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Update 14/05/2'19

master
João Narciso 3 years ago
parent
commit
a6ad9b0c74
  1. 15
      Code/CardiacPhase.m
  2. 12
      Code/Phase.m
  3. 13
      Code/RespiratoryPhase.m
  4. 139
      Code/test_OOP.m

15
Code/CardiacPhase.m

@ -4,7 +4,6 @@ classdef CardiacPhase < Phase @@ -4,7 +4,6 @@ classdef CardiacPhase < Phase
IMF = uint32(0);
SystolePositions = [];
DiastolePositions = [];
end
properties % (GetAccess = private) should become private
@ -18,6 +17,7 @@ classdef CardiacPhase < Phase @@ -18,6 +17,7 @@ classdef CardiacPhase < Phase
% gets properties of superclass
obj.FullPhase = Phase.ModePhases;
obj.Video = Phase.Video;
obj.InstantaneousFreq = Phase.InstantaneousFreq;
end
% Choose the correct IMF depending on the work load
@ -43,6 +43,19 @@ classdef CardiacPhase < Phase @@ -43,6 +43,19 @@ classdef CardiacPhase < Phase
obj.Values = obj.FullPhase(obj.IMF,:); %Phase corresponding to respiratory phase
end
function GetFrequency(obj,time)
heart_inst_freq = (abs(diff(obj.Values))./diff(time))/(2*pi());
obj.InstantaneousFreq = medfilt1(heart_inst_freq,3);
figure
scatter(time,[obj.InstantaneousFreq,0],8);
mean_freq1 = mean(obj.InstantaneousFreq);
hline = refline([0 mean_freq1]); % Reference line for maximum phase
hline.Color = 'm';
title('Cardiac Instantaneous Frequency');
xlabel('Time (sec)')
ylabel('Frequency (Hz)');
end
% Detects the frame's positions of diastolic events
function Diastole(obj)
max_heart_phase = max(obj.Values); % cardiac phase maxima

12
Code/Phase.m

@ -6,6 +6,7 @@ classdef Phase < handle @@ -6,6 +6,7 @@ classdef Phase < handle
IMFs = [];
ModePhases = [];
Values = [];
InstantaneousFreq = [];
NumberOfSlices = uint32(0);
CurrentSlice = uint32(0);
end
@ -92,6 +93,7 @@ classdef Phase < handle @@ -92,6 +93,7 @@ classdef Phase < handle
end
function DisplayIntensity(obj)
figure
plot(obj.MeanIntensity,'-s','LineWidth',0.8,'MarkerSize',4);
end
@ -119,15 +121,17 @@ classdef Phase < handle @@ -119,15 +121,17 @@ classdef Phase < handle
% Shows the frames of the original image sequence specified in the
% array 'positions'
function ShowFrames(obj,positions,title)
function ShowFrames(obj,positions,title,fps)
triggered = [];
triggered = cat(2,triggered,obj.Video(:,:,positions));
video = implay(triggered,3);
set(video.Parent, 'Name', title);
triggered = cat(2,triggered,obj.Video(:,:,positions));
video = implay(triggered,fps);
set(video.Parent, 'Name', title);
end
function DisplayValues(obj)
plot(obj.Values,'-s','LineWidth',0.8,'MarkerSize',4);
xlabel('Time (sec)');
ylabel('Phase(rad)');
end
end

13
Code/RespiratoryPhase.m

@ -37,6 +37,19 @@ classdef RespiratoryPhase < Phase @@ -37,6 +37,19 @@ classdef RespiratoryPhase < Phase
obj.Values = obj.FullPhase(obj.IMF,:); %Phase corresponding to respiratory phase
end
function GetFrequency(obj,time)
resp_inst_freq = (abs(diff(obj.Values))./diff(time))/(2*pi());
obj.InstantaneousFreq = medfilt1(resp_inst_freq,3);
figure
scatter(time,[obj.InstantaneousFreq,0],8);
mean_freq1 = mean(obj.InstantaneousFreq);
hline = refline([0 mean_freq1]); % Reference line for maximum phase
hline.Color = 'm';
title('Respiratory Instantaneous Frequency');
xlabel('Time (sec)')
ylabel('Frequency (Hz)');
end
% Detects the frame's positions of inspiration moments
function Inspiration(obj)
obj.MaxRespPhase = max(obj.Values); % respiratory phase maxima

