diff --git a/Code/AdvancedSettings.m b/Code/AdvancedSettings.m
new file mode 100644
index 0000000..383e1cc
--- /dev/null
+++ b/Code/AdvancedSettings.m
@@ -0,0 +1,1253 @@
+function varargout = AdvancedSettings(varargin)
+% ADVANCEDSETTINGS M-file for AdvancedSettings.fig
+%      ADVANCEDSETTINGS, by itself, creates a new ADVANCEDSETTINGS or raises the existing
+%      singleton*.
+%
+%      H = ADVANCEDSETTINGS returns the handle to a new ADVANCEDSETTINGS or the handle to
+%      the existing singleton*.
+%
+%      ADVANCEDSETTINGS('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in ADVANCEDSETTINGS.M with the given input arguments.
+%
+%      ADVANCEDSETTINGS('Property','Value',...) creates a new ADVANCEDSETTINGS or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before AdvancedSettings_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to AdvancedSettings_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help AdvancedSettings
+
+% Last Modified by GUIDE v2.5 25-Feb-2015 16:00:32
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @AdvancedSettings_OpeningFcn, ...
+                   'gui_OutputFcn',  @AdvancedSettings_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+
+% --- Executes just before AdvancedSettings is made visible.
+function AdvancedSettings_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to AdvancedSettings (see VARARGIN)
+
+%get Settings sent in if this was opened before and is being reopened.
+stemp=load('Settings.mat');
+Settings=stemp.Settings;
+clear stemp
+
+%Read Grain File and get material data
+if strcmp(Settings.Material, 'grainfile')
+    GrainFileVals = ReadGrainFile(Settings.GrainFilePath);
+    allMaterials = unique(lower(GrainFileVals{11}));
+    handles.allMaterials = allMaterials;
+    curMaterial=allMaterials{1};
+else
+    handles.allMaterials = {Settings.Material};
+    curMaterial = Settings.Material;
+end
+guidata(hObject,handles);
+
+%Initialize NumROIs popup
+MaxROINum = 50;
+set(handles.NumberROIsPopUp,'String',num2cell(1:MaxROINum));
+
+%Initialize ROIStyle popup
+ROIStyleList = {'Grid','Radial','Intensity'};
+set(handles.ROIStylePopUp, 'String', ROIStyleList);
+
+%Initialize ROIStyle popup
+ImageFilterTypeList = {'standard','localthresh'};
+set(handles.ImageFilterType, 'String', ImageFilterTypeList);
+
+%Initialize HROIMMEthod popup
+HROIMMethodList = {'Simulated','Real-Grain Ref','Real-Single Ref'};
+set(handles.HROIMMethodPopUp, 'String', HROIMMethodList);
+
+%Initialize FCalcMethod popup
+FCalcMethodList = {'Real Sample','Real Crystal','Collin Sample','Collin Crystal'};
+set(handles.FCalcMethodPopUp, 'String', FCalcMethodList);
+
+%Initialze Real Ref Image Method
+GrainRefImageTypeList = {'Min Kernel Avg Miso','IQ > Fit > CI'};
+set(handles.GrainRefTypePopUp, 'String', GrainRefImageTypeList);
+
+%Initialize DDS Method
+DDSList = {'Nye-Kroner', 'Nye-Kroner (Pantleon)','Distortion Matching'};
+set(handles.DDMethod,'String',DDSList);
+
+if ~isempty(Settings.ROISizePercent)
+    if ~isnumeric(Settings.ROISizePercent) || Settings.ROISizePercent <= 0
+        warndlg('Input ROISizePercent is not a number or is negative','Warning');
+    else
+        set(handles.ROISizeEdit, 'String', num2str(Settings.ROISizePercent) );
+    end
+end
+
+if ~isempty(Settings.NumROIs)
+    if Settings.NumROIs > MaxROINum
+       warndlg('Too many ROI''s attempted','Warning');
+    else
+        NumROIs = Settings.NumROIs;
+        set(handles.NumberROIsPopUp, 'Value', NumROIs);
+    end    
+end
+
+if ~isempty(Settings.ROIStyle)
+    
+    ROIStyle = Settings.ROIStyle;
+    IndList = 1:length(ROIStyleList);
+    SelectedROIStyleInd = IndList(strcmp(ROIStyleList,ROIStyle));
+    set(handles.ROIStylePopUp, 'Value', SelectedROIStyleInd);
+    
+    if strcmp(Settings.ROIStyle,'Grid')
+        
+       set(handles.NumberROIsPopUp,'Enable','off');
+%        set(handles.ROISizeEdit,'Enable','off');
+        
+    end
+    
+end
+
+if strcmp(Settings.ROIStyle,'Intensity')
+
+   set(handles.ROIFilterEdit1,'Enable','off');
+   set(handles.ROIFilterEdit2,'Enable','off');
