function varargout = imlook3d(varargin)
% IMLOOK3D M-file for imlook3d.fig
% IMLOOK3D, by itself, creates a new IMLOOK3D or raises the existing
% singleton*.
%
% H = IMLOOK3D returns the handle to a new IMLOOK3D or the handle to
% the existing singleton*.
%
% IMLOOK3D('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in IMLOOK3D.M with the given input arguments.
%
% IMLOOK3D('Property','Value',...) creates a new IMLOOK3D or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before imlook3d_OpeningFunction gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to imlook3d_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% EXAMPLE:
% Let us first load the mri image in Matlab using
% >load mri;
% and then run imlook3d
% >imlook3d(squeeze(D)); % squeeze removes singleton dimensions
%
% Descriptions of Menus
%
% ImFile:
%
% -READ FROM WORKSPACE: Reads or displays images existing in the
% workspace(base).
%
% -READ A STACK (DISK): Reads (displays)slices of images into a 3D array creating
% a 3D image. It reads them from the disk. A file browser pups up and
% allows the user to pick up the first file in the series. It reads all
% the files in the directory that has similar names except a suffix
% changing for each file.
%
% For example: slice01.tif, slice01.tif,...,slice0N.tif
%
% -READ DICOM SERIES:
% Reads/displays series of DICOM images into a 3D array. A file browser
% pups up and allows users to select the first file in the series.
% It reads all the files in the directory that has similar names
% except a suffix changing for each file.
% -SAVE SLICE AS TIFF:
% Saves the current slice as a tiff image.
% -SAVE INTO WORKSPACE: This saves displayed 3D image into workspace as
% a 3D variable. This may be useful to save the 3D image that is
% read by "read a stack (disk)".
%
% ImTools:
%
% -PIXVAL: Allows looking at pixel intensities.
% -HISTOGRAM: Displays the histogram of the current image (slice).
% -PROFILE: Allows plotting intensity profiles across the image in an
% interactive manner.
% -ADJUST INTENSITY RANGE: Allows adjusting the intensity range for
% the current slice.
% -GLOBAL INTENSITY WINDOWING:
% If not checked,not global, the intensity limits are set to [min(currentslice)
% max(currentslice)]
%
% VIEW MENU:
%
% This pup-up menu allows users to change the view of the image
% from transverse to sagittal or coronal views. It assumes that
% original image is in transverse mode.
%
% Copyright(c) Omer Demirkaya
% Last Modified by GUIDE v2.5 22-May-2007 21:27:00
% Begin initialization code - DO NOT EDIT
% This entire code or part of it could be modified and used if the due
% credit to the original author is given.
%------------------------------------------------------------------
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @imlook3d_OpeningFcn, ...
'gui_OutputFcn', @imlook3d_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin & isstr(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if isempty(varargin)
disp('There was no image to display');
disp('USAGE: >>imlook3d(img) or use ImFile menu to load an image');
varargin{1,1} = zeros(32,32);
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 imlook3d is made visible.
function imlook3d_OpeningFcn(hObject, eventdata, handles, varargin)
% Choose default command line output for imlook3d
if isempty(varargin{:})
return;
end
handles.output = hObject;
Std.Interruptible = 'off';
Std.BusyAction = 'queue';
Ax = Std;
Ax.Units = 'Pixels';
Ax.ydir = 'reverse';
Ax.XLim = [.5 128.5];
Ax.YLim = [.5 128.5];
Ax.XTick = [];
Ax.YTick = [];
Ax.CLimMode = 'auto';
set(handles.axes1,Ax);
Img = Std;Img.CData = [];Img.Xdata = [];Img.Ydata = [];
Img.CDataMapping = 'Scaled';
Img.Erasemode = 'none';
handles.image = Img;
inpargs = varargin{:};
[r,c,z] = size(inpargs);
handles.image.CData = inpargs;
handles.imSize = [r,c,z];
handles.viewtype = 1;
handles.imageModality = [];
handles.hText = [];
handles.global_windowing= 0;
handles.SliceThickness = [];
handles.imageInfo = [];
handles.currentSliceNumber = 1;
handle.image.SliceSensitivityFactor =[];
handles.oimage = handles.image;
cimg = handles.image.CData(:,:,1);
% Create image object and set the properties
handles.ImgObject = image(Img,'Parent',handles.axes1);
set(handles.SliceNumEdit,'String',1);
set(handles.figure1,'Colormap',gray,'Units','Pixels');
% Set the properties of the axes
cclim =[min(cimg(:)) max(cimg(:))];
if (cclim(2)>0 & cclim(2)-cclim(1) ~= 0)
set(handles.axes1,'CLim',cclim,...
'PlotBoxAspectRatio',[c r 1]);
end
set(handles.axes1,'XLim',[1 c],'Ylim',[1 r],...