139
Code/test_OOP.m

@ -10,7 +10,7 @@ phase = Phase; % creates a Phase object @@ -10,7 +10,7 @@ phase = Phase; % creates a Phase object
phase.GetData; % extracts data
%% Visualize data
phase.ShowFrames(:,'cine Images');
phase.ShowFrames(:,'cine Images',13);
%% Time Information
time = 0:1:phase.nFrames-1;
@ -19,28 +19,28 @@ time = repetitionTime*time; % sampling moments in time @@ -19,28 +19,28 @@ time = repetitionTime*time; % sampling moments in time
%% Instantaneous Phase Extraction (cardiac and respiratory)
phase.GetSignal; % gets mean intensity level of the images
% phase.DisplayIntensity;
% title('Mean Intensity Value');
% te=repetitionTime;
% xt=get(gca,'xtick');
% set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
% xlabel('Time (sec)');
phase.DisplayIntensity;
title('Mean Intensity Value');
te=repetitionTime;
xt=get(gca,'xtick');
set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
xlabel('Time (sec)');
phase.GetEMD; % decompose the siganl using EMD
% Complot(phase.IMFs);
% te=repetitionTime;
% xt=get(gca,'xtick');
% set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
% title('Empirical Mode Decomposition');
% xlabel('Time (sec)');
% legend('IMF1','IMF2','IMF3','IMF4','IMF5','IMF6','IMF7');
Complot(phase.IMFs);
te=repetitionTime;
xt=get(gca,'xtick');
set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
title('Empirical Mode Decomposition');
xlabel('Time (sec)');
legend('IMF1','IMF2','IMF3','IMF4','IMF5','IMF6','IMF7');
phase.GetModes; % turn the modes into phase information
figure
Complot(phase.ModePhases)
title('IMF Phases');
title('IMFs Phase');
te=repetitionTime;
xt=get(gca,'xtick');
set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
@ -56,34 +56,20 @@ figure @@ -56,34 +56,20 @@ figure
cardiac_phase.DisplayValues
hold on
respiratory_phase.DisplayValues
% hold on
% hline = refline([0 cardiac_phase.SystoleTreshold]); % Reference line for systole treshold phase
% hline.Color = 'b';
% hline.LineStyle = ':';
% hold on
% hline = refline([0 cardiac_phase.DiastoleTreshold]); % Reference line for diastole treshold phase
% hline.Color = 'b';
% hline.LineStyle = ':'
% hold on
% hline = refline([0 respiratory_phase.InspirationTreshold]); % Reference line for systole treshold phase
% hline.Color = 'r';
% hline.LineStyle = ':';
% hold on
% hline = refline([0 respiratory_phase.ExpirationTreshold]); % Reference line for diastole treshold phase
% hline.Color = 'r';
% hline.LineStyle = ':';
title('Cardiac and Respiratory Phase');
legend('Cardiac Phase','Respiratory Phase');
te=repetitionTime;
xt=get(gca,'xtick');
set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
xlabel('Time (sec)');
ylabel('Phase(rad)');
%% File with Cardiac and Respiratory Phase
file_matrix = [cardiac_phase.Values; respiratory_phase.Values];
csvwrite('phase_file.csv',file_matrix);
%% Instantaneous Frequency
cardiac_phase.GetFrequency(time);
respiratory_phase.GetFrequency(time);
%% Cardiac and Respiratory events
cardiac_phase.Diastole % detects diastolic events
cardiac_phase.Systole % detects systolic events
@ -96,7 +82,8 @@ DI = intersect(cardiac_phase.DiastolePositions,respiratory_phase.InspirationPosi @@ -96,7 +82,8 @@ DI = intersect(cardiac_phase.DiastolePositions,respiratory_phase.InspirationPosi
DE = intersect(cardiac_phase.DiastolePositions,respiratory_phase.ExpirationPositions); % diastole in expiration
% Show frames of the different cardiac/respiratory events
phase.ShowFrames(SI,'End-systolic frames in inpiration');
% Systole in Inpiration
phase.ShowFrames(SI,'End-systolic frames in inpiration',3);
directory = 'Systole in Inspiration'
mkdir(directory);
for i=1:length(SI)
@ -105,7 +92,26 @@ for i=1:length(SI) @@ -105,7 +92,26 @@ for i=1:length(SI)
dicomwrite(phase.Video(:,:,1,SI(i)), fullFileName);
end
phase.ShowFrames(SE,'End-systolic frames in expiration');
