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VisualFluo.m
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VisualFluo.m
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classdef VisualFluo < handle
properties
data
gui
guiFigure
config
ElementProfiles
end
methods
function this = VisualFluo()
initializeGui();
function initializeGui()
configFile = which('visualfluo.config.json');
this.config = loadjson(configFile);
this.ElementProfiles = loadjson(fullfile(getParentDir(which('VisualFluo.m')), 'support-files/element-profiles.json'));
createView();
createController();
this.control('initial-load');
end
function createView()
createFigure();
createBeamlinePanel();
createDataListPanel();
createPlot1();
createPlot2();
createMenus();
createBasicInfoTable();
createCalibrationTable();
createOutputRegion();
createSaveButtons();
function createFigure()
set(0,'units','pixels');
screenSize = get(0,'screensize');
if screenSize(4) * 0.85 > 800
height = 800;
else
height = screenSize(4) * 0.85;
end
this.guiFigure = figure('Visible','off','Name','VisualFluo','NumberTitle','off','Units','pixels',...
'Position',[190,15,1200,height],'Resize','on');
movegui(this.guiFigure, 'center');
this.guiFigure.Visible = 'on';
end
function createBeamlinePanel()
this.gui.specPanel = uipanel(this.guiFigure,'Title','File','Units','normalized',...
'Position',[0.014 0.88 0.16 0.11]);
specPanel = this.gui.specPanel;
this.gui.beamlineMenu = uicontrol(specPanel, 'Style', 'popupmenu', 'String',...
this.config.beamLines, 'Units','normalized', 'Position',[0.05 0.77 0.915 0.16]);
this.gui.loadButton = uicontrol(specPanel, 'Style', 'pushbutton', 'String','Load','Units','normalized',...
'Position',[0.08 0.32 0.25 0.32]);
this.gui.specInput = uicontrol(specPanel,'Style','edit','Enable','inactive','Units','normalized',...
'Position',[0.35 0.36 0.59 0.25]);
this.gui.refreshButton = uicontrol(specPanel,'Style','pushbutton','String','Refresh','Units','normalized',...
'Position',[0.67 0.02 0.27 0.32]);
end
function createDataListPanel()
this.gui.listPanel = uipanel(this.guiFigure,'Title','Data','Units','normalized',...
'Position',[0.014 0.02 0.16 0.85]);
listPanel = this.gui.listPanel;
this.gui.scanText = uicontrol(listPanel,'Style','text','String','Select one or more scans','Units','normalized',...
'Position',[0.05 0.87 0.8 0.12]);
this.gui.scanList = uicontrol(listPanel,'Style','listbox','Units','normalized',...
'Position',[0.05 0.5 0.9 0.46],'Max',2);
this.gui.qzText = uicontrol(listPanel,'Style','text','String','Select the Qz range','Units','normalized',...
'Position',[0.05 0.37 0.8 0.12]);
this.gui.qzList = uicontrol(listPanel,'Style','listbox','Units','normalized',...
'Position',[0.05 0.015 0.9 0.44],'Max',2);
end
function createPlot1()
ax1 = axes('Parent', this.guiFigure, '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;
this.gui.plot1Type = uicontrol(this.guiFigure,'Style','popupmenu','String', this.config.plot1Choices,...
'Units','normalized', 'Position',[0.522 0.97 0.15 0.018]);
end
function createPlot2()
ax2 = axes('Parent',this.guiFigure,'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;
this.gui.plot2Type = uicontrol(this.guiFigure,'Style','popupmenu','String',this.config.plot2Choices,...
'Units','normalized', 'Position',[0.522 0.44 0.15 0.018]);
end
function createMenus()
this.gui.rightPanel = uipanel(this.guiFigure,'Units','normalized','Position',[0.68 0.02 0.31 0.97]);
rightPanel = this.gui.rightPanel;
this.gui.elementMenu = uicontrol(rightPanel,'Style','popupmenu','String',{'Choose Element...'},'Units','normalized',...
'Position',[0.015 0.97 0.46 0.018]);
this.gui.lineShape = uicontrol(rightPanel,'Style','popupmenu','String', {'Gaussian','Lorentzian'},'Units','normalized',...
