flow_gui.m

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

% Last Modified by GUIDE v2.5 09-Jul-2008 16:08:00

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

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

% Update handles structure
guidata(hObject, handles);

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


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


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

update_mask(handles);


function update_mask(handles)

global sMAG;
global sCD;
global sMASK;
global vis_axis;
global vis_alpha;
global wss_axis;
global vis_thresh;
global VELX;
global VELY;
global VELZ;
global m_xlength;
global m_ylength;
global m_zlength;
global XPTS;
global YPTS;
global ZPTS;

global verts;
global norms;
global norm_handle;
global hpatch;

mask_type = get(handles.mask_type,'Value');
%%%VISUAL METHOD DECODING
%   1 = CD
%   2 = MAG

vis_thresh = str2double(get(handles.lumen_thresh,'String'));

new_fig = ishandle(wss_axis);
figure(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;

if mask_type == 1
    hpatch = patch(isosurface(sCD,vis_thresh));
else
    hpatch = patch(isosurface(sMAG,vis_thresh));
end
colormap('jet');
reducepatch(hpatch,0.1);
%reducepatch(hpatch,1000);
set(hpatch,'FaceColor','red','EdgeColor', 'none');

if mask_type == 1
    isonormals(sCD,hpatch)
else
    isonormals(sMAG,hpatch)
end

camlight right;
lighting gouraud
%lighting flat;
alpha(0.9)
set(vis_axis, 'Renderer','OpenGL')
set(vis_axis, 'RendererMode','Manual');
set(gca,'color','black');
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','Visualization Window');
end

hold on
%axis equal tight off vis3d;

axis equal tight vis3d;
set(gca,'XColor','w');
set(get(gca,'XLabel'),'String','L to R?')
set(gca,'YColor','w');
set(get(gca,'YLabel'),'String','A to P?')
set(gca,'ZColor','w');
set(get(gca,'ZLabel'),'String','S to I?') 

% norms = (get(hpatch,'VertexNormals'));
% verts = (get(hpatch,'Vertices'));
%
% scl = 15
% 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',2)

norms = (get(hpatch,'VertexNormals'));
verts = (get(hpatch,'Vertices'));


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


% --- 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.
% 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


% --- 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


% --- 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


% --- 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 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 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


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


% --- Executes during object creation, after setting all properties.
function thresh_CreateFcn(hObject, eventdata, handles)
% hObject    handle to 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 slider movement.
function box_xslide_Callback(hObject, eventdata, handles)
% hObject    handle to box_xslide (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,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

update_box(handles);

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

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end


% --- Executes on slider movement.
function box_yslide_Callback(hObject, eventdata, handles)
% hObject    handle to box_yslide (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,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
update_box(handles);

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

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end


% --- Executes on slider movement.
function box_zslide_Callback(hObject, eventdata, handles)
% hObject    handle to box_zslide (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,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

update_box(handles);

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

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end



function box_xsize_Callback(hObject, eventdata, handles)
% hObject    handle to box_xsize (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_xsize as text
%        str2double(get(hObject,'String')) returns contents of box_xsize as a double
update_box(handles);


% --- Executes during object creation, after setting all properties.
function box_xsize_CreateFcn(hObject, eventdata, handles)
% hObject    handle to box_xsize (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 box_ysize_Callback(hObject, eventdata, handles)
% hObject    handle to box_ysize (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_ysize as text
%        str2double(get(hObject,'String')) returns contents of box_ysize as a double
update_box(handles);

% --- Executes during object creation, after setting all properties.
function box_ysize_CreateFcn(hObject, eventdata, handles)
% hObject    handle to box_ysize (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 box_zsize_Callback(hObject, eventdata, handles)
% hObject    handle to box_zsize (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_zsize as text
%        str2double(get(hObject,'String')) returns contents of box_zsize as a double
update_box(handles);

% --- Executes during object creation, after setting all properties.
function box_zsize_CreateFcn(hObject, eventdata, handles)
% hObject    handle to box_zsize (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 during object creation, after setting all properties.
function velocity_profile_CreateFcn(hObject, eventdata, handles)
% hObject    handle to velocity_profile (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 velocity_profile

%**************************************************************************
%This is where almost all of the calculations are done*********************
%**************************************************************************


function update_box(handles)

%%Anatomical Data
global sMAG;
global sCD;
global sMASK;

%%Visualization Stuff
global vis_axis;
global vis_alpha;
global wss_axis;
global vis_thresh;

%Velocity data
global VELX;
global VELY;
global VELZ;
global VELXt;
global VELYt;
global VELZt;

%%Matrix Size
global m_xlength;
global m_ylength;
global m_zlength;
global tframes

%%Pressure Stuff??
global XPTS;
global YPTS;
global ZPTS;

