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cwepr_code.sh
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#!/bin/sh
# cwepr_code.sh
#
#
# Created by Thomas Casey on 10/6/21.
#
classdef cwEPR < matlab.apps.AppBase
% Properties that correspond to app components
properties (Access = public)
cwEPRapp matlab.ui.Figure
UIAxes matlab.ui.control.UIAxes
OpenDataButton matlab.ui.control.Button
SysTabGroup matlab.ui.container.TabGroup
Sys1Tab matlab.ui.container.Tab
Sys1Switch matlab.ui.control.Switch
Sys1Edit matlab.ui.control.EditField
Sys1ListBox matlab.ui.control.ListBox
Sys2Tab matlab.ui.container.Tab
Sys2Switch matlab.ui.control.Switch
Sys2Edit matlab.ui.control.EditField
Sys2ListBox matlab.ui.control.ListBox
Sys3Tab matlab.ui.container.Tab
Sys3Switch matlab.ui.control.Switch
Sys3Edit matlab.ui.control.EditField
Sys3ListBox matlab.ui.control.ListBox
Sys4Tab matlab.ui.container.Tab
Sys4Switch matlab.ui.control.Switch
Sys4Edit matlab.ui.control.EditField
Sys4ListBox matlab.ui.control.ListBox
ExpTab matlab.ui.container.Tab
ExpEdit matlab.ui.control.EditField
FromDataButton matlab.ui.control.Button
ExpListBox matlab.ui.control.ListBox
FrequencySliderLabel matlab.ui.control.Label
FrequencySlider matlab.ui.control.Slider
StaticExpListBox matlab.ui.control.ListBox
FreqSpinner matlab.ui.control.Spinner
OptTab matlab.ui.container.Tab
OptEdit matlab.ui.control.EditField
OptListBox matlab.ui.control.ListBox
ProcessingTabGroup matlab.ui.container.TabGroup
BaselineTab matlab.ui.container.Tab
LoadButton matlab.ui.control.Button
BackgroundFilenameLabel matlab.ui.control.Label
SpectrumUsageSliderLabel matlab.ui.control.Label
SpectrumUsageSlider matlab.ui.control.Slider
PolynomialFitButton matlab.ui.control.Button
ApplyButton matlab.ui.control.Button
BackgroundButton matlab.ui.control.Button
RevertBaseButton matlab.ui.control.Button
fromendsLabel matlab.ui.control.Label
msbackadjButton matlab.ui.control.Button
RequiresBioinformaticsToolboxLabel matlab.ui.control.Label
NormalizeBaseCheckBox matlab.ui.control.CheckBox
OrderSpinnerLabel matlab.ui.control.Label
PolyOrderSpinner matlab.ui.control.Spinner
SmoothTab matlab.ui.container.Tab
SmoothingOptionsButtonGroup matlab.ui.container.ButtonGroup
MovingAverageButton matlab.ui.control.RadioButton
BinomialButton matlab.ui.control.RadioButton
FlatButton matlab.ui.control.RadioButton
SavitskyGolayButton matlab.ui.control.RadioButton
wdenoiseButton matlab.ui.control.RadioButton
pdifEditFieldLabel matlab.ui.control.Label
pdifEditField matlab.ui.control.EditField
LevelLabel matlab.ui.control.Label
wdOptionsEditField matlab.ui.control.EditField
RequiresWavletToolboxLabel matlab.ui.control.Label
orfloorlog2nPointsLabel matlab.ui.control.Label
SmoothingBusyLabel matlab.ui.control.Label
StepsSpinnerLabel matlab.ui.control.Label
StepsSpinner matlab.ui.control.Spinner
ShowButton matlab.ui.control.Button
SmoothingApplyButton matlab.ui.control.Button
SmoothingRevertButton matlab.ui.control.Button
IntegrateTab matlab.ui.container.Tab
IntegrateButton matlab.ui.control.Button
ShowIntButtonGroup matlab.ui.container.ButtonGroup
SingleButton matlab.ui.control.RadioButton
DoubleButton matlab.ui.control.RadioButton
BothButton matlab.ui.control.RadioButton
NeitherButton matlab.ui.control.RadioButton
BaselineCorrButtonGroup matlab.ui.container.ButtonGroup
NoneButton matlab.ui.control.RadioButton
PolynomialorderButton matlab.ui.control.RadioButton
IntOrderSpinner matlab.ui.control.Spinner
IntegralTextAreaLabel matlab.ui.control.Label
