInPixels(this.gMinLabel, [margin + leftPanelSize, newPosition(4)/3, 30, buttonHeight]);
Figure.setObjectPositionInPixels(this.gMinEditbox, [margin*2 + leftPanelSize + 30, newPosition(4)/3+margin, 60, buttonHeight]);

Figure.setObjectPositionInPixels(this.gMaxLabel, [margin + leftPanelSize + 100, newPosition(4)/3, 30, buttonHeight]);
Figure.setObjectPositionInPixels(this.gMaxEditbox, [margin*2 + leftPanelSize + 130, newPosition(4)/3+margin, 60, buttonHeight]);

Figure.setObjectPositionInPixels(this.gImageDisplay.axisHandle, [margin, newPosition(4)/3+margin, leftPanelSize - colourBarSize, individualImageHeights]);

Figure.setObjectPositionInPixels(this.bDataSelectionBox, [margin, newPosition(4)/3-buttonHeight-margin, leftPanelSize*2, buttonHeight]);
Figure.setObjectPositionInPixels(this.bImageSelectionBox, [margin, newPosition(4)/3-buttonHeight*2-margin, leftPanelSize, buttonHeight]);
Figure.setObjectPositionInPixels(this.bHisteqCheckbox, [margin + leftPanelSize, newPosition(4)/3-buttonHeight*3-margin, leftPanelSize, buttonHeight]);

Figure.setObjectPositionInPixels(this.bMinLabel, [margin + leftPanelSize, 0, 30, buttonHeight]);
Figure.setObjectPositionInPixels(this.bMinEditbox, [margin*2 + leftPanelSize + 30, margin, 60, buttonHeight]);

Figure.setObjectPositionInPixels(this.bMaxLabel, [margin + leftPanelSize + 100, 0, 30, buttonHeight]);
Figure.setObjectPositionInPixels(this.bMaxEditbox, [margin*2 + leftPanelSize + 130, margin, 60, buttonHeight]);

Figure.setObjectPositionInPixels(this.bImageDisplay.axisHandle, [margin, margin, leftPanelSize - colourBarSize, individualImageHeights]);

Figure.setObjectPositionInPixels(this.rgbImageDisplay.axisHandle, [margin+leftPanelSize*2, margin, newPosition(3) - leftPanelSize*2 - margin*2, newPosition(4) - margin*2]);
end
end

function createFigure(this)
% createFigure Create figure.
%
% createFigure()

createFigure@Figure(this);

this.setTitle('RGB Composite');

this.rDataSelectionBox = uicontrol('Parent', this.handle, 'Style', 'popup', ...
'String', {''}, 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.dataSelected(src, event, this.rImageSelectionBox));
this.gDataSelectionBox = uicontrol('Parent', this.handle, 'Style', 'popup', ...
'String', {''}, 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.dataSelected(src, event, this.gImageSelectionBox));
this.bDataSelectionBox = uicontrol('Parent', this.handle, 'Style', 'popup', ...
'String', {''}, 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.dataSelected(src, event, this.bImageSelectionBox));

this.rImageSelectionBox = uicontrol('Parent', this.handle, 'Style', 'popup', ...
'String', {''}, 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.imageSelected(src, event, this.rDataSelectionBox, this.rImageDisplay, this.rMinEditbox, this.rMaxEditbox));
this.gImageSelectionBox = uicontrol('Parent', this.handle, 'Style', 'popup', ...
'String', {''}, 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.imageSelected(src, event, this.gDataSelectionBox, this.gImageDisplay, this.gMinEditbox, this.gMaxEditbox));
this.bImageSelectionBox = uicontrol('Parent', this.handle, 'Style', 'popup', ...
'String', {''}, 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.imageSelected(src, event, this.bDataSelectionBox, this.bImageDisplay, this.bMinEditbox, this.bMaxEditbox));

this.rImageDisplay = ImageDisplay(this, Image(1));
this.rImageDisplay.setColourMap([(0:255)' zeros(256, 1) zeros(256, 1)]./255);
% set(this.rImageDisplay.axisHandle, 'Position', [0.05, 0.5, 0.4, 0.35]);

this.gImageDisplay = ImageDisplay(this, Image(1));
this.gImageDisplay.setColourMap([zeros(256, 1) (0:255)' zeros(256, 1)]./255);
% set(this.gImageDisplay.axisHandle, 'Position', [0.05, 0.5, 0.4, 0.35]);

this.bImageDisplay = ImageDisplay(this, Image(1));
this.bImageDisplay.setColourMap([zeros(256, 1) zeros(256, 1) (0:255)']./255);
% set(this.bImageDisplay.axisHandle, 'Position', [0.05, 0.5, 0.4, 0.35]);

this.rHisteqCheckbox = uicontrol('Parent', this.handle, 'Style', 'checkbox', ...
'String', 'Histogram Equalisation', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.toggleHistogramEqualisation(src, event, this.rImageDisplay));
this.gHisteqCheckbox = uicontrol('Parent', this.handle, 'Style', 'checkbox', ...
'String', 'Histogram Equalisation', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.toggleHistogramEqualisation(src, event, this.gImageDisplay));
this.bHisteqCheckbox = uicontrol('Parent', this.handle, 'Style', 'checkbox', ...
'String', 'Histogram Equalisation', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.toggleHistogramEqualisation(src, event, this.bImageDisplay));