'Position',[0.49 0.97 0.46 0.018], 'Enable', 'off');
this.gui.background = uicontrol(rightPanel,'Style','radiobutton','Enable','off','String','Subtract Background','Units','normalized',...
'Position',[0.025 0.93 0.45 0.022]);
this.gui.integrate = uicontrol(rightPanel,'Style','radiobutton','Enable','off','String','Integrate','Units','normalized',...
'Position',[0.5 0.93 0.45 0.022]);
end
function createBasicInfoTable()
rowName = {'Energy (keV)', 'Slit Height (mm)', 'Scaling (x)'};
colName = {};
columnFormat = {'numeric'};
columnWidth = {120};
basicInfoData = {0; 0; 1e6};
this.gui.basicInfoTable = uitable(this.gui.rightPanel,'Data', basicInfoData,...
'ColumnFormat', columnFormat,'ColumnEditable', true, 'Units', 'normalized',...
'ColumnWidth',columnWidth,'ColumnName', colName, 'RowName',rowName,'RowStriping','off',...
'Position', [.03 .82 .935 .1]);
end
function createCalibrationTable()
this.gui.calibractionText = uicontrol(this.gui.rightPanel, 'Style', 'text',...
'String', 'Vortex Calibration', 'Units', 'normalized', 'Position', [0.03 0.795 0.9 0.02],...
'HorizontalAlignment', 'left');
rowName = {'Constant', 'Linear Term', 'Quadratic Term', 'Cubic Term'};
colName = {};
columnFormat = {'numeric', 'numeric', 'numeric', 'numeric'};
columnWidth = {140};
tableData = {0; 0; 0; 0};
this.gui.calibrationTable = uitable(this.gui.rightPanel, 'Data', tableData, ...
'ColumnName', colName, 'RowName', rowName, 'RowStriping', 'off', ...
'ColumnFormat', columnFormat, 'ColumnWidth', columnWidth, 'ColumnEditable', true, ...
'Units', 'normalized', 'Position', [0.03 0.67 0.935 0.12]);
end
function createOutputRegion()
rightPanel = this.gui.rightPanel;
this.gui.commentText = uicontrol(rightPanel, 'Style', 'text', 'String', 'Comment', ...
'Units', 'normalized', 'Position', [0.03 0.645 0.9 0.02], 'HorizontalAlignment', 'left');
this.gui.comment = uicontrol(rightPanel, 'Style', 'edit', 'String', '', 'Max', 2, ...
'Units', 'normalized', 'Position', [0.03 0.595 0.935 0.05], 'HorizontalAlignment', 'left');
this.gui.saveComment = uicontrol(rightPanel, 'Style', 'pushbutton', 'String', 'Save', ...
'Units', 'normalized', 'Position', [0.86 0.565 0.12 0.03]);
this.gui.systemLogText = uicontrol(rightPanel, 'Style', 'text',...
'String', 'Sysem Log', 'Units', 'normalized', 'Position', [0.03 0.555 0.2 0.02],...
'HorizontalAlignment', 'left');
this.gui.output = uicontrol(rightPanel, 'Style', 'edit', 'Max', 2, 'HorizontalAlignment', 'left','Units','normalized',...
'Position',[0.03 0.07 0.935 0.48]);
this.gui.clearOutputButton = uicontrol(rightPanel,'Style','pushbutton','String','Clear Output','Units','normalized',...
'Position',[0.022 0.04 0.21 0.03]);
this.gui.saveOutputButton = uicontrol(rightPanel,'Style','pushbutton','String','Save Output Text','Units','normalized',...
'Position',[0.24 0.04 0.27 0.03]);
this.gui.saveText = uicontrol(rightPanel,'Style','text','String','Save:','HorizontalAlignment','left','Units','normalized',...
'Position',[0.03 0.01 0.1 0.022]);
end
function createSaveButtons()
rightPanel = this.gui.rightPanel;
this.gui.saveFigure1Button = uicontrol(rightPanel,'Style','pushbutton','String','Figure 1','Units','normalized',...
