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EvalGUI.m
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EvalGUI.m
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function varargout = EvalGUI(varargin)
% GUI to evaluate the registration results
%
% opens from RegiGUI with the current registration results or from the
% command window, then, registration mat-file has to be loaded
%
% For detailed documentation see "Documentation of GUIs for MR image
% registration" (pdf).
%
% Before the first start check the path in th EvalGUI_OpeningFcnResult
%
% -------------------------------------------------------------------------
% (c) 2015: Thomas Kuestner, Verena Neumann
% -------------------------------------------------------------------------
% Last Modified by GUIDE v2.5 07-Jun-2016 16:21:30
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @EvalGUI_OpeningFcn, ...
'gui_OutputFcn', @EvalGUI_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
% -------------------------------------------------------------------------
% basic GUI functions
% -------------------------------------------------------------------------
% --- Executes just before EvalGUI is made visible.
function EvalGUI_OpeningFcn(hObject, eventdata, handles, varargin)
%% standard paths
currpath = fileparts(mfilename('fullpath'));
if(~exist('GUIPreferences.mat','file')) % first run
SPaths.sResults = uigetdir(pwd,'Select default result directory');
SPaths.sData = uigetdir(pwd,'Select default data directory');
SPaths.sCode = currpath;
standardVoxelsize = [1,1,1];
save('GUIPreferences.mat','SPaths','standardVoxelsize');
else
load GUIPreferences.mat;
try
% check if path are reachable
if(~exist(SPaths.sResults,'dir')), error('path not existing'); end;
if(~exist(SPaths.sData,'dir')), error('path not existing'); end;
if(~exist(SPaths.sCode,'dir')), error('path not existing'); end;
catch
% loading failed or paths not reachable
clear 'SPaths' 'standardVoxelsize';
end
end
if(~exist('SPaths','var'))
% if no valid GUIPreferences are set use the standard paths:
if ~exist([currpath,filesep,'Results'],'dir'); mkdir(currpath,'results'); end
SPaths.sResults = [currpath,filesep,'results'];
SPaths.sData = [currpath,filesep,'example'];
SPaths.sCode = currpath;
end
handles.SPaths = SPaths;
% set some folders on the path
addpath(genpath([currpath,filesep,'io']));
addpath(genpath([currpath,filesep,'metrics']));
addpath(genpath([currpath,filesep,'registration']));
addpath(genpath([currpath,filesep,'segmentation']));
addpath(genpath([currpath,filesep,'utils']));
%% read inputs
if(nargin > 3)
for index = 1:2:(nargin-3),
if nargin-3==index, break, end
switch lower(varargin{index})
case 'inarg'
handles.h = varargin{index+1};
case 'egmode'
handles.EGmode = varargin{index+1};
case 'path'
h = fwaitbar(0,'Loading image data ...');
[sPathname, sFilename, sExt] = fileparts(varargin{index+1});
load([sPathname, filesep, sFilename, sExt]); fwaitbar(1,h);
try close(h); catch; end;
handles.h = SRegiResult;
if isempty(sPathname)
handles.closeFigure = true;
% Update handles structure
guidata(hObject, handles);
return;
end
handles.h.sFilename = sFilename;
handles.SPaths.sData = sPathname;
end
end
end
% when opening without data, select a data struct from the hard drive
% originating from registration with RegiGUI
if ~isfield(handles, 'h') || isempty(handles.h)
[handles.h, sPathname, sFilename] = fSelectStruct(handles);
if isempty(sPathname)
handles.closeFigure = true;
% Update handles structure
guidata(hObject, handles);
error('Missing data for viewing!');
end
handles.h.sFilename = sFilename;
handles.SPaths.sData = sPathname;
end
%% set icons
try % Try to apply a nice icon
warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
jframe = get(hObject, 'javaframe');
jIcon = javax.swing.ImageIcon([currpath, filesep, 'icons', filesep, 'EvalGUI_icon.png']);
pause(0.001);
jframe.setFigureIcon(jIcon);
clear jframe jIcon
catch
warning('Could not apply a nice icon to the figure :(');
end
dImage = double(imread([currpath,filesep,'icons',filesep,'layers.png']))./255;
if size(dImage, 3) == 1, dImage = repmat(dImage, [1 1 3]); end
set(handles.pb_DispGates, 'CData', dImage/max(dImage(:)));
dImage = double(imread([currpath,filesep,'icons',filesep,'reset.png']))./255;
if size(dImage, 3) == 1, dImage = repmat(dImage, [1 1 3]); end
set(handles.pb_resetContrast, 'CData', dImage/max(dImage(:)));
dImage = double(imread([currpath,filesep,'icons',filesep,'save.png']))./255;
if size(dImage, 3) == 1, dImage = repmat(dImage, [1 1 3]); end
set(handles.pb_save, 'CData', dImage/max(dImage(:)));