%%Spacings (voxel sizes)
global delX;
global delY;
global delZ;
global tres %%length of tframes in ms
tframes
%%Mask Stuff
global verts;
global norms;
global norm_handle;
global norm_mag_handle;
global norm_cd_handle;
global color_range;
global hpatch;
global Cdata;

%Box stuff
global box_idx;
global box_handle;
global hist_xout;
global hist_nout;

%%%Flow Parameters (control)
global CINE_flag;
global ROI_flag;
global slice_CD;
global slice_VEL;
global slice_MASK;
global thresh;
global flow_mean;

%%%%%%Delete Object or Not %%%%%%%%%%%%%%
new_fig = ishandle(wss_axis);
figure(wss_axis);


%Delete Box
if ishandle(box_handle)
    delete(box_handle);
end

%%Mask Type flag
mask_type = get(handles.mask_type,'Value');
%%%VISUAL METHOD DECODING
%   1 = CD
%   2 = MAG

%%%CINE Flag
CINE_flag = get(handles.cine_flag,'Value');

%%Threshold
thresh = str2num(get(handles.thresh,'String'));

%%Interpolation Number
pol = str2num(get(handles.interp_num,'String'));

%%Manually select ROI?
ROI_flag = get(handles.roi_flag,'Value');

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  get Box Position and Coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

phix = ( (get(handles.box_xrot,'Value')*pi - pi/2 ));
phiy = ( (get(handles.box_yrot,'Value')*pi - pi/2 ));
phiz = ( (get(handles.box_zrot,'Value')*pi - pi/2 ));

xpos = floor(1 + (get(handles.box_xslide,'Value')*( m_ylength-1) ));
ypos = floor(1 + (get(handles.box_yslide,'Value')*( m_xlength-1) ));
zpos = floor(1 + (get(handles.box_zslide,'Value')*( m_zlength-1) ));


xsize = str2num(get(handles.box_xsize,'String'));
ysize = str2num(get(handles.box_ysize,'String'));
zsize = str2num(get(handles.box_zsize,'String'));

[xB,yB,zB] = meshgrid(linspace(-xsize,xsize,2), ...
    linspace(-ysize,ysize,2), ...
    linspace(-zsize,zsize,2));
Tes = [ 1 2 3 4;
    5 6 7 8;
    1 3 5 7;
    2 4 6 8;
    3 4 7 8;
    1 2 5 6];

Rx = [ 1 0        0;
    0 cos(phix) sin(phix);
    0 -sin(phix) cos(phix)];
Ry = [ cos(phiy) 0   -sin(phiy);
    0         1        0;
    sin(phiy) 0    cos(phiy)];
Rz = [ cos(phiz) sin(phiz) 0;
    -sin(phiz) cos(phiz) 0;
    0 0 1];

RT = Rx*Ry*Rz;

XB = [xB(:) yB(:) zB(:)]';
size(XB);
XB = ( RT*XB )' + repmat([xpos ypos zpos],[8 1]);;


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Visualize The Box
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%Visualize Control
box_on = get(handles.box_on,'Value');

%%%VISUAL Box Color DECODING
%   1 = White
%   2 = Blue
%   3 = Yellow
%   4 = Green
%   5 = Red
box_color= get(handles.box_color,'Value');
if box_color == 1
    col = 'w';
elseif box_color == 2
    col = 'b';
elseif box_color == 3
    col = 'y';
elseif box_color == 4
    col = 'g';
elseif box_color == 5
    col = 'r';
end

box_alpha=1.0 - 0.25*(get(handles.box_alpha,'Value')-1);

if(box_on)
    box_handle = tetramesh(Tes,XB,'FaceAlpha',box_alpha,'FaceColor',col,'EdgeColor','none');
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Resample the Image in Box Coordinates (No Cine Yet)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%Find Indices Within the box
[xB,yB,zB] = meshgrid(linspace(-xsize,xsize,pol*xsize*2+1),linspace(-ysize,ysize,pol*ysize*2+1),linspace(-zsize,zsize,pol*zsize*2+1));

Rx = [ 1 0        0;
    0 cos(phix) sin(phix);
    0 -sin(phix) cos(phix)];
Ry = [ cos(phiy) 0   -sin(phiy);
    0         1        0;
    sin(phiy) 0    cos(phiy)];
Rz = [ cos(phiz) sin(phiz) 0;
    -sin(phiz) cos(phiz) 0;
    0 0 1];

RT = Rx*Ry*Rz;

XB = [xB(:) yB(:) zB(:)]';
XB = ( RT*XB )' + repmat([xpos ypos zpos],[numel(XB)/3 1]);;

%**************************************************************************
%Non-CINE data
%**************************************************************************
if(CINE_flag == 1)
    slice_CD = zeros(size(xB));
    vx_slice = zeros(size(xB));
    vy_slice = zeros(size(xB));
    vz_slice = zeros(size(xB));
    vtemp = zeros(size(xB));
    cdtemp = zeros(size(xB));
    magtemp = zeros(size(xB));