DIEditField matlab.ui.control.TextArea
DoubleLabel matlab.ui.control.Label
ndMomentButton matlab.ui.control.Button
TrapzCheckBox matlab.ui.control.CheckBox
SumCheckBox matlab.ui.control.CheckBox
SecondMomentEdit matlab.ui.control.EditField
IntSpectrumUsageSlider matlab.ui.control.Slider
SpectrumUsagefromendsLabel matlab.ui.control.Label
AutoButton matlab.ui.control.Button
AutoBusyLabel matlab.ui.control.Label
QuantifyTab matlab.ui.container.Tab
Step1Label matlab.ui.control.Label
Step2Label matlab.ui.control.Label
DIEditFieldLabel matlab.ui.control.Label
aEditField matlab.ui.control.NumericEditField
x2Label matlab.ui.control.Label
Label matlab.ui.control.Label
bEditField matlab.ui.control.NumericEditField
xLabel matlab.ui.control.Label
EditField_2Label matlab.ui.control.Label
cEditField matlab.ui.control.NumericEditField
Step2Label_2 matlab.ui.control.Label
Step4Label matlab.ui.control.Label
FindconcentrationButton matlab.ui.control.Button
Step3Label matlab.ui.control.Label
SpinCEditField matlab.ui.control.EditField
DIfactorEditField matlab.ui.control.EditField
hintsLabel matlab.ui.control.Label
hint2Label matlab.ui.control.Label
AdjustTab matlab.ui.container.Tab
AddNoiseButton matlab.ui.control.Button
RevertAdjustmentsButton matlab.ui.control.Button
NoiseModelButtonGroup matlab.ui.container.ButtonGroup
fButton matlab.ui.control.RadioButton
UniformButton matlab.ui.control.RadioButton
GaussianButton matlab.ui.control.RadioButton
ApplyAdjustmentsButton matlab.ui.control.Button
InterpolateButton matlab.ui.control.Button
NoisySimButton matlab.ui.control.Button
NoiseDTADSCCheckBox matlab.ui.control.CheckBox
NoiseasciiCheckBox matlab.ui.control.CheckBox
NoisetoworkspaceCheckBox matlab.ui.control.CheckBox
NoisetodataCheckBox matlab.ui.control.CheckBox
SNRSpinnerLabel matlab.ui.control.Label
SNRSpinner matlab.ui.control.Spinner
PointsSpinnerLabel matlab.ui.control.Label
PointsSpinner matlab.ui.control.Spinner
ToolsTab matlab.ui.container.Tab
ExportDataButton matlab.ui.control.Button
ConstantsDropDownLabel matlab.ui.control.Label
ConstantsDropDown matlab.ui.control.DropDown
ConversionToolButton matlab.ui.control.Button
PeriodicTableButton matlab.ui.control.Button
ExportDTADSCCheckBox matlab.ui.control.CheckBox
ExportasciiCheckBox matlab.ui.control.CheckBox
ExporttoworkspaceCheckBox matlab.ui.control.CheckBox
ShowButtonGroup matlab.ui.container.ButtonGroup
DataOnlyButton matlab.ui.control.RadioButton
SimOnlyButton matlab.ui.control.RadioButton
PlotBothButton matlab.ui.control.RadioButton
ResetDataButton matlab.ui.control.Button
ConstantLabel matlab.ui.control.Label
LoadParametersButton matlab.ui.control.Button
SaveParametersButton matlab.ui.control.Button
getesfitfit1Button matlab.ui.control.Button
ExportStructsButton matlab.ui.control.Button
DTab matlab.ui.container.Tab
PausesEditFieldLabel matlab.ui.control.Label
PausesEditField matlab.ui.control.NumericEditField
plambdanPreAvgdeltadirEditFieldLabel matlab.ui.control.Label
ewrlsoptions matlab.ui.control.EditField
ewrlsButton matlab.ui.control.Button
ewrlsBusyLabel matlab.ui.control.Label
ApplyewrlsButton matlab.ui.control.Button
RevertewrlsButton matlab.ui.control.Button
PlayButton matlab.ui.control.StateButton
CompareewrlstooriginalLabel matlab.ui.control.Label
ewrlsSpinner matlab.ui.control.Spinner
ewrlsedLabel matlab.ui.control.Label
totalslicesLabel matlab.ui.control.Label
mainLabel matlab.ui.control.Label
VaryTabGroup matlab.ui.container.TabGroup
Vary1Tab matlab.ui.container.Tab