dImage = double(imread([currpath,filesep,'icons',filesep,'doc_export.png']))./255;
if size(dImage, 3) == 1, dImage = repmat(dImage, [1 1 3]); end
set(handles.pb_SaveAs, 'CData', dImage/max(dImage(:)));
%% check inputs
if ~isfield(handles.h, 'SGeo') || isempty(handles.h.SGeo.cVoxelsize)
handles.h.SGeo.cVoxelsize{1} = standardVoxelsize;
handles.h.SGeo.cOrientation{1} = 'coronal';
end
if(~isfield(handles.h,'nSCT'))
if(~isfield(handles.h.SGeo, 'cOrientation'))
handles.nSCT = 1; % slice orientation (default: coronal)
else
cont = {'coronal', 'sagittal', 'transverse'};
handles.nSCT = find(strcmp(cont,handles.h.SGeo.cOrientation{1}));
end
else
handles.nSCT = handles.h.nSCT;
end
set(handles.pop_SagCorTrans,'Value',handles.nSCT)
if(~isfield(handles.h,'sRegMethod'))
handles.h.sRegMethod = 'N/A';
end
if(~isfield(handles.h, 'sParFile'))
handles.h.sParFile = 'N/A';
end
if(~isfield(handles.h, 'sFilename'))
handles.h.sFilename = 'default';
end
if(~isfield(handles.h,'sShownames'))
handles.h.sShownames = cell(1,size(handles.h.dImg,4));
end
if(~isfield(handles.h,'nRegMethod'))
handles.h.nRegMethod = 1;
end
handles.iActualGates = size(handles.h.dImg,4);
if(handles.iActualGates < 4) % if input has less than four gates
% pad with zeros
handles.h.dImg = cat(4,handles.h.dImg,zeros(size(handles.h.dImg,1),size(handles.h.dImg,2),size(handles.h.dImg,3),4-size(handles.h.dImg,4)));
handles.h.dImgReg = cat(4,handles.h.dImgReg,zeros(size(handles.h.dImgReg,1),size(handles.h.dImgReg,2),size(handles.h.dImgReg,3),4-size(handles.h.dImgReg,4)));
for iI=handles.iActualGates+1:4
handles.h.SDeform(iI).dBx = zeros(size(handles.h.SDeform(2).dBx));
handles.h.SDeform(iI).dBy = zeros(size(handles.h.SDeform(2).dBy));
handles.h.SDeform(iI).dBz = zeros(size(handles.h.SDeform(2).dBz));
handles.h.SDeform(iI).dFx = zeros(size(handles.h.SDeform(2).dFx));
handles.h.SDeform(iI).dFy = zeros(size(handles.h.SDeform(2).dFy));
handles.h.SDeform(iI).dFz = zeros(size(handles.h.SDeform(2).dFz));
handles.h.SGeo.cVoxelsize{iI} = handles.h.SGeo.cVoxelsize{1};
end
end
%% Choose default command line output for EvalGUI
handles.output = hObject;
handles.slice = max([1,floor(size(handles.h.dImg,3)/2)]); % slice number
handles.quiverScale = 1;
handles.quiverFactor = 8;
handles.dStep = [0.25, 1]; % quiverScale, quiverFactor
handles.level_set = 2;
handles.level_set_incr = 0.25;
handles.tcmap=[ 0 0 0; 7 0 17; 14 0 33; 21 0 50; 29 0 67; 36 0 84; 43 0 100; 50 0 117;
57 0 134; 64 0 150; 72 0 167; 80 3 164; 89 7 156; 97 11 149; 106 15 142; 114 19 134;
123 23 127; 131 27 119; 140 31 112; 149 35 105; 157 39 97; 166 43 90; 174 47 82;
183 51 75; 192 55 68; 200 59 60; 209 63 53; 217 67 45; 226 71 38; 234 75 31;
243 79 23; 252 83 16; 255 88 12; 255 95 12; 255 102 11; 255 109 11; 255 116 10;
255 123 10; 255 130 9; 255 137 9; 255 144 8; 255 151 8; 255 158 7; 255 165 7;
255 172 6; 255 179 6; 255 186 5; 255 193 4; 255 200 4; 255 207 3; 255 214 3; 255 221 2;
255 228 2; 255 235 1; 255 242 1; 255 249 0; 255 252 22; 255 252 55; 255 253 88;
255 253 122; 255 254 155; 255 254 188; 255 255 222; 255 255 255]/255;
handles.dView = [-30,60];
handles.dCamlight = [-45,45];
handles.jacDiv = 0; % 'gradient' method to measure change of defField
handles.sImageData='origImage'; % start with original image data (can be changed to registered images)
handles.FButtonDown = 0; % start with no pressed button
handles.newGates = 0; % the gates have not been changed yet
handles.cMetrics = {'smi', 'snmi', 'efinfo', 'rmi', 'rnmi', 'tmi', 'tnmi', 'ejp', 'gre', 'finfo', 'mssim', 'cc', 'zcc', 'spr', 'ket', 'mse', 'nmse', ...
'rmse', 'nrmse', 'psnr', 'tam', 'zca', 'zcr', 'mr', 'ssd', 'msd', 'nssd', 'sad', 'zsad', 'lsad', 'mad', 'shd', 'besov'; ...
'Shannon mutual information', 'Shannon normalized mutual information', 'exclusive F-information', 'Renyi mutual information', 'Renyi normalized mutual information', 'Tsallis mutual information', 'Tsallis normalized mutual information', 'energy of joint probability', 'gradient entropy', ...
'F-information measures', 'Mean structural similarity', '(Pearson) cross correlation', 'zero-mean normalized (Pearson) cross correlation', 'Spearman rank correlation', ...
'Kendall''s tau', 'mean squared error', 'normalized mean squared error', 'root mean squared error', 'normalized root mean squared error', 'peak signal to noise ratio', ...
'Tanimoto measure', 'zero crossings (absolute)', 'zero crossings (relative)', 'minimum ratio', 'sum of squared differences', 'median of squared differences', 'normalized sum of squared differences', ...
