Add filters figures

04-B1/03-Filtering/binder/postBuild

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+#!/bin/bash
+
+git clone https://www.github.com/qMRLab/qMRLab.git ../qMRLab
+cd ../qMRLab
+git checkout f481d86da7272ee0f74abdbe9020cf93be06000f
+cd binder
+

04-B1/03-Filtering/binder/requirements.txt

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+repo2data

04-B1/03-Filtering/content/b1filt_fig1.m

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+clear all
+clc
+close all
+%%
+
+dim = 128;
+x=linspace(1,dim,dim);
+
+signal = 1000;
+
+PulseOpt.slope = dim/100;
+
+b1_func = signal*fermi_pulse(x, dim, PulseOpt);
+
+%%
+
+filtered_obj = filter_map();
+filtered_obj.options.Smoothingfilter_Dimension = '2D';
+data.Raw = repmat(b1_func, dim, 1);
+
+vox_range = 1:25;
+
+gauss_b1_1d = zeros(length(vox_range), dim);
+median_b1_1d = zeros(length(vox_range), dim);
+
+for ii=1:length(vox_range)
+    fwhm_vox = vox_range(ii);
+
+    filtered_obj.options.Smoothingfilter_sizex = fwhm_vox;
+    filtered_obj.options.Smoothingfilter_sizey = fwhm_vox;
+    filtered_obj.options.Smoothingfilter_sizez = fwhm_vox;
+
+    filtered_obj.options.Smoothingfilter_Type = 'gaussian';
+    fit_results = filtered_obj.fit(data);
+    gauss_b1_1d(ii,:) = fit_results.Filtered(1,:);
+
+
+    filtered_obj.options.Smoothingfilter_Type = 'median';
+    fit_results = filtered_obj.fit(data);
+    median_b1_1d(ii,:) = fit_results.Filtered(1,:);
+end
+
+
+order_range = 1:25;
+
+spline_b1_1d = zeros(length(order_range), dim);
+poly_b1_1d = zeros(length(order_range), dim);
+
+
+for ii=1:length(order_range)
+    filtered_obj.options.Smoothingfilter_order = order_range(ii);
+
+    filtered_obj.options.Smoothingfilter_Type = 'spline';
+    fit_results = filtered_obj.fit(data);
+    spline_b1_1d(ii,:) = fit_results.Filtered(1,:);
+
+
+    filtered_obj.options.Smoothingfilter_Type = 'polynomial';
+    fit_results = filtered_obj.fit(data);
+    poly_b1_1d(ii,:) = fit_results.Filtered(1,:);
+end
+
+save("b1filt_fig1.mat", "b1_func", "gauss_b1_1d", "median_b1_1d", "spline_b1_1d", "poly_b1_1d", "vox_range", "order_range")

04-B1/03-Filtering/content/b1filt_fig1_fixed.m

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+clear all
+clc
+close all
+%%
+
+dim = 128;
+x=linspace(1,dim,dim);
+
+signal = 1000;
+
+PulseOpt.slope = dim/100;
+
+b1_func = signal*fermi_pulse(x, dim, PulseOpt);
+
+%%
+
+vox_range = 1:10;
+
+gauss_b1_1d = zeros(length(vox_range), dim);
+median_b1_1d = zeros(length(vox_range), dim);
+spline_b1_1d = zeros(length(vox_range), dim);
+
+for ii=1:length(vox_range)
+
+    % Gaussian
+    w = gausswin(2*vox_range(ii)+1, 2);
+    w = w/sum(w);
+
+    tmp_data = [zeros(1, vox_range(ii)) b1_func zeros(1, vox_range(ii))];
+
+    tmp = filter(w, 1, tmp_data);
+    shifted_tmp_data = [tmp(vox_range(ii)+1:end) zeros(1,vox_range(ii))];
+    shifted_tmp_data(1:vox_range(ii)) = [];
+    shifted_tmp_data(end-vox_range(ii)+1:end) = [];
+    gauss_b1_1d(ii,:) = shifted_tmp_data;
+
+    % Median
+    median_b1_1d(ii,:) = medfilt1(b1_func,vox_range(ii));
+
+    % Spline    
+    spline_b1_1d(ii,:) = smoothn(b1_func, vox_range(ii));
+end
+
+save("b1filt_fig1.mat", "b1_func", "gauss_b1_1d", "median_b1_1d", "spline_b1_1d", "vox_range")