+   set(handles.ROIFilterEdit3,'Enable','off');
+   set(handles.ROIFilterEdit4,'Enable','off');
+%        set(handles.ROISizeEdit,'Enable','off');
+elseif ~isempty(Settings.ROIFilter)
+
+   set(handles.ROIFilterEdit1,'String',num2str(Settings.ROIFilter(1)));
+   set(handles.ROIFilterEdit2,'String',num2str(Settings.ROIFilter(2)));
+   set(handles.ROIFilterEdit3,'String',num2str(Settings.ROIFilter(3)));
+   set(handles.ROIFilterEdit4,'String',num2str(Settings.ROIFilter(4)));
+    
+end
+
+if ~isempty(Settings.ImageFilterType)
+    ImageFilterType = Settings.ImageFilterType;
+    IndList = 1:length(ImageFilterTypeList);
+    Ind = IndList(strcmp(ImageFilterTypeList,ImageFilterType));
+    set(handles.ImageFilterType,'Value',Ind);
+    if strcmp(Settings.ImageFilterType,'localthresh')
+
+        set(handles.ImageFilterEdit1,'Enable','off');
+        set(handles.ImageFilterEdit2,'Enable','off');
+        set(handles.ImageFilterEdit3,'Enable','off');
+        set(handles.ImageFilterEdit4,'Enable','off');
+    %        set(handles.ROISizeEdit,'Enable','off');
+    end
+end
+if ~isempty(Settings.ImageFilter)
+
+   set(handles.ImageFilterEdit1,'String',num2str(Settings.ImageFilter(1)));
+   set(handles.ImageFilterEdit2,'String',num2str(Settings.ImageFilter(2)));
+   set(handles.ImageFilterEdit3,'String',num2str(Settings.ImageFilter(3)));
+   set(handles.ImageFilterEdit4,'String',num2str(Settings.ImageFilter(4)));
+
+end
+if ~isempty(Settings.ROIFilter)
+    
+   set(handles.ROIFilterEdit1,'String',num2str(Settings.ROIFilter(1)));
+   set(handles.ROIFilterEdit2,'String',num2str(Settings.ROIFilter(2)));
+   set(handles.ROIFilterEdit3,'String',num2str(Settings.ROIFilter(3)));
+   set(handles.ROIFilterEdit4,'String',num2str(Settings.ROIFilter(4)));
+    
+end
+if ~isempty(Settings.HROIMMethod)
+    
+    HROIMMethod = Settings.HROIMMethod;
+    if strcmp(HROIMMethod,'Real')
+        if Settings.RefImageInd > 0
+            HROIMMethod = 'Real-Single Ref';
+            set(handles.RefImageIndEdit,'String',num2str(Settings.RefImageInd));
+        else
+            HROIMMethod = 'Real-Grain Ref';
+        end
+    end
+            
+    IndList = 1:length(HROIMMethodList);
+    SelectedHROIMMethodInd = IndList(strcmp(HROIMMethodList,HROIMMethod));
+    if isempty(SelectedHROIMMethodInd)
+        set(handles.HROIMMethodPopUp,'Value',1);
+    else
+        set(handles.HROIMMethodPopUp, 'Value', SelectedHROIMMethodInd);
+    end
+    
+    if ~strcmp(HROIMMethod,'Simulated')
+        set(handles.GrainRefTypePopUp,'Enable','on');
+        set(handles.KernelAvgFilePathEdit,'Enable','on');
+        set(handles.KernelAvgBrowseButton,'Enable','on');
+        set(handles.IterationLabel,'Visible','off');
+        set(handles.IterationLimitEdit,'Enable','off');
+        set(handles.IterationLimitEdit,'Visible','off');
+        set(handles.RefImageIndLabel,'Visible','on');
+        if strcmp(HROIMMethod,'Real-Grain Ref')
+            set(handles.RefImageIndEdit,'Enable','off');
+        else
+            set(handles.RefImageIndEdit,'Enable','on');
+        end
+        set(handles.RefImageIndEdit,'Visible','on');      
+    else
+        set(handles.GrainRefTypePopUp,'Enable','off');
+        set(handles.KernelAvgFilePathEdit,'Enable','off');
+        set(handles.KernelAvgBrowseButton,'Enable','off');
+        set(handles.IterationLabel,'Visible','on');
+        set(handles.IterationLimitEdit,'Enable','on');
+        set(handles.IterationLimitEdit,'Visible','on');
+        set(handles.RefImageIndLabel,'Visible','off');
+        set(handles.RefImageIndEdit,'Enable','off');
+        set(handles.RefImageIndEdit,'Visible','off');
+    end
+    
+end
+if isfield(Settings,'DoDDS')
+    set(handles.SplitDD, 'Value', Settings.DoDDS)
+else
+    set(handles.SplitDD, 'Value', 0);
+end
+if isfield(Settings,'DDSMethod')
+    switch Settings.DDSMethod
+        case 1
+            DDSMethodInd = 1;
+        case 9
+            DDSMethodInd = 2;
+        case 2
+            DDSMethodInd = 3;
+    end
+    set(handles.DDMethod,'Value',DDSMethodInd);
+end