'sum of absolute differences', 'zero-mean sum of absolute differences', 'locally scaled sum of absolute differences', 'median of absolute differences', 'sum of hamming distance', 'besov norm'};
if(~exist('lEvalMetrics','var'))
handles.lEvalMetrics = logical([0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0]); % default to be evaluated intensity-based metrics
else
handles.lEvalMetrics = lEvalMetrics;
end
if(~isfield(handles.h.SDeform(2),'dBx'))
set(handles.rbBackward, 'Visible', 'off');
end
handles.iShown = 1:4;
handles.methods = {'elastix', 'halar', 'grics', 'LAP', 'demons'};
% normalize image data to [0,1]
for k = 1:size(handles.h.dImg,4)
dImgData = handles.h.dImg(:,:,:,k);
handles.h.dImg(:,:,:,k) = (dImgData-min(dImgData(:)))./(max(dImgData(:))-min(dImgData(:)));
dImgData = handles.h.dImgReg(:,:,:,k);
dImgData(dImgData<0) = 0;
handles.h.dImgReg(:,:,:,k) = (dImgData-min(dImgData(:)))./(max(dImgData(:))-min(dImgData(:)));
end
if isfield(handles, 'EGmode') && strcmp(handles.EGmode,'auto')
fEvalAuto(hObject,handles);
handles.closeFigure = true;
% Update handles structure
guidata(hObject, handles);
else
set(handles.cb_showQuiver,'Value',1)
% set(handles.textFilename, 'String', ['Dataset: ',handles.h.sFilename(1:min(end,94))])
% methods = {'elastix', 'halar', 'grics', 'LAP', 'demons'};
% method = methods{handles.h.nRegMethod};
handles.RegMParam = ['Registration Method: ', handles.h.sRegMethod];
handles.RegMParam = [handles.RegMParam, ', Parameter: ',handles.h.sParFile];
set(handles.tRegMParm, 'String', handles.RegMParam)
sStandardLabel = {'Image 01 (reference/fixed)'; 'Image 02'; 'Image 03'; 'Image 04'};
for iI=1:4
if(iI <= length(handles.h.sShownames) && ~isempty(handles.h.sShownames{iI}))
eval(sprintf('set(handles.txGate0%d,''String'',{sStandardLabel{iI}, handles.h.sShownames{iI}});',iI));
else % if iNGates < 4
eval(sprintf('set(handles.txGate0%d,''String'',sStandardLabel(iI));',iI));
end
end
% compute det(Jac), divergence and arrow length of deformation field
handles = fComputeDiv(handles);
% Update handles structure
guidata(hObject, handles);
% plot all gates
fPlotImageAndDefField(hObject, handles);
drawnow update;
end
function EvalGUI_ResizeFcn(hObject, eventdata, handles)
function varargout = EvalGUI_OutputFcn(hObject, eventdata, handles)
try varargout{1}= handles.output; catch; end;
if(isfield(handles,'closeFigure') && handles.closeFigure)
EvalGUI_CloseRequestFcn(hObject, eventdata, handles)
end
function EvalGUI_CloseRequestFcn(hObject, ~, handles)
% save GUIPreference
try
currpath = fileparts(mfilename('fullpath'));
if(isfield(handles,'SPaths'))
SPaths = handles.SPaths;
standardVoxelsize = [1 1 1];
lEvalMetrics = handles.lEvalMetrics;
if(exist([currpath, filesep, 'GUIPreferences.mat'],'file'))
save([currpath, filesep, 'GUIPreferences.mat'],'SPaths','standardVoxelsize', 'lEvalMetrics', '-append');
else
save([currpath, filesep, 'GUIPreferences.mat'],'SPaths','standardVoxelsize', 'lEvalMetrics');
end
end
delete(hObject);
catch
end
%% ------------------------------------------------------------------------
% callback functions
% -------------------------------------------------------------------------
function pop_SagCorTrans_Callback(hObject, eventdata, handles)
% change view between sagital, coronal and transverse slices
% get selected slice orientation
contents = cellstr(get(handles.pop_SagCorTrans,'String'));
lead=contents{get(handles.pop_SagCorTrans,'value')};
% get image array and deformation fields
dImg = handles.h.dImg;
dImgReg = handles.h.dImgReg;
dFx2 = handles.h.SDeform(2).dFx;
dFy2 = handles.h.SDeform(2).dFy;
dFz2 = handles.h.SDeform(2).dFz;
dFx3 = handles.h.SDeform(3).dFx;
dFy3 = handles.h.SDeform(3).dFy;
dFz3 = handles.h.SDeform(3).dFz;
dFx4 = handles.h.SDeform(4).dFx;
dFy4 = handles.h.SDeform(4).dFy;
dFz4 = handles.h.SDeform(4).dFz;
if(strcmp(get(handles.rbForward,'Visible'),'on'))
dBx2 = handles.h.SDeform(2).dBx;
dBy2 = handles.h.SDeform(2).dBy;
dBz2 = handles.h.SDeform(2).dBz;
dBx3 = handles.h.SDeform(3).dBx;
dBy3 = handles.h.SDeform(3).dBy;
dBz3 = handles.h.SDeform(3).dBz;
dBx4 = handles.h.SDeform(4).dBx;
dBy4 = handles.h.SDeform(4).dBy;
dBz4 = handles.h.SDeform(4).dBz;
lBackward = true;
else
lBackward = false;
end
% permutation vector for orientation changes
CorSag = [1,3,2,4];
CorTra = [3,2,1,4];
SagCor = [1,3,2,4];
SagTra = [2,3,1,4];
TraCor = [3,2,1,4];
TraSag = [3,1,2,4];
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% very sensitive code: be attentive when changing it!
% especially Fx/Fy/Fz permutation is tricky!