Vary1Switch matlab.ui.control.Switch
Vary1Edit matlab.ui.control.EditField
Vary1ListBox matlab.ui.control.ListBox
Vary1RemoveButton matlab.ui.control.Button
Vary2Tab matlab.ui.container.Tab
Vary2Switch matlab.ui.control.Switch
Vary2Edit matlab.ui.control.EditField
Vary2ListBox matlab.ui.control.ListBox
Vary2RemoveButton matlab.ui.control.Button
Vary3Tab matlab.ui.container.Tab
Vary3Switch matlab.ui.control.Switch
Vary3Edit matlab.ui.control.EditField
Vary3ListBox matlab.ui.control.ListBox
Vary3RemoveButton matlab.ui.control.Button
Vary4Tab matlab.ui.container.Tab
Vary4Switch matlab.ui.control.Switch
Vary4Edit matlab.ui.control.EditField
Vary4ListBox matlab.ui.control.ListBox
Vary4RemoveButton matlab.ui.control.Button
FitOptTab matlab.ui.container.Tab
FitOptEdit matlab.ui.control.EditField
MethodDropDownLabel matlab.ui.control.Label
FitMethodDropDown matlab.ui.control.DropDown
TargetDropDownLabel matlab.ui.control.Label
TargetDropDown matlab.ui.control.DropDown
ScalingDropDownLabel matlab.ui.control.Label
FitScalingDropDown matlab.ui.control.DropDown
DDataButtonGroup matlab.ui.container.ButtonGroup
AllParallelButton matlab.ui.control.RadioButton
AllSequentialButton matlab.ui.control.RadioButton
OnlyCurrentButton matlab.ui.control.RadioButton
FitOptListBox matlab.ui.control.ListBox
SimulateButton matlab.ui.control.Button
Spinner matlab.ui.control.Spinner
SliceLabel matlab.ui.control.Label
DataFilenameLabel matlab.ui.control.Label
gvaluesButton matlab.ui.control.StateButton
SimTimeLabel matlab.ui.control.Label
FittingSliceLabel matlab.ui.control.Label
StopFittingButton matlab.ui.control.StateButton
esfitButton matlab.ui.control.Button
FunctionDropDown matlab.ui.control.DropDown
SimMethodDropDown matlab.ui.control.DropDown
FitGUICheckBox matlab.ui.control.CheckBox
RescaleDropDown matlab.ui.control.DropDown
RescaleLabel matlab.ui.control.Label
v33Label matlab.ui.control.Label
RealCheckBox matlab.ui.control.CheckBox
ImaginaryCheckBox matlab.ui.control.CheckBox
end
properties (Access = public)
currslice=1;
data=[];
dataexists='n';
simexists='n';
whchS=[];
fitexists='n';
params=[];
tags={};
xlab='Field (mT)';
inp={};
SysStr={'function=','method=','weight=','S=','g=','gFrame=','lw=','lwpp=',...
'Nucs=','n=','A_=','A=','AFrame=','tcorr=','logtcorr=','Diff=','logDiff=','DiffFrame=',...
'lambda=','Potential=','Exchange=','J=','ee=','eeFrame=','D=','DFrame=','DStrain=',...
'DStrainCorr=','HStrain=','gStrain=','Abund=','AStrain=','gAStrainCorr=',...
'dvec=','eeD=','ee2=','Q=','QFrame=','nn=','nnFrame=',...
'aF=','B0=','B2=','B4=','B6=','B8=','B10=','B12=','L=','CF0=','CF2=','CF4=','CF6=',...
'CF8=','CF10=','CF12=','orf=','soc=','Ham='};
ExpStr={'mwFreq=','Range=','nPoints=','ModAmp=','Mode=','CenterSweep=','Temperature=',...
'mwCenterSweep=','mwRange=','Harmonic=','mwPhase=','mwPolarization=',...
'CrystalOrientation=','CrystalSymmetry=','MolFrame=','Ordering='};
StaticExpStr={'Q Value=','Power (mW)=','Power (dB)=','Reciever Gain=',...
'Time Constant=','Conversion Time=','Averages=','Temperature='};
OptStr={'Output=','Verbosity=','LLKM=','LLMK=','evenK=','highField=','pImax=','GridSize=','nKnots=','Transitions=',...
'Sites=','Threshold=','Symmetry=','Enhancement=','Intensity=','Freq2Field=',...
'IsoCutoff=','HybridCoreNuclei=','PostConvNucs=','AccumMethod='};
rangeLH=[];
FitOptStr={'FitRange=','maxTime=','PrintLevel=','OutArg=','RandomStart=','TolEdgeLength=',...
'TolFun=','SimplexPars=','delta=','TolStep=','lambda=','nTrials=','PopulationSize=',...