+if isfield(Settings,'CalcDerivatives')
+    
+    set(handles.CalcDerivativesCheckBox, 'Value', Settings.CalcDerivatives)
+    CalcDerivativesCheckBox_Callback(handles.CalcDerivativesCheckBox, eventdata, handles)
+    
+end
+if ~isempty(Settings.NumSkipPts)
+    
+    set(handles.NumSkipPtsBox, 'String', Settings.NumSkipPts);
+    
+end
+if ~isempty(Settings.MisoTol)
+    
+    set(handles.MisoTolBox, 'String', Settings.MisoTol)
+    
+end
+if ~isempty(Settings.IQCutoff)
+    
+    set(handles.IQCutoffBox, 'String', Settings.IQCutoff)
+    
+end
+if ~isempty(Settings.FCalcMethod)
+    
+    FCalcMethod = Settings.FCalcMethod;
+    IndList = 1:length(FCalcMethodList);
+    SelectedFCalcMethodInd = IndList(strcmp(FCalcMethodList,FCalcMethod));
+    set(handles.FCalcMethodPopUp, 'Value', SelectedFCalcMethodInd);
+    
+end
+
+if ~isempty(Settings.IterationLimit)
+   set(handles.IterationLimitEdit,'String',num2str(Settings.IterationLimit));    
+end
+
+if ~isempty(Settings.StandardDeviation)
+    set(handles.StdDevEdit,'String',num2str(Settings.StandardDeviation))
+end
+
+if ~isempty(Settings.RefImageInd)
+    set(handles.RefImageIndEdit,'String',num2str(Settings.RefImageInd));
+end
+
+if ~isempty(Settings.GrainRefImageType)
+    
+    GrainRefImageType = Settings.GrainRefImageType;
+    IndList = 1:length(GrainRefImageTypeList);
+    SelectedGrainRefImageTypeInd = IndList(strcmp(GrainRefImageTypeList,GrainRefImageType));
+    set(handles.GrainRefTypePopUp, 'Value', SelectedGrainRefImageTypeInd);
+    if strcmp(GrainRefImageType,'IQ > Fit > CI')
+        set(handles.KernelAvgFilePathEdit, 'Enable', 'off');
+        set(handles.KernelAvgBrowseButton, 'Enable', 'off');
+    else
+        set(handles.KernelAvgFilePathEdit, 'Enable', 'on');
+        set(handles.KernelAvgBrowseButton, 'Enable', 'on');
+    end
+end
+
+if ~isempty(Settings.KernelAvgMisoPath)
+   set(handles.KernelAvgFilePathEdit, 'String', Settings.KernelAvgMisoPath);
+end
+
+
+%Read in first image, if that does not work, read in demo image
+Image = ReadEBSDImage(Settings.FirstImagePath, Settings.ImageFilter);
+if isempty(Image)
+    Image = ReadEBSDImage('demo.bmp', Settings.ImageFilter);
+end
+
+Material = ReadMaterial(curMaterial);
+Av = Settings.AccelVoltage*1000; %put it in eV from KeV
+sampletilt = Settings.SampleTilt;
+elevang = Settings.CameraElevation;
+pixsize = size(Image,1);
+disp(Settings.AngFilePath)
+[SquareFileVals ScanParams] = ReadAngFile(Settings.AngFilePath);
+paramspat={ScanParams.xstar;ScanParams.ystar;ScanParams.zstar;pixsize;Av;sampletilt;elevang;Material.Fhkl;Material.dhkl;Material.hkl};
+Angles(:,1) = SquareFileVals{1};
+Angles(:,2) = SquareFileVals{2};
+Angles(:,3) = SquareFileVals{3};
+g=euler2gmat(Angles(1,1),Angles(1,2),Angles(1,3));
+
+GenImage = genEBSDPatternHybrid(g,paramspat,eye(3),Material.lattice,Material.a1,Material.b1,Material.c1,Material.axs);
+GenImage = custimfilt(GenImage, Settings.ImageFilter(1), Settings.ImageFilter(2),Settings.ImageFilter(3),Settings.ImageFilter(4));
+handles.GenImage=GenImage;
+handles.Image = Image;
+handles.Settings = Settings;
+UpdateImageDisplay(handles,Settings.ImageFilter);
+% UpdateROIDisplay(handles,Settings.ImageFilter);
+axes(handles.OriginalImage);
+imagesc(imread(Settings.FirstImagePath))
+drawnow
+set(gca,'xcolor',get(gcf,'color'));
+set(gca,'ycolor',get(gcf,'color'));
+set(gca,'ytick',[]);
+set(gca,'xtick',[]);
+axis equal
+
+axes(handles.SimPat);
+imagesc(GenImage)
+drawnow
+set(gca,'xcolor',get(gcf,'color'));
+set(gca,'ycolor',get(gcf,'color'));
+set(gca,'ytick',[]);
+set(gca,'xtick',[]);
+axis equal
+% Choose default command line output for AdvancedSettings
+handles.output = hObject;
+
+% Update handles structure
+guidata(hObject, handles);
+% keyboard
+% UIWAIT makes AdvancedSettings wait for user response (see UIRESUME)
+% uiwait(handles.figure1);
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = AdvancedSettings_OutputFcn(hObject, eventdata, handles) 
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+
+
+% --- Executes on selection change in NumberROIsPopUp.
