wss_gui.m

function varargout = wss_gui(varargin)
% WSS_GUI M-file for wss_gui.fig
%      WSS_GUI, by itself, creates a new WSS_GUI or raises the existing
%      singleton*.
%
%      H = WSS_GUI returns the handle to a new WSS_GUI or the handle to
%      the existing singleton*.
%
%      WSS_GUI('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in WSS_GUI.M with the given input arguments.
%
%      WSS_GUI('Property','Value',...) creates a new WSS_GUI or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before wss_gui_OpeningFunction gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to wss_gui_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

% Copyright 2002-2003 The MathWorks, Inc.

% Edit the above text to modify the response to help wss_gui

% Last Modified by GUIDE v2.5 27-Jun-2017 08:59:03

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
    'gui_Singleton',  gui_Singleton, ...
    'gui_OpeningFcn', @wss_gui_OpeningFcn, ...
    'gui_OutputFcn',  @wss_gui_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 wss_gui is made visible.
function wss_gui_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 wss_gui (see VARARGIN)

% Choose default command line output for wss_gui
handles.output = hObject;

%%Load Velocity Data%%%%%%%%%%
if numel(varargin)==0
    [wss_file,pathname] = uigetfile({'*.mat'},'Select WSS Input File');
    load(fullfile(pathname,wss_file));
    
    set(handles.box_filename,'String',wss_file);
else
    save('WSS_Input.mat','varargin');
end
handles.MAG= varargin{1};
handles.VX = varargin{2};
handles.VY = varargin{3};
handles.VZ = varargin{4};

handles.VXt = varargin{5};
handles.VYt = varargin{6};
handles.VZt = varargin{7};

handles.CD = varargin{8};
handles.MASK=varargin{9};
handles.STL_MASK=varargin{10};
handles.delX = varargin{11};
handles.delY = varargin{12};
handles.delZ = varargin{13};
handles.delT = varargin{14};


handles.norm_handle =[];
handles.wss_axis = 11;


handles.avg_wss_mean = 0;
handles.avg_wss_std = 0;
handles.avg_wss_med = 0;
handles.avg_wss_lq = 0;
handles.avg_wss_uq =0;
handles.wss_mean = 0;
handles.wss_std = 0;
handles.wss_med = 0;
handles.wss_lq = 0;
handles.wss_uq =0;
handles.osi_mean = 0;
handles.osi_std = 0;
handles.osi_med = 0;
handles.osi_lq = 0;
handles.osi_uq = 0;

handles.average_velocity = 0;
handles.volume = 0;
handles.kinetic_energy = 0;
handles.visc_energy_loss = 0;


% Setup volume to select
count =1;
handles.mask_type_key(1) = 0;
handles.mask_type_pos(1) = 1;
voptions = {'PC-MRA'};
for pos = 1:numel(handles.MAG)
    voptions{end+1} = handles.MAG{pos}.Name;
    count = count +1;
    handles.mask_type_key(count) = 1; %MAG
    handles.mask_type_pos(count) = pos;
    
end
noptions = voptions;

for pos = 1:numel(handles.STL_MASK)
    voptions{end+1} = handles.STL_MASK{pos}.Name;
    count = count +1;
    handles.mask_type_key(count) = 2; %STL
    handles.mask_type_pos(count) = pos;
end
set(handles.mask_type,'String',voptions);

noptions{end+1} = 'Base on Mask';
set(handles.normal_type,'String',noptions);



% Surface plot types
vtype_options = {'Avg WSS','OSI','Time Resolved WSS'};
for pos = 1:numel(handles.MAG)
    vtype_options{end+1} = handles.MAG{pos}.Name;
end
set(handles.visual_type,'String',vtype_options);




% volume to select
count =1;
handles.volume_type_key(1) = 0;
handles.volume_type_pos(1) = 1;
voptions = {'PC-MRA'};
for pos = 1:numel(handles.MAG)
    voptions{end+1} = handles.MAG{pos}.Name;
    count = count +1;
    handles.volume_type_key(count) = 1; %MAG
    handles.volume_type_pos(count) = pos;
end
for pos = 1:numel(handles.MASK)
    voptions{end+1} = handles.MASK{pos}.Name;
    count = count +1;
    handles.volume_type_key(count) = 2; %MASK
    handles.volume_type_pos(count) = pos;
end
set(handles.volume_type,'String',voptions);


% Update handles structure
guidata(hObject, handles);

% UIWAIT makes wss_gui wait for user response (see UIRESUME)
% uiwait(handles.figure1);


% --- Outputs from this function are returned to the command line.
function varargout = wss_gui_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;

function update_mask(hObject,handles)

mask_type = get(handles.mask_type,'Value');
%%%VISUAL METHOD DECODING
%   1 = CD
%   2 = MAG
%   3 = STL
vis_thresh = str2double(get(handles.lumen_thresh,'String'));

new_fig = ishandle(handles.wss_axis);
figobj = figure(handles.wss_axis);

if new_fig == 1
    cmpos = campos;
    cmva  = camva;
    zoom reset
end

set(gca,'CameraPositionMode','manual');
set(gca,'CameraTargetMode','manual');
set(gca,'CameraUpVectorMode','manual');
set(gca,'CameraViewAngleMode','manual');
clf;
hold on

if handles.mask_type_key(mask_type) == 0
    VOL = handles.CD;
    hpatch = patch(isosurface(VOL,vis_thresh*max(VOL(:)) ) );
    fv = isosurface(VOL,vis_thresh*max(VOL(:)));
    disp(['CD X:',num2str(min(fv.vertices(:,1))),' to ',num2str(max(fv.vertices(:,1)))]);
    disp(['CD Y:',num2str(min(fv.vertices(:,2))),' to ',num2str(max(fv.vertices(:,2)))]);
    disp(['CD Z:',num2str(min(fv.vertices(:,3))),' to ',num2str(max(fv.vertices(:,3)))]);
    isonormals(VOL,hpatch)
    
