%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% To run: Edit user options in npscalc.m and execute the code.
%
% This code is intended to accompany the manuscript entitled:
%
% A simple approach to measure computed tomography (CT) modulation transfer
% function (MTF) and noise-power spectrum (NPS) using the American College
% of Radiology (ACR) accreditation phantom
%
% Please do not distribute.
%
% This program requires the following 4 files:
% npscalc.m
% SliceBrowser.m
% SliceBrowser.fig
% license.txt
%
% Purpose: To calculate the 3D NPS using CT data of the American College
% of Radiology (ACR) accreditation phantom.
%
% Input: Two consecutive scans of the phantom are needed. The program
% requires a data directory to be selected in which there are
% only two subdirectories containing only CT slices corresponding
% to the third module of the phantom. Be careful of partial
% volume effects with surrounding modules.
%
% i.e., datadir
% |-> scan 1 dir
% | | -> only module 3 slices
% |
% |-> scan 2 dir
% |-> only module 3 slices
%
% Copyright 2012 Saul N. Friedman
% Distributed under the terms of the "New BSD License." Please see
% license.txt.
%
% N.B.: SliceBrowser.m is an altered version of code by Marian Uhercik.
% Please see license.txt.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% ======================================================================
%> SLICEBROWSER M-file for SliceBrowser.fig
%> SliceBrowser is an interactive viewer of 3D volumes,
%> it shows 3 perpendicular slices (XY, YZ, ZX) with 3D pointer.
%> Input: a) VOLUME - a 3D matrix with volume data
%> b) VOLUME - a 4D matrix with volume data over time
%> Control:
%> - Clicking into the window changes the location of 3D pointer.
%> - 3D pointer can be moved also by keyboard arrows.
%> - Pressing +/- will switch to next/previous volume.
%> - Pressing 1,2,3 will change the focus of current axis.
%> - Pressing 'e' will print the location of 3D pointer.
%> - Pressing 'c' switches between color-mode and grayscale.
%> - Pressing 'q' switches scaling of axis (equal/normal).
%> Example of usage:
%> load mri.dat
%> volume = squeeze(D);
%> SliceBrowser(volume);
%>
%> Last modified by Saul N. Friedman
% ======================================================================
function varargout = SliceBrowser(varargin)
% Documentation generated GUIDE:
%
%SLICEBROWSER M-file for SliceBrowser.fig
% SLICEBROWSER, by itself, creates a new SLICEBROWSER or raises the existing
% singleton*.
%
% H = SLICEBROWSER returns the handle to a new SLICEBROWSER or the handle to
% the existing singleton*.
%
% SLICEBROWSER('Property','Value',...) creates a new SLICEBROWSER using the
% given property value pairs. Unrecognized properties are passed via
% varargin to SliceBrowser_OpeningFcn. This calling syntax produces a
% warning when there is an existing singleton*.
%
% SLICEBROWSER('CALLBACK') and SLICEBROWSER('CALLBACK',hObject,...) call the
% local function named CALLBACK in SLICEBROWSER.M with the given input
% arguments.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help SliceBrowser
% Last Modified by GUIDE v2.5 01-Sep-2008 13:14:20
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @SliceBrowser_OpeningFcn, ...
'gui_OutputFcn', @SliceBrowser_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 SliceBrowser is made visible.
function SliceBrowser_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 unrecognized PropertyName/PropertyValue pairs from the
% command line (see VARARGIN)
% Choose default command line output for SliceBrowser
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes SliceBrowser wait for user response (see UIRESUME)
% uiwait(handles.figure1);
if (length(varargin) <=0)
error('Input volume has not been specified.');
end;
volume = varargin{1};
if (ndims(volume) ~= 3 && ndims(volume) ~= 4)
error('Input volume must have 3 or 4 dimensions.');
end;
handles.volume = volume;
handles.axis_equal = 0;
handles.color_mode = 1;
if (size(volume,4) ~= 3)
handles.color_mode = 0;
end;
% set main wnd title
set(gcf, 'Name', 'Slice Viewer')
% init 3D pointer
vol_sz = size(volume);
if (ndims(volume) == 3)
vol_sz(4) = 1;
end;
pointer3dt = floor(vol_sz/2)+1;
handles.pointer3dt = pointer3dt;
handles.vol_sz = vol_sz;
plot3slices(hObject, handles);
% stores ID of last axis window
% (0 means that no axis was clicked yet)
handles.last_axis_id = 0;
% Update handles structure
guidata(hObject, handles);
% --- Outputs from this function are returned to the command line.