+function NumberROIsPopUp_Callback(hObject, eventdata, handles)
+% hObject    handle to NumberROIsPopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = get(hObject,'String') returns NumberROIsPopUp contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from NumberROIsPopUp
+% Update handles structure
+guidata(hObject, handles);
+% UpdateROIDisplay(handles);
+
+% --- Executes during object creation, after setting all properties.
+function NumberROIsPopUp_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to NumberROIsPopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+% --- Executes on selection change in ROISizePopUp.
+function ROISizePopUp_Callback(hObject, eventdata, handles)
+% hObject    handle to ROISizePopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = get(hObject,'String') returns ROISizePopUp contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from ROISizePopUp
+% Update handles structure
+guidata(hObject, handles);
+% UpdateROIDisplay(handles);
+
+% --- Executes during object creation, after setting all properties.
+function ROISizePopUp_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ROISizePopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+% --- Executes on selection change in HROIMMethodPopUp.
+function HROIMMethodPopUp_Callback(hObject, eventdata, handles)
+% hObject    handle to HROIMMethodPopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = get(hObject,'String') returns HROIMMethodPopUp contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from HROIMMethodPopUp
+HROIMMethodList = get(hObject,'String');
+Ind = get(hObject,'Value');
+HROIMMethod = HROIMMethodList(Ind);
+
+if ~strcmp(HROIMMethod,'Simulated') %Either type of Real
+    
+    GrainRefTypeList = get(handles.GrainRefTypePopUp,'String');
+    GrainRefType = GrainRefTypeList(get(handles.GrainRefTypePopUp,'Value'));
+    if strcmp(GrainRefType, 'Min Kernel Avg Miso')
+        set(handles.KernelAvgFilePathEdit,'Enable','on');
+        set(handles.KernelAvgBrowseButton,'Enable','on');
+    end
+    set(handles.GrainRefTypePopUp,'Enable','on');
+    set(handles.IterationLimitEdit,'Enable','off');
+    set(handles.IterationLimitEdit,'Visible','off');
+    set(handles.IterationLabel,'Visible','off');
+    set(handles.RefImageIndLabel,'Visible','on');
+    if strcmp(HROIMMethod,'Real-Single Ref')
+        set(handles.RefImageIndEdit,'Enable','on');
+        set(handles.RefImageIndEdit,'Visible','on');
+    else
+        set(handles.RefImageIndEdit,'Enable','off');
+        set(handles.RefImageIndEdit,'Visible','on');
+    end
+else %Simulated
+    set(handles.GrainRefTypePopUp,'Enable','off');
+    set(handles.KernelAvgFilePathEdit,'Enable','off');
+    set(handles.KernelAvgBrowseButton,'Enable','off');
+    set(handles.RefImageIndLabel,'Visible','off')
+    set(handles.IterationLimitEdit,'Enable','on');
+    set(handles.IterationLimitEdit,'Visible','on');
+    set(handles.IterationLabel,'Visible','on');
+    set(handles.RefImageIndEdit,'Enable','off');
+    set(handles.RefImageIndEdit,'Visible','off');
+end
+
+% --- Executes during object creation, after setting all properties.
+function HROIMMethodPopUp_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to HROIMMethodPopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+% --- Executes on selection change in ROIStylePopUp.
