Assign_Read_Vis_Biosignals_Images
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Simon Fraser University *
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Apr 3, 2024
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%% CMPT340 Assignment - Reading & Visualizing Bio-signals
% ============================ Goal =========================:
% In this activity, you will load and visualize different data % types acquired from different modalities. %
% ===================== Download Data ==============================
%
% First, download and unzip the BioData from Canvas: %
%
% The data folder contains 5 files:
%
% (1) emg_myopathy.txt (EMG)
%
% (2) bMode.mat (B-mode Ultrasound)
%
% (3) vol4d.mat (fMRI)
%
% (4) XYStripes20x20Noise_9_L_3.mat (tensor field)
% % (5) clathrin_ROI_cmpt340.csv (SMLM data)
clc;
disp('Hamoudi Ohan Saleh Baratta')
disp('SFU ID # 301540229')
% %% ============================ Task 1 ===============================
% (1) EMG Data % Data Description: EMG is short for electromyogram, which measures electrical activity in muscles
% Requirement: % Load the data from emg_myopathy.txt and extract the two columns of values: % i) First column -- time
% ii) Second column -- the amplitude of an EMG signal. close all; clear;
% Load data into MATLAB:
% Write your own code here:
EMG = importdata('emg_myopathy.txt');
% Q1: What are the dimensions of the loaded variable (eg. 5 x 3 x 10)? % Write your own code here: sizeEMG = size(EMG);
fprintf('\nVariable dimensions:\n %d x %d\n\n', sizeEMG(1), sizeEMG(2));
% How many EMG amplitude values does the signal contain?
% Write your own code here:
fprintf('Number of amplitudes:\n %d values\n\n', sizeEMG(1));
% Plot the amplitude vs time using the values in the two columns. % Properly label both axes. Add a suitable title to your figure.
figure(1)
time = EMG(:, 1);
amplitude = EMG(:, 2);
plot(time, amplitude);
xlabel('Time (s)');
ylabel('Amplitude (mV)');
title('EMG Signal');
% There is a period of time with a clearly reduced EMG amplitude. % Examine the previous plot, use the "Zoom In" icon on the toolbar % to close up on this region of the plot. % Visually (roughly) identify the approximate starting and ending % time for this period.
% Display these values :
% Write your own code here
fprintf('Start:\n 16.7667\n\n');
fprintf('End:\n 16.9965\n\n');
% What are the time and amplitude values of the 100th sample of the data? % Write your own code here
disp('Time_100th = ');
display(EMG(100, 1));
disp('Amp_100th = ');
display(EMG(100, 2));
% Plot the EMG signal from the 100th sample (in (1d)) up until the 1100th
% sample. Give a title to your figure. figure(2)
time_100_1100 = EMG(100:1100, 1);
amplitude_100_1100 = EMG(100:1100, 2);
plot(time_100_1100, amplitude_100_1100);
xlabel('Time (s)');
ylabel('Amplitude (mV)');
title('EMG Signal from the 100th to 1100th sample');
%% ============================ Task 2 ===============================
% (2) B-mode Ultrasound sequence % Data Description: This data represent an B-mode ultrasound video sequence (B stands for Brightness)
% Requirement: Load the data in bMode.mat into MATLAB, explore the video frames and
create a GIF
% close all; clear;
% Load data into MATLAB:
% Write your own code here:
load("bMode.mat");
% What are the dimensions of the loaded variable (eg. 5 x 3 x 10)? % You should output the variable dim_bMode as a vector of size 1x3.. % Write your own code here
disp('bMode dimensions: '); % display your answers
dim_bMode = size(bMode); % get the dimensions of bMode
disp(dim_bMode); % display the dimensions
% How many frames (2D images) do we have in the video? % Write your own code here
disp('Number of frames: '); % display your answer
num_frames = dim_bMode(3); % get the number of frames from the third dimension
disp(num_frames); % display the number of frames
% What is the size (rows and columns) of each frame?
