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lunge.m
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function lunge %%% -- INFO -- the function file name is what matters, so lets make this equal
figObject = createMainFigure();
%Create Navigation Axes
navigationAxesObjects = createNavigationAxes(figObject);
%Create Information Texts
informationTextsObjects = createInformationTexts(navigationAxesObjects.informationAxesObject);
%Create Menus
createMenuObjects(figObject);
createControlSideBar(figObject);
handles.gui = guihandles(figObject);
guidata(figObject, handles);
end
%%%%%%%%%%%% GUI RELATED FUNCTIONS %%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function figObject = createMainFigure()
%Get the screen size
screenSize = get(0, 'ScreenSize');
figObject = figure('Tag', 'mainFig',...
'MenuBar', 'None',...
'NumberTitle', 'Off',...
'Name', 'New CT Processing V 0.0.1dev',...
'units', 'normalized', ...
'OuterPosition', [0 0.03 1 0.97], ... %%% -- INFO -- in my laptop I can not see the top of the window, only after manually risize. I think it is a problem with windows, anyway a chaged the dimensions, is ok in your screen?
'Color', 'black',...
'WindowScrollWheelFcn', @refreshSlicePosition,...
'WindowButtonMotionFcn', @mouseMove);
end
function navigationAxesObjectStructure = createNavigationAxes(parentFigureObject)
navigationAxesObjectStructure.navigationAxesObject = axes('Parent', parentFigureObject,...
'Units', 'Normalized',...
'Position', [0.16, 0.15, 0.6, 0.8],...
'Color', 'black',...
'XtickLabel', '',...
'YtickLabel', '',...
'Tag', 'navigationAxes');
navigationAxesObjectStructure.informationAxesObject = axes('Parent', parentFigureObject,...
'Units', 'Normalized',...
'Position', [0.11, 0.08, 0.7, 0.9],...
'XtickLabel', '',...
'YtickLabel', '',...
'Color', 'black');
end
function informationTextsObjectsStructure = createInformationTexts(parentAxesObject)
informationTextsObjectsStructure.patientName = text(0.5, 0.98, 'Patient''s Name',...
'Color', 'white',...
'Fontsize', 12,...
'Fontweight', 'bold',...
'Tag', 'patientNameTag',...
'HorizontalAlignment', 'center',...
'Visible', 'Off');
informationTextsObjectsStructure.slicePosition = text(0.01, 0.02, '1/-',...
'Color', 'white',...
'Fontsize', 12,...
'Fontweight', 'bold',...
'Visible', 'Off',...
'Tag', 'slicePositionTag');
informationTextsObjectsStructure.numberOfRows = text(0.01, 0.06, 'Image Size: -',...
'Color', 'white',...
'Fontsize', 12,...
'Fontweight', 'bold',...
'Visible', 'Off',...
'Tag', 'numberOfRowsTag');
informationTextsObjectsStructure.pixelValue = text(0.14, 0.02, 'Pixel Value = -',...
'Color', 'white',...
'Fontsize', 12,...
'Fontweight', 'bold',...
'Visible', 'Off',...
'Tag', 'pixelValueTag');
end
function createMenuObjects(parentFigureObject)
%Create Menu Objects
%%%FILE MENU
fileMenu = uimenu('Parent', parentFigureObject,...
'Label', 'File');
openGroup = uimenu('Parent', fileMenu, 'Label', 'Open');
%Load Patient Menu
uimenu('Parent', openGroup,...
'Label', 'Open Patient',...
'Acc', 'P',...
'Callback', @openPatient);
%Load Frame Menu
uimenu('Parent', openGroup,...
'Label', 'Open Frame',...
'Acc', 'O',...
'Callback', @openDicom);
%Load Masks Menu
uimenu('Parent', openGroup,...
'Label', 'Open Masks',...
'Acc', 'M',...
'Enable', 'Off',...
'Tag', 'openMaskMenu',...
'Callback', @openMask);
%Save data Menu
uimenu('Parent', fileMenu,...
'Label', 'Save Data',...
'Enable', 'Off',...
'Tag', 'saveDataMenu',...
'Callback', @saveData);
%Close Patient Menu
uimenu('Parent', fileMenu,...