this.rMinLabel = uicontrol('Parent', this.handle, 'Style', 'text', ...
'String', 'Min', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1]);
this.rMinEditbox = uicontrol('Parent', this.handle, 'Style', 'edit', ...
'String', '', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.editMinValue(src, event, this.rImageDisplay));
this.rMaxLabel = uicontrol('Parent', this.handle, 'Style', 'text', ...
'String', 'Max', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1]);
this.rMaxEditbox = uicontrol('Parent', this.handle, 'Style', 'edit', ...
'String', '', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.editMaxValue(src, event, this.rImageDisplay));

this.gMinLabel = uicontrol('Parent', this.handle, 'Style', 'text', ...
'String', 'Min', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1]);
this.gMinEditbox = uicontrol('Parent', this.handle, 'Style', 'edit', ...
'String', '', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.editMinValue(src, event, this.gImageDisplay));
this.gMaxLabel = uicontrol('Parent', this.handle, 'Style', 'text', ...
'String', 'Max', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1]);
this.gMaxEditbox = uicontrol('Parent', this.handle, 'Style', 'edit', ...
'String', '', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.editMaxValue(src, event, this.gImageDisplay));

this.bMinLabel = uicontrol('Parent', this.handle, 'Style', 'text', ...
'String', 'Min', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1]);
this.bMinEditbox = uicontrol('Parent', this.handle, 'Style', 'edit', ...
'String', '', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.editMinValue(src, event, this.bImageDisplay));
this.bMaxLabel = uicontrol('Parent', this.handle, 'Style', 'text', ...
'String', 'Max', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1]);
this.bMaxEditbox = uicontrol('Parent', this.handle, 'Style', 'edit', ...
'String', '', 'Units', 'normalized', 'Position', [0.05, 0.85, 0.3, 0.1], 'Callback', @(src, event) this.editMaxValue(src, event, this.bImageDisplay));

this.rgbImageDisplay = ImageDisplay(this, Image(1));
this.rgbImageDisplay.setColourBarOn(0);

set(this.handle, 'units','normalized','outerposition',[0.2 0.4 0.5 0.5]);
% columnNames = {'ROI', 'Mean', 'SD', '# Pixels', 'Max', 'Min'};
% columnFormat = {'char', 'numeric', 'numeric', 'numeric', 'numeric', 'numeric'};
% columnEditable = [false, false, false, false, false, false];
%
% this.imageListSelection = uicontrol('Parent', this.handle, 'Style', 'popup', ...
% 'String', {''}, 'Units', 'normalized', 'Position', [0.05, 0.85, 0.7, 0.1], 'Callback', @(src, event) this.imageSelected(src, event));
%
% this.allDataButton = uicontrol('Parent', this.handle, ...
% 'String', 'View all data', 'Units', 'normalized', 'Position', [0.75, 0.9, 0.2, 0.05], 'Callback', @(src, event) this.viewAllData());
%
% this.imageDisplay = ImageDisplay(this, Image(1));
% set(this.imageDisplay.axisHandle, 'Position', [0.05, 0.5, 0.4, 0.35]);
%
% this.roiPlot = axes(this.handle, 'Units', 'normalized', 'Position', [0.525, 0.525, 0.425, 0.325]);
%
% this.regionOfInterestTable = uitable('Parent', this.handle, ...
% 'ColumnName', columnNames, 'ColumnFormat', columnFormat, 'ColumnEditable', columnEditable, ...
% 'RowName', [], 'Units', 'normalized', 'Position', [0.05 0.15 0.9 0.3]);
%
% this.copyToClipboardButton = uicontrol('Parent', this.handle, ...
% 'String', 'Copy to clipboard', 'Units', 'normalized', 'Position', [0.05, 0.05, 0.2, 0.05], 'Callback', @(src, event) this.copyToClipboard());
% this.exportButton = uicontrol('Parent', this.handle, ...
% 'String', 'Export', 'Units', 'normalized', 'Position', [0.75, 0.05, 0.2, 0.05], 'Callback', @(src, event) this.export());
end
end
end
8 changes: 8 additions & 0 deletions src/gui/SpectralAnalysisInterface.m
View file
Expand Up @@ -13,6 +13,7 @@
properties (Access = private)
openFileMenu;
convertMenu;
toolsMenu;
memoryMenu;

progressBarAxis;
Expand Down Expand Up @@ -204,6 +205,10 @@ function showDataListViewer(this)
end
end

function showRGBCompositeGenerator(this)
OverlayFigure(this.dataViewerList);
end

function dataRepresentations = getDataRepresentations(this)
% getDataRepresentations Get data representations associated with this SpectralAnalysisInterface.
%
Expand Down Expand Up @@ -331,6 +336,9 @@ function createMenu(this)
'Callback', @(src, evnt) this.convertToBinary(this.toBinaryConverterMethods{i}));
end

this.toolsMenu = uimenu(this.handle, 'Label', 'Tools');
uimenu(this.toolsMenu, 'Label', 'RGB Composite Generator', 'Callback', @(src, evnt) this.showRGBCompositeGenerator());

% Add in memory menu
this.memoryMenu = uimenu(this.handle, 'Label', 'Memory');
uimenu(this.memoryMenu, 'Label', 'Memory Usage', 'Callback', @(src, evnt) this.showDataListViewer());
Expand Down

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