'Position',[0.12 0.008 0.15 0.03]);
this.gui.saveFigure2Button = uicontrol(rightPanel,'Style','pushbutton','String','Figure 2','Units','normalized',...
'Position',[0.28 0.008 0.15 0.03]);
this.gui.saveWorkspaceButton = uicontrol(rightPanel,'Style','pushbutton','String','Workspace','Units','normalized',...
'Position',[0.44 0.008 0.17 0.03]);
this.gui.exportDataButton = uicontrol(rightPanel,'Style','pushbutton','String','Export Selected Data','Units','normalized',...
'Position',[0.62 0.008 0.32 0.03]);
end
end
function createController()
% left panel
this.gui.loadButton.Callback = @(varargin) this.control('load');
this.gui.refreshButton.Callback = @(varargin) this.control('refresh');
this.gui.scanList.Callback = @(varargin) this.control('scan');
this.gui.qzList.Callback = @(varargin) this.control('qz');
% central panel
this.gui.plot1Type.Callback = @(varargin) this.control('plot1-type');
this.gui.plot2Type.Callback = @(varargin) this.control('plot2-type');
% right panel before the output
this.gui.elementMenu.Callback = @(varargin) this.control('element');
this.gui.lineShape.Callback = @(varargin) this.control('line-shape');
this.gui.background.Callback = @(varargin) this.control('background');
this.gui.integrate.Callback = @(varargin) this.control('integrate');
% tables and comment
this.gui.basicInfoTable.CellEditCallback = @(source, eventdata) this.control('basic-info', eventdata);
this.gui.calibrationTable.CellEditCallback = @(source, eventdata) this.control('calibration', eventdata);
this.gui.saveComment.Callback = @(varargin) this.control('comment');
% buttons below the output
this.gui.clearOutputButton.Callback = @(varargin) this.control('clear-output');
this.gui.saveOutputButton.Callback = @(varargin) this.control('save-output');
this.gui.saveFigure1Button.Callback = @(varargin) this.control('save-figure-1');
this.gui.saveFigure2Button.Callback = @(varargin) this.control('save-figure-2');
this.gui.saveWorkspaceButton.Callback = @(varargin) this.control('save-workspace');
this.gui.exportDataButton.Callback = @(varargin) this.control('export-data');
end
end
function model(this, state, trigger, varargin)
switch state
case 'element'
switch trigger
case {'element', 'line-shape'}
elementProfile = varargin{1};
lineShape = varargin{2};
fitElement(elementProfile, lineShape);
otherwise
warning(['case not found for model, with state = ', state, ' and trigger = ', trigger]);
end
otherwise
warning(['case not found for model, with state = ', state]);
end
function fitElement(elementProfile, lineShape)
x = this.data;
for i = 1:length(x)
xFit(x{i}, elementProfile, lineShape);
end
end
end
function view(this, state, trigger, varargin)
switch state
case 'empty'
switch trigger
case 'initial-load'
this.gui.elementMenu.String = getElementMenuItems();
this.gui.specInput.String = this.data{1}.specFile;
this.gui.scanList.String = getScanListString();
this.gui.qzList.String = getQzList();
displayTableInfo();
displayScanInfo();
displayComment();
upperPlot();
plotParameter();
otherwise
warning(['case not found for view, with state = ', state, ' and trigger = ', trigger]);
end
case 'whole'
turnElementFeatures('off');
switch trigger
case 'scan'
this.gui.qzList.String = getQzList();
displayTableInfo();
displayScanInfo();
displayComment();
upperPlot();
plotParameter();
case 'qz'
upperPlot();
plotParameter();
case {'plot1-type', 'element', 'basic-info', 'calibration'}