function varargout = SliceBrowser_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 mouse press over axes background.
function Subplot1_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to Subplot1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% This object contains the XY slice
xaxis = getappdata(0,'uaxis');
yaxis = getappdata(0,'vaxis');
zaxis = getappdata(0,'waxis');
axlabel = getappdata(0,'axlabel');
deltayaxis = yaxis(2) - yaxis(1);
deltaxaxis = xaxis(2) - xaxis(1);
deltazaxis = zaxis(2) - zaxis(1);
%disp('Subplot1:BtnDown');
pt=get(gca,'currentpoint');
if length(xaxis) > 0 && length(yaxis)
xpos=round((pt(1,2)+xaxis(end))/deltaxaxis); ypos=round((pt(1,1)+yaxis(end))/deltayaxis);
else
xpos=round(pt(1,2)); ypos=round(pt(1,1));
end
zpos = handles.pointer3dt(3);
tpos = handles.pointer3dt(4);
handles.pointer3dt = [xpos ypos zpos tpos];
handles.pointer3dt = clipointer3d(handles.pointer3dt,handles.vol_sz);
plot3slices(hObject, handles);
% store this axis as last clicked region
handles.last_axis_id = 1;
% Update handles structure
guidata(hObject, handles);
% --- Executes on mouse press over axes background.
function Subplot2_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to Subplot2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% This object contains the YZ slice
xaxis = getappdata(0,'uaxis');
yaxis = getappdata(0,'vaxis');
zaxis = getappdata(0,'waxis');
axlabel = getappdata(0,'axlabel');
deltayaxis = yaxis(2) - yaxis(1);
deltaxaxis = xaxis(2) - xaxis(1);
deltazaxis = zaxis(2) - zaxis(1);
%disp('Subplot2:BtnDown');
pt=get(gca,'currentpoint');
if length(xaxis) > 0 && length(zaxis)
xpos=round((pt(1,2)+xaxis(end))/deltaxaxis); zpos=round((pt(1,1)+zaxis(end))/deltazaxis);
else
xpos=round(pt(1,2)); zpos=round(pt(1,1));
end
ypos = handles.pointer3dt(2);
tpos = handles.pointer3dt(4);
handles.pointer3dt = [xpos ypos zpos tpos];
handles.pointer3dt = clipointer3d(handles.pointer3dt,handles.vol_sz);
plot3slices(hObject, handles);
% store this axis as last clicked region
handles.last_axis_id = 2;
% Update handles structure
guidata(hObject, handles);
% --- Executes on mouse press over axes background.
function Subplot3_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to Subplot3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% This object contains the XZ slice
xaxis = getappdata(0,'uaxis');
yaxis = getappdata(0,'vaxis');
zaxis = getappdata(0,'waxis');
axlabel = getappdata(0,'axlabel');
deltayaxis = yaxis(2) - yaxis(1);
deltaxaxis = xaxis(2) - xaxis(1);
deltazaxis = zaxis(2) - zaxis(1);
%disp('Subplot3:BtnDown');
pt=get(gca,'currentpoint');
if length(xaxis) > 0 && length(zaxis)
ypos=round((pt(1,1)+yaxis(end))/deltayaxis); zpos=round((pt(1,2)+zaxis(end))/deltazaxis);
else
zpos=round(pt(1,2)); ypos=round(pt(1,1));
end
xpos = handles.pointer3dt(1);
tpos = handles.pointer3dt(4);
handles.pointer3dt = [xpos ypos zpos tpos];
handles.pointer3dt = clipointer3d(handles.pointer3dt,handles.vol_sz);
plot3slices(hObject, handles);
% store this axis as last clicked region
handles.last_axis_id = 3;
% Update handles structure
guidata(hObject, handles);
% --- Executes on key press with focus on SliceBrowserFigure and no controls selected.
