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XeRay3.m
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XeRay3.m
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classdef XeRay3 < handle
properties
data
gui
const
handles
call
config
ElementProfiles
end
methods
function this = XeRay3(filenames)
initializeGui();
function initializeGui()
parent = getParentDir(which('XeRayGUI.m'));
this.config = loadjson(fullfile(parent, 'support-files/xeray-config.json'));
this.config.ScatteringFactorFolder = fullfile(parent, this.config.ScatteringFactorFolder);
this.ElementProfiles = loadjson(fullfile(getParentDir(which('XeRayGUI.m')), 'support-files/element-profiles.json'));
set(0, 'units', this.config.units);
pix = get(0, 'screensize');
if pix(4) * 0.85 <= this.config.window(4)
this.config.window(4) = pix(4)*0.85;
end
this.handles = figure('Visible','off','Name','XeRay','NumberTitle','off','Units','pixels', 'Position', this.config.window, 'Resize', 'on');
movegui(this.handles, 'center');
this.handles.Visible = 'on';
this.const = XeRayControl();
createView();
createController();
this.control('initialize');
end
function createView()
handle0 = this.handles;
createListPanel();
createAxes();
createRightPanel();
createElementEditPanel();
createDataControl();
createBasicInfoTalbe();
createParametersTable();
createLayersTable();
createFittingControls();
createOutputandSaveButtons();
function createListPanel()
listPanel = uipanel(handle0,'Title','X-ray Fluorescence Data','Units','normalized',...
'Position',[0.014 0.02 0.16 0.97]);
this.gui.scanText = uicontrol(listPanel,'Style','text','String','Select data sets to begin','Units','normalized',...
'Position',[0.05 0.965 0.8 0.03]);
this.gui.fileList = uicontrol(listPanel,'Style','listbox','Units','normalized',...
'Position',[0.05 0.56 0.9 0.405],'Max',2);
this.gui.loadButton = uicontrol(listPanel,'Style','pushbutton','String','Load','Units','normalized',...
'Position',[0.035 0.52 0.3 0.032]);
this.gui.deleteButton = uicontrol(listPanel,'Style','pushbutton','String','Delete','Units','normalized',...
'Position',[0.38 0.52 0.3 0.032]);
uicontrol(listPanel,'Style','text','String','Select angle range','Units','normalized',...
'Position',[0.05 0.49 0.8 0.03]);
this.gui.angleList = uicontrol(listPanel,'Style','listbox','Units','normalized',...
'Position',[0.05 0.015 0.9 0.48],'Max',2);
end
function createAxes()
this.gui.showError = uicontrol(handle0,'Style','checkbox','String','Show Error','Units','normalized','Visible','on',...
'Position',[0.6 0.965 0.1 0.018]);
this.gui.likelihoodChi2 = uicontrol(handle0,'Style','popupmenu','String',{'Likelihood','Chi^2'},'Visible','off',...
'Units','normalized',...
'Position',[0.572 0.97 0.1 0.018]);
this.gui.showCal = uicontrol(handle0,'Style','checkbox','String','Show Calc.','Units','normalized',...
'Position',[0.6 0.437 0.08 0.018]);
this.gui.showFit = uicontrol(handle0,'Style','checkbox','String','Show Fit','Units','normalized',...
'Position',[0.54 0.437 0.06 0.018]);
ax1 = axes('Parent',handle0,'Units','normalized','Position',[0.215 0.52 0.45 0.44]);
ax1.XLim = [0 10];
ax1.YLim = [0 10];
ax1.XTick = [0 2 4 6 8 10];
ax1.YTick = [0 2 4 6 8 10];
ax1.XLabel.String = 'x1';
ax1.YLabel.String = 'y1';
this.gui.ax1 = ax1;
% plot region 2
ax2 = axes('Parent',handle0,'Units','normalized','Position',[0.215 0.08 0.45 0.35]);
ax2.XLim = [0 10];
ax2.YLim = [0 10];
ax2.XTick = [0 2 4 6 8 10];
ax2.YTick = [0 2 4 6 8 10];
ax2.XLabel.String = 'x2';
ax2.YLabel.String = 'y2';
this.gui.ax2 = ax2;
end
function createRightPanel()
this.gui.rightPanel = uipanel(handle0,'Units','normalized','Position',[0.68 0.02 0.31 0.97]);
this.gui.elementEditPanel = uipanel(handle0,'Title', 'Element Management', 'Visible', 'off', 'Units', 'normalized', 'Position',[0.685 0.03 0.3 0.95]);
end
function createElementEditPanel()
elementEditPanel = this.gui.elementEditPanel;
elementNames = fieldnames(this.ElementProfiles);
if ~isempty(elementNames)
status = 'on';
else
status = 'off';
end
base = 0.965;
textHeight = 0.025;
btnHeight = 0.035;
uicontrol(elementEditPanel,'Style','text','String','Existing Elements','Units','normalized',...