'Label', 'Close Patient',...
'Enable', 'Off',...
'Tag', 'closePatientMenu',...
'Callback', @closePatient);
%Quit Menu
uimenu('Parent', fileMenu,...
'Label', 'Quit',...
'Callback', '');
%%%ANALYSIS MENU
analysisMenu = uimenu('Parent', parentFigureObject,...
'Label', 'Analysis');
massAndVolume = uimenu('Parent', analysisMenu,...
'Label', 'Mass and Volume',... ..
'Enable', 'Off',...
'Tag', 'massAndVolumeCalculation');
uimenu('Parent', massAndVolume,...
'Label', 'Cranio-Caudal',...
'Callback', @massAndVolumeCalculation);
uimenu('Parent', massAndVolume,...
'Label', 'Antero-Posterior',...
'Callback', '');
uimenu('Parent', massAndVolume,...
'Label', 'Latero-Lateral',...
'Callback', '');
uimenu('Parent',analysisMenu,...
'Enable', 'Off',...
'Tag', 'p15Calculation',...
'Callback', @p15Calculation,...
'Label', 'P15');
uimenu('Parent',analysisMenu,...
'Enable', 'Off',...
'Tag', 'toSUV',...
'Callback', @toSUV,...
'Label', 'PET to SUV');
%%%PLUGINS MENU
pluginsMenu = uimenu('Parent', parentFigureObject,...
'Label', 'Plugins');
end
function createControlSideBar(parentFigureObject)
mainPanel = uipanel('Parent', parentFigureObject,...
'Units', 'Normalized',...
'Position', [0.8, 0, 0.2, 1],...'
'BackGroundColor', 'black',...
'Visible', 'On',...
'Tag', 'sideBarMainPanel');
%Side Bar Sliders
uicontrol('Parent', mainPanel,...
'Style', 'Slider',...
'Units', 'Normalized',...
'Position', [0.1, 0.45, 0.1, 0.2],...
'Tag', 'windowWidthSlider',...
'Callback', @windowWidthCallback);
uicontrol('Parent', mainPanel,...
'Style', 'Slider',...
'Units', 'Normalized',...
'Position', [0.35, 0.45, 0.1, 0.2],...
'Tag', 'windowCenterSlider',...
'Callback', @windowCenterCallback);
uicontrol('Parent',mainPanel,...
'Style', 'Edit',...
'Units', 'Normalized',...
'Position', [0.12, 0.67, 0.11, 0.02],...
'HorizontalAlignment', 'Center',...
'String', '0',...
'BackGroundColor', 'black',...
'ForeGroundColor', 'white',...
'Tag', 'windowWidthText',...
'Callback', @windowWidthTextCallback);
uicontrol('Parent',mainPanel,...
'Style', 'Edit',...
'Units', 'Normalized',...
'Position', [0.37, 0.67, 0.11, 0.02],...
'HorizontalAlignment', 'Center',...
'String', '0',...
'BackGroundColor', 'black',...
'ForeGroundColor', 'white',...
'Tag', 'windowCenterText',...
'Callback', @windowCenterTextCallback);
%Window Width and Center Buttons
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.48, 0.45, 0.28, 0.06],...
'String', 'Reset',...
'Callback', @resetWindowWidthCenter);
%HU Ranges textfields
uicontrol('Parent', mainPanel,...
'Units', 'Normalized', ...
'Position', [0.3, 0.2, 0.45, 0.05],...
'Style', 'Text',...
'Backgroundcolor', 'black',...
'Foregroundcolor', 'white',...
'Fontsize', 13,...
'Fontweight', 'bold',...
'String', 'HU Ranges');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized', ...
'Position', [0.01 , 0.16, 0.45, 0.03],...
'Style', 'Text',...
'Backgroundcolor', 'black',...
'Foregroundcolor', 'white',...
'Fontsize', 11,...
'HorizontalAlignment', 'left',...
'String', 'Hyper Aerated:');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized', ...
'Position', [0.01 , 0.12, 0.5, 0.03],...
'Style', 'Text',...
'Backgroundcolor', 'black',...
'Foregroundcolor', 'white',...
'Fontsize', 11,...