+function ROIStylePopUp_Callback(hObject, eventdata, handles)
+% hObject    handle to ROIStylePopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = get(hObject,'String') returns ROIStylePopUp contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from ROIStylePopUp
+guidata(hObject, handles);
+% UpdateROIDisplay(handles);
+StyleList = get(hObject,'String');
+Ind = get(hObject,'Value');
+ROIStyle = StyleList{Ind};
+if strcmp(ROIStyle,'Grid')
+        
+       set(handles.NumberROIsPopUp,'Enable','off');
+%        set(handles.ROISizeEdit,'Enable','off');
+else
+        set(handles.NumberROIsPopUp,'Enable','on');
+%        set(handles.ROISizeEdit,'Enable','off');
+end
+if strcmp(ROIStyle,'Intensity')
+   set(handles.ROIFilterEdit1,'Enable','off');
+   set(handles.ROIFilterEdit2,'Enable','off');
+   set(handles.ROIFilterEdit3,'Enable','off');
+   set(handles.ROIFilterEdit4,'Enable','off');
+else    
+   set(handles.ROIFilterEdit1,'Enable','on');
+   set(handles.ROIFilterEdit2,'Enable','on');
+   set(handles.ROIFilterEdit3,'Enable','on');
+   set(handles.ROIFilterEdit4,'Enable','on');
+end
+
+
+% --- Executes during object creation, after setting all properties.
+function ROIStylePopUp_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ROIStylePopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function IterationLimitEdit_Callback(hObject, eventdata, handles)
+% hObject    handle to IterationLimitEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of IterationLimitEdit as text
+%        str2double(get(hObject,'String')) returns contents of IterationLimitEdit as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function IterationLimitEdit_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to IterationLimitEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+% --- Executes on selection change in FCalcMethodPopUp.
+function FCalcMethodPopUp_Callback(hObject, eventdata, handles)
+% hObject    handle to FCalcMethodPopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = get(hObject,'String') returns FCalcMethodPopUp contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from FCalcMethodPopUp
+
+
+% --- Executes during object creation, after setting all properties.
+function FCalcMethodPopUp_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to FCalcMethodPopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+function KernelAvgFilePathEdit_Callback(hObject, eventdata, handles)
+% hObject    handle to KernelAvgFilePathEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of KernelAvgFilePathEdit as text
+%        str2double(get(hObject,'String')) returns contents of KernelAvgFilePathEdit as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function KernelAvgFilePathEdit_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to KernelAvgFilePathEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+% --- Executes on button press in KernelAvgBrowseButton.
+function KernelAvgBrowseButton_Callback(hObject, eventdata, handles)
+% hObject    handle to KernelAvgBrowseButton (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+[picname picpath] = uigetfile('*.txt','OIM Map Data');
+set(handles.KernelAvgFilePathEdit,'String', [picpath picname]);
+
+
+
+% --- Executes on button press in SaveAndCloseButton.
+function SaveAndCloseButton_Callback(hObject, eventdata, handles)
+% hObject    handle to SaveAndCloseButton (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+%Read in all items relevant to Settings and save them to a .mat file
+Settings = handles.Settings;
+
+Settings.ROISizePercent = str2double(get(handles.ROISizeEdit,'String'));
+
+Settings.NumROIs = get(handles.NumberROIsPopUp,'Value');
+
+ROIStyleList = get(handles.ROIStylePopUp,'String');
+StyleInd = get(handles.ROIStylePopUp,'Value');
+Settings.ROIStyle = ROIStyleList{StyleInd};
+
+ImageFilterTypeList = get(handles.ImageFilterType,'String');
+TypeInd = get(handles.ImageFilterType,'Value');
+Settings.ImageFilterType = ImageFilterTypeList{TypeInd};
+
+ROIFilt(1) = str2double(get(handles.ROIFilterEdit1,'String'));
+ROIFilt(2) = str2double(get(handles.ROIFilterEdit2,'String'));
+ROIFilt(3) = str2double(get(handles.ROIFilterEdit3,'String'));
+ROIFilt(4) = str2double(get(handles.ROIFilterEdit4,'String'));
+Settings.ROIFilter = ROIFilt;
+
+ImageFilt(1) = str2double(get(handles.ImageFilterEdit1,'String'));
+ImageFilt(2) = str2double(get(handles.ImageFilterEdit2,'String'));
+ImageFilt(3) = str2double(get(handles.ImageFilterEdit3,'String'));
+ImageFilt(4) = str2double(get(handles.ImageFilterEdit4,'String'));
+Settings.ImageFilter = ImageFilt;
+
+HROIMMethodList = get(handles.HROIMMethodPopUp,'String');
+MethodInd = get(handles.HROIMMethodPopUp,'Value');
+switch HROIMMethodList{MethodInd}
+    case 'Simulated'
+        Settings.HROIMMethod = HROIMMethodList{MethodInd};
+        Settings.RefImageInd = 0;
+    case 'Real-Grain Ref'