'HorizontalAlignment','left','Position',[0.0200 base 0.3000 textHeight]);
this.gui.closeTabButton = uicontrol(elementEditPanel,'Style','pushbutton','String','Close','Units','normalized',...
'Position',[0.88 0.01 0.11 btnHeight]);
this.gui.elementListbox = uicontrol(elementEditPanel,'Style','listbox','String', elementNames, 'Units','normalized',...
'Position',[0.02 0.02 0.2 0.94],'Max',1);
uicontrol(elementEditPanel,'Style','text','String','Element Name:','Units','normalized',...
'HorizontalAlignment','left','Position',[0.25 0.94 0.25 textHeight]);
this.gui.elementNameInput = uicontrol(elementEditPanel,'Style','edit','String', elementNames{1},'Units','normalized',...
'HorizontalAlignment','left','Position',[0.45 0.935 0.15 btnHeight]);
columnName = {'1','2'};
columnFormat = {'numeric','numeric'};
columnWidth = {60,60};
rowName = {'Range (keV)','Peaks (keV)','FWHM (keV)'};
elementTableData = getDataForElementTable(elementNames{1});
this.gui.elementTable = uitable(elementEditPanel,'ColumnName', columnName,'Data',elementTableData,...
'ColumnFormat', columnFormat,'ColumnEditable', [true true],'Units','normalized',...
'ColumnWidth',columnWidth,'RowName',rowName,'RowStriping','off',...
'Position',[0.25 0.78 0.7 0.15]);
uicontrol(elementEditPanel,'Style','text','String','Note: (1) FWHM is optinal, (2) enter both the lower and upper bounds, (3) enter 1 or 2 peaks.',...
'Units','normalized','HorizontalAlignment','left','Position',[0.25 0.72 0.65 0.05]);
this.gui.addElement = uicontrol(elementEditPanel, 'Style', 'pushbutton', 'String', 'Add', 'Units', 'normalized', 'Position',[0.81 base-0.03 0.15 btnHeight]);
this.gui.removeElement = uicontrol(elementEditPanel, 'Style', 'pushbutton', 'String', 'Remove', 'Units', 'normalized', 'Position',[0.65 base-0.03 0.15 btnHeight], 'Enable', status);
function data = getDataForElementTable(elementName)
data = cell(3,2);
profile = this.ElementProfiles.(elementName);
data{1,1} = profile.range(1);
data{1,2} = profile.range(2);
data{2,1} = profile.peak(1);
if length(profile.peak) > 1
data{2,2} = profile.peak(2);
else
data{2,2} = NaN;
end
if ~isempty(profile.width)
data{3,1} = profile.width(1);
if length(profile.width) > 1
data{3,2} = profile.width(2);
else
data{3,2} = NaN;
end
else
data{3,1} = NaN;
data{3,2} = NaN;
end
end
end
function createDataControl()
elementNames = fieldnames(this.ElementProfiles);
rightPanel = this.gui.rightPanel;
this.gui.elementPopup = uicontrol(rightPanel,'Style','popupmenu','String',[{'Choose element...'}, elementNames', {'Add or modify...'}],'Units','normalized',...