'PlotBoxAspectRatio',[c r 1]);
set(handles.ImgObject,'Xdata',[1 c],'Ydata',[1 r],'CData',cimg);
drawnow
% Set the slider's value and step size
if z > 1
turnDisplayButtons(handles,'on')
set(handles.SliceNumSlider,'Min',1,'Max',z,'Value',...
1,'SliderStep',[1.0/double(z-1) 1.0/double(z-1)]);
end
% Define the line and associate it with the context menu
set(handles.ImgObject,'UIContextMenu',handles.ImMaps);
% Update handles structure
%--------------------------------------------------------------------------
%% Set appdata for the inntensity adjustment GUI
setappdata(0 , 'hMainGui' , gcf);
hMainGui = getappdata(0, 'hMainGui');
maxINT = max(max(max(handles.image.CData)));
minINT = min(min(min(handles.image.CData)));
intensityParam = struct('lowerLimit',cclim(1),'upperLimit',cclim(2),...
'maxIntensity', maxINT, 'minIntensity',minINT);
handles.intensityParam = intensityParam;
setappdata(hMainGui, 'intensityParam' ,intensityParam);
%% Read and display logo image
% ----------------------------------------------------------------
fdir = which('imlook3d');
txt = [fdir(1:end-10) '\imlook3d.png'];
imlogo = imread(txt);
Sz= size(imlogo);
flogo = figure('Position',[10000 10000 Sz(2) + 4 Sz(1) + 4],'name','Imlook3D',...
'numbertitle','off','menubar','none');
movegui(flogo,'center');
set(flogo,'Units', 'pixels');
image(imlogo(:,:,1:3))
set(gca, ...
'Visible', 'off', ...
'Units', 'pixels', ...
'Position', [2 2 Sz(2) Sz(1)]);
text(220,16,'3D Image Display Tool','Fontsize',12);
text(130,355,'Version 1.2: Copyright 2006, Omer Demirkaya','Fontsize',8);
pause(3);delete(flogo);clear imlogo
%% ------------------------------------
%--------------------------------------------------------------------------
guidata(hObject, handles);
%--------------------------------------------------------------------------
% --- Outputs from this function are returned to the command line.
function varargout = imlook3d_OutputFcn(hObject, eventdata, handles)
varargout{1} = handles.output;
% --- Executes during object creation, after setting all properties.
function SliceNumSlider_CreateFcn(hObject, eventdata, handles)
usewhitebg = 1;
if usewhitebg
set(hObject,'BackgroundColor',[.9 .9 .9]);
else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end
% --- Executes on slider movement.
%------------------------------------------------------------
function SliceNumSlider_Callback(hObject, eventdata, handles)
NewVal= round(get(hObject,'Value'));
cimg = handles.image.CData(:,:,NewVal);
if ~(handles.global_windowing)
cclim = [min(cimg(:)) max(cimg(:))];
if (cclim(2)>0 & cclim(2)-cclim(1) ~= 0)
set(handles.axes1,'CLim',[min(cimg(:)) max(cimg(:))])
end
else
set(handles.axes1,'CLim',[handles.intensityParam.lowerLimit handles.intensityParam.upperLimit])
end
set(handles.ImgObject,'Cdata',cimg);
set(handles.SliceNumEdit,'String',num2str(NewVal));
drawnow
guidata(hObject, handles);
% --- Executes during object creation, after setting all properties.
function SliceNumEdit_CreateFcn(hObject, eventdata, handles)
if ispc
set(hObject,'BackgroundColor','white');
else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end
%--------------------------------------------------------------------------
function SliceNumEdit_Callback(hObject, eventdata, handles)
z= size(handles.image.CData,3);
strg = get(hObject,'String');
if str2num(strg)>=1 & str2num(strg)<=z
set(handles.SliceNumSlider,'Value',str2num(strg));
cimg = handles.image.CData(:,:,str2num(strg));
set(handles.ImgObject,'Cdata',cimg);
handles.currentSliceNumber = str2num(strg);
drawnow
end
if ~(handles.global_windowing)
cclim = [min(cimg(:)) max(cimg(:))];
if (cclim(2)>0 & cclim(2)-cclim(1) ~= 0)
set(handles.axes1,'CLim',[min(cimg(:)) max(cimg(:))])
end
else
set(handles.axes1,'CLim',[handles.intensityParam.lowerLimit handles.intensityParam.upperLimit])
end
guidata(hObject, handles);
% --------------------------------------------------------------------
% --------------------------------------------------------------------
function changeColorMaps_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function petColormaps_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function CTcolormaps_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
% --------------------------------------------------------------------
function Hot_Callback(hObject, eventdata, handles)
htable = feval('hot');