upperPlot();
case 'plot2-type'
plotParameter();
case 'clear-output'
this.gui.output.String = {};
otherwise
warning(['case not found for view, with state = ', state, ' and trigger = ', trigger]);
end
case 'element'
turnElementFeatures('on');
switch trigger
case {'element', 'line-shape', 'plot1-type', 'background', 'basic-info', 'calibration'}
upperPlot();
case 'qz'
upperPlot();
plotParameter();
case 'scan'
displayTableInfo();
displayScanInfo();
displayComment();
upperPlot();
case 'integrate'
upperPlot();
case 'plot2-type'
plotParameter();
case 'clear-output'
this.gui.output.String = {};
otherwise
warning(['case not found for view, with state = ', state, ' and trigger = ', trigger]);
end
end
function scanList = getScanListString()
n = length(this.data);
scanList = cell(n, 1);
for i = 1 : n
scanList{i} = ['Scan #', num2str(this.data{i}.scanNumber)];
end
end
function qzList = getQzList()
indices = this.gui.scanList.Value;
m = length(indices);
n = zeros(1, m);
for i = 1 : m
n(i) = length(this.data{indices(i)}.q);
end
ind = find(min(n)==n,1);
qzList = num2cell(this.data{indices(ind)}.q);
end
function items = getElementMenuItems()
items = ['Choose Element...'; fieldnames(this.ElementProfiles); 'Add Element'];
end
function plotParameter()
ax = this.gui.ax2;
plot2Type = this.gui.plot2Type;
scanList = this.gui.scanList;
qzList = this.gui.qzList;
x = this.data;
switch plot2Type.String{plot2Type.Value}
case this.config.plot2Choices{1}
for i = 1:length(scanList.Value)
plot(ax,x{scanList.Value(i)}.q(qzList.Value),x{scanList.Value(i)}.influx(qzList.Value),this.config.spec2{i},'markersize',8,'linewidth',2);
xlabel(ax,'Qz');
ylabel(ax,'Influx Counts');
title(ax,'Influx - Qz Relation');
hold(ax,'on');
end
case this.config.plot2Choices{2}
for i = 1:length(scanList.Value)
plot(ax,x{scanList.Value(i)}.q(qzList.Value),x{scanList.Value(i)}.T(qzList.Value),this.config.spec2{i},'markersize',8,'linewidth',2);
xlabel(ax,'Qz');
ylabel(ax,'Count Time');
title(ax,'Count Time - Qz Relation');
hold(ax,'on');
end
case this.config.plot2Choices{3}
for i = 1:length(scanList.Value)
plot(ax,x{scanList.Value(i)}.q(qzList.Value),x{scanList.Value(i)}.countTime(qzList.Value)./x{scanList.Value(i)}.T(qzList.Value),this.config.spec2{i},'markersize',8,'linewidth',2);
xlabel(ax,'Qz');
ylabel(ax,'Detector Live Ratio');
title(ax,'Detector Live Ratio - Qz Relation');
hold(ax,'on');
end
case this.config.plot2Choices{4}
for i = 1:length(scanList.Value)
plot(ax,x{scanList.Value(i)}.q(qzList.Value),x{scanList.Value(i)}.absorber,this.config.spec2{i},'markersize',8,'linewidth',2);
xlabel(ax,'Qz');
ylabel(ax,'Absorber');
title(ax,'Absorber');
hold(ax,'on');
end
case this.config.plot2Choices{5}
for i = 1:length(scanList.Value)
plot(ax,x{scanList.Value(i)}.scanNumber,sum(x{scanList.Value(i)}.sx),this.config.spec2{i},'markersize',8,'linewidth',2);
xlabel(ax,'Scan Number');
ylabel(ax,'Detector Footprint (mm)');
title(ax,'Detector Footprint');
hold(ax,'on');
end
case this.config.plot2Choices{6}
for i = 1:length(scanList.Value)
plot(ax,x{scanList.Value(i)}.scanNumber,sum(x{scanList.Value(i)}.s1(1:2)),this.config.spec2{i},'markersize',8,'linewidth',2);
xlabel(ax,'Scan Number');
ylabel(ax,'Slit height (mm)');
title(ax,'Slit height');
hold(ax,'on');
end
case this.config.plot2Choices{7}
for i = 1:length(scanList.Value)
plot(ax,x{scanList.Value(i)}.scanNumber,sum(x{scanList.Value(i)}.s1(3:4)),this.config.spec2{i},'markersize',8,'linewidth',2);