'HorizontalAlignment', 'left',...
'String', 'Normally Aerated:');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized', ...
'Position', [0.01 , 0.08, 0.45, 0.03],...
'Style', 'Text',...
'Backgroundcolor', 'black',...
'Foregroundcolor', 'white',...
'Fontsize', 11,...
'HorizontalAlignment', 'left',...
'String', 'Poorly Aerated:');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized', ...
'Position', [0.01 , 0.04, 0.45, 0.03],...
'Style', 'Text',...
'Backgroundcolor', 'black',...
'Foregroundcolor', 'white',...
'Fontsize', 11,...
'HorizontalAlignment', 'left',...
'String', 'Non Aerated:');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.55, 0.16, 0.15, 0.03],...
'Style', 'Edit',...
'Tag', 'upperHyperValue',...
'String', '-1000');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.75, 0.16, 0.15, 0.03],...
'Style', 'Edit',...
'Tag', 'lowerHyperValue',...
'String', '-900');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.55, 0.12, 0.15, 0.03],...
'Style', 'Edit',...
'Tag', 'upperNormallyValue',...
'String', '-900');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.75, 0.12, 0.15, 0.03],...
'Style', 'Edit',...
'Tag', 'lowerNormallyValue',...
'String', '-500');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.55, 0.08, 0.15, 0.03],...
'Style', 'Edit',...
'Tag', 'upperPoorlyValue',...
'String', '-500');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.75, 0.08, 0.15, 0.03],...
'Style', 'Edit',...
'Tag', 'lowerPoorlyValue',...
'String', '-100');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.55, 0.04, 0.15, 0.03],...
'Style', 'Edit',...
'Tag', 'upperNonValue',...
'String', '-100');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.75, 0.04, 0.15, 0.03],...
'Style', 'Edit',...
'Tag', 'lowerNonValue',...
'String', '100');
%Side Bar Slice Range
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.3, 0.35, 0.4, 0.05],...
'Style', 'Text',...
'BackGroundColor', 'black',...
'ForeGroundColor', 'white',...
'FontSize', 13,...
'FontWeight', 'bold',...
'String', 'Slice Range');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.01, 0.33, 0.2, 0.025],...
'Style', 'Text',...
'String', 'From:',...
'BackGroundColor', 'black',...
'ForeGroundColor', 'white');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.4, 0.33, 0.2, 0.025],...
'Style', 'Text',...
'String', 'To:',...
'BackGroundColor', 'black',...
'ForeGroundColor', 'white');
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.25, 0.33, 0.15, 0.025],...
'Style', 'Edit',...
'String', '1',....
'Tag', 'sliceRangeFrom',...
'Callback', @sliceRangeFromToCallback);
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.6, 0.33, 0.15, 0.025],...
'Style', 'Edit',...
'String', '1',...
'Tag', 'sliceRangeTo',...
'Callback', @sliceRangeFromToCallback);
% Overlay checkboxes
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.1, 0.95, 0.8, 0.025],...
'Style', 'CheckBox',...
'String', 'Show Mask',...
'FontSize', 13,...
'BackGroundColor', 'black',...
'ForeGroundColor', 'white',...
'Enable','off',...
'Tag', 'maskChk',...
'Callback', @maskChkCallback);
uicontrol('Parent', mainPanel,...
'Units', 'Normalized',...
'Position', [0.1, 0.92, 0.8, 0.025],...
'Style', 'CheckBox',...
'String', 'Show PET',...
'FontSize', 13,...
'BackGroundColor', 'black',...
'ForeGroundColor', 'white',...
'Enable','off',...
'Tag', 'petChk',...