    %%Get a starting point
    XF = floor(XB(:,1));
    YF = floor(XB(:,2));
    ZF = floor(XB(:,3));

    %%find points outside matrix
    MASK = (XF < 1 ) | (YF < 1) | (ZF < 1) | (XF > m_ylength-1) | (YF > m_xlength-1) | (ZF > m_zlength-1);
    idx2 = find(MASK == 0);
    XF = XF(idx2);
    YF = YF(idx2);
    ZF = ZF(idx2);

    dx = XB(idx2,1) - XF;
    dy = XB(idx2,2) - YF;
    dz = XB(idx2,3) - ZF;
    mdx = 1 - dx;
    mdy = 1 - dy;
    mdz = 1 - dz;

    CDtemp = sCD(:,:,:);
    idx = sub2ind(size(CDtemp),YF,XF,ZF);
    cdtemp(idx2)= cdtemp(idx2)+  mdy.*mdx.*mdz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF,XF+1,ZF);
    cdtemp(idx2)= cdtemp(idx2)+  mdy.*dx.*mdz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF+1,XF,ZF);
    cdtemp(idx2)= cdtemp(idx2)+  dy.*mdx.*mdz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF+1,XF+1,ZF);
    cdtemp(idx2)= cdtemp(idx2)+  dy.*dx.*mdz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF,XF,ZF+1);
    cdtemp(idx2)= cdtemp(idx2)+  mdy.*mdx.*dz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF,XF+1,ZF+1);
    cdtemp(idx2)= cdtemp(idx2)+  mdy.*dx.*dz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF+1,XF,ZF+1);
    cdtemp(idx2)= cdtemp(idx2)+  dy.*mdx.*dz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF+1,XF+1,ZF+1);
    cdtemp(idx2)= cdtemp(idx2)+  dy.*dx.*dz.*CDtemp(idx);
    slice_CD(:,:,:)=cdtemp;


    MAGtemp = sMAG(:,:,:);
    idx = sub2ind(size(MAGtemp),YF,XF,ZF);
    magtemp(idx2)= magtemp(idx2)+  mdy.*mdx.*mdz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF,XF+1,ZF);
    magtemp(idx2)= magtemp(idx2)+  mdy.*dx.*mdz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF+1,XF,ZF);
    magtemp(idx2)= magtemp(idx2)+  dy.*mdx.*mdz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF+1,XF+1,ZF);
    magtemp(idx2)= magtemp(idx2)+  dy.*dx.*mdz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF,XF,ZF+1);
    magtemp(idx2)= magtemp(idx2)+  mdy.*mdx.*dz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF,XF+1,ZF+1);
    magtemp(idx2)= magtemp(idx2)+  mdy.*dx.*dz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF+1,XF,ZF+1);
    magtemp(idx2)= magtemp(idx2)+  dy.*mdx.*dz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF+1,XF+1,ZF+1);
    magtemp(idx2)= magtemp(idx2)+  dy.*dx.*dz.*MAGtemp(idx);
    slice_MAG(:,:,:)=magtemp;


    vtemp(:) = 0;
    Vtemp = VELX(:,:,:);
    idx = sub2ind(size(Vtemp),YF,XF,ZF);
    vtemp(idx2)= vtemp(idx2)+  mdy.*mdx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF+1,ZF);
    vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF,ZF);
    vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF);
    vtemp(idx2)= vtemp(idx2)+  dy.*dx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  mdy.*mdz.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF+1,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  dy.*dx.*dz.*Vtemp(idx);
    vx_slice(:,:,:)=vtemp;

    vtemp(:) = 0;
    Vtemp = VELY(:,:,:);
    idx = sub2ind(size(Vtemp),YF,XF,ZF);
    vtemp(idx2)= vtemp(idx2)+  mdy.*mdx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF+1,ZF);
    vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF,ZF);
    vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF);
    vtemp(idx2)= vtemp(idx2)+  dy.*dx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  mdy.*mdx.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF+1,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  dy.*dx.*dz.*Vtemp(idx);
    vy_slice(:,:,:)=vtemp;

    vtemp(:) = 0;
    Vtemp = VELZ(:,:,:);
    idx = sub2ind(size(Vtemp),YF,XF,ZF);
    vtemp(idx2)= vtemp(idx2)+  mdx.*mdy.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF+1,ZF);
    vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF,ZF);
    vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF);
    vtemp(idx2)= vtemp(idx2)+  dy.*dx.*mdz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  mdy.*mdx.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF,XF+1,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*dz.*Vtemp(idx);
    idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF+1);
    vtemp(idx2)= vtemp(idx2)+  dy.*dx.*dz.*Vtemp(idx);
    vz_slice(:,:,:)=vtemp;