figure
cardiac_phase.DisplayValues
hold on
respiratory_phase.DisplayValues
hold on
hline = refline([0 cardiac_phase.SystoleTreshold]); % Reference line for systole treshold phase
hline.Color = 'b';
hline.LineStyle = ':';
hold on
hline = refline([0 respiratory_phase.InspirationTreshold]); % Reference line for systole treshold phase
hline.Color = 'r';
hline.LineStyle = ':';
title('Systole in Inspiration');
legend('Cardiac Phase','Respiratory Phase');
te=repetitionTime;
xt=get(gca,'xtick');
set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
%Systole in Expiration
phase.ShowFrames(SE,'End-systolic frames in expiration',3);
directory = 'Systole in Expiration'
mkdir(directory);
for i=1:length(SE)
@ -114,7 +120,26 @@ for i=1:length(SE) @@ -114,7 +120,26 @@ for i=1:length(SE)
dicomwrite(phase.Video(:,:,1,SE(i)), fullFileName);
end
phase.ShowFrames(DI,'End-diastolic frames in inpiration');
figure
cardiac_phase.DisplayValues
hold on
respiratory_phase.DisplayValues
hold on
hline = refline([0 cardiac_phase.SystoleTreshold]); % Reference line for systole treshold phase
hline.Color = 'b';
hline.LineStyle = ':';
hold on
hline = refline([0 respiratory_phase.ExpirationTreshold]); % Reference line for diastole treshold phase
hline.Color = 'r';
hline.LineStyle = ':';
title('Systole in Expiration');
legend('Cardiac Phase','Respiratory Phase');
te=repetitionTime;
xt=get(gca,'xtick');
set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
% Disatole in Inspiration
phase.ShowFrames(DI,'End-diastolic frames in inpiration',3);
directory = 'Diastole in Inspiration'
mkdir(directory);
for i=1:length(DI)
@ -123,7 +148,26 @@ for i=1:length(DI) @@ -123,7 +148,26 @@ for i=1:length(DI)
dicomwrite(phase.Video(:,:,1,DI(i)), fullFileName);
end
phase.ShowFrames(DE,'End-diastolic frames in expiration');
figure
cardiac_phase.DisplayValues
hold on
respiratory_phase.DisplayValues
hold on
hline = refline([0 cardiac_phase.DiastoleTreshold]); % Reference line for diastole treshold phase
hline.Color = 'b';
hline.LineStyle = ':'
hold on
hline = refline([0 respiratory_phase.InspirationTreshold]); % Reference line for systole treshold phase
hline.Color = 'r';
hline.LineStyle = ':';
title('Disatole in Inspiration');
legend('Cardiac Phase','Respiratory Phase');
te=repetitionTime;
xt=get(gca,'xtick');
set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
% Distole in Expiration
phase.ShowFrames(DE,'End-diastolic frames in expiration',3);
directory = 'Diastole in Expiration'
mkdir(directory);
for i=1:length(DE)
@ -132,6 +176,25 @@ for i=1:length(DE) @@ -132,6 +176,25 @@ for i=1:length(DE)
dicomwrite(phase.Video(:,:,1,DE(i)), fullFileName);
end
figure
cardiac_phase.DisplayValues
hold on
respiratory_phase.DisplayValues
hold on
hline = refline([0 cardiac_phase.DiastoleTreshold]); % Reference line for diastole treshold phase
hline.Color = 'b';
hline.LineStyle = ':'
hold on
hline = refline([0 respiratory_phase.ExpirationTreshold]); % Reference line for diastole treshold phase
hline.Color = 'r';
hline.LineStyle = ':';
title('Diastole in Expiration');
legend('Cardiac Phase','Respiratory Phase');
te=repetitionTime;
xt=get(gca,'xtick');
set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
%% Heart Beat Reconstruction
n_ranges = 30; % number of phase ranges
ranges = linspace(respiratory_phase.MinRespPhase,respiratory_phase.MaxRespPhase,n_ranges+1); % splits the respiratory phase in n_ranges equal parts
@ -151,4 +214,4 @@ for i=1:1:n_ranges @@ -151,4 +214,4 @@ for i=1:1:n_ranges
new_index{i} = k(j); % ordered indexes
end
selected_range = n_ranges-2; % optional range
phase.ShowFrames(new_index{selected_range},'Heart Beat Reconstruction');
phase.ShowFrames(new_index{selected_range},'Heart Beat Reconstruction',3);

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