'Callback', @petChkCallback);
end
%%%%%%%%%%%% GUI RELATED FUNCTIONS - END %%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function handles = displayCurrentDicom(handles, dicomImage, slicePosition)
axes(handles.gui.navigationAxes)
set(findobj(handles.gui.navigationAxes,'type','image'),'CData',dicomImage(:, :, slicePosition))
set(handles.gui.navigationAxes, 'Clim', [handles.data.displayLow, handles.data.displayHigh]);
colormap(gray)
end
function handles = createDisplayDicom(handles, dicomImage, slicePosition)
axes(handles.gui.navigationAxes)
set(handles.gui.navigationAxes,'nextPlot','replace')
handles.gui.imagePlot = imagesc(dicomImage(:, :, slicePosition));
set(handles.gui.navigationAxes, 'Clim', [handles.data.displayLow, handles.data.displayHigh]);
colormap(gray)
end
function refreshPatientsInfo(handles, info)
patientName = info.PatientName.FamilyName;
%Check if Patient has Give Name
if isfield(info.PatientName, 'GivenName')
patientName = [info.PatientName.GivenName ' ' patientName];
end
set(handles.gui.patientNameTag, 'String', patientName)
set(handles.gui.numberOfRowsTag, 'String', sprintf('Image Size: %d x %d', info.Rows, info.Columns));
end
function refreshSlicePosition(hObject, eventdata)
slicePositionPlaceHolder = '%d/%d';
handles = guidata(hObject);
if isfield(handles, 'data')
nSlices = size(handles.data.dicomImage, 3);
currentSlicePosition = get(handles.gui.slicePositionTag, 'String');
%Get the new slice position based on the displayed values using regexp
newSlicePosition = getSlicePosition(currentSlicePosition,...
eventdata.VerticalScrollCount);
%Make sure that the slice number return to 1 if it is bigger than the
%number of slices
newSlicePosition = mod(newSlicePosition, nSlices);
%Make sure that the slice number return to nSlices if it is smaller than the
%number of slices
if ~newSlicePosition && eventdata.VerticalScrollCount < 0
newSlicePosition = nSlices;
elseif ~newSlicePosition && eventdata.VerticalScrollCount >= 0 %%% -- INFO -- matlab has some hard time with the scroll of my laptop, in this case VerticalScrollCount == 0, it get an error latter in this function and this is error realy I need to restart matlab. I changed > to >=
newSlicePosition = 1;
end
%Refresh slice position information.
set(handles.gui.slicePositionTag, 'String',...
sprintf(slicePositionPlaceHolder, newSlicePosition, nSlices));
if handles.gui.petDisplay
if isfield(handles.dataPET,'CT')
handles = displayCurrentDicom(handles, handles.dataPET.CT, newSlicePosition);
end
else
handles = displayCurrentDicom(handles, handles.data.dicomImage, newSlicePosition);
end
% refresh overlay if needed
if get(handles.gui.maskChk,'value')
if handles.gui.petDisplay
refreshOverlay(handles.dataPET.masks,handles)
else
refreshOverlay(handles.data.masks,handles)
end
elseif get(handles.gui.petChk,'Value') && handles.gui.petDisplay
refreshOverlay(handles.dataPET.dicomImage,handles)
end
%Refresh pixel value information.
refreshPixelPositionInfo(handles, handles.gui.navigationAxes)
guidata(hObject, handles)
end
end
function newSlicePosition = getSlicePosition(slicePositionString, direction)
tempSlicePosition = regexp(slicePositionString, '/', 'split');
if direction > 0
newSlicePosition = str2double(tempSlicePosition(1)) + 1;
else
newSlicePosition = str2double(tempSlicePosition(1)) - 1;
end
end
function openPatient(hObject, eventdata)
handles = guidata(hObject);
if isfield(handles, 'data')
dirPath = uigetdir(handles.data.dicomImagePath, 'Select Patient''s Folder');
else
dirPath = uigetdir('Select Patient''s Folder');
end
if dirPath
%Display Wait window
figObj = createLogFrame();
displayLog(figObj, sprintf('%s', 'Searching patient data files...'), 0)
set(handles.gui.mainFig,'Pointer','watch'); drawnow('expose');
% Look for available CT,mask and PET files
[mask,ct,pet]=find_files(dirPath,{},[],[]);
%Close log frame
close(figObj)
% Now load CT, mask and PET
% TODO no data found case
if ~isempty(ct)
openDicom(hObject, [], fileparts(ct))
end
% TODO case with more than one possible mask
if ~isempty(mask)
[folder name ext] = fileparts(mask{1});
openMask(hObject, [], [name ext], [folder filesep])
end
if ~isempty(pet)
openDicom(hObject, [], fileparts(pet))
end
set(handles.gui.mainFig,'Pointer','arrow'); drawnow('expose');
end
end
function openDicom(hObject, eventdata, dirPath)
handles = guidata(hObject);
if ~exist('dirPath','var')
if isfield(handles, 'data')
dirPath = uigetdir(handles.data.dicomImagePath, 'Select Patient''s Dicom Folder');
else
dirPath = uigetdir('Select Patient''s Dicom Folder');
end
end
if dirPath
%Display Wait window
figObj = createLogFrame();
displayLog(figObj, sprintf('%s', 'Loading Images...'), 0)
set(handles.gui.mainFig,'Pointer','watch'); drawnow('expose');
listOfFiles = dir(dirPath);
%Try to open every file with dicomread. If possible use as a Dicom
nFiles = length(listOfFiles);
found = false;
counter = 0;
%Create a function to insert this piece of code.