%     %%Interpolation
%     if size(xB,3) == 1
%         slice_CD = interp2(slice_CD,pol);
%         vx_slice = interp2(vx_slice,pol);
%         vy_slice = interp2(vy_slice,pol);
%         vz_slice = interp2(vz_slice,pol);
%     else
%         slice_CD = interp3(slice_CD,pol);
%         vx_slice = interp3(vx_slice,pol);
%         vy_slice = interp3(vy_slice,pol);
%         vz_slice = interp3(vz_slice,pol);
%     end

    %%%Test Plot Normal
    Norm = RT*[0; 0; 1];
    slice_VEL = Norm(1)*vy_slice + Norm(2)*vx_slice + Norm(3)*vz_slice;

    %**************************************************************************
else %%if CINE data set%%%%%%%%%%%%%%%%%%%%
    %**************************************************************************

    slice_CD = zeros(size(xB));
    slice_VEL = zeros(size(xB,1),size(xB,2),size(xB,3),tframes);
    vx_slice = zeros(size(xB,1),size(xB,2),size(xB,3),tframes);
    vy_slice = zeros(size(xB,1),size(xB,2),size(xB,3),tframes);
    vz_slice = zeros(size(xB,1),size(xB,2),size(xB,3),tframes);
    vtemp = zeros(size(xB,1),size(xB,2),size(xB,3));
    cdtemp = zeros(size(xB,1),size(xB,2),size(xB,3));
    magtemp = zeros(size(xB,1),size(xB,2),size(xB,3));

    %%Get a starting point
    XF = floor(XB(:,1));
    YF = floor(XB(:,2));
    ZF = floor(XB(:,3));

    %%find points outside matrix
    MASK = (XF < 1 ) | (YF < 1) | (ZF < 1) | (XF > m_ylength-1) | (YF > m_xlength-1) | (ZF > m_zlength-1);
    idx2 = find(MASK == 0);
    XF = XF(idx2);
    YF = YF(idx2);
    ZF = ZF(idx2);

    dx = XB(idx2,1) - XF;
    dy = XB(idx2,2) - YF;
    dz = XB(idx2,3) - ZF;
    mdx = 1 - dx;
    mdy = 1 - dy;
    mdz = 1 - dz;

    CDtemp = sCD(:,:,:);
    idx = sub2ind(size(CDtemp),YF,XF,ZF);
    cdtemp(idx2)= cdtemp(idx2)+  mdy.*mdx.*mdz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF,XF+1,ZF);
    cdtemp(idx2)= cdtemp(idx2)+  mdy.*dx.*mdz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF+1,XF,ZF);
    cdtemp(idx2)= cdtemp(idx2)+  dy.*mdx.*mdz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF+1,XF+1,ZF);
    cdtemp(idx2)= cdtemp(idx2)+  dy.*dx.*mdz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF,XF,ZF+1);
    cdtemp(idx2)= cdtemp(idx2)+  mdy.*mdx.*dz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF,XF+1,ZF+1);
    cdtemp(idx2)= cdtemp(idx2)+  mdy.*dx.*dz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF+1,XF,ZF+1);
    cdtemp(idx2)= cdtemp(idx2)+  dy.*mdx.*dz.*CDtemp(idx);
    idx = sub2ind(size(CDtemp),YF+1,XF+1,ZF+1);
    cdtemp(idx2)= cdtemp(idx2)+  dy.*dx.*dz.*CDtemp(idx);
    slice_CD(:,:,:)=cdtemp;

    MAGtemp = sMAG(:,:,:);
    idx = sub2ind(size(MAGtemp),YF,XF,ZF);
    magtemp(idx2)= magtemp(idx2)+  mdy.*mdx.*mdz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF,XF+1,ZF);
    magtemp(idx2)= magtemp(idx2)+  mdy.*dx.*mdz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF+1,XF,ZF);
    magtemp(idx2)= magtemp(idx2)+  dy.*mdx.*mdz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF+1,XF+1,ZF);
    magtemp(idx2)= magtemp(idx2)+  dy.*dx.*mdz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF,XF,ZF+1);
    magtemp(idx2)= magtemp(idx2)+  mdy.*mdx.*dz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF,XF+1,ZF+1);
    magtemp(idx2)= magtemp(idx2)+  mdy.*dx.*dz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF+1,XF,ZF+1);
    magtemp(idx2)= magtemp(idx2)+  dy.*mdx.*dz.*MAGtemp(idx);
    idx = sub2ind(size(MAGtemp),YF+1,XF+1,ZF+1);
    magtemp(idx2)= magtemp(idx2)+  dy.*dx.*dz.*MAGtemp(idx);
    slice_MAG(:,:,:)=magtemp;

    for t=1:tframes

        %interpolation in x
        vtemp(:) = 0;
        Vtemp = VELXt(:,:,:,t);
        idx = sub2ind(size(Vtemp),YF,XF,ZF);
        vtemp(idx2)= vtemp(idx2)+  mdy.*mdx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF+1,ZF);
        vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF,ZF);
        vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF);
        vtemp(idx2)= vtemp(idx2)+  dy.*dx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  mdy.*mdz.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF+1,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  dy.*dx.*dz.*Vtemp(idx);
        vx_slice(:,:,:,t)=vtemp;