'maxGenerations=','GridSize=','nParticles=','SwarmParams=',};
whchV=[];
dlw=1.1;
slw=1.5;
plw=1.5;
dclr=[0.00,0.45,0.74];
sclr={[0.64,0.08,0.18],[0.47,0.67,0.19],[0.49,0.18,0.56],[0.93,0.69,0.13],'r'};
pclr={[0.85,0.33,0.10],[0.49,0.18,0.56]};
end
methods (Access = private)
function [B0,spec,pars,scnD] = opendata(~,name,exten)
switch exten
case '.DTA'
[B,spc,pars]=eprload(name);
typ='Bruker DTA';
case '.DSC'
[B,spc,pars]=eprload(name);
typ='Bruker DTA';
case '.YGF'
name=replace(name,'YGF','DTA');
[B,spc,pars]=eprload(name);
typ='Bruker DTA';
case '.spc'
[B,spcH,pars]=eprload(name);
if iscell(B)
B{1,2}=B{1,2}';
spc=spcH;
else
B=B';
spc=spcH';
end
typ='Bruker spc';
case '.par'
[B,spcH,pars]=eprload(name);
if iscell(B)
B{1,2}=B{1,2}';
spc=spcH;
else
B=B';
spc=spcH';
end
typ='Bruker spc';
case '.ESR'
[B,spc,pars]=eprload(name);
typ='ActiveSpectrum';
case '.xml'
[BNaN,spcNaN,pars]=eprload(name);
BNaN=BNaN.*10;
m=1;
for i=1:length(BNaN)
if ~isnan(BNaN(i)) && BNaN(i)~=0
Bm(m,1)=BNaN(i);
spcm(m,1)=spcNaN(i);
m=m+1;
else
end
end
B=Bm;
spc=spcm;
typ='magnettech';
otherwise
original=readmatrix(name);
B=original(:,1);
spc=original(:,2:end);
typ='ascii';
end
if length(spc(1,:))>1
switch typ
case 'ascii'
B_(:,1)=B;
scnD1=1:1:length(spc(1,:));
otherwise
B_(:,1)=B{1,1};
scnD1=B{1,2};
end
k=1;
%assignin("base",'spc',spc)
for i=1:length(spc(1,:))
if sum(abs(spc(:,i)))~=0
spk(:,k)=spc(:,i);
scnD(k)=scnD1(i);
k=k+1;
else
end
end
%assignin("base",'spk',spk)
else
B_=B;
spk=spc;
scnD=[];
end
B1=B_;
for i=2:length(B_)+1
if i>=length(B_)
break
else
if B_(i)==B_(i-1) || B_(i)==B_(i+1)
B1(i,1)=(B_(i-1)+B_(i+1))/2;
else
B1(i,1)=B_(i);
end
end
end
if max(B1)<1000
B0=B1;
else
B0=B1/10;
end
if length(spk(1,:))>1
for i=1:length(spk(1,:))
[spec(:,i),~]=basecorr(spk(:,i),1,0);
end
else
[spec,~]=basecorr(spk,1,0);
end
try
pars.MFQ=num2str(pars.MWFQ/1e9);
catch
try
pars.MFQ=num2str(pars.MF);
catch
try
pars.MFQ=num2str(pars.MwFreq);
catch
pars.MFQ='';
end
end
end
try
[modA_,~]=strtok(pars.ModAmp,' G');
modA=str2double(modA_)/10;
pars.modA=num2str(modA);
catch
try
[modA,~]=strtok(pars.Modulation,' G');
pars.modA=num2str(modA/10);
catch
try
pars.modA=num2str(pars.RMA/10);
catch
pars.modA='';
end
end
end
try
[ct,~]=strtok(pars.ConvTime,' ms');
pars.CT=num2str(ct);
catch
try
pars.CT=num2str(pars.RCT);
catch
pars.CT='';
end
end
try
[tc,~]=strtok(pars.TimeConst,' ms');
pars.TC=num2str(tc);
catch
try
pars.TC=num2str(pars.RTC);
catch
pars.TC='';
end
end
try
[rg,~]=strtok(pars.Gain,' dB');
pars.RG=num2str(rg);
catch
try
pars.RG=num2str(pars.RRG);
catch
pars.RG='';
end
end
try
[pow,~]=strtok(pars.Power,' mW');
pars.POW=num2str(pow);
catch
try
pars.POW=num2str(pars.MP);
catch
pars.POW='';
end
end
try
[attn,~]=strtok(pars.PowerAtten,' dB');
pars.ATTN=num2str(attn);
catch
try
pars.ATTN=num2str(pars.MPD);
catch
pars.ATTN='';
end
end
try
pars.QVal=num2str(pars.QValue);
catch
pars.QVal='';
end
try
pars.Harm=num2str(pars.Harmonic);
catch
pars.Harm='';
end
try
pars.nScans=num2str(pars.AVGS);
catch
pars.nScans='';
end
try
[temper,~]=strtok(pars.Temperature,' K');
pars.Temp = num2str(temper);
catch
pars.Temp = '';
end
end
function [sys,fncmeth_f,fncmeth_m]=getsyss(~,syslst)
l=1;
SysValues=[];
for i=1:numel(syslst)
syslst_f=strsplit(syslst{i},'=');
syslst_f{2} = erase(syslst_f{2},"'");
switch syslst_f{1}
case 'function'
fncmeth_f=syslst_f{2};
case 'method'
fncmeth_m=syslst_f{2};
otherwise
if ~isempty(syslst_f{2})