set(handles.figure1,'Colormap',htable);
if handles.imSize(3)> 1
set(handles.SliceNumEdit,'BackgroundColor',[.1 .1 .1],'ForegroundColor','r');
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function Gray_Callback(hObject, eventdata, handles)
htable = feval('gray');
set(handles.figure1,'Colormap',htable);
if handles.imSize(3)> 1
set(handles.SliceNumEdit,'BackgroundColor','k','ForegroundColor','w');
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function InvGray_Callback(hObject, eventdata, handles)
htable = 1-feval('gray');
set(handles.figure1,'Colormap',htable);
if handles.imSize(3)> 1
set(handles.SliceNumEdit,'BackgroundColor','w','ForegroundColor','k');
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function Jet_Callback(hObject, eventdata, handles)
htable = feval('jet');
set(handles.figure1,'Colormap',htable);
if handles.imSize(3)> 1
set(handles.SliceNumEdit,'BackgroundColor','b','ForegroundColor','y');
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function boneWindow_Callback(hObject, eventdata, handles)
handles.intensityParam.lowerLimit = -250;
handles.intensityParam.upperLimit = 1250;
set(handles.axes1,'CLim',[-300 1250])
guidata(hObject,handles);
% --------------------------------------------------------------------
function lungWindow_Callback(hObject, eventdata, handles)
handles.intensityParam.lowerLimit = -2500;
handles.intensityParam.upperLimit = 1100;
set(handles.axes1,'CLim',[-2500 1100])
guidata(hObject,handles);
% --------------------------------------------------------------------
function mediasitnalWindow_Callback(hObject, eventdata, handles)
handles.intensityParam.lowerLimit = -450;
handles.intensityParam.upperLimit = 350;
set(handles.axes1,'CLim',[-450 350])
guidata(hObject,handles);
% --------------------------------------------------------------------
%---------------------------------------------------------
% Callbacks for imtoolsmenu
%----------------------------------------------------------
function imToolsMenu_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function imPixval_Callback(hObject, eventdata, handles)
if isempty(handles.hText)
handles.hText = impixelinfoval(handles.figure1,handles.ImgObject);
set(handles.hText,'FontWeight','bold');
set(handles.hText,'FontSize',10);
else
delete(handles.hText);
handles.hText =[];
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function imHistogram_Callback(hObject, eventdata, handles)
myhistogram(1)
%-------------------------------------------------------------
function imProfile_Callback(hObject, eventdata, handles)
improfile;
title('Intensity profile');
ylabel('Intensity');
xlabel('Pixel position');
%------------------------------------------------
% Histogram function
% -----------------------------------------------
function myhistogram(htype)
img = getimage(gcbf);
if (htype==1)
figure;hist(double(img(:)),64);
title('Slice histogram');
ylabel('Frequency');
xlabel('Intensity');
elseif (htype == 2)
figure;hist(log(double(img(:))+1),64);
else
htype = 0;
end
return;
% --- Executes during object creation, after setting all properties.
function popup_view_CreateFcn(hObject, eventdata, handles)
if ispc
set(hObject,'BackgroundColor','white');
else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end
%-------------------------------------------------------------
% --- Executes on selection change in popup_view.
%-------------------------------------------------------------
function popup_view_Callback(hObject, eventdata, handles)
v = get(hObject,'value');
if v ~=1
nimg = convert_view(handles.oimage.CData,v);
else
nimg = handles.oimage.CData;
end
[r,c,z]=size(nimg);
handles.image.CData = nimg;
handles.image.Xdata = [1 c];
handles.image.Ydata = [1 r];
handles.viewtype = v;
handles.imSize = [r,c,z];
reset(handles.axes1); axis off;
set(handles.SliceNumSlider,'Min',1,'Max',z,'Value',...
round(z/2),'SliderStep',[1.0/double(z-1) 1.0/double(z-1)]);
set(handles.ImgObject,'Xdata',[1 c],'Ydata',[1 r]);
% Set the properties of the axes
set(handles.axes1,'XLim',[1 c],'YLim',[1 r],'PlotBoxAspectRatio',[c r 1]);
if ~isempty(handles.imageInfo)
Sthick = handles.imageInfo.SliceThickness;
if v == 2
psize = handles.imageInfo.PixelSpacing(1);
set(handles.axes1,'DataAspectRatio',[1 psize/Sthick 1]);
elseif v == 3
psize = handles.imageInfo.PixelSpacing(2);
set(handles.axes1,'DataAspectRatio',[1 psize/Sthick 1]);
else
