diff --git a/rfPulseTools/2drfPulseTools/b0map.npy b/rfPulseTools/2drfPulseTools/b0map.npy new file mode 100644 index 00000000..8f87aded Binary files /dev/null and b/rfPulseTools/2drfPulseTools/b0map.npy differ diff --git a/rfPulseTools/2drfPulseTools/readNPY.m b/rfPulseTools/2drfPulseTools/readNPY.m new file mode 100644 index 00000000..9095d003 --- /dev/null +++ b/rfPulseTools/2drfPulseTools/readNPY.m @@ -0,0 +1,37 @@ + + +function data = readNPY(filename) +% Function to read NPY files into matlab. +% *** Only reads a subset of all possible NPY files, specifically N-D arrays of certain data types. +% See https://github.com/kwikteam/npy-matlab/blob/master/tests/npy.ipynb for +% more. +% + +[shape, dataType, fortranOrder, littleEndian, totalHeaderLength, ~] = readNPYheader(filename); + +if littleEndian + fid = fopen(filename, 'r', 'l'); +else + fid = fopen(filename, 'r', 'b'); +end + +try + + [~] = fread(fid, totalHeaderLength, 'uint8'); + + % read the data + data = fread(fid, prod(shape), [dataType '=>' dataType]); + + if length(shape)>1 && ~fortranOrder + data = reshape(data, shape(end:-1:1)); + data = permute(data, [length(shape):-1:1]); + elseif length(shape)>1 + data = reshape(data, shape); + end + + fclose(fid); + +catch me + fclose(fid); + rethrow(me); +end diff --git a/rfPulseTools/2drfPulseTools/readNPYheader.m b/rfPulseTools/2drfPulseTools/readNPYheader.m new file mode 100644 index 00000000..7776de52 --- /dev/null +++ b/rfPulseTools/2drfPulseTools/readNPYheader.m @@ -0,0 +1,72 @@ + + +function [arrayShape, dataType, fortranOrder, littleEndian, totalHeaderLength, npyVersion] = readNPYheader(filename) +% function [arrayShape, dataType, fortranOrder, littleEndian, ... +% totalHeaderLength, npyVersion] = readNPYheader(filename) +% +% parse the header of a .npy file and return all the info contained +% therein. +% +% Based on spec at http://docs.scipy.org/doc/numpy-dev/neps/npy-format.html + +fid = fopen(filename); + +% verify that the file exists +if (fid == -1) + if ~isempty(dir(filename)) + error('Permission denied: %s', filename); + else + error('File not found: %s', filename); + end +end + +try + + dtypesMatlab = {'uint8','uint16','uint32','uint64','int8','int16','int32','int64','single','double', 'logical'}; + dtypesNPY = {'u1', 'u2', 'u4', 'u8', 'i1', 'i2', 'i4', 'i8', 'f4', 'f8', 'b1'}; + + + magicString = fread(fid, [1 6], 'uint8=>uint8'); + + if ~all(magicString == [147,78,85,77,80,89]) + error('readNPY:NotNUMPYFile', 'Error: This file does not appear to be NUMPY format based on the header.'); + end + + majorVersion = fread(fid, [1 1], 'uint8=>uint8'); + minorVersion = fread(fid, [1 1], 'uint8=>uint8'); + + npyVersion = [majorVersion minorVersion]; + + headerLength = fread(fid, [1 1], 'uint16=>uint16'); + + totalHeaderLength = 10+headerLength; + + arrayFormat = fread(fid, [1 headerLength], 'char=>char'); + + % to interpret the array format info, we make some fairly strict + % assumptions about its format... + + r = regexp(arrayFormat, '''descr''\s*:\s*''(.*?)''', 'tokens'); + if isempty(r) + error('Couldn''t parse array format: "%s"', arrayFormat); + end + dtNPY = r{1}{1}; + + littleEndian = ~strcmp(dtNPY(1), '>'); + + dataType = dtypesMatlab{strcmp(dtNPY(2:3), dtypesNPY)}; + + r = regexp(arrayFormat, '''fortran_order''\s*:\s*(\w+)', 'tokens'); + fortranOrder = strcmp(r{1}{1}, 'True'); + + r = regexp(arrayFormat, '''shape''\s*:\s*\((.*?)\)', 'tokens'); + shapeStr = r{1}{1}; + arrayShape = str2num(shapeStr(shapeStr~='L')); + + + fclose(fid); + +catch me + fclose(fid); + rethrow(me); +end diff --git a/rfPulseTools/2drfPulseTools/rf2d_bloch_sim.m b/rfPulseTools/2drfPulseTools/rf2d_bloch_sim.m new file mode 100644 index 00000000..d12b0551 --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_bloch_sim.m @@ -0,0 +1,361 @@ +% rf2d_bloch_sim.m +% Jason Rock, Elena Osipyan and Jamie Near, 2025. +% +% USAGE: +% rf2d_bloch_sim.runblochsim(params) +% +% DESCRIPTION: +% This class performs Bloch simulations of two-dimensional RF (2DRF) pulses. +% It supports both simulated pulses generated with rf2d_create.makepulse +% and Siemens-provided RF/gradient waveform data. The simulator models +% magnetization dynamics under off-resonance conditions and can visualize +% excitation maps, magnetization components of +% the Bloch simulation. +% +% INPUTS: +% params.RF_RASTER = RF raster time [s] +% params.GRAD_RASTER = Gradient raster time [s] +% params.tp = Total pulse duration [s] +% params.flip_angle = Flip angle [degrees] (default = 10°) +% cond = Integer flag to select pulse type (e.g., cond=7 for +% rf2d_create.m-generated pulses) +% ppm = Spin system frequency offset definition. Desired off-resonance offset [Hz]. Based off the ppm +% value in params.mat +% file_path = Path to RF pulse text file (default = '2DRFpulse.txt') +% b1_peak = Peak B1 amplitude [Tesla] (default ≈ 8e-6 for 2DRF) +% +% OUTPUTS: +% result = Complex transverse magnetization (Mxy) across spatial grid +% M_z_range = Final z-component magnetization values +% M_x_range = Final x-component magnetization values +% M_y_range = Final y-component magnetization values +% (All outputs can be visualized as images or trajectories of magnetization) +% +% INTERNAL METHODS: +% rot_y() - Rotation matrix about the y-axis +% rot_z() - Rotation matrix about the z-axis +% Bloch_Sim() - Core Bloch simulation routine, computes Mx, My, Mz +% runblochsim()- Main execution function, loads pulse/gradients and runs sim +% +% VISUALIZATIONS: +% - 3D plot of magnetization components (Mx, My, Mz) +% - Transverse excitation map (|Mxy|) +% - RF amplitude/phase vs time +% - Gradient waveforms vs time + + +classdef rf2d_bloch_sim + methods(Static) + +% Rotation Functions +function[res] = rot_y(M_temp,angle) + angle = angle(1); + R = [cos(angle),0,-sin(angle); + 0, 1, 0; + sin(angle), 0, cos(angle)]; + res = R * M_temp(:); + res = res'; +end + +function[res] = rot_z(M_temp, angle) + angle = angle(1); + R = [cos(angle), -sin(angle), 0; + sin(angle), cos(angle), 0; + 0, 0, 1]; + res = R * M_temp(:); % Ensure proper matrix multiplication + res = res'; +end + + +function[result, M_z_range, M_y_range, M_x_range, Mxy] = Bloch_Sim(b0_map_flag, gamma, x_pos, y_pos, grad_x, grad_y, offset, b1, phase, amp, b1_peak) + RF_RASTER = 5*10^-6; + tp = round(length(amp)*RF_RASTER, 5); + b0_map = fliplr(readNPY('b0map.npy')); + b0_map = imresize(b0_map, [length(y_pos), length(x_pos)]); + figure; + imagesc(b0_map); % Scales and displays matrix as image + colormap jet; % Apply the 'jet' colormap + colorbar; % Add colorbar + title('loaded b0 map'); % Set title + axis image; % Optional: makes pixel aspect ratio 1:1 + hold off; + + + fprintf("**Bloch Sim Starting with this offset:" + offset); + for n = 1:length(x_pos) + offset_x = grad_x .* x_pos(n) / 1000; + for ny = 1:length(y_pos) + offset_y = grad_y .* y_pos(ny) / 1000; % + 300/gamma #for off res + offset_b0 = 2*pi*b0_map(ny,n)/gamma; + M_new = [0 0 1]; + for q = 1:length(b1)-1 + phi = phase(q); + + if(b0_map_flag) + B1_eff = sqrt(b1(q).^2 + (offset_x(q) + offset_y(q) + offset/gamma + offset_b0).^2); + alpha = atan2(b1(q), (offset_x(q) + offset_y(q) + offset_b0 + offset/gamma)); + + else + B1_eff = sqrt(b1(q).^2 + (offset_x(q) + offset_y(q) + offset/gamma).^2); + alpha = atan2(b1(q), (offset_x(q) + offset_y(q) + offset/gamma)); + + end + dt = tp / length(amp); + theta = gamma * B1_eff * dt; + M_new = rf2d_bloch_sim.rot_z(M_new, phi); + M_new = rf2d_bloch_sim.rot_y(M_new, alpha); + M_new = rf2d_bloch_sim.rot_z(M_new, theta); + M_new = rf2d_bloch_sim.rot_y(M_new, -alpha); + M_new = rf2d_bloch_sim.rot_z(M_new, -phi); + + end + M_z_range(ny,n) = M_new(3); + M_x_range(ny,n) = M_new(1); + M_y_range(ny,n) = M_new(2); + end + end + % Compute transverse magnetization magnitude + +N = length(M_x_range); +idx = 1:N; + +figure; + +% X component along x-axis +pMx = plot3(idx, M_x_range, zeros(1, N), 'r', 'DisplayName', 'M_x'); +hold on; + +% Y component along y-axis +pMy = plot3(idx, zeros(1, N), M_y_range, 'g', 'DisplayName', 'M_y'); + +% Z component rotated to lie along z-axis +pMz = plot3(idx, M_z_range, zeros(1, N), 'b', 'DisplayName', 'M_z'); + +xlabel('M_z'); +ylabel('M_y'); +zlabel('M_x'); +title('Magnetization Components vs Sample Index'); + +legend([pMx(1) pMy(1) pMz(1)], 'Location', 'northeastoutside'); % compact legend +grid on; +view(45, 30); % adjust viewing angle + +Mxy = M_x_range + 1i * M_y_range; +% --- figure: Transverse excitation map --- +figure; + +imagesc(100 * [min(x_pos), max(x_pos)], ... + 100 * [min(y_pos), max(y_pos)], ... + (abs(Mxy))); +colormap('gray'); +axis image; +set(gca, 'FontSize', 20); +colorbar; +title('Transverse Excitation', 'Interpreter', 'latex'); +xlabel('X position (cm)'); +ylabel('Y position (cm)'); +result = Mxy; +end + +function[] = runblochsim(params) + tic; + load params + load rf2d + if ~strcmp(rf2d.type, '2drf') + ME = MException('ForceStop:ExecutionTerminated', ... + 'You are not creating a 2DRF Pulse! Program stopped.'); + throw(ME); + end + RF_RASTER = params.RF_RASTER; + GRAD_RASTER = params.GRAD_RASTER; + b1_peak = rf2d.b1_peak; %flip_angle/gamma/tp/integral_factor #Tesla #8 for regular pulses + chris_pulse_test = false; + cond = 7; + [amp, phase, g_x, g_y, g_z] = rf2d_pulse_readin.read_pulse_for_bloch(cond); + ppm = params.ppm; + offset = 123.25*ppm*2*pi; + gamma = 267.522*10^6; + +T = params.tp; % seconds - total pulse duration. +t = linspace(0, T, 6000); % rf pulse legnth: 10ms, # of samples +% 6000 = lots of samples + +off_resonance_testing = false; +b0_map_flag = false; + +% Gradients resampled to be same length as the phase and amplitude waveforms. +g_x = resample(g_x, length(amp), length(g_x)); +g_y = resample(g_y, length(amp), length(g_y)); + +b1_peak_approx = 8e-6; +b1 = ((amp) / max(amp))* b1_peak_approx; +b1 = reshape(b1.', 1, []); % transpose first, then reshape into a row vector + + +tp = round(length(amp)*RF_RASTER, 5); +t_axis = linspace(0, tp * 1000, length(amp)); % ms +% % Plot RF amplitude +% figure; +% plot(t_axis, amp, 'LineWidth', 1); +% title("RF Pulse Amplitude"); +% xlabel("Time (ms)"); +% ylabel("Amplitude"); +% grid on; + +% % Plot RF phase +% figure; +% plot(t_axis, phase, 'LineWidth', 1); +% title("RF Pulse Phase"); +% xlabel("Time (ms)"); +% ylabel("Phase (radians or a.u)"); +% grid on; + + +tp = round(length(amp)*RF_RASTER, 5); +dt = tp / length(amp); + + +if(chris_pulse_test) + data = load('sim_noB0.npz'); + data = load('jason_square_B0_23.npz'); + lst = data.files; + new_amp = []; + for i = 1:length(lst) + item = lst{i}; + new_amp{end+1} = data.(item); + end + amp = new_amp{1}; + phase = new_amp{2}; + data = [amp, phase]; % Concatenate as two columns + + lenRF = length(amp); + file_path = '2DRFpulse.txt'; + + %Write the data to a text file with tab separation + + fid = fopen(file_path, 'w'); + fprintf(fid, '%d\n', lenRF); + fclose(fid); + % Append the amplitude and phase data + writematrix(file_path, data, '-append', 'delimiter', '\t', 'precision', '%.6f'); + + fprintf('Complex B1 has been written to {file_path}'); + +end + + +RF_lobe_correction = zeros(size(amp)); +signed_RF = zeros(size(amp)); + +realAmp = 0; +imagAmp = 0; + +if cond == 1 || cond == 2 + for i = 1:length(phase) + if(phase(i) == 0.0) + RF_lobe_correction(i) = 1; + end + if(phase(i) == 180.0) + RF_lobe_correction(i) = -1; + end + signed_RF(i) = amp(i)*RF_lobe_correction(i); + %signed_RF has the arbitrary unit scaling + integral_factor = sum(signed_RF)/(length(signed_RF)*max(signed_RF)); + end +end +if cond == 3 || cond == 4 + %integral_factor = 82 + for i = 1:length(amp) + realAmp = realAmp + amp(i) * cos(phase(i)); + imagAmp = imagAmp + amp(i) * sin(phase(i)); + + end +end + +integral_factor = sqrt(realAmp^2 + imagAmp^2); + + +if(cond == 1 || cond == 2) + grad_x = 0.5595 * ones(size(b1)); % mT/m + grad_y = 0.5595 * ones(size(b1)); +end +if(cond == 3 || cond == 7) %Siemens sequence requirements + grad_x = resample(g_x, length(b1), length(g_x)); + grad_y = resample(g_y, length(b1), length(g_y)); +end + + + +if(cond == 4 || cond == 5 || cond == 6) + t_grad = linspace(0, 1, length(g_x)); + t_b1 = linspace(0, 1, length(b1)); + % Interpolate gradients to match b1 length + grad_x = g_x; % Or 'spline' + grad_y = interp1(t_grad, g_y, t_b1, 'spline'); +end + +flip_angle = params.flip_angle; + +x_fov = params.FOV/100; %meters +y_fov = params.FOV/100; +linspace(x_fov/2, -x_fov/2, params.voxels); +M0 = [0,0,1]; + +b1_unsgn = b1; %(np.array(amp) / max(amp)) * b1_peak +a = 0.40; +beta = pi / 2; + +M_temp = [0 0 1]; +amp = amp(:); +phase = phase(:); + +tp = RF_RASTER * length(amp); % update time duration + + +x_pos = linspace(x_fov/2, -x_fov/2, params.voxels); +y_pos = linspace(y_fov/2, -y_fov/2, params.voxels); + +images = zeros(length(amp), length(x_pos), length(y_pos), 'single'); +images_pha = zeros(length(amp), length(x_pos), length(y_pos), 'single'); + +blochs_simside = {}; +if(off_resonance_testing) + ORs = [0, 66.5, 194.4, 217, 263] .* (2 * pi); + for i = 1:length(ORs) + bloch_simside = rf2d_bloch_sim.Bloch_Sim(b0_map_flag, gamma, x_pos, y_pos, grad_x, grad_y, offset, b1, phase, amp, b1_peak); + end + + instance = 7; + % instance 2 = circle + image = shape(instance); + image = fliplr(image); + mse_onres, roi_integrals, frac_outside = off_res_metrics(image, blochs_simside, '.', FA = 1); + + for i = 1:length(ORs) + figure; + offset_Hz = 0; + titleStr = sprintf('Off-resonance Transverse Excitation M_{xy}, nOffset = %g', offset); + Mxy = M_x_range + 1i*M_y_range; + % Plot the masked image + imagesc(100 * [min(x_pos), max(x_pos)], ... + 100 * [min(y_pos), max(y_pos)], ... + masked_image); + axis image; + colormap gray; + + c = colorbar; + c.Label.String = 'Fraction of \bfM in M_{xy}'; + title(titleStr, 'Interpreter','tex') + xlabel("x position (cm)") + ylabel("y position (cm)") + end + +else + blochs_simside = rf2d_bloch_sim.Bloch_Sim(b0_map_flag, gamma, x_pos, y_pos, grad_x, grad_y, offset, b1, phase, amp, b1_peak); +end + +elapsed = toc; +fprintf('Elapsed time of Bloch Sim: %.3f seconds\n', elapsed); +end +end +end \ No newline at end of file diff --git a/rfPulseTools/2drfPulseTools/rf2d_create.m b/rfPulseTools/2drfPulseTools/rf2d_create.m new file mode 100644 index 00000000..74522e4c --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_create.m @@ -0,0 +1,873 @@ +% rf2d_create.m +% Jason Rock, Elena Osipyan and Jamie Near, 2025. +% +% USAGE: +% rf2d = rf2d_create.makepulse(params) +% +% DESCRIPTION: +% This class provides functions to design, generate, and export 2D RF (2DRF) +% pulses with corresponding gradient trajectories. It implements spiral k-space +% trajectories with gradient and slew rate