switch lead % for all combinations of orientation changes:
case 'coronal'
nSCT=1; % 1. set: - flag for slice orientation
handles.quiverFactor = 8; % - standard quiver densitiy
handles.quiverScale = 1; % - standard quiver length
% set(handles.slider_quiverScale,'value', handles.quiverScale); % - slider positions
% set(handles.slider_quiverFac,'value', handles.quiverFactor);
if handles.nSCT == 2 % sag -> cor
dImgRot = permute(dImg,SagCor); % 2. a) permute all image data according to permutation vector
dImgRegRot = permute(dImgReg,SagCor);
handles.h.SDeform(2).dFx = permute(dFz2,SagCor); % b) permute all deformation fields (x, y and z coordinates)
handles.h.SDeform(2).dFz = permute(dFx2,SagCor); % c) set permuted deformFields into old ones
handles.h.SDeform(2).dFy = permute(dFy2,SagCor); % ! swap names (e.g. y <-> z) according to permutation
handles.h.SDeform(3).dFx = permute(dFz3,SagCor);
handles.h.SDeform(3).dFz = permute(dFx3,SagCor);
handles.h.SDeform(3).dFy = permute(dFy3,SagCor);
handles.h.SDeform(4).dFx = permute(dFz4,SagCor);
handles.h.SDeform(4).dFz = permute(dFx4,SagCor);
handles.h.SDeform(4).dFy = permute(dFy4,SagCor);
if(lBackward)
handles.h.SDeform(2).dBx = permute(dBz2,SagCor); % b) permute all deformation fields (x, y and z coordinates)
handles.h.SDeform(2).dBz = permute(dBx2,SagCor); % c) set permuted deformFields into old ones
handles.h.SDeform(2).dBy = permute(dBy2,SagCor); % ! swap names (e.g. y <-> z) according to permutation
handles.h.SDeform(3).dBx = permute(dBz3,SagCor);
handles.h.SDeform(3).dBz = permute(dBx3,SagCor);
handles.h.SDeform(3).dBy = permute(dBy3,SagCor);
handles.h.SDeform(4).dBx = permute(dBz4,SagCor);
handles.h.SDeform(4).dBz = permute(dBx4,SagCor);
handles.h.SDeform(4).dBy = permute(dBy4,SagCor);
end
if isfield(handles,'divF2')
handles.divF2 = permute(handles.divF2,SagCor);
handles.divF3 = permute(handles.divF3,SagCor);
handles.divF4 = permute(handles.divF4,SagCor);
end
if isfield(handles,'detJ2')
handles.detJ2 = permute(handles.detJ2,SagCor);
handles.detJ3 = permute(handles.detJ3,SagCor);
handles.detJ4 = permute(handles.detJ4,SagCor);
end
if isfield(handles,'arrL2')
handles.arrL2 = permute(handles.arrL2,SagCor);
handles.arrL3 = permute(handles.arrL3,SagCor);
handles.arrL4 = permute(handles.arrL4,SagCor);
end
if isfield(handles,'gradL2')
handles.gradL2 = permute(handles.gradL2,SagCor);
handles.gradL3 = permute(handles.gradL3,SagCor);
handles.gradL4 = permute(handles.gradL4,SagCor);
end
elseif handles.nSCT == 3 % tra -> cor
dImgRot = permute(dImg,TraCor);
dImgRegRot = permute(dImgReg,TraCor);
handles.h.SDeform(2).dFz = permute(dFy2,TraCor);
handles.h.SDeform(2).dFy = permute(dFz2,TraCor);
handles.h.SDeform(2).dFx = permute(dFx2,TraCor);
handles.h.SDeform(3).dFz = permute(dFy3,TraCor);
handles.h.SDeform(3).dFy = permute(dFz3,TraCor);
handles.h.SDeform(3).dFx = permute(dFx3,TraCor);
handles.h.SDeform(4).dFz = permute(dFy4,TraCor);
handles.h.SDeform(4).dFy = permute(dFz4,TraCor);
handles.h.SDeform(4).dFx = permute(dFx4,TraCor);
if(lBackward)
handles.h.SDeform(2).dBz = permute(dBy2,TraCor);
handles.h.SDeform(2).dBy = permute(dBz2,TraCor);
handles.h.SDeform(2).dBx = permute(dBx2,TraCor);
handles.h.SDeform(3).dBz = permute(dBy3,TraCor);
handles.h.SDeform(3).dBy = permute(dBz3,TraCor);
handles.h.SDeform(3).dBx = permute(dBx3,TraCor);
handles.h.SDeform(4).dBz = permute(dBy4,TraCor);
handles.h.SDeform(4).dBy = permute(dBz4,TraCor);
handles.h.SDeform(4).dBx = permute(dBx4,TraCor);
end
if isfield(handles,'divF2')
handles.divF2 = permute(handles.divF2,TraCor);
handles.divF3 = permute(handles.divF3,TraCor);
handles.divF4 = permute(handles.divF4,TraCor);
end
if isfield(handles,'detJ2')
handles.detJ2 = permute(handles.detJ2,TraCor);
handles.detJ3 = permute(handles.detJ3,TraCor);
handles.detJ4 = permute(handles.detJ4,TraCor);
end
if isfield(handles,'arrL2')
handles.arrL2 = permute(handles.arrL2,TraCor);
handles.arrL3 = permute(handles.arrL3,TraCor);
handles.arrL4 = permute(handles.arrL4,TraCor);
end
if isfield(handles,'gradL2')
handles.gradL2 = permute(handles.gradL2,TraCor);
handles.gradL3 = permute(handles.gradL3,TraCor);
handles.gradL4 = permute(handles.gradL4,TraCor);
end
else return % 3. do nothing, if slice orientation did not change