psize = handles.imageInfo.PixelSpacing;
set(handles.axes1,'DataAspectRatio',[psize(1) psize(2) 1]);
end
end
set(handles.SliceNumEdit,'String',num2str(round(z/2)));
cimg = handles.image.CData(:,:,round(z/2));
handles.currentSliceNumber = round(z/2);
set(handles.ImgObject,'Cdata',cimg);
guidata(hObject, handles);
drawnow
%-------------------------------------------------------------
% function s= convert_view(img,desired_view)
% img: input image
% It assumes that the original image is in transverse view(1)
% 1: transverse, 2: coronal, 3: sagittal views
% s: output image
function s= convert_view(img,desired_view)
[r,c,z]=size(img);
switch desired_view
case 2
s = permute(img,[3 2 1]);
s=flipdim(s,1);
case 3
s = permute(img,[3 1 2]);
s=flipdim(s,1);
otherwise;
end
% --------------------------------------------------------------------
function readOrdinaryImageSeries_Callback(hObject, eventdata, handles)
[filename, pathname] = uigetfile({'*.*'},'Image');
if isequal(filename,0)|isequal(pathname,0)
setstatus('File not found');
else
cd(pathname)
k = findstr(filename,'.');
fnames = dir(['*' filename(k+1:end)]);
timg = imread(filename);
[r,c,z] = size(timg);
numSlices = size(fnames,1);
nimg = zeros([r,c,numSlices]);
if z == 3
hw=warndlg('Color images will be converted to gray');
uiwait;
nimg(:,:,1) = rgb2gray(timg);
else
nimg(:,:,1) = timg;
end
hwb = waitbar(0,'Reading Images, please wait...');
for i=2:numSlices
waitbar(i/numSlices, hwb);
timg = imread(fnames(i).name);
[r,c,z] = size(timg);
if z == 3
nimg(:,:,i) = rgb2gray(timg);
else
nimg(:,:,i) = timg;
end
end
close(hwb);
clear timg;
[r,c,z]=size(nimg);
handles.image.CData = nimg;
handles.image.Xdata = [1 c];
handles.image.Ydata = [1 r];
handles.imSize = [r,c,z];
handles.SliceThickness = 1;
if z==1
sliderStep = 1;
else
sliderStep = 1.0/double(z-1);
end
set(handles.SliceNumSlider,'Min',1,'Max',z,'Value',...
round(z/2),'SliderStep',[sliderStep sliderStep]);
set(handles.ImgObject,'Xdata',[1 c],'Ydata',[1 r]);
% Set the properties of the axes
set(handles.axes1,'XLim',[1 c],'YLim',[1 r],'PlotBoxAspectRatio',[c r 1]);
set(handles.SliceNumEdit,'String',num2str(round(z/2)));
cimg = handles.image.CData(:,:,round(z/2));
set(handles.ImgObject,'Cdata',cimg);
handles.oimage = handles.image;
guidata(hObject, handles);
clear nimg;
if z > 1
turnDisplayButtons(handles,'on');
set(handles.popupmenu_imageModality,'visible','off');
end
drawnow
end
% --------------------------------------------------------------------
function saveImageIntoWorkspace_Callback(hObject, eventdata, handles)
assignin('base','IIMG',handles.image.CData);
% --------------------------------------------------------------------
function imfileMenu_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function ImMaps_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
% --------------------------------------------------------------------
function readWorkspaceImage_Callback(hObject, eventdata, handles)
Vars = evalin('base','who;');
if ~isempty (Vars)
[s,v] = listdlg('PromptString','Select an image:',...
'SelectionMode','single',...
'Listsize',[150,200],...
'ListString',Vars);
if (v)
imlook3d(evalin('base',Vars{s}));
end
else
disp('No workspace variable');
end
% --------------------------------------------------------------------
% Reads series of dicom images into a 3D array
% --------------------------------------------------------------------
function readDicomPETSeries_Callback(hObject, eventdata, handles)
[filename, pathname] = uigetfile({'*.dcm';'*.*'},'Image');
if isequal(filename,0)|isequal(pathname,0)
setstatus('File not found');
else
cd(pathname)
k = findstr(filename,'.');
fnames = dir([filename(1:2) '*']);
info = dicominfo(filename);
r = info.Width;
c = info.Height;
numSlices = length(fnames);
nimg = zeros([r,c,numSlices]);
hw = waitbar(0,'Reading volume image, please wait...');
for i=1:numSlices
info = dicominfo(fnames(i).name);
nimg(:,:,info.ImageIndex) = info.RescaleSlope*dicomread(info)+info.RescaleIntercept;
waitbar(i/numSlices,hw);
end
close(hw);
fields = {'Filename','FileModDate','FileSize','ImageType','Width','Height','BitDepth',...
'NumberOfFrames','Rows','Columns','BitsAllocated','SmallestImagePixelValue',...
'LargestImagePixelValue','PixelDataGroupLength','StudyDescription','SeriesDescription',...
'StudyID','ImageID','PatientID','SliceThickness','StudyDate','AcquisitionDate',...