'Position',[0.01 0.96 0.43 0.03], 'TooltipString', 'Choose or add new element.');
this.gui.lineShape = uicontrol(rightPanel,'Style','popupmenu','String',this.const.lineShapes,'Units','normalized', 'Position',[0.5 0.96 0.43 0.03], 'TooltipString', 'Lineshape to fit peaks.');
this.gui.removeBackground = uicontrol(rightPanel,'Style','radiobutton','String','Subtract Background','Units','normalized', 'Position',[0.015 0.925 0.43 0.03]);
this.gui.startFitting = uicontrol(rightPanel,'Style','radiobutton','String','Start Fitting','Units','normalized', 'Position',[0.5 0.925 0.43 0.03]);
end
function createBasicInfoTalbe()
rightPanel = this.gui.rightPanel;
rowName = {'Beam Energy (keV)', 'Slit Size (mm)', 'Detector Footprint (mm)'};
colName = {};
columnFormat = {'numeric'};
columnWidth = {120};
tableData = {10; 0.04; 10.76};
this.gui.basicInfoTable = uitable(rightPanel, 'Data', tableData, 'ColumnName', colName, ...
'ColumnFormat', columnFormat, 'ColumnEditable', true, 'Units','normalized', ...
'ColumnWidth',columnWidth,'RowName',rowName, 'RowStriping','off',...
'Position', [0.025 0.84 0.935 0.08], 'TooltipString', 'Press enter to update value.');
end
function createLayersTable()
rightPanel = this.gui.rightPanel;
rowName = {'Top', 'Bottom'};
colName = {'Formula', 'ED', 'Depth (A)', 'Delete'};
colFormat = {'char', 'numeric', 'numeric', 'logical'};
colWidth = {130, 40, 60, 50};
heliumEd = 101325 / 8.314 / 298 / 1e3 * 6.02e23 * 1e-27 * 2;
tableData = {'He', heliumEd, Inf, false; 'H2O', 0.334, Inf, false};
uicontrol(rightPanel,'Style','text','String','Layer Structure:','Units','normalized','HorizontalAlignment','left',...
'Position',[0.025 0.81 0.8 0.025]);
this.gui.layerTable = uitable(rightPanel,'Data', tableData,'ColumnName', colName,...
'ColumnFormat', colFormat,'ColumnEditable', true(1, 6), 'Units', 'normalized',...
'ColumnWidth',colWidth,'RowName',rowName,'RowStriping','off',...
'Position', [0.025 0.66 0.935 0.15]);
this.gui.addLayer = uicontrol(rightPanel,'Style','pushbutton','String', 'Add', 'Units','normalized', 'Position', [0.725 0.63 0.11 0.03]);
this.gui.deleteLayer = uicontrol(rightPanel,'Style','pushbutton','String', 'Delete','Units','normalized', 'Position', [0.84 0.63 0.12 0.03]);
end
function createParametersTable()
rightPanel = this.gui.rightPanel;
rowName = {'Angle-Offset','Scale-Factor','Decay-Length','Background', 'Conc-Bottom'};
colName = {'Min','Max','Start','Fix','Plot'};
colFormat = {'numeric','numeric','numeric','logical','logical'};
colWidth = {55 55 55 30 30};
tableData = {-0.0001, 0.0001, 0, false, false; 1, 1, 1, true, false; 0, 0, 0, true, false; 0, 0, 0, true, false; 0, 0, 0, true, false};
this.gui.parametersTableTitle = uicontrol(rightPanel,'Style','text','String','Fitting Parameters:','Units','normalized','HorizontalAlignment','left', 'Position', [0.025 0.625 0.8 0.025]);
this.gui.parametersTable = uitable(rightPanel,'Data', tableData,'ColumnName', colName,...
'ColumnFormat', colFormat,'ColumnEditable', [true true true true true],'Units','normalized',...
'ColumnWidth',colWidth,'RowName',rowName,'RowStriping','off', 'Position', [0.025 0.425 0.935 0.2]);
end
function createFittingControls()
rightPanel = this.gui.rightPanel;
h = 0.39;
this.gui.layerTableTitle = uicontrol(rightPanel,'Style','text','String', 'Fitting Control:','Units','normalized','HorizontalAlignment','left',...