SysString{l}=syslst_f{1};
SysValues{l}=str2num(syslst_f{2});
if isempty(SysValues{l})
SysValues{l}=syslst_f{2};
end
l=l+1;
else
end
end
end
if isempty(SysValues)
sys=[];
else
sys=cell2struct(SysValues,SysString,2);
end
end
function [Exp] = getexps(~,explst)
h=1;
ExpValues = [];
for i=1:numel(explst)
explst_f=strsplit(explst{i},'=');
explst_f{2}=erase(explst_f{2},"'");
if ~isempty(explst_f{2})
ExpString{h}=explst_f{1};
ExpValues{h}=str2num(explst_f{2});
if isempty(ExpValues{h})
ExpValues{h}=explst_f{2};
end
h=h+1;
end
end
if isempty(ExpValues)
Exp = [];
else
Exp=cell2struct(ExpValues,ExpString,2);
end
end
function [Opt] = getopts(~,optlst)
k=1;
OptValues=[];
for i=1:numel(optlst)
optlst_f=strsplit(optlst{i},'=');
optlst_f{2}=erase(optlst_f{2},"'");
if ~isempty(optlst_f{2})
OptString{k}=optlst_f{1};
OptValues{k}=str2num(optlst_f{2});
if isempty(OptValues{k})
OptValues{k}=optlst_f{2};
end
k=k+1;
end
end
if isempty(OptValues)
Opt=[];
else
Opt=cell2struct(OptValues,OptString,2);
end
end
function [syslst_new]=sysadd(~,sysstr,syslst)
sysparam=strsplit(sysstr,'=');
syslst_new=syslst;
for i=1:numel(syslst)
syslstf=strsplit(syslst{i},'=');
switch syslstf{1}
case sysparam{1}
syslst_new{i}=[sysparam{1},'=',sysparam{2}];
otherwise
syslst_new{i}=syslst{i};
end
end
end
function syslst_new = getsysstructs(~,syslst,sys_strct,sys_params)
syslst_new=syslst;
for i=1:numel(sys_params)
for j=1:numel(syslst)
syslstf=strsplit(syslst{j},'=');
switch syslstf{1}
case sys_params{i}
if contains(sys_params{i},'function')==1 || contains(sys_params{i},'method')==1 || contains(sys_params{i},'Nucs')==1
syslst_new{j}=[sys_params{i},'=',sys_strct.(sys_params{i})];
else
sys_vals{1}=sys_params{i};
sys_val=sys_strct.(sys_params{i});
if length(sys_val(1,:))==1 && length(sys_val(:,1))==1
sys_vals{2}=num2str(sys_val(1));
elseif length(sys_val(1,:))==2 && length(sys_val(:,1))==1
sys_vals{2}=['[',num2str(sys_val(1)),' ',num2str(sys_val(2)),']'];
elseif length(sys_val(1,:))==1 && length(sys_val(:,1))==2
sys_vals{2}=['[',num2str(sys_val(1)),';',num2str(sys_val(2)),']'];
elseif length(sys_val(1,:))==2 && length(sys_val(:,1))==2
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),';',num2str(sys_val(2,1)),' ',num2str(sys_val(2,2)),']'];
elseif length(sys_val(1,:))==3 && length(sys_val(:,1))==1
sys_vals{2}=['[',num2str(sys_val(1)),' ',num2str(sys_val(2)),' ',num2str(sys_val(3)),']'];
elseif length(sys_val(1,:))==1 && length(sys_val(:,1))==3
sys_vals{2}=['[',num2str(sys_val(1)),';',num2str(sys_val(2)),';',num2str(sys_val(3)),']'];
elseif length(sys_val(1,:))==3 && length(sys_val(:,1))==2
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),' ',num2str(sys_val(1,3)),';',...
num2str(sys_val(2,1)),' ',num2str(sys_val(2,2)),' ',num2str(sys_val(2,3)),']'];
elseif length(sys_val(1,:))==2 && length(sys_val(:,1))==3
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),'; ',num2str(sys_val(2,1)),' ',...
num2str(sys_val(2,2)),'; ',num2str(sys_val(3,1)),' ',num2str(sys_val(3,2)),']'];
elseif length(sys_val(1,:))==3 && length(sys_val(:,1))==3
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),' ',num2str(sys_val(1,3)),';',...
num2str(sys_val(2,1)),' ',num2str(sys_val(2,2)),' ',num2str(sys_val(2,3)),';',...
num2str(sys_val(3,1)),' ',num2str(sys_val(3,2)),' ',num2str(sys_val(3,3)),']'];
elseif length(sys_val(1,:))==5 && length(sys_val(:,1))==2
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),...