elseif handles.mask_type_key(mask_type) == 1
    VOL = handles.MAG{handles.mask_type_pos(mask_type)}.Volume;
    hpatch = patch(isosurface(VOL,vis_thresh*max(VOL(:)) ) );
    isonormals(VOL,hpatch)
else
    vis_thresh = 0.5;
    VOL = handles.CD;
    
    fv = handles.STL_MASK{handles.mask_type_pos(mask_type)};
    
    hpatch = patch('Faces',fv.faces,'Vertices',fv.vertices);
    
    disp(['STL X:',num2str(min(fv.vertices(:,1))),' to ',num2str(max(fv.vertices(:,1)))]);
    disp(['STL Y:',num2str(min(fv.vertices(:,2))),' to ',num2str(max(fv.vertices(:,2)))]);
    disp(['STL Z:',num2str(min(fv.vertices(:,3))),' to ',num2str(max(fv.vertices(:,3)))]);
end

set(hpatch,'FaceColor','red','EdgeColor', 'none');
colormap('parula');
%reducepatch(hpatch,0.4);

c = camlight('headlight');

f2 = @(varargin) camlight(c,'headlight');
set(figobj, 'WindowButtonMotionFcn', f2);

material('dull');
lighting gouraud
alpha(0.9)
set(handles.wss_axis, 'Renderer','OpenGL')
set(handles.wss_axis, 'RendererMode','Manual');
set(gca,'color','w');
set(gcf,'color','black');
daspect([1 1 1])

if new_fig ==1
    campos([cmpos]);
    camva([cmva]);
end

if(new_fig==0)
    view([-1 -1 0]);
    zoom(0.8);
    %xlim([1 (m_ylength)]);
    %ylim([1 (m_xlength)]);
    %zlim([1 (m_zlength)]);
    scrsz = get(0,'ScreenSize');
    SIZE=[(scrsz(3)*1/2-64) scrsz(4)*1/4 scrsz(3)*1/2 scrsz(4)*1/2];
    set(gcf,'Position',SIZE);
    set(gcf,'Name','WSS Window');
end

axis equal tight off vis3d;
handles.hpatch_wall = hpatch;

% Update handles structure
guidata(hObject, handles);

% Update Normals
handles = guidata(hObject);
update_norms(hObject, handles);

% Update the Volume
handles = guidata(hObject);
update_volume(hObject, handles);


function update_volume(hObject,handles)

% Grab the index
volume_type = get(handles.volume_type,'Value');
volume_thresh = str2double(get(handles.volume_thresh,'String'));

if handles.volume_type_key(volume_type) == 0
    handles.VOLUME_MASK = handles.CD > volume_thresh*max( handles.CD(:));
elseif handles.volume_type_key(volume_type) == 1
    VOL = handles.MAG{handles.volume_type_pos(volume_type)}.Volume;
    handles.VOLUME_MASK = handles.CD > volume_thresh*max( handles.CD(:));
else
    handles.VOLUME_MASK = handles.MASK{handles.volume_type_pos(volume_type)}.Volume;
end

% Update handles structure
guidata(hObject, handles);

function lumen_thresh_Callback(hObject, eventdata, handles)
% hObject    handle to lumen_thresh (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 lumen_thresh as text
%        str2double(get(hObject,'String')) returns contents of lumen_thresh as a double
update_mask(hObject,handles);

% --- Executes during object creation, after setting all properties.
function lumen_thresh_CreateFcn(hObject, eventdata, handles)
% hObject    handle to lumen_thresh (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 mask_type.
function mask_type_Callback(hObject, eventdata, handles)
% hObject    handle to mask_type (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 mask_type contents as cell array
%        contents{get(hObject,'Value')} returns selected item from mask_type
update_mask(hObject,handles);

% --- Executes during object creation, after setting all properties.
function mask_type_CreateFcn(hObject, eventdata, handles)
% hObject    handle to mask_type (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 normal_type.
function normal_type_Callback(hObject, eventdata, handles)
% hObject    handle to normal_type (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 normal_type contents as cell array
%        contents{get(hObject,'Value')} returns selected item from normal_type
update_mask(hObject,handles);


% --- Executes during object creation, after setting all properties.
function normal_type_CreateFcn(hObject, eventdata, handles)
% hObject    handle to normal_type (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 normal_plot_type.
function normal_plot_type_Callback(hObject, eventdata, handles)
% hObject    handle to normal_plot_type (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 normal_plot_type contents as cell array
%        contents{get(hObject,'Value')} returns selected item from normal_plot_type
update_mask(hObject,handles);

% --- Executes during object creation, after setting all properties.
function normal_plot_type_CreateFcn(hObject, eventdata, handles)
% hObject    handle to normal_plot_type (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 update_norms(hObject,handles)

normal_type = get(handles.normal_type,'Value');
%%%VISUAL METHOD DECODING
%   3 = base on vector
%   1 = base on data mag
%   2 = base on data cd
norm_plot_type= get(handles.normal_plot_type,'Value');


new_fig = ishandle(handles.wss_axis);
h = figure(handles.wss_axis);
cameratoolbar(h,'Show')

if normal_type == 1
    isonormals(handles.CD,handles.hpatch_wall)
elseif handles.mask_type_key(normal_type) == 1
    isonormals(handles.MAG{handles.mask_type_pos(normal_type)}.Volume,handles.hpatch_wall)
end

if handles.mask_type_key(normal_type) == 2  
    disp('Computing STL vertex normals');
    mask_type = get(handles.mask_type,'Value');
    [vn]=patchnormals(handles.STL_MASK{handles.mask_type_pos(mask_type)});
    
    set(handles.hpatch_wall,'VertexNormals',vn);
    size(vn)
end
   
norms = (get(handles.hpatch_wall,'VertexNormals'));
    size(norms)
verts = (get(handles.hpatch_wall,'Vertices'));