'Position',[0.025 h 0.8 0.025]);
this.gui.loadPara = uicontrol(rightPanel,'Style','pushbutton','String','Load Para','Units','normalized',...
'Position',[0.024 h-0.03 0.17 0.03]);
this.gui.savePara = uicontrol(rightPanel,'Style','pushbutton','String','Save Para','Units','normalized',...
'Position',[0.19 h-0.03 0.17 0.03]);
this.gui.stepInput = uicontrol(rightPanel,'Style','edit','String',20,'Units','normalized',...
'HorizontalAlignment','left','Position',[0.62 h-0.03 0.1 0.03]);
this.gui.stepText = uicontrol(rightPanel,'Style','text','String','Steps','Units','normalized',...
'HorizontalAlignment','left','Position', [0.735 h-0.035 0.08 0.03]);
this.gui.fitButton = uicontrol(rightPanel,'Style','pushbutton','String','Fit','Units','normalized',...
'Position',[0.82 h-0.03 0.15 0.03]);
this.gui.withText = uicontrol(rightPanel,'Style','text','String','With','Units','normalized','HorizontalAlignment','left',...
'Position',[0.025 h-0.065 0.07 0.03]);
this.gui.confidenceInput = uicontrol(rightPanel,'Style','edit','String','95','Units','normalized',...
'HorizontalAlignment','left','Position',[0.1 h-0.06 0.07 0.03]);
this.gui.confidenceText = uicontrol(rightPanel,'Style','text','String','% confidence window','Units','normalized','HorizontalAlignment','left',...
'Position',[0.171 h-0.065 0.28 0.03]);
this.gui.recordFitting = uicontrol(rightPanel,'Style','pushbutton','String','Record Fitting','Units','normalized',...
'Position',[0.452 h-0.06 0.22 0.03]);
this.gui.updateStartButton = uicontrol(rightPanel,'Style','pushbutton','String','Update Starts','Units','normalized',...
'Position',[0.75 h-0.06 0.22 0.03]);
end
function createOutputandSaveButtons()
rightPanel = this.gui.rightPanel;
this.gui.output = uicontrol(rightPanel,'Style','edit','Max',2,'HorizontalAlignment','left','Units','normalized',...
'Position',[0.03 0.07 0.935 0.25]);
this.gui.clearOutput = uicontrol(rightPanel,'Style','pushbutton','String','Clear','Units','normalized',...
'Position',[0.82 0.038 0.15 0.03]);
uicontrol(rightPanel,'Style','text','String','Save:','Units','normalized',...
'HorizontalAlignment','left','Position',[0.025 0.035 0.08 0.025]);
this.gui.saveOutput = uicontrol(rightPanel,'Style','pushbutton','String','Output Text','Units','normalized',...
'Position',[0.024 0.007 0.2 0.03]);
this.gui.saveUpperFigure = uicontrol(rightPanel,'Style','pushbutton','String','Upper Figure','Units','normalized',...
'Position',[0.234 0.007 0.2 0.03]);
this.gui.saveLowerFigure = uicontrol(rightPanel,'Style','pushbutton','String','Lower Figure','Units','normalized',...
'Position',[0.444 0.007 0.2 0.03]);
this.gui.saveData = uicontrol(rightPanel,'Style','pushbutton','String','Data & Fit','Units','normalized',...