        %interpolation in y
        vtemp(:) = 0;
        Vtemp = VELYt(:,:,:,t);
        idx = sub2ind(size(Vtemp),YF,XF,ZF);
        vtemp(idx2)= vtemp(idx2)+  mdy.*mdx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF+1,ZF);
        vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF,ZF);
        vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF);
        vtemp(idx2)= vtemp(idx2)+  dy.*dx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  mdy.*mdx.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF+1,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  dy.*dx.*dz.*Vtemp(idx);
        vy_slice(:,:,:,t)=vtemp;

        %interpolation in z
        vtemp(:) = 0;
        Vtemp = VELZt(:,:,:,t);
        idx = sub2ind(size(Vtemp),YF,XF,ZF);
        vtemp(idx2)= vtemp(idx2)+  mdx.*mdy.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF+1,ZF);
        vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF,ZF);
        vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF);
        vtemp(idx2)= vtemp(idx2)+  dy.*dx.*mdz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  mdy.*mdx.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF,XF+1,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  mdy.*dx.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  dy.*mdx.*dz.*Vtemp(idx);
        idx = sub2ind(size(Vtemp),YF+1,XF+1,ZF+1);
        vtemp(idx2)= vtemp(idx2)+  dy.*dx.*dz.*Vtemp(idx);
        vz_slice(:,:,:,t)=vtemp;
    end

    %%%Test Plot Normal
    Norm = RT*[0; 0; 1];
    slice_VEL = Norm(1)*vy_slice + Norm(2)*vx_slice + Norm(3)*vz_slice;

end


%**************************************************************************
%%%%   Any Processing
%**************************************************************************

%%Get the Mask
mask_type = get(handles.mask_type,'Value');
%%%VISUAL METHOD DECODING
%   1 = CD
%   2 = MAG

sliceMASK = 0;

if (mask_type == 1) %%Mask on CD image**************
    if (ROI_flag == 1)
        threshM = thresh/100*max(slice_CD(:));
        slice_MASK = slice_CD > threshM;
        roi_idx = find(slice_MASK > 0);
        voxels = length(roi_idx(:,:,1));
    else
        figure; imshow(mean(slice_CD,3),'InitialMagnification',2000);
        %figure; imshow(slice_CD(:,:,1),'InitialMagnification',2000);
        [MASK,x_roi,y_roi] = roipoly;
        for i = 1:size(xB,3)
            slice_MASK(:,:,i) = MASK;
        end
    end
else %%***********Mask on MAG image*****************
    if (ROI_flag == 1)
        threshM = thresh/100*max(slice_CD(:));
        slice_MASK = slice_CD > threshM;
        roi_idx = find(slice_MASK > 0);
        voxels = length(roi_idx(:,:,1));
    else
        figure; imshow(slice_CD(:,:,1),'InitialMagnification',2000);
        [slice_MASK,x_roi,y_roi] = roipoly;
    end
end

size(slice_CD);
size_mask = size(slice_MASK);
slice_mask = slice_MASK;

%Calculate max, mean, std velocity
% if(CINE_flag == 1)
%     vel_mean = mean(slice_VEL(slice_MASK));
%     vel_max = max(slice_VEL(slice_MASK));
%     vel_std = std(slice_VEL(slice_MASK));
% else %if CINE data set
%     for t=1:tframes
%     im_vel = double(squeeze(slice_VEL(:,:,:,t)));
%     vel_mean(t) = mean(im_vel(slice_MASK));
%     vel_max(t) = max(im_vel(slice_MASK));
%     vel_std(t) = std(im_vel(slice_MASK));
%     end
% end



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Update the Figures in the GUI
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%Update Figure
mapbw = gray(128);
mapcol = jet(128);
map = [mapbw; mapcol];
axes(handles.cd_axes);
colormap(map);
im = mean(slice_CD,3);
im = 511*im/max(im(:));
im = (mean(slice_MASK,3) == 0).*im +  (mean(slice_MASK,3) > 0)*768;
imagesc(im,[0 1024]);
set(gca,'YTick',[])
set(gca,'XTick',[])
xlabel('');
ylabel('');
daspect([1 1 1]);