function SliceBrowserFigure_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to SliceBrowserFigure (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%disp('SliceBrowserFigure_KeyPressFcn');
curr_char = int8(get(gcf,'CurrentCharacter'));
if isempty(curr_char)
return;
end;
xpos = handles.pointer3dt(1);
ypos = handles.pointer3dt(2);
zpos = handles.pointer3dt(3);
tpos = handles.pointer3dt(4);
% Keys:
% - up: 30
% - down: 31
% - left: 28
% - right: 29
% - '1': 49
% - '2': 50
% - '3': 51
% - 'e': 101
% - plus: 43
% - minus: 45
switch curr_char
case 99 % 'c'
handles.color_mode = 1 - handles.color_mode;
if (handles.color_mode ==1 && size(handles.volume,4) ~= 3)
handles.color_mode = 0;
end;
case 113 % 'q'
handles.axis_equal = 1 - handles.axis_equal;
case 30
switch handles.last_axis_id
case 1
xpos = xpos -1;
case 2
xpos = xpos -1;
case 3
zpos = zpos -1;
case 0
end;
case 31
switch handles.last_axis_id
case 1
xpos = xpos +1;
case 2
xpos = xpos +1;
case 3
zpos = zpos +1;
case 0
end;
case 28
switch handles.last_axis_id
case 1
ypos = ypos -1;
case 2
zpos = zpos -1;
case 3
ypos = ypos -1;
case 0
end;
case 29
switch handles.last_axis_id
case 1
ypos = ypos +1;
case 2
zpos = zpos +1;
case 3
ypos = ypos +1;
case 0
end;
case 43
% plus key
tpos = tpos+1;
case 45
% minus key
tpos = tpos-1;
case 49
% key 1
handles.last_axis_id = 1;
case 50
% key 2
handles.last_axis_id = 2;
case 51
% key 3
handles.last_axis_id = 3;
case 101
disp(['[' num2str(xpos) ' ' num2str(ypos) ' ' num2str(zpos) ' ' num2str(tpos) ']']);
otherwise
return
end;
handles.pointer3dt = [xpos ypos zpos tpos];
handles.pointer3dt = clipointer3d(handles.pointer3dt,handles.vol_sz);
plot3slices(hObject, handles);
% Update handles structure
guidata(hObject, handles);
% --- Plots all 3 slices XY, YZ, XZ into 3 subplots
function [sp1,sp2,sp3] = plot3slices(hObject, handles)
% pointer3d 3D coordinates in volume matrix (integers)
handles.pointer3dt;
size(handles.volume);
value3dt = handles.volume(handles.pointer3dt(1), handles.pointer3dt(2), handles.pointer3dt(3), handles.pointer3dt(4));
text_str = ['[X:' int2str(handles.pointer3dt(1)) ...
', Y:' int2str(handles.pointer3dt(2)) ...
', Z:' int2str(handles.pointer3dt(3)) ...
', Time:' int2str(handles.pointer3dt(4)) '/' int2str(handles.vol_sz(4)) ...
'], value:' num2str(value3dt)];
set(handles.pointer3d_info, 'String', text_str);
guidata(hObject, handles);
if (handles.color_mode ==1)
sliceXY = squeeze(handles.volume(:,:,handles.pointer3dt(3),:));
sliceYZ = squeeze(handles.volume(handles.pointer3dt(1),:,:,:));
sliceXZ = squeeze(handles.volume(:,handles.pointer3dt(2),:,:));
max_xyz = max([ max(sliceXY(:)) max(sliceYZ(:)) max(sliceXZ(:)) ]);
min_xyz = min([ min(sliceXY(:)) min(sliceYZ(:)) min(sliceXZ(:)) ]);
clims = [ min_xyz max_xyz ];
else
sliceXY = squeeze(handles.volume(:,:,handles.pointer3dt(3),handles.pointer3dt(4)));
sliceYZ = squeeze(handles.volume(handles.pointer3dt(1),:,:,handles.pointer3dt(4)));
sliceXZ = squeeze(handles.volume(:,handles.pointer3dt(2),:,handles.pointer3dt(4)));
max_xyz = max([ max(sliceXY(:)) max(sliceYZ(:)) max(sliceXZ(:)) ]);
min_xyz = min([ min(sliceXY(:)) min(sliceYZ(:)) min(sliceXZ(:)) ]);
clims = [ min_xyz max_xyz ];
end;
sliceZY = squeeze(permute(sliceYZ, [2 1 3]));
xaxis = getappdata(0,'uaxis');
yaxis = getappdata(0,'vaxis');
zaxis = getappdata(0,'waxis');
axlabel = getappdata(0,'axlabel');
if length(xaxis) > 0 && length(yaxis) && length(zaxis)
deltayaxis = yaxis(2) - yaxis(1);