'Position',[0.66 0.007 0.17 0.03]);
end
end
function createController()
%% left panel
this.gui.fileList.Callback = @(varargin) this.control('file');
this.gui.loadButton.Callback = @(varargin) this.control('load-file');
this.gui.deleteButton.Callback = @(varargin) this.control('delete-file');
this.gui.angleList.Callback = @(varargin) this.control('angle');
%% plotting
this.gui.showError.Callback = @(varargin) this.control('show-error');
this.gui.likelihoodChi2.Callback = @(varargin) this.control('likelihood-chi2');
this.gui.showFit.Callback = @(varargin) this.control('show-fit');
this.gui.showCal.Callback = @(varargin) this.control('show-cal');
%% data control
this.gui.lineShape.Callback = @(varargin) this.control('line-shape');
this.gui.elementPopup.Callback = @(varargin) this.control('switch-element');
this.gui.removeBackground.Callback = @(varargin) this.control('remove-background');
this.gui.startFitting.Callback = @(varargin) this.control('start-fitting');
%% right panel
this.gui.basicInfoTable.CellEditCallback = @(~, eventdata, varargin) this.control('basic-info', eventdata);
this.gui.layerTable.CellEditCallback = @(~, eventdata, varargin) this.control('layer-table', eventdata);
%% table
this.gui.addLayer.Callback = @(varargin) this.control('add-layer');
this.gui.deleteLayer.Callback = @(varargin) this.control('delete-layers');
this.gui.parametersTable.CellEditCallback = @(~, eventdata, varargin) this.control('parameter-table', eventdata);
%% fitting
this.gui.confidenceInput.Callback = @(varargin) this.control('confidence-input');
this.gui.loadPara.Callback = @(varargin) this.control('load-parameters');
this.gui.savePara.Callback = @(varargin) this.control('save-parameters');
this.gui.recordFitting.Callback = @(varargin) this.control('record-results');
this.gui.fitButton.Callback = @(varargin) this.control('fit');
this.gui.stepInput.Callback = @(varargin) this.control('step-input');
this.gui.updateStartButton.Callback = @(varargin) this.control('update-start');
%% saving
this.gui.saveData.Callback = @(varargin) this.control('save-data');
this.gui.saveUpperFigure.Callback = @(varargin) this.control('save-upper-figure');
this.gui.saveLowerFigure.Callback = @(varargin) this.control('save-lower-figure');
this.gui.saveOutput.Callback = @(varargin) this.control('save-output');
this.gui.clearOutput.Callback = @(varargin) this.control('clear-output');
%% element edits
this.gui.closeTabButton.Callback = @(varargin) this.control('close-tab');
this.gui.elementListbox.Callback = @(varargin) this.control('element-listbox');
this.gui.elementNameInput.Callback = @(source, varargin) this.control('edit-element-name', source);
this.gui.elementTable.CellEditCallback = @(source, eventdata, varargin) this.control('edit-element', source, eventdata);
this.gui.addElement.Callback = @(varargin) this.control('add-element');
this.gui.removeElement.Callback = @(varargin) this.control('remove-element');
end
if nargin == 1
this.control('load-file', filenames);
end
end
function feedback = model(this, state, trigger, varargin)
switch state
case 'empty'
switch trigger
case 'load-file'
files = varargin{1};
paths = varargin{2};
loadNewData(files, paths);
end
case 'whole-spectra'
switch trigger
case 'delete-file'
deleteSelectedFiles();
case 'load-file'
files = varargin{1};
path = varargin{2};
loadNewData(files, path);
case 'delete-layers'
this.processInputs('layer');
case 'inputs'
what = varargin{1};
this.processInputs(what);
case 'switch-element'
newElement = varargin{1};
switch newElement
case 'none'
% do nothing
case 'new'
otherwise
if ~strcmp(newElement, this.const.element)
this.const.element = newElement;
fitSpectraToElement();
end
end
end
case 'element-spectra'