'AcquisitionTime','PixelSpacing'};
myinfo = keepfield(info,fields);
handles.imageInfo = myinfo;
[r,c,z]=size(nimg);
handles.image.CData = nimg;
handles.image.Xdata = [1 c];
handles.image.Ydata = [1 r];
handles.imSize = [r,c,z];
set(handles.SliceNumSlider,'Min',1,'Max',z,'Value',...
round(z/2),'SliderStep',[1.0/double(z-1) 1.0/double(z-1)]);
set(handles.ImgObject,'Xdata',[1 c],'Ydata',[1 r]);
% Set the properties of the axes
set(handles.axes1,'XLim',[1 c],'YLim',[1 r],'PlotBoxAspectRatio',[c r 1]);
set(handles.SliceNumEdit,'String',num2str(round(z/2)));
cimg = handles.image.CData(:,:,round(z/2));
set(handles.ImgObject,'Cdata',cimg);
handles.oimage = handles.image;
guidata(hObject, handles);
clear nimg;
if z>1
turnDisplayButtons(handles,'on')
end
handles.imageModality = 1;
set(handles.popupmenu_imageModality,'visible','on');
set(handles.popupmenu_imageModality,'value',1);
drawnow
end
% --------------------------------------------------------------------
function saveCurrentSlice_Callback(hObject, eventdata, handles)
[filename, pathname,filterindex] = uiputfile({'*.png';'*.tif';'*.jpg'},'Image');
fformat = {'png','tif','jpg'};
if isequal(filename,0) | isequal(pathname,0)
warndlg('No file name entered!');
else
I= getframe(handles.axes1);
I=frame2im(I);
buffer=pwd;
cd(pathname);
imwrite(I,filename,fformat{filterindex});
cd(buffer);
end
% --------------------------------------------------------------------
function adjust_intensity_window_Callback(hObject, eventdata, handles)
setappdata(0 , 'hMainGui' , gcf);
hMainGui = getappdata(0, 'hMainGui');
maxINT = max(max(max(handles.image.CData)));
minINT = min(min(min(handles.image.CData)));
cclim = get(handles.axes1,'CLim');
intensityParam = struct('lowerLimit',cclim(1),'upperLimit',cclim(2),'maxIntensity',maxINT, 'minIntensity',minINT);
setappdata(hMainGui, 'intensityParam', intensityParam);
adjustIntensityRangeGui;
uiwait;
hMainGui = getappdata(0,'hMainGui');
handles.intensityParam = getappdata(hMainGui, 'intensityParam');
guidata(hObject, handles);
% -----------------------------------------------------------------
function global_intensity_windowing_Callback(hObject, eventdata, handles)
str = get(gcbo,'Checked');
if strcmp(str,'off')
handles.global_windowing =1;
set(gcbo,'Checked','on');
else
handles.global_windowing =0;
set(gcbo,'Checked','off');
end
guidata(hObject,handles);
% --------------------------------------------------------------------
function renderVolume_Callback(hObject, eventdata, handles)
img= handles.image.CData;
if size(img,3) > 1
prompt = {'Enter Lower Threshold:','Enter Upper Threshold:'};
dlg_title = 'Enter Thresholds'; num_lines = 1; def = {'1','2'};
answer = inputdlg(prompt,dlg_title,num_lines,def);
T(1) = str2num(answer{1,1});
T(2) = str2num(answer{2,1});
nimg = img >= T(1) & img <= T(2);
s = size(img);
vlim=[1 s(2) 1 s(1) 1 s(3)];
figure;
% set(get(hndl,'CurrentAxes'),'YDir','rev');
[x y z D] = subvolume(nimg,vlim);
p = patch(isosurface(x,y,z,D,0),'FaceColor','r','EdgeColor','none');
p2 = patch(isocaps(x,y,z,D,0),'FaceColor','interp','EdgeColor','none');
set(gca,'XTick',[],'YTick',[],'ZTick',[],'Box','on','Color','c');
isonormals(x,y,z,D,p);
axis tight;
daspect([1 1 1])
lighting gouraud
else
msgbox('This is not a volume image','Error','modal');
end
% --------------------------------------------------------------------
% READS CT DICOM IMAGES
% --------------------------------------------------------------------
function readDicomCTSeries_Callback(hObject, eventdata, handles)
[filename, pathname] = uigetfile({'*.dcm';'*.*'},'Image');
if isequal(filename,0)|isequal(pathname,0)
setstatus('File not found');
else
cd(pathname)
k = findstr(filename,'.');
fnames = dir(['*' filename(k(end)+1:end)]);
info = dicominfo(filename);
r = info.Width;
c = info.Height;
numSlices = length(fnames);
nimg = zeros([r,c,numSlices]);
hwb = waitbar(0,'Reading Images, please wait...');
for i=1:numSlices
waitbar(i/numSlices, hwb);
info = dicominfo(fnames(i).name);
nimg(:,:,i) = info.RescaleSlope*dicomread(info)+info.RescaleIntercept;
end
close(hwb);
fields = {'Filename','FileModDate','FileSize','ImageType','Width','Height','BitDepth',...
'NumberOfFrames','Rows','Columns','BitsAllocated','SmallestImagePixelValue',...
'LargestImagePixelValue','PixelDataGroupLength','StudyDescription','SeriesDescription',...