% Write your own code here
disp('Nb_rows:');
nb_rows = dim_bMode(1); % get the number of rows from the first dimension
disp(nb_rows); % display the number of rows
disp('Nb_cols:');
nb_cols = dim_bMode(2); % get the number of columns from the second dimension
disp(nb_cols); % display the number of columns
% Extract and display the 9-th frame of the sequence in a figure. % Apply the command that ensures that pixels are not stretched % (i.e. maintain aspect ratio of the image). Apply the command % that uses a grey colour-map to display the image.
% Write your own code here
figure(1)
frame_9 = bMode(:, :, 9); % extract the 9-th frame of the sequence
imagesc(frame_9); colormap gray; axis image; % display the frame with the grey colour-map and aspect ratio
% What is the intensity value at row 30 and column 40, at frame 20?
% Write your own code here disp('Intensity_(30,40,20): '); % update the display to show your answer
intensity_30_40_20 = bMode(30, 40, 20); % get the intensity value at row 30, column
40, and frame 20[^23^][23]
disp(intensity_30_40_20); % display the intensity value
% Extract a cropped rectangular region of frame 15. % The cropped part should extend from row 10 to row 30, and from column 45 % to column 60 of the image. Display this cropped region % (also called region of interest or ROI).
% Write your own code here
figure(2) % update the colormap and figure title
frame_15 = bMode(:, :, 15); % extract the 15-th frame of the sequence
roi = frame_15(10:30, 45:60); % extract the cropped region of interest
imagesc(roi); colormap gray; axis image; % display the region of interest
title('Region of interest of frame 15'); % add a title to the figure
% Create an animated GIF that shows the ultrasound sequence
% (like a video clip). % Save this GIF image using the name US_seq.gif . % You can make use of the MATLAB code used during the lectures
% Write your own code here filename = 'US_seq.gif'; % the name of the GIF file
for idx = 1:num_frames % loop over all the frames
frame = bMode(:, :, idx); % get the current frame
[A, map] = gray2ind(frame, 256); % convert the frame to indexed image
if idx == 1 % for the first frame
imwrite(A, map, filename, 'gif', 'LoopCount', Inf, 'DelayTime', 0.1); % write the frame to the GIF file with infinite loop and 0.1 second delay
else % for the subsequent frames
imwrite(A, map, filename, 'gif', 'WriteMode', 'append', 'DelayTime', 0.1); % append the frame to the GIF file with 0.1 second delay
end
end
%% ============================ Task 3 ===============================
% (3) Functional MRI
% Data Description: This is a 3D+time f-MRI data (functional magnetic resonance image). % fMRI captures the changes in oxygenation with time (4th dimension) at every (x,y,z) location of a volume.
% Requirement: Load the data in vol4d.mat into MATLAB, explore how oxygenation level changes with time
% close all; clear;
% Load data into MATLAB:
% Write your own code here:
load('vol4d.mat'); % load the data
% What are the dimensions of the loaded variable (eg. 5 x 3 x 10)? % Write your own code here:
disp('Size fMRI: '); % display your answer
disp(size(vol4d)) % display the dimensions
% Noting that the first 3 dimensions represent the spatial x, y, and z % dimensions, identify how many rows, columns, slices, and time steps % does this fMRI data have?
% Write your own code here:
% update the display:
disp('Rows fMRI: '); % display # of rows in each slice
disp(size(vol4d,1)); disp('Columns fMRI: '); % display # of columns in each slice
disp(size(vol4d,2)); disp('Slices fMRI: '); % display # of slices
disp(size(vol4d,3));
disp('Time fMRI: '); % display time
disp(size(vol4d,4));
% Plot a curve that shows how the oxygenation level changes % with time at voxel location (x=32, y=34 , z=10).
% Define axis and figure title. figure(1) % create a new figure
plot(squeeze(vol4d(32,34,10,:))) % plot the oxygenation level over time at (x=32, y=34, z=10)
xlabel('Time') % label the x-axis
ylabel('Oxygenation level') % label the y-axis
title('Oxygenation level at (x=32, y=34, z=10)') % add a title
% Extract and display the slice in the X-Y plane, at slice % location z=15, of the 10th time sample.
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