% Normalize the normals
norm_mag = sqrt( sum(norms.^2,2));
norms(:,1) = norms(:,1)./norm_mag;
norms(:,2) = norms(:,2)./norm_mag;
norms(:,3) = norms(:,3)./norm_mag;

scl = 5;
if norm_plot_type == 1
    if ishandle(handles.norm_handle) delete(handles.norm_handle); end
elseif norm_plot_type ==2
    if ishandle(handles.norm_handle) delete(handles.norm_handle); end
    handles.norm_handle = plot3( [verts(:,1)  verts(:,1) + scl*norms(:,1)]',[verts(:,2) verts(:,2)+scl*norms(:,2)]',[verts(:,3)  verts(:,3) + scl*norms(:,3)]','b','LineWidth',1.5);
elseif norm_plot_type == 3;
    if normal_type == 2
        handles.norm_handle = plot3( [verts(:,1)  verts(:,1) + scl*norms(:,1)]',[verts(:,2) verts(:,2)+scl*norms(:,2)]',[verts(:,3)  verts(:,3) + scl*norms(:,3)]','b','LineWidth',1.5);
    elseif normal_type ==3
        handles.norm_handle = plot3( [verts(:,1)  verts(:,1) + scl*norms(:,1)]',[verts(:,2) verts(:,2)+scl*norms(:,2)]',[verts(:,3)  verts(:,3) + scl*norms(:,3)]','g','LineWidth',1.5);
    end
end

handles.verts = verts;
handles.norms = norms;

% Update handles structure
guidata(hObject, handles);


function N = patchnormals(FV) 
%Vertex normals of a triangulated mesh, area weighted, left-hand-rule 
% N = patchnormals(FV) -struct with fields, faces Nx3 and vertices Mx3 
%N: vertex normals as Mx3
%face corners index 
A = FV.faces(:,1); 
B = FV.faces(:,2); 
C = FV.faces(:,3);
%face normals 
n = cross(FV.vertices(A,:)-FV.vertices(B,:),FV.vertices(C,:)-FV.vertices(A,:)); %area weighted
%vertice normals 
N = zeros(size(FV.vertices)); %init vertix normals 
for i = 1:size(FV.faces,1) %step through faces (a vertex can be reference any number of times) 
N(A(i),:) = N(A(i),:)+n(i,:); %sum face normals 
N(B(i),:) = N(B(i),:)+n(i,:); 
N(C(i),:) = N(C(i),:)+n(i,:); 
end


function viscosity_value_Callback(hObject, eventdata, handles)
% hObject    handle to viscosity_value (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 viscosity_value as text
%        str2double(get(hObject,'String')) returns contents of viscosity_value as a double


% --- Executes during object creation, after setting all properties.
function viscosity_value_CreateFcn(hObject, eventdata, handles)
% hObject    handle to viscosity_value (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 wss_update.
function wss_update_Callback(hObject, eventdata, handles)
% hObject    handle to wss_update (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

update_wss(hObject,handles,0);


function update_wss(hObject,handles, time_update)

handles

visc = str2double(get(handles.viscosity_value,'String'));
poly_num = str2num(get(handles.poly_num,'String'));
poly_order = str2num(get(handles.poly_order,'String'));
color_range = str2num(get(handles.color_range,'String'))/100;

del = 0.01; %0.0001;
conv = ( visc/1000 ) * ( 1 / 1000 ) / ( handles.delX / 1000 );

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%          TIME RESOLVED WSS UPDATE                    %%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

for time = 1:size(handles.VXt,4)
    
    set(handles.status_text,'String',['Updating time point ',num2str(time)]);
    drawnow
    
    %%%%%%GET VELOCITY POSITIONS%%%%%
    for pos=1:size(handles.verts,1)
        norm_size= sqrt( handles.norms(pos,1).^2 + handles.norms(pos,2).^2 + handles.norms( pos,3).^2);
        handles.norms(pos,1) = handles.norms(pos,1)/norm_size;
        handles.norms(pos,2) = handles.norms(pos,2)/norm_size;
        handles.norms(pos,3) = handles.norms(pos,3)/norm_size;
        
        for poly_pos = 1:poly_num
            
            py = handles.verts(pos,1)- (poly_pos -1.0)*handles.norms(pos,1);
            px = handles.verts(pos,2)- (poly_pos -1.0)*handles.norms(pos,2);
            pz = handles.verts(pos,3)- (poly_pos -1.0)*handles.norms(pos,3);
            
            vx_wss(pos,poly_pos) = lin3dt(handles.VXt,time,px,py,pz);
            vy_wss(pos,poly_pos) = lin3dt(handles.VYt,time,px,py,pz);
            vz_wss(pos,poly_pos) = lin3dt(handles.VZt,time,px,py,pz);
        end
        vx_wss(pos,1) = 0;
        vy_wss(pos,1) = 0;
        vz_wss(pos,1) = 0;
    end
    