' ',num2str(sys_val(1,3)),' ',num2str(sys_val(1,4)),' ',num2str(sys_val(1,5)),...
';',num2str(sys_val(2,1)),' ',num2str(sys_val(2,2)),' ',...
num2str(sys_val(2,3)),' ',num2str(sys_val(2,4)),' ',num2str(sys_val(2,5)),']'];
elseif length(sys_val(1,:))==5 && length(sys_val(:,1))==1
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),' ',num2str(sys_val(1,3)),' ',...
num2str(sys_val(1,4)),' ',num2str(sys_val(1,5)),']'];
elseif length(sys_val(1,:))==6 && length(sys_val(:,1))==2
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),...
' ',num2str(sys_val(1,3)),' ',num2str(sys_val(1,4)),' ',num2str(sys_val(1,5)),...
' ',num2str(sys_val(1,6)),';',num2str(sys_val(2,1)),' ',num2str(sys_val(2,2)),' ',...
num2str(sys_val(2,3)),' ',num2str(sys_val(2,4)),' ',num2str(sys_val(2,5)),' ',num2str(sys_val(2,6)),']'];
elseif length(sys_val(1,:))==6 && length(sys_val(:,1))==1
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),' ',num2str(sys_val(1,3)),' ',...
num2str(sys_val(1,4)),' ',num2str(sys_val(1,5)),' ',num2str(sys_val(1,6)),']'];
elseif length(sys_val(1,:))==9 && length(sys_val(:,1))==1
sys_vals{2}=['[',num2str(sys_val(1)),' ',num2str(sys_val(2)),' ',num2str(sys_val(3)),' ',...
num2str(sys_val(4)),' ',num2str(sys_val(5)),' ',num2str(sys_val(6)),' ',...
num2str(sys_val(7)),' ',num2str(sys_val(8)),' ',num2str(sys_val(9)),']'];
elseif length(sys_val(1,:))==3 && length(sys_val(:,1))==6
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),' ',num2str(sys_val(1,3)),';',...
num2str(sys_val(2,1)),' ',num2str(sys_val(2,2)),' ',num2str(sys_val(2,3)),';',...
num2str(sys_val(3,1)),' ',num2str(sys_val(3,2)),' ',num2str(sys_val(3,3)),']; [',...
num2str(sys_val(4,1)),' ',num2str(sys_val(4,2)),' ',num2str(sys_val(4,3)),';',...
num2str(sys_val(5,1)),' ',num2str(sys_val(5,2)),' ',num2str(sys_val(5,3)),';',...
num2str(sys_val(6,1)),' ',num2str(sys_val(6,2)),' ',num2str(sys_val(6,3)),']'];
elseif length(sys_val(1,:))==6 && length(sys_val(:,1))==3
sys_vals{2}=['[',num2str(sys_val(1,1)),' ',num2str(sys_val(1,2)),' ',num2str(sys_val(1,3)),';',...
num2str(sys_val(2,1)),' ',num2str(sys_val(2,2)),' ',num2str(sys_val(2,3)),';',...
num2str(sys_val(3,1)),' ',num2str(sys_val(3,2)),' ',num2str(sys_val(3,3)),'], [',...
num2str(sys_val(1,4)),' ',num2str(sys_val(1,5)),' ',num2str(sys_val(1,6)),';',...
num2str(sys_val(2,4)),' ',num2str(sys_val(2,5)),' ',num2str(sys_val(2,6)),';',...