while ~found
counter = counter + 1;
fileName = listOfFiles(counter).name;
if ~strcmp(fileName, '.') && ~strcmp(fileName, '..')
completeFileName = [dirPath filesep fileName];
%Try to discover if files without extension are Dicom files
try
info = dicominfo(completeFileName); %%% -- INFO -- I changed the info and handles.data.metadata, because I think this way makes more sense and I need to check is it is a PET image to know were to put the data
handles.gui.petDisplay = strcmpi(info.Modality,'pt');
if handles.gui.petDisplay
% using the string field name we do not need to
% repeat this if in each instance
fieldname = 'dataPET';
else
fieldname = 'data';
end
handles.(fieldname).metadata = dicom_read_header(completeFileName);
%%% -- INFO -- I used a random dicom file I had and it
%%% didn't have the WindowCenter and WindowWidth
%%% infomation - I included the following lines to
%%% garantee
if ~isfield(info,'WindowWidth')
handles.data.metadata.WindowWidth = 1400; % 1400 is a common value used to visualize lung in CT
end
if ~isfield(info,'WindowCenter')
handles.data.metadata.WindowCenter = -600; % -600 is a common value used to visualize lung in CT
end
found = true;
catch
%Do nothing
continue
end
end
end
dicomImage = single(dicom_read_volume(handles.(fieldname).metadata)); %% -- INFO -- for the PET data we can not use int, it will need more memory, but we need single for calculation too
if strcmpi(handles.(fieldname).metadata.Manufacturer,'siemens')
% Siemens data can have different slopes and intercepts for each
% slice (at least in data from Pettsburg)
handles.(fieldname).metadata.RescaleSlope = zeros([1,1,numel(handles.(fieldname).metadata.Filenames)]);
handles.(fieldname).metadata.RescaleIntercept = zeros([1,1,numel(handles.(fieldname).metadata.Filenames)]);
for idx = 1:numel(handles.(fieldname).metadata.Filenames)
aux = dicominfo(handles.(fieldname).metadata.Filenames{idx});
handles.(fieldname).metadata.RescaleSlope(idx) = single(aux.RescaleSlope);
handles.(fieldname).metadata.RescaleIntercept(idx) = single(aux.RescaleIntercept);
end
end
if isfield(info, 'RescaleSlope')
dicomImage = bsxfun(@times,dicomImage,single(handles.(fieldname).metadata.RescaleSlope)); % bsxfun expandes the singleton dimension automaticaly
end
if isfield(info, 'RescaleIntercept')
dicomImage = bsxfun(@plus,dicomImage,single(handles.(fieldname).metadata.RescaleIntercept));
end
% If a PET image was loaded maybe the user want to analyse PET and
% CT together. For this CT must be converted to PET resolution.