    %%%%%%%%%NOW GET WSS%%%%%%%%
    for pos=1:size(handles.verts,1)
        fit_vx = polyfit(1:poly_num,vx_wss(pos,:),poly_order);
        fit_vy = polyfit(1:poly_num,vy_wss(pos,:),poly_order);
        fit_vz = polyfit(1:poly_num,vz_wss(pos,:),poly_order);
        
        vxwall = polyval(fit_vx,1);
        vywall = polyval(fit_vy,1);
        vzwall = polyval(fit_vz,1);
        
        vxplus = polyval(fit_vx,1+del);
        vyplus = polyval(fit_vy,1+del);
        vzplus = polyval(fit_vz,1+del);
        
        vplus = [vxplus vyplus vzplus]; %- (sum([vxplus vyplus vzplus].*[norm(pos,2) norm(pos,1) norm(3,pos)]))*[norm(pos,2) norm(pos,1) norm(3,pos)]
        vwall = [vxwall vywall vzwall]; %- (sum([vxwall vywall vzwall].*[norm(pos,2) norm(pos,1) norm(3,pos)]))*[norm(pos,2) norm(pos,1) norm(3,pos)]
        normal= [handles.norms(pos,2) handles.norms(pos,1) handles.norms(pos,3)];
        
        vtwall = cross(vwall,normal);
        vtplus = cross(vplus,normal);
        
        wsst(pos,time)=abs(conv*( ( sqrt( sum(vtplus.^2))) - ( sqrt( sum(vtwall.^2))) )/del);
    end
    
end


%%%%% Calc OSI (note can fully due without knowing directionality %%%%%%%
osi = std(wsst,1,2)./mean(wsst,2);
idx = find( isnan(osi));
osi(idx)=0.0;

handles.wsst = wsst;
handles.osi = osi;

wss_temporal_avg = mean(wsst,2);
wss2 = sort(wss_temporal_avg);
handles.wss_mean = mean(wss_temporal_avg(:));
handles.wss_std = std(wss_temporal_avg(:));
handles.wss_med = median(wss_temporal_avg(:));
handles.wss_lq = wss2( ceil(numel(wss2)*0.25) );
handles.wss_uq = wss2( floor(numel(wss2)*0.75) );

osi2 = sort(osi);
handles.osi_mean = mean(osi(:));
handles.osi_std = std(osi(:));
handles.osi_med = median(osi(:));
handles.osi_lq = osi2( ceil(numel(osi2)*0.25) );
handles.osi_uq = osi2( floor(numel(osi2)*0.75) );

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%          Average WSS UPDATE                          %%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%GET VELOCITY POSITIONS%%%%%
disp('Getting Norms');
for pos=1:size(handles.verts,1)
    
    if( mod(pos,500)==1)
        disp(['Doing Point ', int2str(pos),' of ',num2str(size(handles.verts,1))]);
    end
    
    norm_size= sqrt( handles.norms(pos,1).^2 + handles.norms(pos,2).^2 + handles.norms( pos,3).^2);
    handles.norms(pos,1) = handles.norms(pos,1)/norm_size;
    handles.norms(pos,2) = handles.norms(pos,2)/norm_size;
    handles.norms(pos,3) = handles.norms(pos,3)/norm_size;
    
    
    for poly_pos = 1:poly_num
        
        py = handles.verts(pos,1)- (poly_pos -1.0)*handles.norms(pos,1);
        px = handles.verts(pos,2)- (poly_pos -1.0)*handles.norms(pos,2);
        pz = handles.verts(pos,3)- (poly_pos -1.0)*handles.norms(pos,3);
        
        vx_wss(pos,poly_pos) = lin3d(handles.VX,px,py,pz);
        vy_wss(pos,poly_pos) = lin3d(handles.VY,px,py,pz);
        vz_wss(pos,poly_pos) = lin3d(handles.VZ,px,py,pz);
    end
    
    vx_wss(pos,1) = 0;
    vy_wss(pos,1) = 0;
    vz_wss(pos,1) = 0;
end

%%%%%%%%%NOW GET WSS%%%%%%%%
disp('Getting Wss');
for pos=1:size(handles.verts,1)
    
    if( mod(pos,500)==1)
        disp(['Doing Point ', int2str(pos),' of ',num2str(size(handles.verts,1))]);
    end
    
    fit_vx = polyfit(1:poly_num,vx_wss(pos,:),poly_order);
    fit_vy = polyfit(1:poly_num,vy_wss(pos,:),poly_order);
    fit_vz = polyfit(1:poly_num,vz_wss(pos,:),poly_order);
    
    vxwall = polyval(fit_vx,1);
    vywall = polyval(fit_vy,1);
    vzwall = polyval(fit_vz,1);
    
    vxplus = polyval(fit_vx,1+del);
    vyplus = polyval(fit_vy,1+del);
    vzplus = polyval(fit_vz,1+del);
    
    vplus = [vxplus vyplus vzplus]; %- (sum([vxplus vyplus vzplus].*[norm(pos,2) norm(pos,1) norm(3,pos)]))*[norm(pos,2) norm(pos,1) norm(3,pos)]
    vwall = [vxwall vywall vzwall]; %- (sum([vxwall vywall vzwall].*[norm(pos,2) norm(pos,1) norm(3,pos)]))*[norm(pos,2) norm(pos,1) norm(3,pos)]
    normal= [handles.norms(pos,2) handles.norms(pos,1) handles.norms(pos,3)];
    
    % Dahan says to fix this so the direction is correct
    vtwall = cross(vwall,normal);
    vtplus = cross(vplus,normal);
    
    wss(pos)=abs( conv*( ( sqrt( sum(vtplus.^2))) - ( sqrt( sum(vtwall.^2))) )/del);
end