xlabel(ax,'Scan Number');
ylabel(ax,'Slit width (mm)');
title(ax,'Slit width');
end
case this.config.plot2Choices{8}
for i = 1:length(scanList.Value)
plot(ax,x{scanList.Value(i)}.scanNumber,x{scanList.Value(i)}.sx,this.config.spec2{i},'markersize',8,'linewidth',2);
xlabel(ax,'Scan Number');
ylabel(ax,'Beam position (mm)');
title(ax,'Beam position (sx)');
hold(ax,'on');
end
otherwise
error('type of plot not found for lower figure');
end
legend(this.config.plot2Legend);
hold(ax,'off');
end
function plotSpectra()
scanList = this.gui.scanList;
qzList = this.gui.qzList;
elementMenu = this.gui.elementMenu;
plot1Type = this.gui.plot1Type;
background = this.gui.background;
ax = this.gui.ax1;
x = this.data;
switch this.gui.plot1Type.String{this.gui.plot1Type.Value}
case this.config.plot1Choices{1}
k = 1;
for i = scanList.Value
for j = qzList.Value
switch lower(elementMenu.String{elementMenu.Value})
case {'choose element...','choose element','choose'}
plot(ax, x{i}.e,x{i}.counts(:,j), this.config.spec1{k});
otherwise
switch background.Value
case 0
plot(ax,x{i}.xe,x{i}.xCounts(:,j),this.config.spec1{k});
case 1
plot(ax,x{i}.xe,x{i}.netCounts(:,j),this.config.spec1{k});
otherwise
error('there should only be two choices: with and without background');
end
end
hold(ax,'on');
k = k+1;
end
end
case this.config.plot1Choices{2} %counts with error
k = 1;
for i = scanList.Value
for j = qzList.Value
switch lower(elementMenu.String{elementMenu.Value})
case {'choose element...','choose element','choose'}
errorbar(ax,x{i}.e,x{i}.counts(:,j),x{i}.countsError(:,j),x{i}.countsError(:,j),this.config.spec1{k});
otherwise
switch background.Value
case 0
errorbar(ax,x{i}.xe,x{i}.xCounts(:,j),x{i}.xCountsError(:,j),x{i}.xCountsError(:,j),this.config.spec1{k});
case 1
errorbar(ax,x{i}.xe,x{i}.netCounts(:,j),x{i}.xCountsError(:,j),x{i}.xCountsError(:,j),this.config.spec1{k});
otherwise
error('there should only be two choices: with and without background');
end
end
hold(ax,'on');
k = k+1;
end
end
case this.config.plot1Choices{3} %normalized
k = 1;
for i = scanList.Value
for j = qzList.Value
switch lower(elementMenu.String{elementMenu.Value})
case {'choose element...','choose element','choose'}
plot(ax,x{i}.e,x{i}.intensity(:,j),this.config.spec1{k});
otherwise
switch background.Value
case 0
plot(ax,x{i}.xe,x{i}.xIntensity(:,j),this.config.spec1{k});
case 1
plot(ax,x{i}.xe,x{i}.netIntensity(:,j),this.config.spec1{k});
otherwise
error('there should only be two choices: with and without background');
end
end
hold(ax,'on');
k = k+1;
end
end
case this.config.plot1Choices{4} %normalized with error
k = 1;
for i = scanList.Value
for j = qzList.Value
switch lower(elementMenu.String{elementMenu.Value})
case {'choose element...','choose element','choose'}
errorbar(ax,x{i}.e,x{i}.intensity(:,j),x{i}.intensityError(:,j),x{i}.intensityError(:,j),this.config.spec1{k});
otherwise
switch background.Value
case 0
errorbar(ax,x{i}.xe,x{i}.xIntensity(:,j),x{i}.xIntensityError(:,j),x{i}.xIntensityError(:,j),this.config.spec1{k});
case 1
errorbar(ax,x{i}.xe,x{i}.netIntensity(:,j),x{i}.xIntensityError(:,j),x{i}.xIntensityError(:,j),this.config.spec1{k});
otherwise
error('there should only be two choices: with and without background');
end
end
hold(ax,'on');
k = k+1;
end
end
otherwise
error('upper plot type not found');
end
legend(ax, this.config.plot1Legend);