constraints, Gaussian k-space filtering, +% B1 peak calibration, and export of Siemens-compatible RF and gradient text files. +% The class also supports visualization of excitation targets, k-space trajectories, +% and the resulting RF pulse amplitude/phase profiles. +% +% INPUTS (params struct): +% params.MAX_GRAD = Maximum gradient amplitude [T/m] (default = 0.08 T/m) +% params.MAX_SLEW = Maximum gradient slew rate [T/m/ms] (default = 0.2 T/m/ms) +% params.RF_RASTER = RF raster time [s] (default = 5e-6 s) +% params.GRAD_RASTER = Gradient raster time [s] (default = 1e-5 s) +% params.type = Type of RF pulse (default = '2drf', anything else yields exception) +% params.shape = Ex citation shape (defined in rf2d_shapes.m). Example: shapes(1) is +% a square. + +% params.FOV = Field of view [cm] (default = 12 cm) +% params.tp = Total pulse duration [s] (default = 0.015 s) +% params.k_us = Transmit k-space trajectory undersampling rate (default = 4) +% params.flip_angle = Flip angle [rad] (default = 10 deg / 0.174533 rad) +% params.ppm = Off-resonance/chemical-shift for simulation [ppm] (on-resonance default = 0) +% params.voxels = Number of spatial samples per axis for design/Bloch sim grid (default = 128) + +% params.calibration = Calibration for calculating the B1 peak. Options: +% 'center' (gets the center pixel of the image), 'brightest' (gets the +% brightest pixel of the image), 'custom' (lets user choose custom pixel of +% image) +% +% OUTPUTS: +% rf2d struct containing: +% .waveform = RF pulse [amplitude, phase, 0] +% .type = '2drf' +% .gradients = Gradient waveforms [gx, gy, gz] +% .b1_peak = Calibrated B1 peak [Tesla] +% .flip_angle = Flip angle [radians] +% .tp = Total pulse duration [s] +% +% FILE OUTPUTS: +% 2DRFpulse.txt = RF amplitude and phase +% 2DGpulse.txt = Gradient waveforms +% rf2d.mat = MATLAB struct containing pulse and gradient information + + +classdef rf2d_create + methods(Static) + function[res] = shift(b1, x0, k) + res = b1 * exp (-1i * dot(x0, k)); +end + +function val = first_zero_crossing(arr) + val = NaN; % Default return value + if length(arr) < 2 + return; + end + arr = arr(isfinite(arr)); + if length(arr) < 2 + return; + end + for i = 1:(length(arr) - 1) + if (arr(i) >= 0 && arr(i+1) < 0) || (arr(i) < 0 && arr(i+1) >= 0) + val = i; + return; + end + end + + % If no zero crossing found, return a reasonable default + val = min(20, floor(length(arr)/4)); +end + +% ===== Helpers (boolean-returning) ===== + +function [ok, b1_peak] = attempt_center(image_in, flip_angle, amp, phase, tp) + % center is (0,0); reject if center is black (no data) + b1_peak = []; + % Get dimensions + [rows, cols] = size(image_in); % Compute center pixel coordinates + cy = round(rows/2); + cx = round(cols/2); + + isBlack = rf2d_create.check_coord(image_in, cx, cy); % true => black/invalid + if isBlack + ok = false; return; + end + offset_x = 0; offset_y = 0; + [ok, b1_peak] = rf2d_create.compute_b1_peak(offset_x, offset_y, flip_angle, amp, phase, tp); +end + +function [ok, b1_peak] = attempt_brightest(image_in, flip_angle, amp, phase, tp, x_axis, y_axis) + b1_peak = []; + try + [cx, cy] = rf2d_create.brightest(image_in); + isBlack = rf2d_create.check_coord(image_in, cx, cy); % true => black/invalid + if isBlack + ok = false; return; + end + catch + ok = false; return; + end + [ok, b1_peak] = rf2d_create.compute_b1_peak(cx/1e6, cy/1e6, flip_angle, amp, phase, tp); +end + +function [ok, b1_peak] = attempt_custom(image_in, flip_angle, amp, phase, tp, x_axis, y_axis) + b1_peak = []; + try + fprintf('Click your preferred pixel for B1 calibration.\n'); + [cx, cy] = rf2d_create.pick_point(image_in); + isBlack = rf2d_create.check_coord(image_in, cx, cy); % true => black/invalid + if isBlack + ok = false; return; + end + catch + ok = false; return; + end + [ok, b1_peak] = rf2d_create.compute_b1_peak(cx/1e6, cy/1e6, flip_angle, amp, phase, tp); +end + +function [ok, b1_peak] = compute_b1_peak(offset_x, offset_y, flip_angle, amp, phase, tp) + % Core boolean computation: no throws, returns ok=false on any invalidity + b1_peak = []; + ok = false; + + % Guard: amp must be nonzero to normalize + if isempty(amp) || all(~isfinite(amp)) || max(abs(amp)) == 0 + return; + end + + % Run calibration sweep via your existing API + try + [b1_peaks, M_z_cal] = rf2d_create.b1_peak_calc( ... + flip_angle, amp, phase, tp, offset_x, offset_y); + catch + return; + end + + % Find first zero crossing + try + idx = rf2d_create.find_zero_crossings(M_z_cal, flip_angle); + catch + idx = []; + end + if isempty(idx) || any(~isfinite(idx)) + return; + end + + cand = b1_peaks(idx(1)); + if isempty(cand) || ~isfinite(cand) || isnan(cand) + return; + end + + b1_peak = cand; + ok = true; +end + + +function[B1_shifted] = modify_rf_pulse_for_shift(B1, kx, ky, shift_x, shift_y) + % RF pulse can be modified to account for object shift, handling phase