% Grab magnitude signal
mag_depth = str2num(get(handles.mag_depth,'String'));
for mask_pos = 1:numel(handles.MAG)
    for pos=1:size(handles.verts,1)
        if( mod(pos,500)==1)
            disp(['Doing Point ', int2str(pos),' of ',num2str(size(handles.verts,1))]);
        end
        
        for poly_pos = -1:mag_depth
            py = handles.verts(pos,1)- (poly_pos)*handles.norms(pos,1);
            px = handles.verts(pos,2)- (poly_pos)*handles.norms(pos,2);
            pz = handles.verts(pos,3)- (poly_pos)*handles.norms(pos,3);
            Wvals(poly_pos+2) = lin3d(handles.MAG{mask_pos}.Volume,px,py,pz);
        end
        
        mag_wall{mask_pos}.Value(pos) = max(Wvals);
        mag_wall{mask_pos}.Name = handles.MAG{mask_pos}.Name;
    end
end

wss2 = sort(wss);
handles.avg_wss_mean = mean(wss);
handles.avg_wss_std = std(wss);
handles.avg_wss_med = median(wss);
handles.avg_wss_lq = wss2( ceil(numel(wss2)*0.25) );
handles.avg_wss_uq = wss2( floor(numel(wss2)*0.75) );

handles.wss = wss;
handles.mag_wall = mag_wall;




% Volume features
idx = handles.VOLUME_MASK > 0;
voxel_volume = handles.delX*handles.delY*handles.delZ;

% Average Velocity [mm/s]
handles.average_velocity = sqrt( mean(handles.VX(idx(:))).^2 + mean(handles.VY(idx(:))).^2 + mean(handles.VZ(idx(:))).^2 );

% Volume [mL]
handles.volume = 0.001*voxel_volume*sum(idx(:));

% Kinetic Energy [J]
density_of_blood = 1060; %kg/M^3
voxel_volume_M3 = (handles.delX/1000)*(handles.delY/1000)*(handles.delZ/1000);
vsquared = handles.VX(idx).^2 +handles.VY(idx).^2 + handles.VZ(idx).^2;
handles.kinetic_energy = 0.5*density_of_blood*voxel_volume_M3*sum( vsquared(:)/1000^2);
for time = 1:size(handles.VXt,4)
    
    VXT = handles.VXt(:,:,:,time);
    VYT = handles.VYt(:,:,:,time);
    VZT = handles.VZt(:,:,:,time);
    
    vsquared = VXT(idx).^2 +VYT(idx).^2 + VZT(idx).^2;
    handles.dyn_kinetic_energy(time) = 0.5*density_of_blood*voxel_volume_M3*sum( vsquared(:)/1000^2);
end
handles.dyn_kinetic_energy


% Viscous Energy Loss [W]
VE = zeros(size(handles.VX),'single');
VX = handles.VX;
VY = handles.VY;
VZ = handles.VZ;
visc = str2double(get(handles.viscosity_value,'String'))/1000;
conv_vel = 1/1000;
for i = 2:size(handles.VX,1)-1
    for j = 2:size(handles.VX,2)-1
        for k = 2:size(handles.VX,3)-1
            if handles.VOLUME_MASK(i,j,k) > 0
                
                x0 = i;
                y0 = j;
                z0 = k;
                
                %%%velocity Terms
                vx = conv_vel*VX(x0,y0,z0);
                vy = conv_vel*VY(x0,y0,z0);
                vz = conv_vel*VZ(x0,y0,z0);
                
                %%First Derivatives
                dvxdx = conv_vel*( VX(x0+1,y0,z0) - VX(x0-1,y0,z0) )/(2*handles.delX/1000);
                dvxdy = conv_vel*( VX(x0,y0+1,z0) - VX(x0,y0-1,z0) )/(2*handles.delY/1000);
                dvxdz = conv_vel*( VX(x0,y0,z0+1) - VX(x0,y0,z0-1) )/(2*handles.delZ/1000);
                
                dvydx = conv_vel*( VY(x0+1,y0,z0) - VY(x0-1,y0,z0) )/(2*handles.delX/1000);
                dvydy = conv_vel*( VY(x0,y0+1,z0) - VY(x0,y0-1,z0) )/(2*handles.delY/1000);
                dvydz = conv_vel*( VY(x0,y0,z0+1) - VY(x0,y0,z0-1) )/(2*handles.delZ/1000);
                
                dvzdx = conv_vel*( VZ(x0+1,y0,z0) - VZ(x0-1,y0,z0) )/(2*handles.delX/1000);
                dvzdy = conv_vel*( VZ(x0,y0+1,z0) - VZ(x0,y0-1,z0) )/(2*handles.delY/1000);
                dvzdz = conv_vel*( VZ(x0,y0,z0+1) - VZ(x0,y0,z0-1) )/(2*handles.delZ/1000);
                
                VE(i,j,k) = 2*visc*( dvxdx^2 + dvydy^2 + dvzdz^2 - 1/3*(dvxdx + dvydy + dvzdz)^2 ) ...
                    + visc*( dvydx+dvxdy)^2 + visc*(dvzdy + dvydz)^2 + visc*(dvxdz + dvzdx)^2;
            end
        end
    end
end

size(VE)
size(handles.VOLUME_MASK)
handles.visc_energy_loss = sum(VE(idx)*voxel_volume_M3);

% Update handles structure
guidata(hObject, handles);

update_wss_text(hObject, handles);
update_image(handles);


figure
time = (0:numel(handles.dyn_kinetic_energy)-1)*handles.delT;
plot(time,handles.dyn_kinetic_energy);
xlabel('Time [s]');
ylabel('Kinetic Energy [J]');


figure
time = (0:numel(handles.dyn_kinetic_energy)-1)*handles.delT;
plot(time, mean(handles.wsst,1));
xlabel('Time [s]');
ylabel('Mean Wall Shear Stress [N/m^2]');


function poly_num_Callback(hObject, eventdata, handles)
% hObject    handle to poly_num (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 poly_num as text
%        str2double(get(hObject,'String')) returns contents of poly_num as a double