+        Settings.HROIMMethod = 'Real';
+        Settings.RefImageInd = 0;
+    case 'Real-Single Ref'
+        Settings.HROIMMethod = 'Real';
+        Settings.RefImageInd = str2double(get(handles.RefImageIndEdit,'String'));
+end
+
+%Derivatives Settings
+Settings.CalcDerivatives = get(handles.CalcDerivativesCheckBox, 'Value');
+Settings.NumSkipPts = get(handles.NumSkipPtsBox, 'String');
+Settings.MisoTol = str2double(get(handles.MisoTolBox, 'String'));
+Settings.IQCutoff = str2double(get(handles.IQCutoffBox, 'String'));
+Settings.DoDDS = get(handles.SplitDD, 'Value');
+DDSMethodList = get(handles.DDMethod, 'String');
+MethodInd = get(handles.DDMethod, 'Value');
+switch DDSMethodList{MethodInd}
+    case 'Nye-Kroner'
+        Settings.DDSMethod = 1;
+    case 'Nye-Kroner (Pantleon)'
+        Settings.DDSMethod = 9;
+    case 'Distortion Matching'
+        Settings.DDSMethod = 2;
+end
+
+Limit = uint8(str2num(get(handles.IterationLimitEdit,'String')));
+if isinteger(Limit) && Limit > 0
+    Settings.IterationLimit = Limit;
+else
+    errordlg('Iteration limit can only be a positive integer','Doy');
+    return;
+end
+
+StdDev = double(str2num(get(handles.StdDevEdit,'String')));
+if StdDev > 0
+    Settings.StandardDeviation = StdDev;
+else
+    errordlg('Standard deviation can only be a positive number','Warning');
+    return;
+end
+
+
+FCalcList = get(handles.FCalcMethodPopUp,'String');
+FCalcInd = get(handles.FCalcMethodPopUp,'Value');
+Settings.FCalcMethod = FCalcList{FCalcInd};
+
+GrainRefTypeList = get(handles.GrainRefTypePopUp,'String');
+GrRefId = get(handles.GrainRefTypePopUp,'Value');
+Settings.GrainRefImageType = GrainRefTypeList{GrRefId};
+
+Settings.KernelAvgMisoPath = get(handles.KernelAvgFilePathEdit,'String');
+
+save('Settings.mat','Settings');
+% keyboard
+delete(handles.figure1);
+
+function ImageFilterEdit1_Callback(hObject, eventdata, handles)
+% hObject    handle to ImageFilterEdit1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% Hints: get(hObject,'String') returns contents of ImageFilterEdit1 as text
+%        str2double(get(hObject,'String')) returns contents of ImageFilterEdit1 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function ImageFilterEdit1_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ImageFilterEdit1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function ImageFilterEdit2_Callback(hObject, eventdata, handles)
+% hObject    handle to ImageFilterEdit2 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% Hints: get(hObject,'String') returns contents of ImageFilterEdit2 as text
+%        str2double(get(hObject,'String')) returns contents of ImageFilterEdit2 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function ImageFilterEdit2_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ImageFilterEdit2 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function ImageFilterEdit3_Callback(hObject, eventdata, handles)
+% hObject    handle to ImageFilterEdit3 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% Hints: get(hObject,'String') returns contents of ImageFilterEdit3 as text
+%        str2double(get(hObject,'String')) returns contents of ImageFilterEdit3 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function ImageFilterEdit3_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ImageFilterEdit3 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function ImageFilterEdit4_Callback(hObject, eventdata, handles)
+% hObject    handle to ImageFilterEdit4 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% Hints: get(hObject,'String') returns contents of ImageFilterEdit4 as text
+%        str2double(get(hObject,'String')) returns contents of ImageFilterEdit4 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function ImageFilterEdit4_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ImageFilterEdit4 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+% --- Executes on selection change in GrainRefTypePopUp.
+function GrainRefTypePopUp_Callback(hObject, eventdata, handles)
+% hObject    handle to GrainRefTypePopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = get(hObject,'String') returns GrainRefTypePopUp contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from GrainRefTypePopUp
+HROIMMethodList = get(handles.HROIMMethodPopUp,'String');
+HROIMMethod = HROIMMethodList(get(handles.HROIMMethodPopUp,'Value'));
+GrainRefTypeList = get(hObject,'String');
+GrainRefType = GrainRefTypeList(get(hObject,'Value'));
+if and(~strcmp(HROIMMethod,'Simulated'), (strcmp(GrainRefType,'Min Kernel Avg Miso')))
+    set(handles.KernelAvgFilePathEdit,'Enable','on');
+    set(handles.KernelAvgBrowseButton,'Enable','on');
+else
+    set(handles.KernelAvgFilePathEdit,'Enable','off');
+    set(handles.KernelAvgBrowseButton,'Enable','off');
+end
+
+% --- Executes during object creation, after setting all properties.