if handles.gui.petDisplay && isfield(handles,'data')
displayLog(figObj, sprintf('%s', 'Converting other data to PET resolution...'), 1)
map = CTPET_CreateMap(handles.data.metadata,handles.dataPET.metadata);
handles.dataPET.CT = CTPET_ApplyMap(handles.data.dicomImage,map);
% if a mask also exist, it should be converted too
if isfield(handles.data,'masks')
handles.dataPET.masks = CTPET_ApplyMap(handles.data.masks,map);
end
end
set(handles.gui.mainFig,'Pointer','arrow'); drawnow('expose');
handles.(fieldname).dicomImage = dicomImage;
%Set the Window Width and Window Center
handles = calculateWindowWidthAndCenter(handles);
configureSliders(handles)
%Refresh Show Mask and Show PET stat
set(handles.gui.maskChk, 'Value', 0)
set(handles.gui.petChk,'Value', 0)
%Display First Slice
cla(handles.gui.navigationAxes)
if handles.gui.petDisplay
if isfield(handles.dataPET,'CT')
handles = createDisplayDicom(handles, handles.dataPET.CT, 1);
set(handles.gui.petChk,'Enable','on')
end
set(handles.gui.toSUV,'Enable','on')
else
handles = createDisplayDicom(handles, dicomImage, 1);
set(handles.gui.petChk,'Enable','off')
end
%Display Patients Information
refreshPatientsInfo(handles, handles.(fieldname).metadata)
%Update Interface Appearene
hideShowImageInformation(handles, 'On')
hideShowSideBar(handles, 'On')
set(handles.gui.openMaskMenu, 'Enable', 'On')
set(handles.gui.saveDataMenu, 'Enable', 'On')
set(handles.gui.closePatientMenu, 'Enable', 'On')
%Create a variable to store the Image folder. This way the Masks
%could be easier located.
handles.(fieldname).dicomImagePath = dirPath;
% -- INFO -- This is redundant with createDisplayDicom
% % set(handles.gui.navigationAxes, 'Clim',...
% % [handles.data.displayLow, handles.data.displayHigh])
% Create the saved field as true, because if the user just load
% files the data should not be saved before close. Every data
% processing function should change saved to false
handles.saved = 1;
guidata(hObject, handles)
%Close log frame
close(figObj)
end
end
function openMask(hObject, eventdata, FileName, PathName)
handles = guidata(hObject);
if ~exist('FileName','var')
[FileName PathName] = uigetfile('*.hdr;*.nrrd',...
'Select the file containing the masks', handles.data.dicomImagePath);
end
if FileName
%Display Wait window
figObj = createLogFrame();
displayLog(figObj, sprintf('%s', 'Loading Masks...'), 0)
set(handles.gui.mainFig,'Pointer','watch'); drawnow('expose');
handles = guidata(hObject);
fileName = [PathName FileName];
if strfind(FileName,'hdr')
masks = analyze75read(fileName);
else
masks = nrrd_read(fileName);
end
% Masks created in 3D Slicer using CIP plugin are labeled, ask user
% wich labels he wants to load
if any(masks(:)>255);
labels = unique(masks(:)); labels = labels(2:end); % exclude 0 fram list of labels
list = interpretCIPCodes(labels);
h=lungeDlg('msgbox',{'You opened a labeld mask file.';'Use the next window to choose structure you want to keep!'},'Instruction!!!','help','modal');
%msgbox({'You opened a labeld mask file.';'Use the next window to choose structure you want to keep!'},'Instruction!!!','help','modal');
uiwait(h);
chosen = lungeDlg('listdlg','ListString',list,'Name','Structures to keep');
%listdlg('ListString',list,'Name','Structures to keep');
notchosen = 1:numel(labels);
notchosen=notchosen(~ismember(notchosen,chosen));
for each=notchosen
masks(masks==labels(each))=0;
end
end
% Mask is converted to logical to reduce memory size
handles.data.masks = logical(masks);
% If there is a PET image loaded and the mask is not of the same
% size as PET, convert it
if isfield(handles,'dataPET')
if ~all(size(handles.dataPET.dicomImage) == size(masks))
map = CTPET_CreateMap(handles.data.metadata, handles.dataPET.metadata);