% --- Executes during object creation, after setting all properties.
function poly_num_CreateFcn(hObject, eventdata, handles)
% hObject    handle to poly_num (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 update_wss_text(hObject, handles)
% hObject    handle to poly_order (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

temp_text{1} = sprintf('WSS [N/m^2] from Time Averaged Data:');
temp_text{end+1} = sprintf('  Median             = %2.2f',handles.avg_wss_med);
temp_text{end+1} = sprintf('  Lower Quartile     = %2.2f',handles.avg_wss_lq);
temp_text{end+1} = sprintf('  Upper Quartile     = %2.2f',handles.avg_wss_uq);
temp_text{end+1} = sprintf('  Mean               = %2.2f',handles.avg_wss_mean);
temp_text{end+1} = sprintf('  Standard Deviation = %2.2f',handles.avg_wss_std);

temp_text{end+1} = sprintf('WSS [N/m^2] from Time Resolved Data:');
temp_text{end+1} = sprintf('  Median             = %2.2f',handles.wss_med);
temp_text{end+1} = sprintf('  Lower Quartile     = %2.2f',handles.wss_lq);
temp_text{end+1} = sprintf('  Upper Quartile     = %2.2f',handles.wss_uq);
temp_text{end+1} = sprintf('  Mean               = %2.2f',handles.wss_mean);
temp_text{end+1} = sprintf('  Standard Deviation = %2.2f',handles.wss_std);

temp_text{end+1} = sprintf('OSI from Time Resolved Data:');
temp_text{end+1} = sprintf('  Median             = %2.2f',handles.osi_med);
temp_text{end+1} = sprintf('  Lower Quartile     = %2.2f',handles.osi_lq);
temp_text{end+1} = sprintf('  Upper Quartile     = %2.2f',handles.osi_uq);
temp_text{end+1} = sprintf('  Mean               = %2.2f',handles.osi_mean);
temp_text{end+1} = sprintf('  Standard Deviation = %2.2f',handles.osi_std);

temp_text{end+1} = sprintf('Native Measures:');
temp_text{end+1} = sprintf('  Avg Velocity [mm/s]     = %f',handles.average_velocity);
temp_text{end+1} = sprintf('  Volume [ml]             = %f',handles.volume);
temp_text{end+1} = sprintf('  Kinetic Energy [mJ]     = %f',1000*handles.kinetic_energy);
temp_text{end+1} = sprintf('  Viscous Energy Loss [mW] = %f',1000*handles.visc_energy_loss);

for pos = 1:numel(handles.mag_wall)
    temp_text{end+1} = sprintf('Wall Magnitude: %s',handles.mag_wall{pos}.Name);
    temp_text{end+1} = sprintf('  Mean:   %f',mean(handles.mag_wall{pos}.Value(:)) );
    temp_text{end+1} = sprintf('  Median: %f',median(handles.mag_wall{pos}.Value(:)) );
    temp_text{end+1} = sprintf('  Max:    %f',max(handles.mag_wall{pos}.Value(:)) );
end
set(handles.wss_text,'string',temp_text);

function poly_order_Callback(hObject, eventdata, handles)
% hObject    handle to poly_order (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 poly_order as text
%        str2double(get(hObject,'String')) returns contents of poly_order as a double


% --- Executes during object creation, after setting all properties.
function poly_order_CreateFcn(hObject, eventdata, handles)
% hObject    handle to poly_order (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 update_time_wss.
function update_time_wss_Callback(hObject, eventdata, handles)
% hObject    handle to update_time_wss (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

update_wss(hObject,handles,1);


function color_range_Callback(hObject, eventdata, handles)
% hObject    handle to color_range (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 color_range as text
%        str2double(get(hObject,'String')) returns contents of color_range as a double


% --- Executes during object creation, after setting all properties.
function color_range_CreateFcn(hObject, eventdata, handles)
% hObject    handle to color_range (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 rot_num_Callback(hObject, eventdata, handles)
% hObject    handle to rot_num (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 rot_num as text
%        str2double(get(hObject,'String')) returns contents of rot_num as a double


% --- Executes during object creation, after setting all properties.
function rot_num_CreateFcn(hObject, eventdata, handles)
% hObject    handle to rot_num (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 rotate_button.
function rotate_button_Callback(hObject, eventdata, handles)
% hObject    handle to rotate_button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

rotfunc(handles,0);


function rotfunc ( handles, save_rot)

num_rot =str2double(get(handles.rot_num,'String'));


new_fig = ishandle(handles.wss_axis);
figure(handles.wss_axis);
set(gcf,'InvertHardCopy','off');
axis manual
axs = [0 0 1];


for n=0:num_rot
    
    
    figure(handles.wss_axis);
    pnt=int2str(n);
    disp(n);
    theta=360/(num_rot+1);
    camorbit(theta,0,'camera');
    
    %rotate(vis_axis,[1 0 0],180)
    
    if save_rot == 1
        fname=['ROTATE',sprintf('%03d',n),'.jpg'];
        print('-opengl','-f1','-r200','-djpeg100',fname);
    end
    
    drawnow
end

% --- Executes on button press in rot_and_save.
function rot_and_save_Callback(hObject, eventdata, handles)
% hObject    handle to rot_and_save (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

rotfunc(handles,1);

function file_name_Callback(hObject, eventdata, handles)
% hObject    handle to file_name (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 file_name as text
%        str2double(get(hObject,'String')) returns contents of file_name as a double