end
case 'sagittal'
nSCT=2;
handles.quiverFactor = 6;
handles.quiverScale = 1;
% set(handles.slider_quiverScale,'value', 4);
% set(handles.slider_quiverFac,'value', 5);
if handles.nSCT == 1 % cor -> sag
dImgRot = permute(dImg,CorSag);
dImgRegRot = permute(dImgReg,CorSag);
handles.h.SDeform(2).dFx = permute(dFz2,CorSag);
handles.h.SDeform(2).dFz = permute(dFx2,CorSag);
handles.h.SDeform(2).dFy = permute(dFy2,CorSag);
handles.h.SDeform(3).dFx = permute(dFz3,CorSag);
handles.h.SDeform(3).dFz = permute(dFx3,CorSag);
handles.h.SDeform(3).dFy = permute(dFy3,CorSag);
handles.h.SDeform(4).dFx = permute(dFz4,CorSag);
handles.h.SDeform(4).dFz = permute(dFx4,CorSag);
handles.h.SDeform(4).dFy = permute(dFy4,CorSag);
if(lBackward)
handles.h.SDeform(2).dBx = permute(dBz2,CorSag);
handles.h.SDeform(2).dBz = permute(dBx2,CorSag);
handles.h.SDeform(2).dBy = permute(dBy2,CorSag);
handles.h.SDeform(3).dBx = permute(dBz3,CorSag);
handles.h.SDeform(3).dBz = permute(dBx3,CorSag);
handles.h.SDeform(3).dBy = permute(dBy3,CorSag);
handles.h.SDeform(4).dBx = permute(dBz4,CorSag);
handles.h.SDeform(4).dBz = permute(dBx4,CorSag);
handles.h.SDeform(4).dBy = permute(dBy4,CorSag);
end
if isfield(handles,'divF2')
handles.divF2 = permute(handles.divF2,CorSag);
handles.divF3 = permute(handles.divF3,CorSag);
handles.divF4 = permute(handles.divF4,CorSag);
end
if isfield(handles,'detJ2')
handles.detJ2 = permute(handles.detJ2,CorSag);
handles.detJ3 = permute(handles.detJ3,CorSag);
handles.detJ4 = permute(handles.detJ4,CorSag);
end
if isfield(handles,'arrL2')
handles.arrL2 = permute(handles.arrL2,CorSag);
handles.arrL3 = permute(handles.arrL3,CorSag);
handles.arrL4 = permute(handles.arrL4,CorSag);
end
if isfield(handles,'gradL2')
handles.gradL2 = permute(handles.gradL2,CorSag);
handles.gradL3 = permute(handles.gradL3,CorSag);
handles.gradL4 = permute(handles.gradL4,CorSag);
end
elseif handles.nSCT == 3 % tra -> sag
dImgRot = permute(dImg,TraSag);
dImgRegRot = permute(dImgReg,TraSag);
handles.h.SDeform(2).dFy = permute(dFz2,TraSag);
handles.h.SDeform(2).dFz = permute(dFx2,TraSag);
handles.h.SDeform(2).dFx = permute(dFy2,TraSag);
handles.h.SDeform(3).dFy = permute(dFz3,TraSag);
handles.h.SDeform(3).dFz = permute(dFx3,TraSag);
handles.h.SDeform(3).dFx = permute(dFy3,TraSag);
handles.h.SDeform(4).dFy = permute(dFz4,TraSag);
handles.h.SDeform(4).dFz = permute(dFx4,TraSag);
handles.h.SDeform(4).dFx = permute(dFy4,TraSag);
if(lBackward)
handles.h.SDeform(2).dBy = permute(dBz2,TraSag);
handles.h.SDeform(2).dBz = permute(dBx2,TraSag);
handles.h.SDeform(2).dBx = permute(dBy2,TraSag);
handles.h.SDeform(3).dBy = permute(dBz3,TraSag);
handles.h.SDeform(3).dBz = permute(dBx3,TraSag);
handles.h.SDeform(3).dBx = permute(dBy3,TraSag);
handles.h.SDeform(4).dBy = permute(dBz4,TraSag);
handles.h.SDeform(4).dBz = permute(dBx4,TraSag);
handles.h.SDeform(4).dBx = permute(dBy4,TraSag);
end
if isfield(handles,'divF2')
handles.divF2 = permute(handles.divF2,TraSag);
handles.divF3 = permute(handles.divF3,TraSag);
handles.divF4 = permute(handles.divF4,TraSag);
end
if isfield(handles,'detJ2')
handles.detJ2 = permute(handles.detJ2,TraSag);
handles.detJ3 = permute(handles.detJ3,TraSag);
handles.detJ4 = permute(handles.detJ4,TraSag);
end
if isfield(handles,'arrL2')
handles.arrL2 = permute(handles.arrL2,TraSag);
handles.arrL3 = permute(handles.arrL3,TraSag);
handles.arrL4 = permute(handles.arrL4,TraSag);
end
if isfield(handles,'gradL2')
handles.gradL2 = permute(handles.gradL2,TraSag);
handles.gradL3 = permute(handles.gradL3,TraSag);
handles.gradL4 = permute(handles.gradL4,TraSag);
end
else return
end
case 'transverse'
nSCT=3;
handles.quiverFactor = 5;
handles.quiverScale = 1;
% set(handles.slider_quiverScale,'value', 4);
% set(handles.slider_quiverFac,'value', 6);
if handles.nSCT == 1 % cor -> tra
dImgRot = permute(dImg,CorTra);
dImgRegRot = permute(dImgReg,CorTra);
handles.h.SDeform(2).dFz = permute(dFy2,CorTra);
handles.h.SDeform(2).dFy = permute(dFz2,CorTra);
handles.h.SDeform(2).dFx = permute(dFx2,CorTra);
handles.h.SDeform(3).dFz = permute(dFy3,CorTra);
handles.h.SDeform(3).dFy = permute(dFz3,CorTra);
handles.h.SDeform(3).dFx = permute(dFx3,CorTra);
handles.h.SDeform(4).dFz = permute(dFy4,CorTra);