handles.dataPET.masks = CTPET_ApplyMap(handles.data.masks,map);
end
end
set(handles.gui.mainFig,'Pointer','arrow'); drawnow('expose');
guidata(hObject, handles)
%UPDATE MENU
set(handles.gui.massAndVolumeCalculation, 'Enable', 'On')
set(handles.gui.p15Calculation, 'Enable', 'On')
set(handles.gui.maskChk, 'Enable', 'On')
%Close wait window
close(figObj);
end
end
function saveData(hObject, eventdata)
handles = guidata(hObject);
if ~isfield(handles.data,'fileName')
[filename, pathname] = uiputfile('*.mat', 'Chose filename');
if isequal(filename,0) || isequal(pathname,0)
return
else
handles.data.fileName = fullfile(pathname, filename);
end
end
%Display Wait window
figObj = createLogFrame();
displayLog(figObj, sprintf('%s', 'Saving data...'), 0)
data = handles.data;
save(handles.data.fileName,'-struct','data')
if isfield(handles,'dataPET')
data = handles.dataPET;
save(handles.data.fileName,'-struct','data','-append')
end
set(handles.gui.saveDataMenu,'Enable','Off')
%Close wait window
close(figObj);
guidata(hObject,handles)
end
function closePatient(hObject, eventdata)
handles = guidata(hObject);
set(handles.gui.mainFig,'Pointer','watch'); drawnow('expose');
if ~handles.saved
% Ask if want to save
btn = lungeDlg('questdlg','You have unsaved data. Want to save before close this patient?','Save','yes','no', 'yes');
%questdlg('You have unsaved data. Want to save before close this patient?','Save','yes','no', 'yes');
if strcmp(btn,'yes')
saveData(hObject)
end
end
handles = rmfield(handles,'data');
if isfield(handles,'dataPET')
handles = rmfield(handles,'dataPET');
end
% Hide patient information and DICOM display
hideShowImageInformation(handles,'off')
cla(handles.gui.navigationAxes)
set(handles.gui.navigationAxes,'color','k')
%UPDATE MENU
set(handles.gui.massAndVolumeCalculation, 'Enable', 'Off')
set(handles.gui.p15Calculation, 'Enable', 'Off')
set(handles.gui.toSUV, 'Enable', 'Off')
set(handles.gui.maskChk, 'Enable', 'Off')
set(handles.gui.petChk, 'Enable', 'Off')
set(handles.gui.openMaskMenu, 'Enable', 'Off')
set(handles.gui.closePatientMenu, 'Enable', 'Off')
set(handles.gui.saveDataMenu,'Enable','Off')
set(handles.gui.mainFig,'Pointer','arrow'); drawnow('expose');
guidata(hObject, handles)
end
function mouseMove(hObject, eventdata)
handles = guidata(hObject);
mainAxes = handles.gui.navigationAxes;
refreshPixelPositionInfo(handles, mainAxes);
end
function refreshPixelPositionInfo(handles, mainAxes)
if isfield(handles, 'data')
C = get(mainAxes,'currentpoint');
xlim = get(mainAxes,'xlim');
ylim = get(mainAxes,'ylim');
row = round(C(1));
col = round(C(1, 2));
%Check if pointer is inside Navigation Axes.
outX = ~any(diff([xlim(1) C(1,1) xlim(2)])<0);
outY = ~any(diff([ylim(1) C(1,2) ylim(2)])<0);
if outX && outY
%Get the current Slice
currentSlicePositionString = get(handles.gui.slicePositionTag, 'String');
tempSlicePosition = regexp(currentSlicePositionString, '/', 'split');
slicePosition = str2double(tempSlicePosition(1));
currentSlice = handles.data.dicomImage(:, :, slicePosition);
pixelValue = currentSlice(col, row);
set(handles.gui.pixelValueTag, 'String', sprintf('Pixel Value = %.2f', double(pixelValue)))
else
set(handles.gui.pixelValueTag, 'String', sprintf('Pixel Value = -'))
end
end
end
function windowWidthCallback(hObject, eventdata)
handles = guidata(hObject);
windowWidth = get(handles.gui.windowWidthSlider, 'Value');
windowCenter = get(handles.gui.windowCenterSlider, 'Value');
if isfield(handles,'data') %%% -- INFO -- if you try to use the sliders before load data there was an error. Other option is to start with disabled sliders
set(handles.gui.windowWidthText, 'String',sprintf('%.2f', windowWidth));
handles = calculateWindowWidthAndCenter(handles,...