xlabel(ax, 'Energy (keV)');
ylabel(ax, 'Signal');
switch lower(elementMenu.String{elementMenu.Value})
case {'choose element...','choose element','choose'}
set(ax, 'xlim',[min(x{scanList.Value(1)}.e) max(x{scanList.Value(1)}.e)]);
titleText = sprintf('%s %s','Whole Spec -',plot1Type.String{plot1Type.Value});
otherwise
titleText = sprintf('%s %s %s',this.config.element,'-',plot1Type.String{plot1Type.Value});
switch plot1Type.String{plot1Type.Value}
case {this.config.plot1Choices{1},this.config.plot1Choices{2}}
k = 1;
for i = scanList.Value
for j = qzList.Value
color = this.config.spec1{k}(1);
switch background.Value
case 0
plot(ax,x{i}.fitE,x{i}.countFit(:,j),color);
case 1
plot(ax,x{i}.fitE,x{i}.netCountFit(:,j),color);
otherwise
end
k = k+1;
end
end
case {this.config.plot1Choices{3},this.config.plot1Choices{4}}
k = 1;
for i = scanList.Value
for j = qzList.Value
color = this.config.spec1{k}(1);
switch background.Value
case 0
plot(ax,x{i}.fitE,x{i}.intensityFit(:,j),color);
case 1
plot(ax,x{i}.fitE,x{i}.netIntensityFit(:,j),color);
otherwise
end
k = k+1;
end
end
end
end
title(ax,titleText);
hold(ax,'off');
end
function plotSignal()
% plot the integrated signal for a given element
ax = this.gui.ax1;
scanList = this.gui.scanList;
qzList = this.gui.qzList;
lineShape = this.gui.lineShape;
x = this.data;
for i = 1:length(scanList.Value)
errorbar(ax,x{scanList.Value(i)}.angle(qzList.Value),x{scanList.Value(i)}.signal(qzList.Value),...
x{scanList.Value(i)}.signalError(qzList.Value),x{scanList.Value(i)}.signalError(qzList.Value),...
this.config.spec2{i},'markersize',8,'linewidth',2);
hold(ax,'on');
end
hold(ax,'off');
xlabel(ax,'Angle (radian)');
ylabel(ax,'Fluorescence Intensity (a.u.)');
switch lower(lineShape.String{lineShape.Value})
case {'gauss','gaussian'}
titleText = sprintf('%s %s',this.config.element,'Integrated Intensity (Gaussian Fit)');
case {'lorentz','lorentzian'}
titleText = sprintf('%s %s',this.config.element,'Integrated Intensity (Lorentzian Fit)');
otherwise
titleText = sprintf('%s %s',this.config.element,'Integrated Intensity (unkown curve type)');
end
title(ax,titleText);
legend(ax,this.config.plot2Legend);
end
function upperPlot()
switch this.gui.elementMenu.Value
case 1
plotSpectra();
case length(this.gui.elementMenu.String)
otherwise
switch this.gui.integrate.Value
case 0
plotSpectra();
case 1
plotSignal();
end
end
end
function turnElementFeatures(mode)
this.gui.lineShape.Enable = mode;
this.gui.background.Enable = mode;
this.gui.integrate.Enable = mode;
end
function displayTableInfo()
this.gui.calibrationTable.Data = getCalibarationTableData();
this.gui.basicInfoTable.Data = getBasicInfoTableData();
function dat = getCalibarationTableData()
calibration = this.data{this.gui.scanList.Value(1)}.calibration;
dat = zeros(1, 4);
dat(1:length(calibration)) = calibration;
dat = dat';
end
function dat = getBasicInfoTableData()
dat = cell(3, 1);
n = this.gui.scanList.Value(1);
dat{1} = this.data{n}.E;
dat{2} = sum(this.data{n}.s1(1:2));
dat{3} = this.data{n}.A;
end
end
function displayScanInfo()
%display the important information
scanList = this.gui.scanList;
output = this.gui.output;
x = this.data;
%the text box
oldText = output.String;
outputText = cell(6,1);
outputText{1} = '';
outputText{2} = repmat('-',1,68);
outputText{3} = sprintf('%s %s','Spec file location:',x{scanList.Value(1)}.specPath);
outputText{4} = sprintf('%s %s','Time of experiment:',x{scanList.Value(1)}.time);