deltaxaxis = xaxis(2) - xaxis(1);
deltazaxis = zaxis(2) - zaxis(1);
end
sp1 = subplot(2,2,1);
%colorbar;
if length(xaxis) > 0 && length(yaxis)
imagesc([yaxis(1) yaxis(end)],[xaxis(1) xaxis(end)],sliceXY,clims)
else
imagesc(sliceXY, clims);
end
if (handles.axis_equal == 1)
axis image;
else
axis normal;
end;
title('Slice XY');
if exist('axlabel')
xlabel(['Y',axlabel]);ylabel(['X',axlabel])
else
ylabel('X');xlabel('Y');
end
if length(xaxis) > 0 && length(yaxis)
line([handles.pointer3dt(2).*deltayaxis - yaxis(end) handles.pointer3dt(2).*deltayaxis - yaxis(end)], [-size(handles.volume,1) size(handles.volume,1)]);
line([-size(handles.volume,2) size(handles.volume,2)], [handles.pointer3dt(1).*deltaxaxis - xaxis(end) handles.pointer3dt(1).*deltaxaxis - xaxis(end)]);
else
line([handles.pointer3dt(2) handles.pointer3dt(2)], [0 size(handles.volume,1)]);
line([0 size(handles.volume,2)], [handles.pointer3dt(1) handles.pointer3dt(1)]);
end
%set(allchild(gca),'ButtonDownFcn',@Subplot1_ButtonDownFcn);
set(allchild(gca),'ButtonDownFcn','SliceBrowser(''Subplot1_ButtonDownFcn'',gca,[],guidata(gcbo))');
sp2 = subplot(2,2,2);
if length(xaxis) > 0 &&length(zaxis) > 0
imagesc([zaxis(1) zaxis(end)],[xaxis(1) xaxis(end)],sliceXZ,clims)
else
imagesc(sliceXZ, clims);
end
if (handles.axis_equal == 1)
axis image;
else
axis normal;
end;
title('Slice XZ');
if exist('axlabel')
ylabel(['X',axlabel]);xlabel(['Z',axlabel])
else
ylabel('X');xlabel('Z');
end
if length(xaxis) > 0 && length(zaxis)
line([handles.pointer3dt(3).*deltazaxis - zaxis(end) handles.pointer3dt(3).*deltazaxis - zaxis(end)], [-size(handles.volume,1).*deltaxaxis size(handles.volume,1).*deltaxaxis]);
line([-size(handles.volume,3).*deltazaxis size(handles.volume,3).*deltazaxis], [handles.pointer3dt(1).*deltaxaxis - xaxis(end) handles.pointer3dt(1).*deltaxaxis - xaxis(end)]);
else
line([handles.pointer3dt(3) handles.pointer3dt(3)], [0 size(handles.volume,1)]);
line([0 size(handles.volume,3)], [handles.pointer3dt(1) handles.pointer3dt(1)]);
end
%set(allchild(gca),'ButtonDownFcn',@Subplot2_ButtonDownFcn);
set(allchild(gca),'ButtonDownFcn','SliceBrowser(''Subplot2_ButtonDownFcn'',gca,[],guidata(gcbo))');
sp3 = subplot(2,2,3);
if length(yaxis) > 0 && length(zaxis) > 0
imagesc([yaxis(1) yaxis(end)],[zaxis(1) zaxis(end)],sliceZY,clims)
else
imagesc(sliceZY, clims);
end
if (handles.axis_equal == 1)
axis image;
else
axis normal;
end;
title('Slice ZY');
if exist('axlabel')
ylabel(['Z',axlabel]);xlabel(['Y',axlabel])
else
ylabel('Z');xlabel('Y');
end
if length(yaxis) > 0 && length(zaxis)
line([-size(handles.volume,2) size(handles.volume,2)], [handles.pointer3dt(3).*deltazaxis - zaxis(end) handles.pointer3dt(3).*deltazaxis - zaxis(end)]);
line([handles.pointer3dt(2).*deltayaxis - yaxis(end) handles.pointer3dt(2).*deltayaxis - yaxis(end)], [-size(handles.volume,3).*deltazaxis size(handles.volume,3).*deltazaxis]);
else
line([0 size(handles.volume,2)], [handles.pointer3dt(3) handles.pointer3dt(3)]);
line([handles.pointer3dt(2) handles.pointer3dt(2)], [0 size(handles.volume,3)]);
end
%set(allchild(gca),'ButtonDownFcn',@Subplot3_ButtonDownFcn);
set(allchild(gca),'ButtonDownFcn','SliceBrowser(''Subplot3_ButtonDownFcn'',gca,[],guidata(gcbo))');
function pointer3d_out = clipointer3d(pointer3d_in,vol_size)
pointer3d_out = pointer3d_in;
for p_id=1:4
if (pointer3d_in(p_id) > vol_size(p_id))
pointer3d_out(p_id) = vol_size(p_id);
end;
if (pointer3d_in(p_id) < 1)
pointer3d_out(p_id) = 1;
end;
end;