switch trigger
case 'line-shape'
this.const.lineShape = varargin{1};
fitSpectraToElement();
case 'switch-element'
newElement = varargin{1};
if ~strcmp(this.const.element, newElement)
this.const.element = newElement;
fitSpectraToElement();
end
end
case 'fitting'
switch trigger
case 'start-fitting'
end
case 'edit-element'
switch trigger
case 'add-element'
newname = varargin{1};
table = this.gui.elementTable;
this.ElementProfiles.(newname).range = cell2mat(table.Data(1, :));
this.ElementProfiles.(newname).peak = cell2mat(table.Data(2, :));
this.ElementProfiles.(newname).width = cell2mat(table.Data(3, :));
case 'remove-element'
elementName = varargin{1};
this.ElementProfiles = rmfield(this.ElementProfiles, elementName);
end
end
% model functions
function deleteSelectedFiles()
fileList = this.gui.fileList;
if ~isempty(fileList.String)
if isa(fileList.String, 'char')
n = true;
else
n = true(1, length(fileList.String));
end
m = fileList.Value;
n(m) = false(1, length(m));
this.data = this.data(n);
feedback = n;
end
end
function loadNewData(files, paths)
if ~isempty(files)
% convert to cell array
if isa(files, 'char')
files = {files};
paths = {paths};
else
if isa(paths, 'char')
paths = repmat({paths}, 1, length(files));
end
end
% load data
n = length(files);
newData = cell(1, n);
for i = 1:n
newData{i} = XeLayers(fullfile(paths{i}, files{i}), this.config.ScatteringFactorFolder);
end
this.data = [this.data, newData];
end
end
function fitSpectraToElement()
element = this.const.element;
lineshape = this.const.lineShape;
for i = 1 : length(this.data)
this.data{i}.selectElement(element, lineshape);
end
end
end
function view(this, state, trigger, varargin)
switch state
case 'empty'
switch trigger
case 'initialize'
switchToWholeSpectra();
case 'load-file'
olds = varargin{1};
news = varargin{2};
this.gui.fileList.String = [olds; news];
displayAngles();
replot('upper');
end
case 'whole-spectra'
switch trigger
case 'file'
displayAngles();
replot('upper');
case 'angle'
replot('upper');
case 'delete-file'
indices = varargin{1};
deleteSelectedFiles(indices);
replot('upper');
case 'load-file'
olds = varargin{1};
news = varargin{2}';
this.gui.fileList.String = [olds; news];
case 'show-error'
replot('upper');
case 'switch-element'
switchToWholeSpectra();
replot('both');
otherwise
warning('Case not fonund for XeRayGUI.view() - whole-spectra state.');
end
case 'element-spectra'
switch trigger
case 'file'
replot('both');
case 'angle'
replot('both');
case 'line-shape'
replot('both');
case 'show-error'
replot('upper');
case 'remove-background'
replot('upper');
case 'switch-element'
switch this.const.element
case 'new'
this.gui.elementEditPanel.Visible = 'on';
otherwise
switchElementInspectionOn();
this.gui.startFitting.Value = 0;
replot('both');
end
case 'start-fitting'
switchElementFitting('off');
replot('lower');
end
case 'fitting'
switch trigger
case 'angle'
replot('both');
case 'start-fitting'
switchElementFitting('on');
case 'show-cal'
replot('lower');
case 'layer-table'
replot('lower');
case 'basic-info'
replot('lower');
case 'parameter-table'
what = varargin{1};
replot(what);
case 'add-layer'
addLayer();
case 'add-layer-update'
replot('lower');
case 'delete-layers'
deleteLayers();
case 'delete-layers-update'
replot('lower');
case 'load-parameters'
loadParameters();
case 'load-parameters-update'
replot('lower');
case 'fit'
this.gui.showFit.Enable = 'on';
this.gui.showFit.Value = 1;
replot();
recordFittingResults(0);
case 'show-fit'
replot('lower');
case 'update-start'
replot('lower');
case 'clear-output'
this.gui.output.String = {};
case 'record-results'
confidence = str2double(this.gui.confidenceInput.String) / 100;
recordFittingResults(confidence);