outputText{5} = sprintf('%s %s','Beam energy:',num2str(x{scanList.Value(1)}.E));
theVector = zeros(1,length(scanList.Value));
scanNumber = theVector;
k = 1;
for i = scanList.Value
scanNumber(k) = x{i}.scanNumber;
k = k+1;
end
outputText{6} = sprintf('%s %s','Scan number:',num2str(scanNumber));
outputText = [oldText;outputText];
output.String = outputText;
end
function displayComment()
this.gui.comment.String = this.data{this.gui.scanList.Value(1)}.comment;
end
end
function control(this, trigger, varargin)
state = getGuiState();
switch state
case 'empty'
switch trigger
case 'initial-load'
specFile = getSpecFileAt(pwd);
if loadDataAt(pwd, specFile)
getLineSpecAndLegendFirstTime();
this.view(state, trigger);
end
case 'load'
[specFile, specFilePath] = uigetfile('*', 'Select the spec file');
if specFile ~= 0
if loadDataAt(specFile, specFilePath)
getLineSpecAndLegendFirstTime();
this.view(state, trigger);
end
end
otherwise
warning(['case not found for view, with state = ', state, ' and trigger = ', trigger]);
end
case 'whole'
switch trigger
case 'load'
[specFile, specFilePath] = uigetfile('*', 'Select the spec file');
if specFile ~= 0
if loadDataAt(specFile, specFilePath)
getLineSpecAndLegendFirstTime();
this.view(state, trigger);
end
end
case 'refresh'
refreshScans();
case {'scan', 'qz'}
getLineSpecAndLegend();
this.view(state, trigger);
case {'plot1-type', 'plot2-type', 'element', 'clear-output'}
this.view(state, trigger);
case 'basic-info'
eventdata = varargin{1};
updateViewNeeded = processBasicInfoTable(eventdata);
if updateViewNeeded
this.view(state, trigger);
end
case 'calibration'
eventdata = varargin{1};
updateViewNeeded = processCalibrationTable(eventdata);
if updateViewNeeded
this.view(state, trigger);
end
case 'comment'
saveComment();
case 'save-output'
saveOutputText();
case 'save-figure-1'
saveFigure1();
case 'save-figure-2'
saveFigure2();
case 'save-workspace'
saveDataset();
case 'export-data'
exportSelectedData();
otherwise
warning(['case not found for view, with state = ', state, ' and trigger = ', trigger]);
end
case 'element'
switch trigger
case 'load'
disp('will build up the loading');
case 'refresh'
refreshScans();
case {'scan', 'qz'}
getLineSpecAndLegend();
this.view(state, trigger);
case 'element'
this.config.element = this.gui.elementMenu.String{this.gui.elementMenu.Value};
lineShape = this.gui.lineShape.String{this.gui.lineShape.Value};
elementProfile = this.ElementProfiles.(this.config.element);
this.model(state, trigger, elementProfile, lineShape);
this.view(state, trigger);
case 'line-shape'
lineShape = this.gui.lineShape.String{this.gui.lineShape.Value};
elementProfile = this.ElementProfiles.(this.config.element);
this.model(state, trigger, elementProfile, lineShape);
this.view(state, trigger);
case {'plot1-type', 'plot2-type', 'background', 'integrate', 'clear-output'}
this.view(state, trigger);
case 'basic-info'
eventdata = varargin{1};
updateViewNeeded = processBasicInfoTable(eventdata);
if updateViewNeeded
this.view(state, trigger);
end
case 'calibration'
eventdata = varargin{1};
updateViewNeeded = processCalibrationTable(eventdata);
if updateViewNeeded
this.view(state, trigger);
end
case 'comment'
saveComment();
case 'save-output'
saveOutputText();
case 'save-figure-1'
saveFigure1();
case 'save-figure-2'
saveFigure2();
case 'save-workspace'
saveDataset();
case 'export-data'
