107 lines
3.7 KiB
Matlab
107 lines
3.7 KiB
Matlab
classdef Phase < handle
|
||
|
||
properties
|
||
MeanIntensity = [];
|
||
Video = [];
|
||
WorkLoad = '';
|
||
IMFs = [];
|
||
ModePhases = [];
|
||
Values = [];
|
||
end
|
||
|
||
properties % (GetAccess = private) should become private
|
||
nFrames = uint32(0);
|
||
xImageSize = uint16(0);
|
||
yImageSize = uint16(0);
|
||
end
|
||
|
||
properties(Constant)
|
||
InitialDirectory = 'C:\Uss\Jero<72>o\Desktop\Tese\Data';
|
||
end
|
||
|
||
methods %constructor
|
||
function obj=Phase(varargin)
|
||
if nargin==0;return;end
|
||
end
|
||
end
|
||
|
||
methods %set methods
|
||
function set.WorkLoad(obj,str)
|
||
obj.WorkLoad = str;
|
||
% if indx == 1
|
||
% obj.WorkLoad = 'Rest';
|
||
% else if indx == 2
|
||
% obj.WorkLoad = 'Exercise';
|
||
% else
|
||
% obj.WorkLoad = 'Continuous Acquisition';
|
||
% end
|
||
end
|
||
end
|
||
|
||
methods
|
||
% Extracts the image sequence from the folder
|
||
function GetData(obj)
|
||
directory = uigetdir(obj.InitialDirectory); % Choose the cineMRI folder
|
||
dicomFiles = dir(fullfile(directory, '*.dcm' ));
|
||
obj.nFrames = length(dicomFiles); % Number of frames of the cineMRI
|
||
info = dicominfo(fullfile(directory,dicomFiles(1).name));
|
||
obj.xImageSize = info.Width; % Image width
|
||
obj.yImageSize = info.Height; % Image height
|
||
obj.Video = zeros(obj.xImageSize, obj.yImageSize, 1, obj.nFrames, 'uint8');
|
||
for p=1:obj.nFrames
|
||
filename = fullfile(directory, dicomFiles(p).name );
|
||
Info=dicominfo(filename);
|
||
if Info.Width~=obj.xImageSize || Info.Height~=obj.yImageSize
|
||
error('invalid image dimensions')
|
||
end
|
||
obj.Video(:,:,1,p) = dicomread(filename); % Read the DICOM files in the folder
|
||
end
|
||
end
|
||
|
||
% Gets the mean intensity value of the image sequence usin the
|
||
% central point in k-space for all the images
|
||
function GetSignal(obj)
|
||
d2IFT = ifft2(obj.Video); % performs Inverse Fourier Transform
|
||
d2IFT_shifted = fftshift(d2IFT);
|
||
for i=1:obj.nFrames
|
||
obj.MeanIntensity(:,i) = d2IFT_shifted(floor(obj.yImageSize/2),floor(obj.xImageSize/2),i); % extracts intensity of the central point in k-space for every frame
|
||
end
|
||
obj.MeanIntensity = abs(obj.MeanIntensity);
|
||
end
|
||
|
||
% Perfomrs Empirical Mode Decomposition
|
||
function GetEMD(obj)
|
||
obj.IMFs = rParabEmd__L(obj.MeanIntensity,40,40,1);
|
||
obj.IMFs = obj.IMFs.';
|
||
end
|
||
|
||
% Apply Hilber Transform to all the IMFs and extract the
|
||
% instantneous phase from each one of them
|
||
function GetModes(obj)
|
||
[number_imf lenght] = size(obj.IMFs);
|
||
analytic_EMD = zeros(number_imf,lenght);
|
||
for i=1:1:number_imf
|
||
analytic_EMD(i,:) = hilbert(obj.IMFs(i,:)); %Apply Hilbert Transform
|
||
obj.ModePhases(i,:) = angle(analytic_EMD(i,:))/pi; % Get instataneous phase
|
||
end
|
||
end
|
||
|
||
function GetPhase(obj,imf)
|
||
obj.Values = obj.ModePhases(imf,:);
|
||
end
|
||
|
||
% Shows the frames of the original image sequence specified in the
|
||
% array 'positions'
|
||
function ShowFrames(obj,positions,title)
|
||
triggered = [];
|
||
triggered = cat(2,triggered,obj.Video(:,:,positions));
|
||
video = implay(triggered,3);
|
||
set(video.Parent, 'Name', title);
|
||
end
|
||
|
||
function Display(obj)
|
||
plot(obj.Values,'-s','LineWidth',0.8,'MarkerSize',4);
|
||
end
|
||
|
||
end
|
||
end |