windowWidth, windowCenter);
set(handles.gui.navigationAxes, 'Clim', [handles.data.displayLow handles.data.displayHigh])
end
guidata(hObject, handles);
end
function windowWidthTextCallback(hObject, eventdata)
handles = guidata(hObject);
windowWidth = str2double(get(hObject, 'String'));
set(handles.gui.windowWidthSlider, 'Value',windowWidth);
windowCenterCallback(hObject)
end
function windowCenterCallback(hObject, eventdata)
handles = guidata(hObject);
windowWidth = get(handles.gui.windowWidthSlider, 'Value');
windowCenter = get(handles.gui.windowCenterSlider, 'Value');
if isfield(handles,'data') %%% -- INFO -- if you try to use the sliders before load data there was an error. Other option is to start with disabled sliders
set(handles.gui.windowCenterText, 'String',sprintf('%.2f', windowCenter));
handles = calculateWindowWidthAndCenter(handles, windowWidth, windowCenter);
set(handles.gui.navigationAxes, 'Clim', [handles.data.displayLow handles.data.displayHigh])
end
guidata(hObject, handles);
end
function windowCenterTextCallback(hObject, eventdata)
handles = guidata(hObject);
windowCenter = str2double(get(hObject, 'String'));
set(handles.gui.windowCenterSlider, 'Value',windowCenter);
windowCenterCallback(hObject)
end
function resetWindowWidthCenter(hObject, eventdata)
handles = guidata(hObject);
if isfield(handles,'data') %%% -- INFO -- if you try to use the button before load data there was an error. Other option is to start with disabled button
windowWidth = handles.data.metadata.WindowWidth(1);
windowCenter = handles.data.metadata.WindowCenter(1);
handles = calculateWindowWidthAndCenter(handles, windowWidth, windowCenter);
set(handles.gui.navigationAxes, 'Clim', ...
[handles.data.displayLow, handles.data.displayHigh]);
set(handles.gui.windowWidthSlider, 'Value', windowWidth);
set(handles.gui.windowWidthText, 'String',sprintf('%.2f', windowWidth));
set(handles.gui.windowCenterSlider, 'Value', windowCenter);
set(handles.gui.windowCenterText, 'String',sprintf('%.2f', windowCenter));
end
guidata(hObject, handles)
end
function hideShowSideBar(handles, hideOrShow)
set(handles.gui.sideBarMainPanel, 'Visible', hideOrShow)
end
function maskChkCallback(hObject, eventdata)
handles = guidata(hObject);
if get(hObject,'Value')
set(handles.gui.petChk,'enable','off')
if handles.gui.petDisplay
handles.gui.overlayPlot = createOverlay(handles.dataPET.masks,handles);
else
handles.gui.overlayPlot = createOverlay(handles.data.masks,handles);
end
else
if handles.gui.petDisplay
set(handles.gui.petChk,'enable','on')
end
if ishandle(handles.gui.overlayPlot)
set(handles.gui.overlayPlot,'visible','off')
end
end
guidata(hObject,handles)
end
function petChkCallback(hObject, eventdata)
handles = guidata(hObject);
if get(hObject,'Value')
if handles.gui.petDisplay
set(handles.gui.maskChk,'enable','off')
handles.gui.overlayPlot = createOverlay(handles.dataPET.dicomImage,handles);
end
else
set(handles.gui.maskChk,'enable','on')
if ishandle(handles.gui.overlayPlot)
set(handles.gui.overlayPlot,'visible','off')
end
end
guidata(hObject,handles)
end
function hideShowImageInformation(handles, hideOrShow)
set(handles.gui.patientNameTag, 'Visible', hideOrShow)
set(handles.gui.slicePositionTag, 'Visible', hideOrShow)
set(handles.gui.numberOfRowsTag, 'Visible', hideOrShow)
set(handles.gui.pixelValueTag, 'Visible', hideOrShow)
end
function sliceRangeFromToCallback(hObject, eventdata)
handles = guidata(hObject);
%totalNumberOfSlices = size(handles.data.lung, 3);
totalNumberOfSlices = 10;
fromRange = get(handles.gui.sliceRangeFrom, 'String');
toRange = get(handles.gui.sliceRangeTo, 'String');
try
validateSliceRangeValues(handles, fromRange, toRange, totalNumberOfSlices)
catch