exportSelectedData();
otherwise
warning(['case not found for view, with state = ', state, ' and trigger = ', trigger]);
end
otherwise
warning(['case not found for control, with state = ', state]);
end
function state = getGuiState()
if isempty(this.gui.scanList.String)
state = 'empty';
else
if this.gui.elementMenu.Value == 1
state = 'whole';
else
state = 'element';
end
end
end
function flag = loadDataAt(thePath, specFile)
%try to load data, returns 0 if not successufl, 1 if successful
%searches for scan data files in thePath and 'vortex' folder
flag = 0;
if nargin == 1
specFile = getSpecFileAt(thePath);
end
if ~isempty(specFile)
specPath = thePath;
scanPath = thePath;
scanFiles = getScanFilesAt(specPath, specFile);
if isempty(scanFiles)
newPath = fullfile(specPath, 'vortex');
scanFiles = getScanFilesAt(newPath, specFile);
scanPath = newPath;
end
%if found both spec files and scan files, try importing data
if ~isempty(scanFiles)
A = this.gui.basicInfoTable.Data{3};
try
this.data = importData(specFile, specPath, scanFiles, scanPath, A);
this.config.specFile = specFile;
this.config.specPath = specPath;
this.config.scanFiles = scanFiles;
this.config.scanPath = scanPath;
flag = 1;
catch
warning('Was not able to import data.');
end
end
end
end
function refreshScans()
% refresh data without losing current work
x = this.data;
if ~isempty(x)
n = length(x);
scanFiles = cell(1, n);
for i = 1 : length(x)
scanFiles{i} = x{i}.scanFile;
if i == 1
scanPath = x{i}.scanPath;
currentSpecFile = x{i}.specFile;
specPath = x{i}.specPath;
end
end
oldScanNumbers = getScanNumbers(scanFiles);
newScanFiles = getScanFilesAt(scanPath, currentSpecFile);
newScanNumbers = getScanNumbers(newScanFiles);
if length(newScanNumbers) > length(oldScanNumbers)
newScanFiles = newScanFiles(length(oldScanNumbers)+1 : end);
A = str2double(this.gui.basicInfoTable.Data{3});
y = importData(currentSpecFile, specPath, newScanFiles, scanPath, A);
%combine the newly added data with the old data set
this.data = {x{1:end},y{1:end}};
this.gui.scanList.String = {scanFiles{1:end}, newScanFiles{1:end}};
end
end
end
function updateViewNeeded = processBasicInfoTable(eventdata)
updateViewNeeded = false;
indices = eventdata.Indices;
table = this.gui.basicInfoTable;
if ~isnumeric(eventdata.NewData) || indices(1) == 2
table.Data{indices(1), indices(2)} = eventdata.PreviousData;
else
selected = this.gui.scanList.Value;
switch indices(1)
case 1
for i = selected
this.data{i}.E = table.Data{1};
end
case 3
updateViewNeeded = true;
for i = selected
adjustScaleFactor(this.data{i}, table.Data{3});
end
end
end
end
function updateViewNeeded = processCalibrationTable(eventdata)
updateViewNeeded = false;
indices = eventdata.Indices;
table = this.gui.calibrationTable;
if ~isnumeric(eventdata.NewData)
table.Data{indices(1), indices(2)} = eventdata.PreviousData;
else
updateViewNeeded = true;
selected = this.gui.scanList.Value;
for i = selected
this.data{i}.calibration = table.Data';
adjustEnergyCalibration(this.data{i});
end
end
end
function saveOutputText()
[fileName, path] = uiputfile('visualfluo-output.txt','Save output text as');
file = fullfile(path, fileName);
text = this.gui.output.String;
fid = fopen(file, 'a');
fprintf(fid, strcat(datestr(datetime), '\n'));
for i = 1:length(text)
fprintf(fid, strcat(text{i}, '\n'));
end
fprintf(fid,'\n');
fclose(fid);
message = {'Output text save at:'; path; 'File name is:'; fileName};