wrapping. + phase_shift = exp(-1i * (kx * shift_x + ky * shift_y)); + phase_shift_wrapped = angle(phase_shift); % Wraps the phase to -pi to pi + phase_shift_corrected = exp(1i * phase_shift_wrapped); + + B1_shifted = B1 * phase_shift_corrected; +end + +function idx = find_zero_crossings(arr, flip_angle) + idx = find(diff(sign(arr - cos(flip_angle)))); +end + +function isBlack = check_coord(image_in, x, y) +% CHECK_COORD Return true if a given pixel in a double image is zero (black). +% isBlack = check_coord(image_in, x, y) +% +% Inputs: +% image_in : 2D or 3D numeric array (double image) +% x : column index (cx) +% y : row index (cy) +% Output: +% isBlack : logical true/false + + % If RGB double image, convert to grayscale + if ndims(image_in) == 3 && size(image_in,3) == 3 + img = mean(image_in, 3); % simple grayscale conversion + elseif ndims(image_in) == 2 + img = image_in; + else + error('Unsupported input: must be 2D grayscale or 3D RGB double image.'); + end + + % Ensure indices are valid integers inside the image + [rows, cols] = size(img); + if x < 1 || x > cols || y < 1 || y > rows + error('Coordinates (x=%d, y=%d) out of image bounds.', x, y); + end + + % Logical check (allow small tolerance for floating-point) + tol = 1e-12; + isBlack = (abs(img(round(y), round(x))) < tol); + +end +function [cx, cy, isBlack] = pick_point(imgIn) +% PICK_POINT Let the user click a location on the image. Returns (cx, cy). +% [cx, cy] = pick_point(imgIn) +% - imgIn: image array or filename (grayscale or RGB) +% - cx, cy: clicked coordinates (x=column, y=row), double precision + + % Load image if filename given + if ischar(imgIn) || isstring(imgIn), img = imread(imgIn); else, img = imgIn; end + + % Convert per your rule + if ndims(img) == 2 + I = im2gray(img); + elseif ndims(img) == 3 && size(img,3) == 3 + I = rgb2gray(img); + else + error('Unsupported image format: use 2D grayscale or 3D RGB.'); + end + + % Show image and get one click + hFig = figure('Name','Click a point'); + imshow(I, []); axis image; hold on; + title('Click your preferred point (press Enter/Esc to cancel)'); + try + [x, y, btn] = ginput(1); % one click + catch + close(hFig); error('Click canceled.'); + end + if isempty(x) || isempty(y) || ~isscalar(btn) + close(hFig); error('Click canceled.'); + end + + % Clip to image bounds and return + [H, W] = size(I); + cx = min(max(x, 1), W); + cy = min(max(y, 1), H); + % Visual feedback + plot(cx, cy, 'r+', 'MarkerSize', 15, 'LineWidth', 2); + drawnow; +end + +function result = mod_custom(p) + result = p - 2 * pi * floor(p / (2 * pi)); +end + +function[ft] = calculate_2dft(image_in) + image_in = im2gray(image_in); % Convert to grayscale if RGB + ft = ifftshift(image_in); + ft = fft2(ft); + ft = fftshift(ft); +end + +function[b1_peaks, M_z_cal] = b1_peak_calc(flip_angle, amp, phase, tp, offset_x, offset_y) + b1_min = 1e-8; + b1_max = 25e-5; + disp(['*** Flip angle: ', num2str(rad2deg(flip_angle)), ' deg']) + + dt = tp / length(amp); % tp should be defined earlier + M_z_cal = zeros(1, 500); + b1_peaks = linspace(b1_min, b1_max, 500); + gamma = 267.522*10^6; + + for i = 1:length(b1_peaks) + b1 = (amp / max(amp)) * b1_peaks(i); % Normalized B1 amplitude + M_temp = [0;0;1]; + for m = 1:length(b1) + phi1 = phase(m); % phase in radians + B1_eff = sqrt(b1(m)^2 + (offset_x + offset_y)^2); + alpha1 = atan2(b1(m), (offset_x + offset_y)); + theta1 = gamma * B1_eff * dt; + + M_temp = rf2d_bloch_sim.rot_z(M_temp, phi1); + M_temp = rf2d_bloch_sim.rot_y(M_temp, alpha1); + M_temp = rf2d_bloch_sim.rot_z(M_temp, theta1); + M_temp = rf2d_bloch_sim.rot_y(M_temp, -alpha1); + M_temp = rf2d_bloch_sim.rot_z(M_temp, -phi1); + end + + M_z_cal(i) = M_temp(3); % Store z-component + end +end + +function[var] = G(T, t, N, k_max) % grad trajectory - Rf pulse = Rf(interpolation) * |G| + var = sqrt((2*N*pi*(1 - t/T)).^2 + 1); +end + +function kx = k_x(t, A, n, T, variable_density) +% k_x - Computes x-component of a spiral k-space trajectory +% +% Inputs: +% t - time array +% A - amplitude (k_max) +% n - number of spiral turns +% T - total RF pulse durationmath +% variable_density - 1x2 logical+numeric array: [true/false, density_param] +% +% Output: +% kx - k-space x-component trajectory + + if nargin < 5 + variable_density = [false, 0]; % default: uniform density + end + + is_vd = variable_density(1); % true or false + density_param = variable_density(2); + + if is_vd + kx = A * (1 - t/T) .* cos(2 * pi * t * n / T) .* exp(density_param * t / T); + else + kx = A * (1 - t/T) .* cos(2 * pi * t * n / T); + end + +end + +function ky = k_y(t, A, n, T, variable_density) +% k_y - Computes y-component of a spiral k-space trajectory +% +% Inputs: +% t - time array +% A - amplitude (k_max) +% n - number of spiral turns +% T - total RF pulse duration +% variable_density - 1x2 logical+numeric array: [true/false, density_param] +% +% Output: +% ky - k-space y-component trajectory + + if nargin < 5 + variable_density = [false, 0]; % default: uniform density + end + + is_vd = variable_density(1); % true or false + density_param = variable_density(2); + + if is_vd + ky = A * (1 - t/T) .