case 'confidence-input'
confidence = str2double(this.gui.confidenceInput.String) / 100;
recordFittingResults(confidence);
end
case 'edit-element'
switch trigger
case 'close-tab'
this.gui.elementEditPanel.Visible = 'off';
case 'switch-element'
this.gui.elementEditPanel.Visible = 'on';
case 'element-listbox'
displayElementTable();
case 'add-element'
addElement();
case 'remove-element'
removeElement();
end
case 'any'
switch trigger
case 'output'
message = varargin{1};
appendToOutput(message);
end
end
% view functions
function deleteSelectedFiles(indices)
fileList = this.gui.fileList;
angleList = this.gui.angleList;
if sum(indices)
fileList.String = fileList.String(indices);
fileList.Value = 1;
angleList.Value = 1;
displayAngles();
else
fileList.Value = 1;
fileList.String = {};
angleList.String = {};
end
end
function switchToWholeSpectra()
set(findall(this.gui.rightPanel, '-property', 'Enable'), 'Enable', 'off');
this.gui.elementPopup.Enable = 'on';
this.gui.fileList.Enable = 'on';
this.gui.showFit.Enable = 'off';
this.gui.showCal.Enable = 'off';
this.gui.loadButton.Enable = 'on';
this.gui.deleteButton.Enable = 'on';
this.gui.startFitting.Value = 0;
end
function switchElementInspectionOn()
set(findall(this.gui.rightPanel, '-property', 'Enable'), 'Enable', 'off');
this.gui.lineShape.Enable = 'on';
this.gui.startFitting.Enable = 'on';
this.gui.removeBackground.Enable = 'on';
this.gui.elementPopup.Enable = 'on';
this.gui.fileList.Enable = 'on';
this.gui.showCal.Enable = 'off';
this.gui.showFit.Enable = 'off';
this.gui.showFit.Value = false;
this.gui.showError.Visible = 'on';
this.gui.likelihoodChi2.Visible = 'off';
this.gui.loadButton.Enable = 'off';
this.gui.deleteButton.Enable = 'off';
end
function switchElementFitting(status)
if strcmp(status, 'on')
antiStatus = 'off';
else
antiStatus = 'on';
this.gui.showFit.Enable = 'off';
this.gui.showFit.Value = 0;
this.gui.parametersTable.Data(:, end) = num2cell(false(size(this.gui.parametersTable.Data, 1), 1));
end
set(findall(this.gui.rightPanel, '-property', 'Enable'), 'Enable', status);
this.gui.showCal.Enable = status;
this.gui.startFitting.Enable = 'on';
this.gui.fileList.Enable = antiStatus;
this.gui.elementPopup.Enable = antiStatus;
this.gui.lineShape.Enable = antiStatus;
this.gui.removeBackground.Enable = antiStatus;
% this.gui.loadButton.Enable = antiStatus;
% this.gui.deleteButton.Enable = antiStatus;
end
function loadParameters()
[filename, pathname] = uigetfile('*.xeraypara', 'Load a saved parameter file.');
if ~isnumeric(filename)
file = fullfile(pathname, filename);
para = loadjson(file);
% load the basic info table
this.gui.basicInfoTable.Data = num2cell(para.basic);
% load the layer table
dat = para.layer;
if ~ischar(dat{1})
n = length(dat);
m = length(dat{1});
newdata = cell(n, m);
for i = 1 : n
newdata(i, :) = dat{i};
end
dat = newdata;
end
for i = 1 : size(dat, 1)
dat{i, end} = logical(dat{i, end});
end
this.gui.layerTable.Data = dat;
assignLayerTableRowName();
% load the parameters table
dat = num2cell(para.parameter);
n = size(dat, 1);
for i = 1 : n
dat{i, 4} = logical(dat{i, 4});
dat{i, 5} = logical(dat{i, 5});
end
this.gui.parametersTable.Data = dat;
assignParameterTableRowName();
end
end
function displayElementTable()
listbox = this.gui.elementListbox;
if isempty(listbox.String)
this.gui.elementNameInput.String = '';
this.gui.elementTable.Data = {};
else
name = listbox.String{listbox.Value};
this.gui.elementNameInput.String = name;
dat = this.ElementProfiles.(name);
tabledata = convertProfileToTableData;
this.gui.elementTable.Data = tabledata;
end
function tabledata = convertProfileToTableData
tabledata = cell(3, 2);
tabledata(1, :) = num2cell(dat.range);
tabledata(2, 1:length(dat.peak)) = num2cell(dat.peak);