'StudyID','ImageID','PatientID','SliceThickness','StudyDate','AcquisitionDate','AcquisitionTime','PixelSpacing'};
myinfo = keepfield(info,fields);
handles.imageInfo = myinfo;
[r,c,z]=size(nimg);
handles.image.CData = nimg;
handles.image.Xdata = [1 c];
handles.image.Ydata = [1 r];
handles.imSize = [r,c,z];
set(handles.SliceNumSlider,'Min',1,'Max',z,'Value',...
round(z/2),'SliderStep',[1.0/double(z-1) 1.0/double(z-1)]);
set(handles.ImgObject,'Xdata',[1 c],'Ydata',[1 r]);
% Set the properties of the axes
set(handles.axes1,'XLim',[1 c],'YLim',[1 r],'PlotBoxAspectRatio',[c r 1]);
set(handles.SliceNumEdit,'String',num2str(round(z/2)));
cimg = handles.image.CData(:,:,round(z/2));
set(handles.ImgObject,'Cdata',cimg);
handles.oimage = handles.image;
guidata(hObject, handles);
clear nimg;
handles.imageModality = 4;
if z>1
turnDisplayButtons(handles,'on')
end
handles.imageModality = 2;
set(handles.popupmenu_imageModality,'visible','on');
set(handles.popupmenu_imageModality,'value',2);
drawnow
end
% --------------------------------------------------------------------
function imageProcessMenu_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function imageThresholdManual_Callback(hObject, eventdata, handles)
img = getimage(gcbf);
th = cell2mat(inputdlg('Enter Threshold','Threshold',1,{'100'}));
if ~isempty(th)
th = str2num(th);
figure;imagesc(img>th);axis image;axis off
title('Thresholded Image');
end
% --------------------------------------------------------------------
function automatedThresholding_Callback(hObject, eventdata, handles)
img = getimage(gcbf);
th=otsu_th(single(img(:)),64);
figure;imagesc(img>th);axis image;axis off
title('Thresholded Image');
% --------------------------------------------------------------------
% READS DICOM IMAGE SINGLE OR VOLUME
% --------------------------------------------------------------------
function readSingleDicomImage_Callback(hObject, eventdata, handles)
[filename, pathname] = uigetfile({'*.dcm';'*.*'},'Image');
if isequal(filename,0)|isequal(pathname,0)
setstatus('File not found');
else
cd(pathname)
info = dicominfo(filename);
if isfield(info,'NumberOfSlices')
z = info.NumberOfSlices;
elseif isfield(info,'NumberOfFrames')
z = info.NumberOfFrames;
end
if isfield(info,'SliceThickness')
handles.SliceThickness= info.SliceThickness;
end
% Reading dicom image
nimg = squeeze(dicomread(info));
[r,c,z]=size(nimg);
handles.image.CData = nimg;
handles.image.Xdata = [1 c];
handles.image.Ydata = [1 r];
handles.imSize = [r,c,z];
if z >1
turnDisplayButtons(handles,'on');
set(handles.SliceNumSlider,'Min',1,'Max',z,'Value',...
round(z/2),'SliderStep',[1.0/double(z-1) 1.0/double(z-1)]);
set(handles.SliceNumEdit,'String',num2str(round(z/2)));
turnDisplayButtons(handles,'on');
cimg = handles.image.CData(:,:,round(z/2));
else
turnDisplayButtons(handles,'off');
cimg = handles.image.CData;
end
fields = {'Filename','FileModDate','FileSize','ImageType','Width','Height','BitDepth',...
'NumberOfFrames','Rows','Columns','BitsAllocated','SmallestImagePixelValue',...
'LargestImagePixelValue','PixelDataGroupLength','StudyDescription','SeriesDescription',...
'StudyID','ImageID','PatientID','SliceThickness','StudyDate','AcquisitionDate','AcquisitionTime','PixelSpacing'};
myinfo = keepfield(info,fields);
handles.imageInfo = myinfo;
% Set the properties of the axes and image object
set(handles.ImgObject,'XData',[1 c],'YData',[1 r],'CData',cimg);
set(handles.axes1,'XLim',[1 c],'YLim',[1 r],'PlotBoxAspectRatio',[c r 1],'DataAspectRatio',...
[1 info.PixelSpacing(2)/info.PixelSpacing(1) 1]);
handles.oimage = handles.image;
guidata(hObject, handles);
clear nimg;
drawnow
end
% --------------------------------------------------------------------
% --- Executes on selection change in popup_flip.
function popup_flip_Callback(hObject, eventdata, handles)
v = get(hObject,'value');
switch v
case 1
handles.image.CData = flipdim(handles.image.CData,2);
case 2
handles.image.CData = flipdim(handles.image.CData,1);
case 3
handles.image.CData = flipdim(handles.image.CData,3);
case 4
handles.image.CData = handles.oimage.CData;
otherwise
end
guidata(hObject,handles);
% --- Executes during object creation, after setting all properties.
function popup_flip_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function turnDisplayButtons(handles,bmode)
set(handles.SliceNumSlider,'visible',bmode);
set(handles.SliceNumEdit,'visible',bmode);
set(handles.popup_view,'visible',bmode);
set(handles.popup_flip,'visible',bmode);
set(handles.text1,'visible',bmode);
set(handles.text2,'visible',bmode);
set(handles.text3,'visible',bmode);
set(handles.popup_flip,'visible',bmode);
return
% --------------------------------------------------------------------
function helpCallback_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
% --------------------------------------------------------------------
function helpMenu_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function helpAboutImlook3d_Callback(hObject, eventdata, handles)
s = sprintf(['IMLOOK3D: 3D Image Display Tool\n',...