handles.h.SDeform(4).dFy = permute(dFz4,CorTra);
handles.h.SDeform(4).dFx = permute(dFx4,CorTra);
if(lBackward)
handles.h.SDeform(2).dBz = permute(dBy2,CorTra);
handles.h.SDeform(2).dBy = permute(dBz2,CorTra);
handles.h.SDeform(2).dBx = permute(dBx2,CorTra);
handles.h.SDeform(3).dBz = permute(dBy3,CorTra);
handles.h.SDeform(3).dBy = permute(dBz3,CorTra);
handles.h.SDeform(3).dBx = permute(dBx3,CorTra);
handles.h.SDeform(4).dBz = permute(dBy4,CorTra);
handles.h.SDeform(4).dBy = permute(dBz4,CorTra);
handles.h.SDeform(4).dBx = permute(dBx4,CorTra);
end
if isfield(handles,'divF2')
handles.divF2 = permute(handles.divF2,CorTra);
handles.divF3 = permute(handles.divF3,CorTra);
handles.divF4 = permute(handles.divF4,CorTra);
end
if isfield(handles,'detJ2')
handles.detJ2 = permute(handles.detJ2,CorTra);
handles.detJ3 = permute(handles.detJ3,CorTra);
handles.detJ4 = permute(handles.detJ4,CorTra);
end
if isfield(handles,'arrL2')
handles.arrL2 = permute(handles.arrL2,CorTra);
handles.arrL3 = permute(handles.arrL3,CorTra);
handles.arrL4 = permute(handles.arrL4,CorTra);
end
if isfield(handles,'gradL2')
handles.gradL2 = permute(handles.gradL2,CorTra);
handles.gradL3 = permute(handles.gradL3,CorTra);
handles.gradL4 = permute(handles.gradL4,CorTra);
end
elseif handles.nSCT == 2 % sag -> tra
dImgRot = permute(dImg,SagTra);
dImgRegRot = permute(dImgReg,SagTra);
handles.h.SDeform(2).dFz = permute(dFy2,SagTra);
handles.h.SDeform(2).dFx = permute(dFz2,SagTra);
handles.h.SDeform(2).dFy = permute(dFx2,SagTra);
handles.h.SDeform(3).dFz = permute(dFy3,SagTra);
handles.h.SDeform(3).dFx = permute(dFz3,SagTra);
handles.h.SDeform(3).dFy = permute(dFx3,SagTra);
handles.h.SDeform(4).dFz = permute(dFy4,SagTra);
handles.h.SDeform(4).dFx = permute(dFz4,SagTra);
handles.h.SDeform(4).dFy = permute(dFx4,SagTra);
if(lBackward)
handles.h.SDeform(2).dBz = permute(dBy2,SagTra);
handles.h.SDeform(2).dBx = permute(dBz2,SagTra);
handles.h.SDeform(2).dBy = permute(dBx2,SagTra);
handles.h.SDeform(3).dBz = permute(dBy3,SagTra);
handles.h.SDeform(3).dBx = permute(dBz3,SagTra);
handles.h.SDeform(3).dBy = permute(dBx3,SagTra);
handles.h.SDeform(4).dBz = permute(dBy4,SagTra);
handles.h.SDeform(4).dBx = permute(dBz4,SagTra);
handles.h.SDeform(4).dBy = permute(dBx4,SagTra);
end
if isfield(handles,'divF2')
handles.divF2 = permute(handles.divF2,SagTra);
handles.divF3 = permute(handles.divF3,SagTra);
handles.divF4 = permute(handles.divF4,SagTra);
end
if isfield(handles,'detJ2')
handles.detJ2 = permute(handles.detJ2,SagTra);
handles.detJ3 = permute(handles.detJ3,SagTra);
handles.detJ4 = permute(handles.detJ4,SagTra);
end
if isfield(handles,'arrL2')
handles.arrL2 = permute(handles.arrL2,SagTra);
handles.arrL3 = permute(handles.arrL3,SagTra);
handles.arrL4 = permute(handles.arrL4,SagTra);
end
if isfield(handles,'gradL2')
handles.gradL2 = permute(handles.gradL2,SagTra);
handles.gradL3 = permute(handles.gradL3,SagTra);
handles.gradL4 = permute(handles.gradL4,SagTra);
end
else return
end
otherwise
error('unexpected error');
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
set(handles.slider_quiverScale,'value', handles.quiverScale); % - slider positions
set(handles.tQuiverSize,'String',num2str(handles.quiverScale));
dVal = get(handles.slider_quiverFac, 'Max') - handles.quiverFactor + 1;
set(handles.slider_quiverFac,'value', dVal);
set(handles.txtDens,'String',num2str(1/handles.quiverFactor,'%.3f'));
% set new values in handle structure.
handles.h.dImg = dImgRot;
handles.h.dImgReg = dImgRegRot;
handles.nSCT = nSCT;
handles.slice= floor(size(handles.h.dImg,3)/2);
if(isfield(handles,'hI1'))
if(ishandle(handles.hI1))
delete(handles.hI1);
end
handles.hI1 = [];
end
if(isfield(handles,'hI'))
for n=2:4
if(ishandle(handles.hI(n)))
delete(handles.hI(n));
end
handles.hI(n) = -1;
end
end
if(isfield(handles,'hQ'))
for n=2:4
if(ishandle(handles.hQ(n)))
delete(handles.hQ(n));
end
handles.hQ(n) = -1;
end
end
% plot new slice orientation
fPlotImageAndDefField(hObject, handles)
function pb_SegLung_Callback(hObject, eventdata, handles)
% segment lung
if handles.nSCT == 2 || handles.nSCT == 3
errordlg('Please segment the lungs in the coronal view.')
return
end
% which type of image shall be segmented?