num2str(sys_val(3,4)),' ',num2str(sys_val(3,5)),' ',num2str(sys_val(3,6)),']'];
end
syslst_fil=[sys_vals(1),'=',sys_vals(2)];
syslst_new{j}=[syslst_fil{1},syslst_fil{2},syslst_fil{3}];
end
otherwise
syslst_new{j}=syslst{j};
end
end
syslst=syslst_new;
end
end
function [vary]=getvarys(~,varypars,t)
j=1;
for i=1:t
varypar=strsplit(varypars{i},'=');
VaryString{j}=varypar{1};
VaryValues{j}=str2num(varypar{2});
j=j+1;
end
vary=cell2struct(VaryValues,VaryString,2);
end
function [FitOpt, fitrange] = getfitopts(~,fitoptlst)
l=1;
fitOptValues=[];
for i=1:numel(fitoptlst)
fitoptlst_f=strsplit(fitoptlst{i},'=');
fitoptlst_f{2}=erase(fitoptlst_f{2},"'");
switch fitoptlst_f{1}
case 'FitRange'
fitrange=str2num(fitoptlst_f{2});
otherwise
if ~isempty(fitoptlst_f{2})
fitOptString{l}=fitoptlst_f{1};
fitOptValues{l}=str2num(fitoptlst_f{2});
if isempty(fitOptValues{l})
fitOptValues{l}=fitoptlst_f{2};
end
l=l+1;
end
end
end
if isempty(fitOptValues)
FitOpt=[];
else
FitOpt=cell2struct(fitOptValues,fitOptString,2);
end
end
function [varylst_new]=varyadd(~,varystr,varylst1)
if isempty(varylst1)
varylst_new{1}=varystr;
else
varylst_new=varylst1;
varylst=varylst1;
varyparam=strsplit(varystr,'=');
if ~isempty(varylst1)
vn=numel(varylst);
n=0;
for i=1:vn
varylstf=strsplit(varylst{i},'=');
switch varylstf{1}
case varyparam{1}
varylst_new{i}=[varylstf{1},'=',varyparam{2}];
otherwise
varylst_new{i}=varylst{i};
n=n+1;
end
end
if n==vn
varylst_new{vn+1}=[varyparam{1},'=',varyparam{2}];
end
end
end
end
function [parlst_new]=paradd(~,parstr,parlst)
parparam=strsplit(parstr,'=');
parlst_new=parlst;
for i=1:numel(parlst)
parlstf=strsplit(parlst{i},'=');
switch parlstf{1}
case parparam{1}
parlst_new{i}=[parparam{1},'=',parparam{2}];
otherwise
parlst_new{i}=parlst{i};
end
end
end
function [simX,sim]=custom_twomethods(~,Sys,Exp,options)
l=length(Sys);
sim=zeros(Exp.nPoints,l);
if l==1
Opt = options;
switch options.fnc{1}
case 'garlic'
Opt.Method=options.meth{1};
[simX(:,1),sim(:,1)] = garlic(Sys,Exp,Opt);
case 'chili'
Opt.LiouvMethod=options.meth{1};
[simX(:,1),sim(:,1)] = chili(Sys,Exp,Opt);
case 'pepper'
Opt.Method=options.meth{1};
[simX(:,1),sim(:,1)] = pepper(Sys,Exp,Opt);
end
%simout(:,1)=sim(Opt.rangeL:Opt.rangeH);
else
for i=1:l
Opt = options;
switch options.fnc{i}
case 'garlic'
Opt.Method=options.meth{i};
[simX(:,1),sim(:,i)] = garlic(Sys{i},Exp,Opt);
case 'chili'
Opt.LiouvMethod=options.meth{i};
[simX(:,1),sim(:,i)] = chili(Sys{i},Exp,Opt);
case 'pepper'
Opt.Method=options.meth{i};
[simX(:,1),sim(:,i)] = pepper(Sys{i},Exp,Opt);
end
%simout(:,i)=sim(Opt.rangeL:Opt.rangeH);
end
end
end
function simout=custom_fittwomethods(~,Sys,Exp,options)
l=length(Sys);
sim=zeros(Exp.nPoints,l);
if l==1
Opt = options;
switch options.fnc{1}
case 'garlic'
Opt.Method=options.meth{1};
[~,sim] = garlic(Sys,Exp,Opt);
case 'chili'
Opt.LiouvMethod=options.meth{1};
[~,sim] = chili(Sys,Exp,Opt);
case 'pepper'
Opt.Method=options.meth{1};
[~,sim] = pepper(Sys,Exp,Opt);
end
simspc=sim;
else
for i=1:l
Opt = options;
switch options.fnc{i}
case 'garlic'
Opt.Method=options.meth{i};
[~,sim(:,i)] = garlic(Sys{i},Exp,Opt);
case 'chili'
Opt.LiouvMethod=options.meth{i};
[~,sim(:,i)] = chili(Sys{i},Exp,Opt);
case 'pepper'
Opt.Method=options.meth{i};
[~,sim(:,i)] = pepper(Sys{i},Exp,Opt);
end
%sim(:,i)=system.weight.*(sim(:,i)./max(sim(:,i)));
end
simspc=sum(sim,2);
end
simout=zeros(length(simspc),1);
simout(options.rangeLH(1):options.rangeLH(2))=...