* sin(2 * pi * t * n / T) .* exp(density_param * t / T); + else + ky = A * (1 - t/T) .* sin(2 * pi * t * n / T); + end + +end + +function[conv] = G_x(kx, dt) + % gamma in rad/(s*T) = 267.522e6 rad/(s*T) + gamma = 267.522e6; + + % Convert k-space trajectory to gradient + % kx is in cm^-1, need to convert to m^-1 (multiply by 100) + % Then divide by gamma to get gradient in T/m + %conv = (gradient(kx * 1000)/dt) / gamma / pi; % T/m + + conv = 1/gamma / (pi) * gradient(1000*kx, dt); + + % Convert to mT/m for display (multiply by 1000) + %conv = conv * 1000; % mT/m +end + +function[conv] = G_y(ky, dt) + % Fixed gradient calculation for Y + % gamma in rad/(s*T) = 267.522e6 rad/(s*T) + gamma = 267.522e6; + + % Convert k-space trajectory to gradient + % ky is in cm^-1, need to convert to m^-1 (multiply by 100) + % Then divide by gamma to get gradient in T/m + %conv = (gradient(ky * 1000)/dt) / gamma / pi; % T/m + conv = 1/gamma / (pi) * gradient(1000*ky, dt); + % Convert to mT/m for display (multiply by 1000) + %conv = conv * 1000; % mT/m +end + +function [cx, cy] = brightest(imgIn) +% BRIGHTEST: Mark the brightest location in an image with a box. +% [cx, cy, peakVal] = brightest (imgIn, boxSizePx) +% - imgIn: image array or filename +% - boxSizePx: optional, side length of the box in pixels (auto if omitted) +% Returns centroid (cx,cy) in image coordinates (x=col, y=row) and peak value. + + % --- Load + if ischar(imgIn) || isstring(imgIn), img = imread(imgIn); else, img = imgIn; end + + % --- Convert per your rule + if ndims(img) == 2 + I = im2gray(img); + elseif ndims(img) == 3 && size(img,3) == 3 + I = rgb2gray(img); + else + error('Unsupported image format. Use 2D grayscale or 3D RGB.'); + end + + % --- Safe double image in [0,1], handle NaNs + I = im2double(I); + I(isnan(I)) = -inf; % exclude NaNs from the max + + % --- Find brightest location(s) + peakVal = max(I(:)); + if ~isfinite(peakVal) + error('Image has no finite pixels.'); + end + [rows, cols] = find(I == peakVal); % all ties + cy = mean(rows); % average if multiple maxima + cx = mean(cols); +end + + +function[absolute_values, phase_values] = write_b1(amp, pha) + absolute_values = amp(:); + phase_values = pha(:); + lenRF = length(absolute_values); + file_path = fullfile('2DRFpulse.txt'); + fid = fopen(file_path, 'w'); + fprintf(fid, '%d\n', lenRF); % write the header line + for i = 1:lenRF + fprintf(fid, '%.6f\t%.6f\n', absolute_values(i), phase_values(i)); % fixed 6 decimal places + end + fclose(fid); + + fprintf("Complex B1 has been written to %s\n", file_path); +end + +function[gx,gy] = write_grad(gx, gy) + % Siemens requires gradients to be normalized + gx = gx(:); % Ensure column vector + gy = gy(:); % Ensure column vector + + gx_max_raw = max(abs(gx)); + gy_max_raw = max(abs(gy)); + gx = gx / gx_max_raw; + gy = gy / gy_max_raw; + gz = zeros(length(gx), 1); + % For Siemens requirements - ensure last elements are zero + if length(gx) > 0 + gx(end) = 0.00; + gy(end) = 0.00; + gz(end) = 0.00; + end + Gx_max = round(gx_max_raw, 3); % in mT/m + Gy_max = round(gy_max_raw, 3); + % Preparing the variables for header + lenGrad = int32(length(gx)); + header = [Gx_max, Gy_max, 0]; + header_row = reshape(header, 1, numel(header)); + % Main data table + data = [gx(:), gy(:), gz(:)]; + %Define the file path + file_path = fullfile('2DGpulse.txt'); + % % Write lenGrad as the first row + fid = fopen(file_path, 'w'); % Overwrite to start clean + fprintf(fid, '%d\n', lenGrad); + % + % % Write header row + fprintf(fid, '%.6f\t%.6f\t%.6f\n', header_row); + + % Write data + fprintf(fid, '%.6f\t%.6f\t%.6f\n', data'); + fclose(fid); + + fprintf("Gradient data written to %s\n", file_path); + end + + + function[gx,gy] = write_files(amp, pha, b1, kx, ky, dt, withRamp, gx, gy, T, RF_RASTER, GRAD_RASTER) + + RF_samples = round(T / RF_RASTER); + Grad_samples = round(T / GRAD_RASTER); + % Ensure inputs are column vectors + amp = amp(:); + pha = pha(:); + gx = gx(:)*1000; + gy = gy(:)*1000; + len_padding = rf2d_create.first_zero_crossing(gy); + if withRamp + len_padding_global = len_padding; + b1_new_amp = zeros(1, len_padding + length(amp)); + b1_new_amp(len_padding+1:end) = amp; + + b1_new_pha = zeros(1, len_padding + length(pha)); + b1_new_pha(len_padding+1:end) = pha; + + % Resampling + RF_samples = round(T / RF_RASTER); + b1_new_amp = b1_new_amp / max(b1_new_amp); + rf2d_create.write_b1(b1_new_amp, b1_new_pha); + + gx_new = zeros(len_padding + length(gx), 1); + gx_new(len_padding + 1:end) = gx; + gy_new = zeros(len_padding + length(gy), 1); + + % Create ramp part - ensure we don't exceed array bounds + ramp_length = min(len_padding, length(gy)); + if