%%%Update Figure: velocity
if(CINE_flag == 1)
    axes(handles.flow_axes);
    im = mean(slice_VEL,3);
    im = im/max(abs(im(:)));
    im = 768 + im*255;
    imagesc(im,[0 1024]);
    set(gca,'YTick',[])
    set(gca,'XTick',[])
    xlabel('');
    ylabel('');
    colorbar;
    daspect([1 1 1]);

else
    axes(handles.flow_axes);
    vel = mean(slice_VEL,4);
    im = mean(vel,3);
    im = im/max(abs(im(:)));
    im = 768 + im*255;
    imagesc(im,[0 1024]);
    set(gca,'YTick',[])
    set(gca,'XTick',[])
    xlabel('');
    ylabel('');
    colorbar;
    daspect([1 1 1]);
end

%%%Update Figure: velocity profile%%%
if(CINE_flag == 1)
    axes(handles.velocity_profile);
    profile = slice_VEL(:,:,1);
    size_prof = size(profile);
    prof_slice = round(size_prof(1)/2);
    vel_profile = profile(:,prof_slice);
    plot(vel_profile);
    xlabel('distance');
    ylabel('velocity [mm/s]');
else
    axes(handles.velocity_profile);
    %vel_slice = mean(slice_VEL,4);
    vel_slice = slice_VEL(:,:,:,1);
    profile = vel_slice(:,:,1);
    size_prof = size(profile);
    prof_slice = round(size_prof(1)/2);
    vel_profile = profile(:,prof_slice);
    % flow_profile = vel_profile * delX * delY / 1000;
    plot(vel_profile);
    xlabel('distance');
    ylabel('velocity [mm/s]');
end

tres
%%%%Update figure: Mean flow over time for CINE data
axes(handles.mean_flow);
delX_pol = delX / pol;
delY_pol = delY / pol;

global max_vel_t;
global flow_t;

if CINE_flag==2
   for t = 1:tframes
        masked_vel_t = slice_VEL(:,:,:,t).*double(slice_MASK);
        flow_t(t) = sum( masked_vel_t(:))/size(slice_MASK,3)*delX_pol*delY_pol / 1000;
        max_vel_t(t) = max(masked_vel_t(:)); 
        time(t) = t*tres;
    end

    %plot(flow_mean);
    plot(time,flow_t);
    xlabel('time [ms]');
    ylabel('velocity [ml/s]');

    max_vel = max(max_vel_t(:));
    set(handles.max_velocity,'String',num2str(max_vel));
    total_flow = trapz(flow_t)*tres/1000;
    set(handles.total_flow,'String',num2str(total_flow));
else
    masked_vel_t = slice_VEL.*double(slice_MASK);
    flow_t = sum( masked_vel_t(:))/size(slice_MASK,3)*delX_pol*delY_pol / 1000;
    max_vel_t = max(masked_vel_t(:)); 
    
    set(handles.max_velocity,'String',num2str(max_vel_t));
    set(handles.total_flow,'String',num2str(flow_t));  
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 selection change in box_color.
function box_color_Callback(hObject, eventdata, handles)
% hObject    handle to box_color (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 box_color contents as cell array
%        contents{get(hObject,'Value')} returns selected item from box_color


update_box(handles);


% --- Executes during object creation, after setting all properties.
function box_color_CreateFcn(hObject, eventdata, handles)
% hObject    handle to box_color (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 box_on.
function box_on_Callback(hObject, eventdata, handles)
% hObject    handle to box_on (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 box_on
update_box(handles)




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

% --- Executes during object creation, after setting all properties.
function hist_bin_CreateFcn(hObject, eventdata, handles)
% hObject    handle to hist_bin (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 box_alpha.
function box_alpha_Callback(hObject, eventdata, handles)
% hObject    handle to box_alpha (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 box_alpha contents as cell array
%        contents{get(hObject,'Value')} returns selected item from box_alpha
update_box(handles)

% --- Executes during object creation, after setting all properties.
function box_alpha_CreateFcn(hObject, eventdata, handles)
% hObject    handle to box_alpha (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 slider movement.
function box_xrot_Callback(hObject, eventdata, handles)
% hObject    handle to box_xrot (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,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
update_box(handles)

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

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

set(hObject,'Value',0.5);


% --- Executes on slider movement.
function box_yrot_Callback(hObject, eventdata, handles)
% hObject    handle to box_yrot (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,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
update_box(handles)

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

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end


set(hObject,'Value',0.5);

% --- Executes on slider movement.
function box_zrot_Callback(hObject, eventdata, handles)
% hObject    handle to box_zrot (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,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
update_box(handles)

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

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

set(hObject,'Value',0.5);