if(isfield(eventdata,'autoMode'))
qSegImg = 'transformed images';
else
qSegImg = questdlg('Which images shall be segmented?', ' ', 'original images', 'transformed images', 'transformed images');
end
switch qSegImg
case 'original images'
dImg2Seg = handles.h.dImg(:,:,:,1:handles.iActualGates);
isOrigImg = 1;
case 'transformed images'
dImg2Seg = handles.h.dImgReg(:,:,:,1:handles.iActualGates);
dImg2Seg(:,:,:,1) = handles.h.dImg(:,:,:,1);
isOrigImg = 0;
case ''
return
end
% segment lungs in the 4 gates and display overlap measures
h = fwaitbar(0,'Segmenting lungs. Please wait...'); st = 0; steps = 2*size(dImg2Seg,4)-1;
% check if there are already masks and if the gates have changed since the last computation
if (~isfield(handles,'lung3d') || handles.newGates == 1 || ~strcmp(qSegImg, handles.qSegImg))
for iI=1:size(dImg2Seg,4)
handles.lung3d{iI} = fLungSegmKohlm(dImg2Seg,iI,1); st= st+1;fwaitbar(st/steps,h);
end
else
st= size(dImg2Seg,4);fwaitbar(st/steps,h);
end
if isOrigImg % transform images according to deformation field
for iI = 2:size(dImg2Seg,4)
uB = {handles.h.SDeform(iI).dBy,handles.h.SDeform(iI).dBx,handles.h.SDeform(iI).dBz};
handles.lung3d{iI} = imshift_3D(handles.lung3d{iI},uB,'bilinear');
end
end
handles.newGate = 0; % flag reset to 0
hData.dImg = dImg2Seg;
hData.lung3d = handles.lung3d;
hData.nGate = 1;
CutOffValue = CutLungGUI('inarg', hData);
if CutOffValue == 1; try close(h); catch; end; return; end;
handles.lung3dcut = handles.lung3d;
for iI=1:size(dImg2Seg,4)
handles.lung3dcut{iI}(1:CutOffValue,:,:)= 0;
end
dice = zeros(size(dImg2Seg,4)-1,1);
jac = zeros(size(dImg2Seg,4)-1,1);
for k = 1:size(dImg2Seg,4)-1
[dice(k), jac(k)] = fEvalOverlap(handles.lung3dcut{1},handles.lung3dcut{k+1}); st= st+1;fwaitbar(st/steps,h);
end
try close(h); catch; end;
handles.qSegImg = qSegImg;
if(isOrigImg) % starting from original image
if(isfield(handles,'lung'))
handles.lung.isPerformed = handles.lung.isPerformed | [true, false]; % original images, transformed images
else
handles.lung.isPerformed = [true, false];
end
handles.lung.diceOri = dice;
handles.lung.jacOri = jac;
else
if(isfield(handles,'lung'))
handles.lung.isPerformed = handles.lung.isPerformed | [false, true]; % original images, transformed images
else
handles.lung.isPerformed = [false, true];
end
handles.lung.diceReg = dice;
handles.lung.jacReg = jac;
end
iInd = get(handles.pm_Gate,'Value');
lMap = repmat(handles.iShown,2,1);
lMap = lMap(:);
if(mod(iInd,2) == 0) % even -> transformed
if(handles.lung.isPerformed(2))
set(handles.textDice,'String',num2str(handles.lung.diceReg(lMap(iInd)-1),'%6.4g'));
set(handles.textJac,'String',num2str(handles.lung.jacReg(lMap(iInd)-1),'%6.4g'));
else
set(handles.textDice,'String', '');
set(handles.textJac,'String', '');
end
else % odd -> original
if(handles.lung.isPerformed(1))
set(handles.textDice,'String',num2str(handles.lung.diceOri(lMap(iInd)-1),'%6.4g'));
set(handles.textJac,'String',num2str(handles.lung.jacOri(lMap(iInd)-1),'%6.4g'));
else
set(handles.textDice,'String', '');
set(handles.textJac,'String', '');
end
end
guidata(hObject, handles);
function pb_lmPoints_Callback(hObject, eventdata, handles)
% open landmarkpoint GUI
h.dImg = handles.h.dImg(:,:,:,1:handles.iActualGates);
h.dImgReg = handles.h.dImgReg(:,:,:,1:handles.iActualGates);
h.SDeform = handles.h.SDeform(1:handles.iActualGates);
h.nRegMethod = handles.h.nRegMethod;
h.sFilename = handles.h.sFilename;
h.sParFile = handles.h.sParFile;
h.nSCT = handles.nSCT;
try h.SPaths = handles.h.SPaths; catch; end;
try h.SPaths = handles.SPaths; catch; end;
h.SGeo = handles.h.SGeo;
LandmarkGUI('inarg', h);
function slider_quiverFac_Callback(hObject, eventdata, handles)
% Slider for quiver Factor manipulation (density)
% get slider position and compute corresponding standard quiver Factor
x = get(hObject,'Max') - get(hObject,'Value') + 1;
% x = get(hObject,'Value');
k = get(hObject,'Min'):handles.dStep(2):get(hObject,'Max');
y = interp1(k,k,x,'nearest');
% dStep = get(hObject,'SliderStep');
% y = get(hObject,'Min'):dStep(1):get(hObject,'Max');
% y = 20:-1:1;
% y = [12,10,8,7,6,5,4,3,2,1];
% get deformation field arrays
if(get(handles.rbForward,'Value') > 0)
dFx2 = handles.h.SDeform(2).dFx;
dFy2 = handles.h.SDeform(2).dFy;
dFx3 = handles.h.SDeform(3).dFx;
dFy3 = handles.h.SDeform(3).dFy;
dFx4 = handles.h.SDeform(4).dFx;
dFy4 = handles.h.SDeform(4).dFy;
else % backward
dFx2 = handles.h.SDeform(2).dBx;
dFy2 = handles.h.SDeform(2).dBy;
dFx3 = handles.h.SDeform(3).dBx;
dFy3 = handles.h.SDeform(3).dBy;
dFx4 = handles.h.SDeform(4).dBx;
dFy4 = handles.h.SDeform(4).dBy;
end
% for different slice orientation adjust quiver Factor
% handles.quiverFactor = y(round(x));
% handles.quiverFactor = round(1/x);
handles.quiverFactor = y;
set(handles.txtDens,'String',num2str(1/handles.quiverFactor,'%.3f'));
% get new positions for quiver arrows
iX = 1:handles.quiverFactor:size(dFx2, 2);
iY = 1:handles.quiverFactor:size(dFy2, 1);
% draw new quiver arrows
% if(isfield(handles,'hQ') && handles.hQ(2) > 0 && ishandle(handles.hQ(2)))
% delete(handles.hQ(2));
% end
try
delete(handles.hQ(2));
catch
end
axes(handles.Gate02)
hold on
handles.hQ(2)=quiver(iX, iY, handles.quiverScale*dFx2(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice),...