% --- Executes during object creation, after setting all properties.
function file_name_CreateFcn(hObject, eventdata, handles)
% hObject    handle to file_name (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 save_button.
function save_button_Callback(hObject, eventdata, handles)
% hObject    handle to save_button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

figure(handles.wss_axis);
set(gcf,'InvertHardCopy','off');
fname = get(handles.file_name,'String');
print('-opengl','-f1','-r200','-djpeg100',fname);



% --- Executes on button press in update_image.
function update_image_Callback(hObject, eventdata, handles)
% hObject    handle to update_image (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

update_image(handles);


function update_image(handles)

color_range = str2num(get(handles.color_range,'String'))/100;
visual_type = get(handles.visual_type,'Value');
%%%%Visual Type Decoding%%%%%
% 1 - Steady WSS
% 2 - Osilatory WSS
% 3 - Time WSS
% 4+- Wall Signal
%%%%%%ASSIGN COLORS %%%%%%%%%%%%%%

if visual_type == 1 %%%%AVERAGE
    max_wss = max(handles.wss(:));
    cmap = parula(512);
    Cdata = zeros(size(handles.verts(1),1),3);
    for pos =1:size(handles.verts,1)
        cpos = 1+floor(512*abs(handles.wss(pos))/max_wss/color_range);
        if(cpos>512)
            cpos = 512;
        end
        Cdata(pos,:) = cmap(cpos,:);
    end
    
    new_fig = ishandle(handles.wss_axis);
    figure(handles.wss_axis);
    
    set(handles.hpatch_wall,'FaceColor','interp','EdgeColor', 'none','FaceVertexCData',Cdata);
    
    t = colorbar('YLim',[0.0 1.0],'YTick',[0.0 1.0],'YTickLabel',{'0',num2str(max_wss*color_range)},'FontSize',22);
    set(get(t,'Label'),'String','Shear Stress (N/m^2)');
    
elseif visual_type == 2
    max_osi = max(handles.osi(:));
    cmap = parula(512);
    Cdata = zeros(size(handles.verts(1),1),3);
    for pos =1:size(handles.verts,1)
        cpos = 1+floor(512*abs(handles.osi(pos))/max_osi/color_range);
        if(cpos>512)
            cpos = 512;
        end
        Cdata(pos,:) = cmap(cpos,:);
    end
    
    new_fig = ishandle(handles.wss_axis);
    figure(handles.wss_axis);
    % hpatch = patch(isosurface(sCD,vis_thresh));
    % reducepatch(hpatch,0.4);
    set(handles.hpatch_wall,'FaceColor','interp','EdgeColor', 'none','FaceVertexCData',Cdata);
    %set(hpatch,'FaceVertexCData',Cdata);
    
    t = colorbar('YLim',[0.0 1.0],'YTick',[0.0 1.0],'YTickLabel',{'0',num2str(max_osi*color_range)},'FontSize',22);
    set(get(t,'Label'),'String','Oscillator Shear Stress (N/m^2)','Color','w');
    
elseif ( visual_type == 3 )
    max_wss = max(handles.wsst(:));
    cmap = parula(512);
    Cdata = zeros(size(handles.verts(1),1),3);
    
    for time = 1:size(handles.wsst,2)
        for pos =1:size(handles.verts,1)
            cpos = 1+floor(512*abs(handles.wsst(pos,time))/max_wss/color_range);
            if(cpos>512)
                cpos = 512;
            end
            Cdata(pos,:) = cmap(cpos,:);
        end
        
        new_fig = ishandle(handles.wss_axis);
        figure(handles.wss_axis);
        % hpatch = patch(isosurface(sCD,vis_thresh));
        % reducepatch(hpatch,0.4);
        set(handles.hpatch_wall,'FaceColor','interp','EdgeColor', 'none','FaceVertexCData',Cdata);
        %set(hpatch,'FaceVertexCData',Cdata);
        
        t = colorbar('YLim',[0.0 1.0],'YTick',[0.0 1.0],'YTickLabel',{'0',num2str(max_wss*color_range)},'FontSize',22);
        set(get(t,'Label'),'String','Shear Stress (N/m^2)','Color','w');
        
        pause(0.5);
        set(gcf,'InvertHardCopy','off');
        fname=['TIME_WSS',sprintf('%03d',time),'.jpg'];
        print('-opengl','-f1','-r200','-djpeg100',fname);
    end
elseif ( visual_type >= 4 )
    
    max_mag_wall = max(handles.mag_wall{visual_type-3}.Value(:));
    disp(['Max Mag Wall',num2str(max_mag_wall)]);
    cmap = parula(512);
    Cdata = zeros(size(handles.verts(1),1),3);
    for pos =1:size(handles.verts,1)
        cpos = 1+floor(512*abs(handles.mag_wall{visual_type-3}.Value(pos))/max_mag_wall/color_range);
        if(cpos>512)
            cpos = 512;
        end
        if(cpos < 1)
            cpos = 1;
        end
        Cdata(pos,:) = cmap(cpos,:);
    end
    
    new_fig = ishandle(handles.wss_axis);
    figure(handles.wss_axis);
    set(handles.hpatch_wall,'FaceColor','interp','EdgeColor', 'none','FaceVertexCData',Cdata);
    
    t = colorbar('YLim',[0.0 1.0],'YTick',[0.0 1.0],'YTickLabel',{'0',num2str(max_mag_wall*color_range)},'FontSize',22);
    set(get(t,'Label'),'String','Oscillator Shear Stress (N/m^2)','Color','w');
    
end



% --- Executes on selection change in visual_type.
function visual_type_Callback(hObject, eventdata, handles)
% hObject    handle to visual_type (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 visual_type contents as cell array
%        contents{get(hObject,'Value')} returns selected item from visual_type


% --- Executes during object creation, after setting all properties.
function visual_type_CreateFcn(hObject, eventdata, handles)
% hObject    handle to visual_type (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 popupmenu5.
function popupmenu5_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu5 (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 popupmenu5 contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu5