04-B1/03-Filtering/content/b1filt_fig2.m

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+clear all
+clc
+close all
+%%
+
+dim = 128;
+x=linspace(1,dim,dim);
+
+signal = 1000;
+
+PulseOpt.slope = dim/100;
+
+b1_func = signal*fermi_pulse(x, dim, PulseOpt);
+
+%% Add noise
+
+SNR_range = 1:100;
+noisy_b1_1d = zeros(length(SNR_range), dim);
+
+%%
+
+filtered_obj = filter_map();
+filtered_obj.options.Smoothingfilter_Dimension = '2D';
+
+fwhm_vox = 5;
+filtered_obj.options.Smoothingfilter_sizex = fwhm_vox;
+filtered_obj.options.Smoothingfilter_sizey = fwhm_vox;
+filtered_obj.options.Smoothingfilter_sizez = fwhm_vox;
+
+filtered_obj.options.Smoothingfilter_order = 6;
+
+noisy_b1 = zeros(length(SNR_range), dim);
+gauss_b1_1d = zeros(length(SNR_range), dim);
+median_b1_1d = zeros(length(SNR_range), dim);
+spline_b1_1d = zeros(length(SNR_range), dim);
+poly_b1_1d = zeros(length(SNR_range), dim);
+
+for ii=1:length(SNR_range)
+    noisy_b1(ii,:) = addNoise(b1_func, SNR_range(ii));
+    data.Raw = repmat(noisy_b1(ii,:), dim, 1);
+
+
+    filtered_obj.options.Smoothingfilter_Type = 'gaussian';
+    fit_results = filtered_obj.fit(data);
+    gauss_b1_1d(ii,:) = fit_results.Filtered(1,:);
+
+
+    filtered_obj.options.Smoothingfilter_Type = 'median';
+    fit_results = filtered_obj.fit(data);
+    median_b1_1d(ii,:) = fit_results.Filtered(1,:);
+
+
+    filtered_obj.options.Smoothingfilter_Type = 'spline';
+    fit_results = filtered_obj.fit(data);
+    spline_b1_1d(ii,:) = fit_results.Filtered(1,:);
+
+
+    filtered_obj.options.Smoothingfilter_Type = 'polynomial';
+    fit_results = filtered_obj.fit(data);
+    poly_b1_1d(ii,:) = fit_results.Filtered(1,:);
+end
+
+save("b1filt_fig2.mat", "b1_func", "noisy_b1", "gauss_b1_1d", "median_b1_1d", "spline_b1_1d", "poly_b1_1d", "SNR_range")

04-B1/03-Filtering/content/b1filt_fig2_fixed.m

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+clear all
+clc
+close all
+%%
+
+dim = 128;
+x=linspace(1,dim,dim);
+
+signal = 1000;
+
+PulseOpt.slope = dim/100;
+
+b1_func = signal*fermi_pulse(x, dim, PulseOpt);
+
+%% Add noise
+
+SNR_range = 1:100;
+noisy_b1_1d = zeros(length(SNR_range), dim);
+
+%%
+
+filtered_obj = filter_map();
+filtered_obj.options.Smoothingfilter_Dimension = '2D';
+
+fwhm_vox = 5;
+filtered_obj.options.Smoothingfilter_sizex = fwhm_vox;
+filtered_obj.options.Smoothingfilter_sizey = fwhm_vox;
+filtered_obj.options.Smoothingfilter_sizez = fwhm_vox;
+
+smoothingfilter_order = 6;
+
+noisy_b1 = zeros(length(SNR_range), dim);
+gauss_b1_1d = zeros(length(SNR_range), dim);
+median_b1_1d = zeros(length(SNR_range), dim);
+spline_b1_1d = zeros(length(SNR_range), dim);
+poly_b1_1d = zeros(length(SNR_range), dim);
+
+for ii=1:length(SNR_range)
+
+    noisy_b1(ii,:) = addNoise(b1_func, SNR_range(ii));
+    data.Raw = repmat(noisy_b1(ii,:), dim, 1);
+
+    % Gaussian
+    w = gausswin(2*fwhm_vox+1, 2);
+    w = w/sum(w);
+
+    tmp_data = [zeros(1, fwhm_vox) noisy_b1(ii,:) zeros(1, fwhm_vox)];
+
+    tmp = filter(w, 1, tmp_data);
+    shifted_tmp_data = [tmp(fwhm_vox+1:end) zeros(1,fwhm_vox)];
+    shifted_tmp_data(1:fwhm_vox) = [];
+    shifted_tmp_data(end-fwhm_vox+1:end) = [];
+    gauss_b1_1d(ii,:) = shifted_tmp_data;
+
+    % Median
+    median_b1_1d(ii,:) = medfilt1(noisy_b1(ii,:),fwhm_vox);
+
+    % Spline    
+    spline_b1_1d(ii,:) = smoothn(noisy_b1(ii,:), smoothingfilter_order);
+end
+
+save("b1filt_fig2.mat", "b1_func", "noisy_b1", "gauss_b1_1d", "median_b1_1d", "spline_b1_1d", "SNR_range")