ramp_length > 0 + ramp_part = flipud(gy(1:ramp_length)); + gy_new(1:ramp_length) = ramp_part; + end + + % Fill the rest of gy_new with original gy values + remaining_start = len_padding + 1; + remaining_end = length(gy_new); + source_start = 1; + source_end = min(length(gy), remaining_end - remaining_start + 1); + + if source_end > 0 && remaining_start <= remaining_end + gy_new(remaining_start:remaining_start + source_end - 1) = gy(source_start:source_end); + end + + gx = resample(gx_new, (Grad_samples + floor(len_padding * Grad_samples / (T/RF_RASTER))), length(gx_new)); + gy = resample(gy_new, (Grad_samples + floor(len_padding * Grad_samples / (T/RF_RASTER))), length(gy_new)); + + rf2d_create.write_grad(gx, gy); + + + else + % Non-ramping version + Grad_samples = int32(round(T / GRAD_RASTER)); + % === Resample b1 amplitude === + + gx = resample(gx, Grad_samples, length(gx)); + gy = resample(gy, Grad_samples, length(gy)); + + pha(pha > 2*pi) = 2*pi; + pha(pha < 0) = 0; + + %plot(pha); + %title('Pha After Write Files'); + rf2d_create.write_b1(amp, pha); + rf2d_create.write_grad(gx, gy); % Non-ramping + end +end +function[rf2d] = makepulse(params) + clear; + tic; + load params + image_in = params.shape; + image_in = fliplr(image_in); + FOV = params.FOV; % cm. FOV = dr * Nx + dr = (FOV / (2 * size(image_in, 2))); + k_us = params.k_us; + MAX_GRAD = params.MAX_GRAD; %T/m, could be much higher. Up for the user to change! + MAX_SLEW = params.MAX_SLEW; % T/m/ms figure out, will affect spiral density N + % raster times - minimum hardware discretization + RF_RASTER = params.RF_RASTER; + GRAD_RASTER = params.GRAD_RASTER; + T = params.tp; % seconds - total pulse duration +% high spatial frequencies are hard to capture - multiply k space by gaussian. +% if we don't filter signal - lots of ripples in image. hence we gauss blur the k space + save_it = true; + withRamp = true; + b1_peak_algo = true; + if ~strcmp(params.type, '2drf') + ME = MException('ForceStop:ExecutionTerminated', ... + 'You are not creating a 2DRF Pulse! Program stopped.'); + throw(ME); + end +t = linspace(0, T, T/RF_RASTER); + +dt = t(2) - t(1); +image_in = fliplr(image_in); + +ft = rf2d_create.calculate_2dft(image_in); +[rows, cols] = size(ft); + +%Create a meshgrid of the same size as the Fourier transform +x1 = linspace(-floor(cols/2), floor(cols/2), cols); +y1 = linspace(-floor(rows/2), floor(rows/2), rows); +[X1, Y1] = meshgrid(x1, y1); + + +% the k space trajectory is calculated through the parametric equation. the gradient of the spiral +no_amp_restriction = false; +% gets you a set of gradient. there is a max amplitude, the rate of change of the gradient is also limited. +% always check that the slope of gradient is the max +% ex. n=26, kmax is prop to res +variable_density = [false, 1]; + +if (no_amp_restriction) + N = 26; % Arbitrary number + k_max = 1 / (2 * dr); % cm^-1 + % k_max = N / FOV + % num of spirals too low while kmax is high = aliasing + + kx_axis = linspace(-k_max, k_max, size(image_in, 2)); + ky_axis = linspace(-k_max, k_max, size(image_in, 1)); + [KX, KY] = meshgrid(kx_axis, ky_axis); + kx = rf2d_create.k_x(t, k_max / k_us, N, T, variable_density); + ky = rf2d_create.k_y(t, k_max / k_us, N, T, variable_density); + +else + % restriction with grad amplitude and slew + % can either restrict number of spirals and k_max for fixed FOV + + restrict_N = true; + + if (restrict_N) + + % for brain/circle, effective FOV = 1 + max_of_max_slew = 0.95; % 80% of MAX SLEW + % N_list = np.linspace(30,2, 30-2+1) + N_list = 30:-0.2:1.8; % list of spirals, increments of .2 + + k_max = 1 / (2 * dr); % cm^-1 + kx_axis = linspace(-k_max, k_max, size(image_in, 2)); + ky_axis = linspace(-k_max, k_max, size(image_in, 1)); + [KX, KY] = meshgrid(kx_axis, ky_axis); + + + for i = 1:(length(N_list)) + kx = rf2d_create.k_x(t, k_max/k_us, N_list(i), T); + ky = rf2d_create.k_y(t, k_max/k_us, N_list(i), T); + if (max(rf2d_create.G_x(kx, dt)) < MAX_GRAD && max(rf2d_create.G_y(ky, dt)) < MAX_GRAD) + %grad_gx = gradient(G_x(kx, dt), dt); + if (max(abs(gradient(rf2d_create.G_x(kx, dt), dt)))/1000) < MAX_SLEW*max_of_max_slew && max(abs(gradient(rf2d_create.G_y(ky, dt), dt))/1000) < MAX_SLEW*max_of_max_slew + N = N_list(i); + %plot(kx); hold on; plot(ky); + fprintf("restricted k_x, k_y found with: N = %d\n", N); + break + end + end + end + end + +end + + +% Define the standard deviation for the Gaussian +% 0.03 more blurry than 0.05 +% Adjust this value as needed, here scaled with the size +sigma = 0.08 * min(rows, cols); + +% Create the Gaussian filter +gaussian_filter = exp(-(X1.^2 + Y1.^2) / (2 * sigma^2)); + +% Apply the Gaussian filter to the Fourier transform +ft = ft .