+function GrainRefTypePopUp_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to GrainRefTypePopUp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function ROIFilterEdit1_Callback(hObject, eventdata, handles)
+% hObject    handle to ROIFilterEdit1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of ROIFilterEdit1 as text
+%        str2double(get(hObject,'String')) returns contents of ROIFilterEdit1 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function ROIFilterEdit1_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ROIFilterEdit1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function ROIFilterEdit2_Callback(hObject, eventdata, handles)
+% hObject    handle to ROIFilterEdit2 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of ROIFilterEdit2 as text
+%        str2double(get(hObject,'String')) returns contents of ROIFilterEdit2 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function ROIFilterEdit2_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ROIFilterEdit2 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function ROIFilterEdit3_Callback(hObject, eventdata, handles)
+% hObject    handle to ROIFilterEdit3 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of ROIFilterEdit3 as text
+%        str2double(get(hObject,'String')) returns contents of ROIFilterEdit3 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function ROIFilterEdit3_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ROIFilterEdit3 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function ROIFilterEdit4_Callback(hObject, eventdata, handles)
+% hObject    handle to ROIFilterEdit4 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of ROIFilterEdit4 as text
+%        str2double(get(hObject,'String')) returns contents of ROIFilterEdit4 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function ROIFilterEdit4_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ROIFilterEdit4 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function ROISizeEdit_Callback(hObject, eventdata, handles)
+% hObject    handle to ROISizeEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of ROISizeEdit as text
+%        str2double(get(hObject,'String')) returns contents of ROISizeEdit as a double
+guidata(hObject, handles);
+% UpdateROIDisplay(handles);
+
+
+% --- Executes during object creation, after setting all properties.
+function ROISizeEdit_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ROISizeEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function StdDevEdit_Callback(hObject, eventdata, handles)
+% hObject    handle to StdDevEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of StdDevEdit as text
+%        str2double(get(hObject,'String')) returns contents of StdDevEdit as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function StdDevEdit_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to StdDevEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+% --- Executes on button press in RefreshImage.
+function RefreshImage_Callback(hObject, eventdata, handles)
+% hObject    handle to RefreshImage (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+guidata(hObject, handles);
+ImageFilt(1) = str2double(get(handles.ImageFilterEdit1,'String'));
+ImageFilt(2) = str2double(get(handles.ImageFilterEdit2,'String'));
+ImageFilt(3) = str2double(get(handles.ImageFilterEdit3,'String'));
+ImageFilt(4) = str2double(get(handles.ImageFilterEdit4,'String'));
+UpdateImageDisplay(handles,ImageFilt)
+
+% --- Executes on button press in Help.
+function Help_Callback(hObject, eventdata, handles)
+% hObject    handle to Help (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% --- Executes on selection change in ImageFilterType.
+function ImageFilterType_Callback(hObject, eventdata, handles)
+% hObject    handle to ImageFilterType (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = cellstr(get(hObject,'String')) returns ImageFilterType contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from ImageFilterType
+ImageFilterTypeList = get(hObject,'String');
+Ind = get(hObject,'Value');
+handles.ImageFilterType=ImageFilterTypeList(Ind);
+disp(ImageFilterTypeList(Ind))
+if strcmp(ImageFilterTypeList(Ind),'localthresh')
+
+    set(handles.ImageFilterEdit1,'Enable','off');
+    set(handles.ImageFilterEdit2,'Enable','off');
+    set(handles.ImageFilterEdit3,'Enable','off');
+    set(handles.ImageFilterEdit4,'Enable','off');
+else
+   
+    set(handles.ImageFilterEdit1,'Enable','on');
+    set(handles.ImageFilterEdit2,'Enable','on');
+    set(handles.ImageFilterEdit3,'Enable','on');
+    set(handles.ImageFilterEdit4,'Enable','on');
+end
+
+% --- Executes during object creation, after setting all properties.
+function ImageFilterType_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to ImageFilterType (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+% --- Executes on button press in RefreshROIs.
+function RefreshROIs_Callback(hObject, eventdata, handles)
+% hObject    handle to RefreshROIs (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+guidata(hObject, handles);
+ImageFilt(1) = str2double(get(handles.ImageFilterEdit1,'String'));
+ImageFilt(2) = str2double(get(handles.ImageFilterEdit2,'String'));
+ImageFilt(3) = str2double(get(handles.ImageFilterEdit3,'String'));
+ImageFilt(4) = str2double(get(handles.ImageFilterEdit4,'String'));
+UpdateROIDisplay(handles,ImageFilt)
+
+
+% --- Executes during object creation, after setting all properties.