% --- Executes on button press in auto_center.
function auto_center_Callback(hObject, eventdata, handles)
% hObject    handle to auto_center (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global sMAG;
global sCD;
global sMASK;
global vis_axis;
global vis_alpha;
global wss_axis;
global vis_thresh;
global VELX;
global VELY;
global VELZ;
global m_xlength;
global m_ylength;
global m_zlength;
global XPTS;
global YPTS;
global ZPTS;
global tframes;
global delX;
global delY;
global delZ;
global verts;
global norms;
global norm_handle;
global norm_mag_handle;
global norm_cd_handle;
global color_range;
global hpatch;
global Cdata;
global visc;
global wss;
global wsst;
global osi;
global box_idx;
global box_handle;
global hist_xout;
global hist_nout;

xpos = floor(1 + (get(handles.box_xslide,'Value')*( m_ylength-1) ));
ypos = floor(1 + (get(handles.box_yslide,'Value')*( m_xlength-1) ));
zpos = floor(1 + (get(handles.box_zslide,'Value')*( m_zlength-1) ));

xsize = str2num(get(handles.box_xsize,'String'));
ysize = str2num(get(handles.box_ysize,'String'));
zsize = str2num(get(handles.box_zsize,'String'));

phix = ( (get(handles.box_xrot,'Value')*pi/2 ));
phiy = ( (get(handles.box_yrot,'Value')*pi/2 ));
phiz = ( (get(handles.box_zrot,'Value')*pi/2 ));

[xB,yB,zB] = meshgrid((-xsize:xsize),(-ysize:ysize),(-zsize:zsize));

Rx = [ 1 0        0;
    0 cos(phix) sin(phix);
    0 -sin(phix) cos(phix)];
Ry = [ cos(phiy) 0   -sin(phiy);
    0         1        0;
    sin(phiy) 0    cos(phiy)];
Rz = [ cos(phiz) sin(phiz) 0;
    -sin(phiz) cos(phiz) 0;
    0 0 1];

RT = Rx*Ry*Rz;

XB = [xB(:) yB(:) zB(:)]';
size(XB)
XB = ( RT*XB )' + repmat([xpos ypos zpos],[numel(XB)/3 1]);;

%%%%Find Values in Box
COMx=0;
COMy=0;
COMz=0;
M0=0;

for pos=1:numel(xB)
    X = XB(pos,:);
    V = lin3d(sCD,X(2),X(1),X(3));
    M0 = M0 + V;
    COMx = X(1)*V + COMx;
    COMy = X(2)*V + COMy;
    COMz = X(3)*V + COMz;
end
COMx= COMx/M0
COMy= COMy/M0
COMz= COMz/M0
set(handles.box_xslide,'Value',round(COMx-1)/( m_ylength-1));
set(handles.box_yslide,'Value',round(COMy-1)/( m_xlength-1));
set(handles.box_zslide,'Value',round(COMz-1)/( m_zlength-1));
update_box(handles)

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

global sMAG;
global sCD;
global sMASK;
global vis_axis;
global vis_alpha;
global wss_axis;
global vis_thresh;
global VELX;
global VELY;
global VELZ;
global m_xlength;
global m_ylength;
global m_zlength;
global XPTS;
global YPTS;
global ZPTS;
global tframes;
global delX;
global delY;
global delZ;
global verts;
global norms;
global norm_handle;
global norm_mag_handle;
global norm_cd_handle;
global color_range;
global hpatch;
global Cdata;
global visc;
global wss;
global wsst;
global osi;
global box_idx;
global box_handle;
global hist_xout;
global hist_nout;

xpos = floor(1 + (get(handles.box_xslide,'Value')*( m_ylength-1) ));
ypos = floor(1 + (get(handles.box_yslide,'Value')*( m_xlength-1) ));
zpos = floor(1 + (get(handles.box_zslide,'Value')*( m_zlength-1) ));

xsize = str2num(get(handles.box_xsize,'String'));
ysize = str2num(get(handles.box_ysize,'String'));
zsize = str2num(get(handles.box_zsize,'String'));

phix = ( (get(handles.box_xrot,'Value')*pi - pi/2 ));
phiy = ( (get(handles.box_yrot,'Value')*pi - pi/2 ));
phiz = ( (get(handles.box_zrot,'Value')*pi - pi/2 ));

MIN_ERR = 1e99;

for pass =1:2
    if pass ==1
        res = 5;
        range = linspace( -pi/4,pi/4,res);
        phix0 = phix;
        phiy0 = phiy;
    else
        res = 5;
        maxp = pi / res / 4;
        range = linspace( -maxp,maxp,res);
        phix0 = phix;
        phiy0 = phiy;
    end

    for cphix = range + phix0
        for cphiy = range + phiy0

            [xB,yB,zB] = meshgrid((-xsize:xsize),(-ysize:ysize),(-zsize:zsize));

            Rx = [ 1 0        0;
                0 cos(cphix) sin(cphix);
                0 -sin(cphix) cos(cphix)];
            Ry = [ cos(cphiy) 0   -sin(cphiy);
                0         1        0;
                sin(cphiy) 0    cos(cphiy)];
            Rz = [ cos(phiz) sin(phiz) 0;
                -sin(phiz) cos(phiz) 0;
                0 0 1];
            RT = Rx*Ry*Rz;