handles.quiverScale*dFy2(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice), 0);
set(handles.hQ(2), 'Linewidth', 1.5, 'Color', 'y');
hold off
% if(isfield(handles,'hQ') && handles.hQ(3) > 0 && ishandle(handles.hQ(3)))
% delete(handles.hQ(3));
% end
try
delete(handles.hQ(3));
catch
end
axes(handles.Gate03)
hold on
handles.hQ(3)=quiver(iX, iY, handles.quiverScale*dFx3(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice),...
handles.quiverScale*dFy3(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice), 0);
set(handles.hQ(3), 'Linewidth', 1.5, 'Color', 'y');
hold off
% if(isfield(handles,'hQ') && handles.hQ(4) > 0 && ishandle(handles.hQ(4)))
% delete(handles.hQ(4));
% end
try
delete(handles.hQ(4));
catch
end
axes(handles.Gate04)
hold on
handles.hQ(4)=quiver(iX, iY, handles.quiverScale*dFx4(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice),...
handles.quiverScale*dFy4(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice), 0);
set(handles.hQ(4), 'Linewidth', 1.5, 'Color', 'y');
hold off
guidata(hObject, handles)
function slider_quiverScale_Callback(hObject, eventdata, handles)
% Slider for quiver size
% get slider position and set standard scale value
x = get(hObject,'Value');
% dStep = get(hObject,'SliderStep');
k = get(hObject,'Min'):handles.dStep(1):get(hObject,'Max');
% k = [0.25 0.5 0.75 1 1.5 2 2.5 3 4 5 6];
% y = k(round(x));
y = interp1(k,k,x,'nearest');
set(handles.tQuiverSize, 'String', num2str(y))
handles.quiverScale = y;
% get deformation field arrays
if(get(handles.rbForward,'Value') > 0)
dFx2 = handles.h.SDeform(2).dFx;
dFy2 = handles.h.SDeform(2).dFy;
dFx3 = handles.h.SDeform(3).dFx;
dFy3 = handles.h.SDeform(3).dFy;
dFx4 = handles.h.SDeform(4).dFx;
dFy4 = handles.h.SDeform(4).dFy;
else % backward
dFx2 = handles.h.SDeform(2).dBx;
dFy2 = handles.h.SDeform(2).dBy;
dFx3 = handles.h.SDeform(3).dBx;
dFy3 = handles.h.SDeform(3).dBy;
dFx4 = handles.h.SDeform(4).dBx;
dFy4 = handles.h.SDeform(4).dBy;
end
% get new positions for quiver arrows
iX = 1:handles.quiverFactor:size(dFx2, 2);
iY = 1:handles.quiverFactor:size(dFy2, 1);
% draw new quiver arrows
% if(isfield(handles,'hQ') && handles.hQ(2) > 0 && ishandle(handles.hQ(2)))
% delete(handles.hQ(2));
% end
try
delete(handles.hQ(2));
catch
end
axes(handles.Gate02)
hold on
handles.hQ(2)=quiver(iX, iY, handles.quiverScale*dFx2(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice),...
handles.quiverScale*dFy2(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice), 0);
set(handles.hQ(2), 'Linewidth', 1.5, 'Color', 'y');
hold off
% if(isfield(handles,'hQ') && handles.hQ(3) > 0 && ishandle(handles.hQ(3)))
% delete(handles.hQ(3));
% end
try
delete(handles.hQ(3));
catch
end
axes(handles.Gate03)
hold on
handles.hQ(3)=quiver(iX, iY, handles.quiverScale*dFx3(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice),...
handles.quiverScale*dFy3(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice), 0);
set(handles.hQ(3), 'Linewidth', 1.5, 'Color', 'y');
hold off
% if(isfield(handles,'hQ') && handles.hQ(4) > 0 && ishandle(handles.hQ(4)))
% delete(handles.hQ(4));
% end
try
delete(handles.hQ(4));
catch
end
axes(handles.Gate04)
hold on
handles.hQ(4)=quiver(iX, iY, handles.quiverScale*dFx4(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice),...
handles.quiverScale*dFy4(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice), 0);
set(handles.hQ(4), 'Linewidth', 1.5, 'Color', 'y');
hold off
guidata(hObject, handles)
function cb_showQuiver_Callback(hObject, eventdata, handles)
% checkbox for quivers
if(get(handles.rbForward,'Value') > 0)
dFx2 = handles.h.SDeform(2).dFx;
dFy2 = handles.h.SDeform(2).dFy;
dFx3 = handles.h.SDeform(3).dFx;
dFy3 = handles.h.SDeform(3).dFy;
dFx4 = handles.h.SDeform(4).dFx;
dFy4 = handles.h.SDeform(4).dFy;
else % backward
dFx2 = handles.h.SDeform(2).dBx;
dFy2 = handles.h.SDeform(2).dBy;
dFx3 = handles.h.SDeform(3).dBx;
dFy3 = handles.h.SDeform(3).dBy;
dFx4 = handles.h.SDeform(4).dBx;
dFy4 = handles.h.SDeform(4).dBy;
end
iX = 1:handles.quiverFactor:size(dFx2, 2);
iY = 1:handles.quiverFactor:size(dFy2, 1);
if get(hObject, 'Value')
axes(handles.Gate02)
hold on
handles.hQ(2)=quiver(iX, iY, handles.quiverScale*dFx2(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice),...
dFy2(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice), 0);
set(handles.hQ(2), 'Linewidth', 1.5, 'Color', 'y');
hold off
axes(handles.Gate03)
hold on
handles.hQ(3)=quiver(iX, iY, handles.quiverScale*dFx3(1:handles.quiverFactor:end, 1:handles.quiverFactor:end, handles.slice),...