+function OriginalImage_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to OriginalImage (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: place code in OpeningFcn to populate OriginalImage
+
+
+% --- Executes during object creation, after setting all properties.
+function SimPat_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to SimPat (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: place code in OpeningFcn to populate SimPat
+
+
+% --- Executes during object creation, after setting all properties.
+function FilteredImage_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to FilteredImage (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: place code in OpeningFcn to populate FilteredImage
+
+
+% --- Executes on button press in CalcDerivativesCheckBox.
+function CalcDerivativesCheckBox_Callback(hObject, eventdata, handles)
+% hObject    handle to CalcDerivativesCheckBox (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of CalcDerivativesCheckBox
+value = get(hObject, 'Value');
+if value == 0
+    set(handles.NumSkipPtsBox, 'Enable', 'off');
+    set(handles.MisoTolBox, 'Enable', 'off');
+    set(handles.IQCutoffBox, 'Enable', 'off');
+    set(handles.SplitDD, 'Enable', 'off');
+    set(handles.SplitDD, 'Value', 0);
+elseif value == 1
+    set(handles.NumSkipPtsBox, 'Enable', 'on');
+    set(handles.MisoTolBox, 'Enable', 'on');
+    set(handles.IQCutoffBox, 'Enable', 'on');
+    set(handles.SplitDD, 'Enable', 'on');
+end
+SplitDD_Callback(handles.SplitDD, eventdata, handles);
+
+
+
+function NumSkipPtsBox_Callback(hObject, eventdata, handles)
+% hObject    handle to NumSkipPtsBox (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of NumSkipPtsBox as text
+%        str2double(get(hObject,'String')) returns contents of NumSkipPtsBox as a double
+
+%Input validation
+Settings = handles.Settings;
+UserInput = get(hObject,'String');
+if isempty(str2num(UserInput))
+    if ~strcmp(UserInput, 'a') && ~strcmp(UserInput, 't')
+        set(hObject, 'String', Settings.NumSkipPts);
+        warndlg('Input must be numerical, "a" or "t"');
+    end
+elseif str2double(UserInput) < 0
+    set(hObject, 'String', Settings.NumSkipPts);
+    warndlg('Input must be positive');
+else
+    set(hObject, 'String', round(str2double(UserInput)));
+end
+    
+%Updates handles object
+guidata(hObject, handles);
+
+
+% --- Executes during object creation, after setting all properties.
+function NumSkipPtsBox_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to NumSkipPtsBox (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function MisoTolBox_Callback(hObject, eventdata, handles)
+% hObject    handle to MisoTolBox (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of MisoTolBox as text
+%        str2double(get(hObject,'String')) returns contents of MisoTolBox as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function MisoTolBox_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to MisoTolBox (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+function IQCutoffBox_Callback(hObject, eventdata, handles)
+% hObject    handle to IQCutoffBox (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of IQCutoffBox as text
+%        str2double(get(hObject,'String')) returns contents of IQCutoffBox as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function IQCutoffBox_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to IQCutoffBox (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+function RefImageIndEdit_Callback(hObject, eventdata, handles)
+% hObject    handle to RefImageIndEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of RefImageIndEdit as text
+%        str2double(get(hObject,'String')) returns contents of RefImageIndEdit as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function RefImageIndEdit_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to RefImageIndEdit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+% --- Executes on button press in skippointshelp.
+function skippointshelp_Callback(hObject, eventdata, handles)
+% hObject    handle to skippointshelp (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+SkipPointsHelp();
+
+
+% --- Executes on button press in SplitDD.
+function SplitDD_Callback(hObject, eventdata, handles)
+% hObject    handle to SplitDD (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of SplitDD
+valid = 0;
+j = 1;
+for i = 1:length(handles.allMaterials)
+    M = ReadMaterial(handles.allMaterials{i});
+    if isfield(M,'SplitDD')
+        valid = 1;
+    else
+        valid = 0;
+        invalidInd(j) = i;
+        j = j + 1;
+    end
+end
+
+if get(hObject,'Value') == 1
+    if valid
+        set(handles.DDMethod, 'Enable', 'on');
+    else
+        warndlg(['Split Dislocation data not available for ' handles.allMaterials{invalidInd(1)}],'OpenXY');
+        set(hObject,'Value',0);
+        set(handles.DDMethod, 'Enable', 'off');
+    end
+else
+    set(hObject,'Value',0);
+    set(handles.DDMethod, 'Enable', 'off');
+end
+
+% --- Executes on selection change in DDMethod.
+function DDMethod_Callback(hObject, eventdata, handles)
+% hObject    handle to DDMethod (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = cellstr(get(hObject,'String')) returns DDMethod contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from DDMethod
+
+
+% --- Executes during object creation, after setting all properties.
+function DDMethod_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to DDMethod (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end