% --- Executes during object creation, after setting all properties.
function popupmenu5_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu5 (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 box_filename_Callback(hObject, eventdata, handles)
% hObject    handle to box_filename (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 box_filename as text
%        str2double(get(hObject,'String')) returns contents of box_filename as a double


% --- Executes during object creation, after setting all properties.
function box_filename_CreateFcn(hObject, eventdata, handles)
% hObject    handle to box_filename (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 box_save.
function box_save_Callback(hObject, eventdata, handles)
% hObject    handle to box_save (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Saving .mat file
out_name = get(handles.box_filename,'String')
save(out_name,'handles');

% Saving 
col_header = '';
row_header = { out_name};
data = [];
[col_header,data] = insert_xls_entry('Avg WWS Median',handles.avg_wss_med,col_header,data);
[col_header,data] = insert_xls_entry('Avg WWS Lower Quartile',handles.avg_wss_lq,col_header,data);
[col_header,data] = insert_xls_entry('Avg WWS Upper Quartile',handles.avg_wss_uq,col_header,data);
[col_header,data] = insert_xls_entry('Avg WWS Mean',handles.avg_wss_mean,col_header,data);
[col_header,data] = insert_xls_entry('Avg WWS Standard Deviation',handles.avg_wss_std,col_header,data);

[col_header,data] = insert_xls_entry('WSS Median',handles.wss_med,col_header,data);
[col_header,data] = insert_xls_entry('WSS Median Lower Quartile',handles.wss_lq,col_header,data);
[col_header,data] = insert_xls_entry('WSS Median Upper Quartile',handles.wss_uq,col_header,data);
[col_header,data] = insert_xls_entry('WSS Median Mean',handles.wss_mean,col_header,data);
[col_header,data] = insert_xls_entry('WSS Median Standard Deviation',handles.wss_std,col_header,data);

[col_header,data] = insert_xls_entry('OSI Median',handles.osi_med,col_header,data);
[col_header,data] = insert_xls_entry('OSI Median Lower Quartile',handles.osi_lq,col_header,data);
[col_header,data] = insert_xls_entry('OSI Median Upper Quartile',handles.osi_uq,col_header,data);
[col_header,data] = insert_xls_entry('OSI Median Mean',handles.osi_mean,col_header,data);
[col_header,data] = insert_xls_entry('OSI Median Standard Deviation',handles.osi_std,col_header,data);

[col_header,data] = insert_xls_entry('Avg Velocity [mm/s]',handles.average_velocity,col_header,data);
[col_header,data] = insert_xls_entry('Volume [ml]',handles.volume,col_header,data);
[col_header,data] = insert_xls_entry('Kinetic Energy [mJ]',1000*handles.kinetic_energy,col_header,data);
[col_header,data] = insert_xls_entry('Viscous Energy Loss [mW]',1000*handles.visc_energy_loss,col_header,data);

for pos = 1:numel(handles.mag_wall)
   [col_header,data] = insert_xls_entry([handles.mag_wall{pos}.Name,' Mean'],mean(handles.mag_wall{pos}.Value(:)),col_header,data);
   [col_header,data] = insert_xls_entry([handles.mag_wall{pos}.Name,' Median'],median(handles.mag_wall{pos}.Value(:)),col_header,data);
   [col_header,data] = insert_xls_entry([handles.mag_wall{pos}.Name,' Max'],max(handles.mag_wall{pos}.Value(:)),col_header,data);
   [col_header,data] = insert_xls_entry([handles.mag_wall{pos}.Name,' Std'],std(handles.mag_wall{pos}.Value(:)),col_header,data);
end


xlswrite([out_name,'.xls'],data,'Sheet1','B2');        %Write data
xlswrite([out_name,'.xls'],col_header,'Sheet1','B1');  %Write column header
xlswrite([out_name,'.xls'],row_header,'Sheet1','A2');  %Write row header

function [col_header,data] = insert_xls_entry(name,value,col_header,data)
col_header{end+1} = name;
data{end+1} = value;

% --- Executes during object creation, after setting all properties.
function update_image_CreateFcn(hObject, eventdata, handles)
% hObject    handle to update_image (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called


% --- Executes during object creation, after setting all properties.
function hist_axes_CreateFcn(hObject, eventdata, handles)
% hObject    handle to hist_axes (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 hist_axes


% --- Executes during object creation, after setting all properties.
function wss_text_CreateFcn(hObject, eventdata, handles)
% hObject    handle to wss_text (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

set(hObject,'max',999);




% --- Executes on selection change in volume_type.
function volume_type_Callback(hObject, eventdata, handles)
% hObject    handle to volume_type (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 volume_type contents as cell array
%        contents{get(hObject,'Value')} returns selected item from volume_type
update_mask(hObject,handles);


% --- Executes during object creation, after setting all properties.
function volume_type_CreateFcn(hObject, eventdata, handles)
% hObject    handle to volume_type (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 volume_thresh_Callback(hObject, eventdata, handles)
% hObject    handle to volume_thresh (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 volume_thresh as text
%        str2double(get(hObject,'String')) returns contents of volume_thresh as a double


% --- Executes during object creation, after setting all properties.
function volume_thresh_CreateFcn(hObject, eventdata, handles)
% hObject    handle to volume_thresh (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 mag_depth_Callback(hObject, eventdata, handles)
% hObject    handle to mag_depth (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 mag_depth as text
%        str2double(get(hObject,'String')) returns contents of mag_depth as a double


% --- Executes during object creation, after setting all properties.
function mag_depth_CreateFcn(hObject, eventdata, handles)
% hObject    handle to mag_depth (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