tabledata(3, 1:length(dat.width)) = num2cell(dat.width);
end
end
function displayAngles()
fileList = this.gui.fileList;
angleList = this.gui.angleList;
n = zeros(size(fileList.Value));
for i = 1:length(fileList.Value)
n(i) = length(this.data{fileList.Value(i)}.rawdata.angle);
end
angleStrings = cell(1, sum(n));
k = 0;
for i = 1:length(n)
for j = 1 : n(i)
k = k + 1;
angleStrings{k} = sprintf('%s %s %f',fileList.String{fileList.Value(i)}(1:end-6), '@angle: ',this.data{fileList.Value(i)}.rawdata.angle(j));
end
end
if max(angleList.Value) > length(angleStrings)
angleList.Value = 1;
end
angleList.String = angleStrings;
end
function assignLayerTableRowName()
table = this.gui.layerTable;
n = size(table.Data, 1);
rowNames = cell(1, n);
for i = 1 : n
rowNames{i} = ['Layer-', num2str(n-i)];
end
rowNames{1} = 'Top';
rowNames{end} = 'Bottom';
table.RowName = rowNames;
end
function assignParameterTableRowName()
table = this.gui.parametersTable;
n = size(table.Data, 1);
rowNames = cell(n, 1);
N = 4;
rowNames(1:N) = {'Angle-Offset', 'Scale-Factor', 'Decay-Length', 'Background'};
for i = N+1 : n-1
rowNames{i} = strcat('Conc-', num2str(n - i));
end
rowNames{end} = 'Conc-Bottom';
table.RowName = rowNames;
end
function n = chosenPlotPara()
n = sum(cell2mat(this.gui.parametersTable.Data(:, end)));
end
function indices = indicesInFit()
dat = cell2mat(this.gui.parametersTable.Data(:, 4:5));
fixed = ~dat(:, 1);
plotting = dat(:, 2);
if sum(plotting)
indices = zeros(1, sum(plotting));
plotting = find(plotting);
for i = 1 : length(plotting)
indices(i) = sum(fixed(1 : plotting(i)));
end
end
end
function [n, m, rankn, rankm] = getSelectionIndex()
% 4 indices for each selected spectrum
% n is the position within the x{} data set, m is the position for
% the angle, rankn is the position of n within selected n, and rankm is
% the position of m within selected m for that specific n
fileList = this.gui.fileList;
angleList = this.gui.angleList;
n = zeros(size(angleList.Value));
m = n;
rankn = n;
rankm = n;
cn = cumsum(dataLengths(fileList.Value));
for i = 1:length(angleList.Value)
rankn(i) = find(cn >= angleList.Value(i),1);
n(i) = fileList.Value(rankn(i));
if rankn(i) > 1
m(i) = angleList.Value(i) - cn(rankn(i)-1);
else
m(i) = angleList.Value(i);
end
if i == 1 || rankn(i) > rankn(i-1)
rankm(i) = 1;
else
rankm(i) = rankm(i-1)+1;
end
end
end
function [fileIndex, angleIndices] = getSelectedSignalIndices()
[n, m, ~, ~] = getSelectionIndex();
n1 = n;
n1(2:end) = n1(2:end)-n1(1:end-1);
ind = find(n1~=0);
fileIndex = zeros(size(ind));
angleIndices = cell(size(ind));
for i = 1:length(ind)-1
fileIndex(i) = n(ind(i));
angleIndices{i} = m(ind(i):ind(i+1)-1);
end
fileIndex(end) = n(ind(end));
angleIndices{end} = m(ind(end):end);
end
function [styles1, legends1, styles2, legends2] = getSpectraStylesAndLegends()
angleList = this.gui.angleList;
fileList = this.gui.fileList;
%obtain line spec for plotting, and legends
styles1 = cell(size(angleList.Value));
legends1 = styles1;
[~,~,rankn,rankm] = getSelectionIndex();
rankn = mod(rankn,length(this.const.symbols));
rankn(rankn==0) = length(this.const.symbols);
rankm = mod(rankm,length(this.const.colors));
rankm(rankm==0) = length(this.const.colors);
for i = 1:length(angleList.Value)
styles1{i} = strcat(this.const.symbols(rankn(i)),this.const.colors(rankm(i)));
legends1{i} = angleList.String{angleList.Value(i)};
end
uniqueN = unique(rankn,'stable');
styles2 = cell(size(uniqueN));
legends2 = styles2;
for i = 1:length(uniqueN)
styles2{i} = this.const.symbols(uniqueN(i));
legends2{i} = fileList.String{fileList.Value(uniqueN(i))};
end
end
function lengths = dataLengths(indices)
if ~isempty(this.data)
if nargin == 1