'Version 1.2, Copyright (2006 - Inf and Beyond)\n',...
'Omer Demirkaya, KFSH&RC']);
msgbox(s,'About IMLOOK3D Tool','modal');
% --------------------------------------------------------------------
function helpDisclaimer_Callback(hObject, eventdata, handles)
s = {'This SOFTWARE DOES NOT (A) MAKE ANY WARRANTY, EXPRESS OR IMPLIED',
'WITH RESPECT TO THE USE OF THE INFORMATION PROVIDED HEREBY; NOR (B)',
'GUARANTEE THE ACCURACY,COMPLETENESS,USEFULNESS,OR ADEQUACY OF ANY',
'RESOURCES, INFORMATION,SYSTEM,PRODUCT,OR PROCESS AVAILABLE - AT OR',
'THROUGH THIS SOFTWARE.'};
msgbox(s,'Disclaimer','modal');
% --------------------------------------------------------------------
function imageInformation_Callback(hObject, eventdata, handles)
if ~isempty(handles.imageInfo)
imageinfo(handles.imageInfo);
else
msgbox('There is no image or no information about it','Image Info..','modal');
end
% --------------------------------------------------------------------
function readSingleOrdinaryImage_Callback(hObject, eventdata, handles)
[filename, pathname] = uigetfile({'*.*'},'Image');
if isequal(filename,0)|isequal(pathname,0)
setstatus('File not found');
else
cd(pathname)
info = imfinfo(filename);
[img, map]=imread(filename);
[r,c,z] = size(img);
handles.image.CData = img;
handles.image.Xdata = [1 c];
handles.image.Ydata = [1 r];
handles.imSize = [r,c,z];
if z > 1 % single slice
set(handles.SliceNumSlider,'Min',1,'Max',z,'Value',...
round(z/2),'SliderStep',[1.0/double(z-1) 1.0/double(z-1)]);
set(handles.SliceNumEdit,'String',num2str(round(z/2)));
turnDisplayButtons(handles,'on');
cimg = handles.image.CData(:,:,round(z/2));
else
turnDisplayButtons(handles,'off');
cimg = handles.image.CData;
end
handles.imageInfo = info;
% Set the properties of the axes and image object
set(handles.ImgObject,'XData',[1 c],'YData',[1 r],'CData',cimg);
set(handles.axes1,'XLim',[1 c],'YLim',[1 r],'PlotBoxAspectRatio',[c r 1],'DataAspectRatio',[1 1 1]);
handles.oimage = handles.image;
guidata(hObject, handles);
clear nimg;
drawnow
end
% --------------------------------------------------------------------
% SMOOTH IMAGE
% --------------------------------------------------------------------
function smoothVolume_Callback(hObject, eventdata, handles)
if size(handles.image.CData,3) > 1
h = waitbar(0,'Smoothing, please wait...');
handles.image.CData= smooth3(handles.image.CData,'gaussian');
close(h);
set(handles.ImgObject,'Cdata',handles.image.CData(:,:,handles.currentSliceNumber));
guidata(hObject,handles);
end
% --------------------------------------------------------------------
% Voxel dimensions
% --------------------------------------------------------------------
function voxelSize_Callback(hObject, eventdata, handles)
prompt = {'X Size:','Y Size:', 'Z Size'};
dlg_title = 'Enter Voxel Sizes'; num_lines = 1; def = {'1','1','1'};
answer = inputdlg(prompt,dlg_title,num_lines,def);
if ~isempty(answer)
voxdim(1) = str2num(cell2mat(answer(1,1)));
voxdim(2) = str2num(cell2mat(answer(2,1)));
voxdim(3) = str2num(cell2mat(answer(3,1)));
bw = voxdim > 0; % checking for zero or negative
if prod(double(bw))
handles.imageInfo.PixelSpacing(1) = voxdim(1);
handles.imageInfo.PixelSpacing(2) = voxdim(2);
handles.imageInfo.SliceThickness = voxdim(3);
if handles.viewtype == 2
set(handles.axes1,'DataAspectRatio',[1 voxdim(1)/voxdim(3) 1]);
elseif handles.viewtype == 3
set(handles.axes1,'DataAspectRatio',[1 voxdim(2)/voxdim(3) 1]);
else
set(handles.axes1,'DataAspectRatio',[1 voxdim(2)/voxdim(1) 1]);
end
end
end
guidata(hObject,handles);
% --------------------------------------------------------------------
% Horizontal Profile
% --------------------------------------------------------------------
function horizontalProfile_Callback(hObject, eventdata, handles)
h = warndlg('Double-click on the row','Pixel Selection');
uiwait;
[c,r,P] = impixel;
f = get(findobj(gcf,'Type','image'));
txt = ['Profile for row: ' num2str(r)];
figure;
plot(f.CData(r,:));title(txt);xlabel('Pixel location');ylabel('Intensity');
% --------------------------------------------------------------------