            XB = [xB(:) yB(:) zB(:)]';
            XB = ( RT*XB )' + repmat([xpos ypos zpos],[numel(XB)/3 1]);;

            for slice = 1:size(xB,3)
                COMx(slice)=0;
                COMy(slice)=0;
                M0=0;

                for x=1:xsize*2+1
                    for y=1:ysize*2+1
                        pos = sub2ind(size(xB),y,x,slice);
                        X = XB(pos,:);
                        V = lin3d(sCD,X(2),X(1),X(3));
                        M0 = M0 + V;
                        COMx(slice) =x*V + COMx(slice);
                        COMy(slice) =y*V + COMy(slice);
                    end
                end
                COMx(slice) = COMx(slice)/M0;
                COMy(slice) = COMy(slice)/M0;
            end
            ERR = abs(std(COMx)^2 + std(COMy)^2);

            if ERR < MIN_ERR
                phix = cphix;
                phiy = cphiy;
                MIN_ERR =ERR;
            end
        end
    end
    disp(['Pass ',int2str(pass),': ',num2str(MIN_ERR)]);

end

set(handles.box_xrot,'Value',(phix+pi/2)/(pi));
set(handles.box_yrot,'Value',(phiy+pi/2)/(pi));

update_box(handles)


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


% --- Executes during object creation, after setting all properties.
function cine_flag_CreateFcn(hObject, eventdata, handles)
% hObject    handle to cine_flag (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 interp_num_Callback(hObject, eventdata, handles)
% hObject    handle to interp_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 interp_num as text
%        str2double(get(hObject,'String')) returns contents of interp_num as a double


% --- Executes during object creation, after setting all properties.
function interp_num_CreateFcn(hObject, eventdata, handles)
% hObject    handle to interp_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 during object creation, after setting all properties.
function slider9_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider9 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
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



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





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


% --- Executes during object creation, after setting all properties.
function mean_flow_CreateFcn(hObject, eventdata, handles)
% hObject    handle to mean_flow (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 save_name_Callback(hObject, eventdata, handles)
% hObject    handle to save_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 save_name as text
%        str2double(get(hObject,'String')) returns contents of save_name as a double

%%%%Base name for saved files%%%%
% --- Executes during object creation, after setting all properties.
function save_name_CreateFcn(hObject, eventdata, handles)
% hObject    handle to save_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)
global ROI_flag;
global CINE_flag;
global slice_CD;
global slice_VEL;
global slice_MASK;
global thresh;
global delX;
global delY;
global delZ;
global flow_mean;
global tframes;
global tres;

base_name = get(handles.save_name,'string');

global max_vel_t;
global flow_t;

fid = fopen([base_name,'.txt'],'w');
fprintf(fid,'Time\tFlow(ml/s)\tMaxVel(mm/s)\t\n');
if(CINE_flag == 1)
    fprintf(fid,'Avg\t%5f\t%5f\t\n',flow_t,max_vel_t);
else
    for t=1:tframes
        fprintf(fid,'%5f\t%5f\t%5f\t\n',t*tres,flow_t(t),max_vel_t(t));
    end
    fprintf(fid,'Overall\t%5f\t%5f\t\n', mean(flow_t),max(max_vel_t(:)));
end
fclose(fid);


% if(CINE_flag == 1)
%     vel_xy = slice_VEL(:,:,1);
%     size(vel_xy)
%     size_prof = size(vel_xy);
%     prof_slice = round(size_prof(1)/2);
%     vel_profile = vel_xy(:,prof_slice);
% else
%     vel_xyz = mean(slice_VEL,4);  %%average velocity over time frames
%     vel_xy = vel_xyz(:,:,1);  %%average velocity over z within mask
% 
%     size_prof = size(vel_xy);
%     prof_slice = round(size_prof(1)/2);
%     vel_profile = vel_xy(:,prof_slice);
% 
%     %%Save mean flow for each time frame
%     flow_name  = [base_name,'.mean_velt'];
%     csvwrite(flow_name,flow_mean);
% 
%     %%Save total flow (area under mean flow curve)
%     flow_total_name = [base_name,'.total_flow'];
%     total_flow = trapz(flow_mean)*tres/1000;
%     csvwrite(flow_total_name,total_flow);
% end
% 
% vel_name = [base_name,'.vel_mean'];
% csvwrite(vel_name,vel_xy);
% 
% profile_name = [base_name,'.vel_profile'];
% csvwrite(profile_name,vel_profile);
% 
% %%Save voxel sizes
% parameters = [delX, delY, delZ];
% voxel_size = [base_name,'.voxel_size'];
% csvwrite(voxel_size,parameters);
% 

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




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


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