simspc(options.rangeLH(1):options.rangeLH(2));
end
function simout=custom_fit2D(~,Sys,Exp,options)
l=length(Sys);
simout=zeros(1,Exp.nP*Exp.nSpcs);
Exp.nPoints=Exp.nP;
for i=1:Exp.nSpcs
k=((i-1)*Exp.nP)+1;
kk=((i)*Exp.nP);
sim=zeros(Exp.nP,l);
if l==1
Opt = options;
switch options.fnc{1}
case 'garlic'
Opt.Method=options.meth{1};
[~,sim] = garlic(Sys,Exp,Opt);
case 'chili'
Opt.LiouvMethod=options.meth{1};
[~,sim] = chili(Sys,Exp,Opt);
case 'pepper'
Opt.Method=options.meth{1};
[~,sim] = pepper(Sys,Exp,Opt);
end
simSpc=sim./max(sim);
else
for j=1:l
Opt = options;
switch options.fnc{j}
case 'garlic'
Opt.Method=options.meth{j};
[~,sim(:,j)] = garlic(Sys{j},Exp,Opt);
case 'chili'
Opt.LiouvMethod=options.meth{j};
[~,sim(:,j)] = chili(Sys{j},Exp,Opt);
case 'pepper'
Opt.Method=options.meth{i};
[~,sim(:,j)] = pepper(Sys{j},Exp,Opt);
end
% sim(:,i)=str2num(Opt.wght{i}).*(sim(:,i)./max(sim(:,i)));
end
simspc=sum(sim,2);
simSpc=simspc./max(simspc);
end
sim_spc=zeros(length(simSpc),1);
sim_spc(options.rangeLH(1):options.rangeLH(2))=...
simSpc(options.rangeLH(1):options.rangeLH(2));
simout(1,k:kk)=sim_spc;
end
end
%{
function simout=custom_fitALL(~,Sys,Exp,Opt)
Exp.nPoints = Exp.nP;
for i=1:Exp.nSpcs
k=((i-1)*Exp.nP)+1;
kk=((i)*Exp.nP);
switch Exp.func
case 'garlic'
[~,simSpc]=garlic(Sys,Exp,Opt);
case 'chili'
[~,simSpc]=chili(Sys,Exp,Opt);
case 'pepper'
[~,simSpc]=pepper(Sys,Exp,Opt);
case 'salt'
[~,simSpc]=salt(Sys,Exp,Opt);
case 'saffron'
[~,simSpc]=saffron(Sys,Exp,Opt);
end
simout(1,k:kk)=simSpc;
end
end
%}
function showplots(app,selbutton,whch,onORoff)
switch app.simexists
case 'y'
l=length(whch);
if l~=0
k=1;
for i=1:4
switch onORoff{i}
case 'On'
inti(k)=max(app.data.simspc(:,i));
simspci(:,k)=app.data.simspc(:,i);
k=k+1;
end
end
totsimspc_=sum(simspci,2);
intsim=max(totsimspc_);
totsimspc=totsimspc_./intsim;
for i=1:length(simspci(1,:))
simspci(:,i)=(simspci(:,i)./max(app.data.simspc(:,i))).*(inti(i)/intsim);
end
end
case 'n'
selbutton='Data Only';
set(app.SimOnlyButton,'Value',0)
set(app.DataOnlyButton,'Value',1)
set(app.PlotBothButton,'Value',0)
end
switch app.dataexists
case 'y'
dataspc=app.data.spc(:,app.currslice);
switch selbutton
case 'Data Only'
plot(app.UIAxes,app.data.B,dataspc,'linewidth',app.dlw,'color',app.dclr);
xlim(app.UIAxes,[min(app.data.B) max(app.data.B)]);
ylim(app.UIAxes,[min(dataspc) max(dataspc)].*1.05);
legend(app.UIAxes,'Data','location','northeast')
case 'Sim Only'
if l~=0
for i=1:l
plot(app.UIAxes,app.data.simB, simspci(:,i),'linewidth',app.slw,'color',app.sclr{i})
lg{i}=['SYS',num2str(whch(i))];
hold(app.UIAxes,'on');
end
if l>1
plot(app.UIAxes,app.data.simB,totsimspc,'linewidth',app.slw,'color',app.sclr{5});
lg{l+1}='Sim';
end
xlim(app.UIAxes,[min(app.data.simB) max(app.data.simB)]);
ylim(app.UIAxes,[min(totsimspc) max(totsimspc)].*1.05);
legend(app.UIAxes,lg,'location','northeast')
hold(app.UIAxes,'off');
end
case 'Both'
lg{1}='Data';
plot(app.UIAxes,app.data.B,dataspc,'linewidth',app.dlw,'color',app.dclr);
xlim(app.UIAxes,[min(app.data.B) max(app.data.B)]);
ylim(app.UIAxes,[min(dataspc) max(dataspc)].*1.05);
legend(app.UIAxes,lg,'location','northeast')
if l~=0
switch app.RescaleDropDown.Value
case 'none'
totsimspc=totsimspc_;
otherwise
try
totsimspc=rescaledata(totsimspc_,dataspc, app.RescaleDropDown.Value);
catch
totsimspc=rescale(totsimspc_,dataspc, app.RescaleDropDown.Value);
end
end