% Vertical Profile
% --------------------------------------------------------------------
function verticalProfile_Callback(hObject, eventdata, handles)
h = warndlg('Double-click on the column','Pixel Selection');
uiwait;
[c,r,P] = impixel;
f = get(findobj(gcf,'Type','image'));
txt = ['Profile for column: ' num2str(c)];
figure;
plot(f.CData(:,c));title(txt);xlabel('Pixel location');ylabel('Intensity');
% --------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
% --------------------------------------------------------------------
function popupmenu_imageModality_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --------------------------------------------------------------------
% --- Image modality selection
% --------------------------------------------------------------------
function popupmenu_imageModality_Callback(hObject, eventdata, handles)
imMod = get(hObject,'value');
handles.imageModality = imMod;
% --------------------------------------------------------------------
% Executes MATLAB IMTOOL
% --------------------------------------------------------------------
function imtoolMATLAB_Callback(hObject, eventdata, handles)
f = get(findobj(gcf,'Type','image'));
imtool(f.CData,[min(f.CData(:)) max(f.CData(:))]);
% --------------------------------------------------------------------
% helpMenu on Imlook3D
% --------------------------------------------------------------------
function helpIMLOOK3D_Callback(hObject, eventdata, handles)
warndlg('Under Construction and needs help :)');
% --------------------------------------------------------------------
% Reading MRI images
% --------------------------------------------------------------------
function readDICOMMRISeries_Callback(hObject, eventdata, handles)
[filename, pathname] = uigetfile({'*.dcm';'*.*'},'Image');
if isequal(filename,0)|isequal(pathname,0)
setstatus('File not found');
else
cd(pathname)
k = findstr(filename,'.');
fnames = dir(['*' filename(k+1:end)]);
info = dicominfo(filename);
r = info.Width;
c = info.Height;
numSlices = length(fnames);
nimg = zeros([r,c,numSlices]);
hwb = waitbar(0,'Reading Images, please wait...');
for i=1:numSlices
waitbar(i/numSlices, hwb);
info = dicominfo(fnames(i).name);
nimg(:,:,i) = dicomread(info);
end
close(hwb);
fields = {'Filename','FileModDate','FileSize','ImageType','Width','Height','BitDepth',...
'NumberOfFrames','Rows','Columns','BitsAllocated','SmallestImagePixelValue',...
'LargestImagePixelValue','PixelDataGroupLength','StudyDescription','SeriesDescription',...
'StudyID','ImageID','PatientID','SliceThickness','StudyDate','AcquisitionDate','AcquisitionTime','PixelSpacing'};
myinfo = keepfield(info,fields);
handles.imageInfo = myinfo;
[r,c,z]=size(nimg);
handles.image.CData = nimg;
handles.image.Xdata = [1 c];
handles.image.Ydata = [1 r];
handles.imSize = [r,c,z];
set(handles.SliceNumSlider,'Min',1,'Max',z,'Value',...
round(z/2),'SliderStep',[1.0/double(z-1) 1.0/double(z-1)]);
set(handles.ImgObject,'Xdata',[1 c],'Ydata',[1 r]);
% Set the properties of the axes
set(handles.axes1,'XLim',[1 c],'YLim',[1 r],'PlotBoxAspectRatio',[c r 1]);
set(handles.SliceNumEdit,'String',num2str(round(z/2)));
cimg = handles.image.CData(:,:,round(z/2));
set(handles.ImgObject,'Cdata',cimg);
handles.oimage = handles.image;
guidata(hObject, handles);
clear nimg;
if z>1
turnDisplayButtons(handles,'on')
end
handles.imageModality = 4;
set(handles.popupmenu_imageModality,'visible','on');
set(handles.popupmenu_imageModality,'value',4);
drawnow
end
% --------------------------------------------------------------------
function cropVolume_Callback(hObject, eventdata, handles)
% hObject handle to cropVolume (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[I,rect] = imcrop;
s = handles.image.CData;
switch handles.viewtype
case 1
[r,c,z] = size(s);
oimg = crop3d(s,rect,[1 z]);
case 2
% s = permute(img,[3 2 1]);
% s = flipdim(s,1);
[r,c,z] = size(s);
oimg = crop3d(s,rect,[1 z]);
case 3
% s = permute(img,[3 1 2]);
% s = flipdim(s,1);
[r,c,z] = size(s);
oimg = crop3d(s,rect,[1 z]);
otherwise;
end
imlook3d(oimg);