* gaussian_filter; +% --- Setup --- +figure; +% Manually move title upward by increasing the y-position +sgtitle('RF Pulse Design'); + +% --- Parameters --- +kx = kx(:); +ky = ky(:); + +% --- Axis vectors (assumes square image) --- +x_axis = linspace(-dr * size(image_in, 2), dr * size(image_in, 2), size(image_in, 2)); +y_axis = x_axis; +[X, Y] = meshgrid(x_axis, y_axis); + +% --- Left Plot: Original Image --- +nexttile; +imagesc(x_axis, y_axis, rot90(image_in, 2)); +axis equal tight; +colormap gray; +xlabel('[cm]'); +ylabel('[cm]'); +title('Target Excitation Region'); + +% --- Right Plot: k-space & Trajectory Overlay --- +nexttile; + +% Convert k-space coordinates to pixel units +kx_pixels = ((kx / k_us) * (dr * size(image_in, 1) / 2)); +ky_pixels = ((ky / k_us) * (dr * size(image_in, 2)/ 2)); + +% Determine bounding box of the k-space trajectory +ft_logabs = log(abs(ft)); +% Display Fourier transform of image within trajectory bounds +imagesc([min(x_axis(1,:)), max(x_axis(1,:))], [min(y_axis(1,:)), max(y_axis(1,:))], ft_logabs); + +% Display Fourier transform of image within trajectory bounds +hold on; +plot(kx_pixels/3, ky_pixels/3, 'r-', 'LineWidth', 2); +xlim([min(x_axis(1,:)) max(x_axis(1,:))]); +axis equal tight; +colormap gray; +alpha(0.8); % Make FT image semi-transparent +xlabel('$k_x$ [cm$^{-1}$]', 'Interpreter', 'latex'); +ylabel('$k_y$ [cm$^{-1}$]', 'Interpreter', 'latex'); +title('k-space trajectory over $\mathcal{FT}$', 'Interpreter', 'latex'); +set(gca, 'TickLabelInterpreter', 'latex'); +set(gcf, 'Color', 'w'); + + +grad_gx = gradient(rf2d_create.G_x(kx, dt), dt); +max_slew = max(abs(grad_gx)) / 1000; % T/m/ms +fprintf("Slew rate MAX for G_x: %.3f T/m/ms\n", max_slew); +% Print info +%fprintf('Slew rate MAX for G_x: %.3f T/m/ms\n', max(abs(grad_gx)) / 1000); +fprintf('Slew rate MAX: 0.200 T/m/ms\n'); +fprintf('Gradient frequency: N / T = %.2f Hz\n', N/T); +fprintf('Forbidden gradient frequency ranges:\n'); +fprintf(' * 1140 Hz +/- 110 Hz\n'); +fprintf(' * 590 Hz +/- 50 Hz\n'); + +if (N/T <= 1250 && N/T >= 1030) || ... + (N/T <= 640 && N/T >= 540) + fprintf('You are within a forbidden gradient frequency range!\n'); +end + +% Reconstruct matching k-space grid for interpolation +kx_axis = linspace(-k_max, k_max, size(ft, 2)); % 64 points +ky_axis = linspace(-k_max, k_max, size(ft, 1)); % 64 points +[KX, KY] = meshgrid(kx_axis, ky_axis); % KX, KY are 64x64 + +% Flatten data for griddata +points = [KX(:), KY(:)]; % (4096, 2) +values = ft(:); % (4096, 1) + +% Confirm shape match +assert(size(points,1) == length(values), 'griddata input mismatch'); + +%b1 = griddata(points(:,1), points(:,2), values, kx(:), ky(:), 'linear'); + +% Apply G modulation +G_vector = rf2d_create.G(T, t, N, k_max); +% Use 1D query points +b1 = griddata(points(:,1), points(:,2), values, kx(:), ky(:), 'cubic'); + +%b1_unfixed = griddata(points(:,1), points(:,2), values, kx(:), ky(:), 'nearest'); +%b1_unfixed = b1_unfixed .* G_vector; + +b1 = b1(:, 1); +time_axis = linspace(0, T, length(b1)); + +% Plot b1 against time_axis (converted to ms) + + +G_vector = reshape(rf2d_create.G(T, t, N, k_max), [], 1); +if isvector(G_vector) && isequal(numel(G_vector), numel(b1)) + b1 = b1 .* G_vector; +elseif isscalar(G_vector) + b1 = b1 * G_vector; +else + error('Size mismatch between b1 and G(t, T, N, k_max)'); +end + + +% ---- +len_padding_global = 0; + +gx = rf2d_create.G_x(kx, dt); % good here +gy = rf2d_create.G_y(ky, dt); +amp = abs(b1) / max(abs(b1)); +pha = rf2d_create.mod_custom(unwrap(angle(b1))); + +if (save_it) + + [g_x, g_y] = rf2d_create.write_files(amp, pha, b1, kx, ky, dt, withRamp, gx, gy, T, RF_RASTER, GRAD_RASTER); +end + +% Open and read the file +pulsedata = readmatrix('2DRFpulse.txt'); +amp_data = pulsedata(:,1); +phase_data = pulsedata(:,2); + +hold off; + +tp = T; + +flip_angle = params.flip_angle; +phase = phase_data; +amp = amp_data; +b1_peak = 8e-6; +b1 = ((amp) / max(amp))* b1_peak; +b1 = reshape(b1.', 1, []); % transpose first, then reshape into a row vector +offset_x = 0; +offset_y = 0; +% ===== Entry point ===== +if b1_peak_algo + method = lower(strtrim(params.calibration)); % 'center' | 'custom' | 'brightest' + valid = any(strcmp(method, {'center','custom','brightest'})); + assert(valid, 'Invalid params.calibration: %s', params.calibration); + + done = false; + max_loops = 3; % upper bound to avoid accidental infinite loops + loops = 0; + + while ~done + loops = loops + 1; + if loops > max_loops + error('B1Peak:AllFailed','B1 Peak cannot be found based on provided excitation shape. Switch excitation shape.'); + end + + switch method + case 'center' + [ok, b1_peak] = rf2d_create.attempt_center(image_in, flip_angle, amp, phase, tp); + if ok + done = true; + else + resp = input('B1 Calibration based on center voxel failed. Select the brightest pixel (b) or a custom pixel (c) to perform the b1 peak calculation: ', 's'); + switch resp + case {'b','B'} + fprintf('You chose brightest pixel option.\n'); + method = 'brightest'; + % --- call your brightest pixel routine here --- + case {'c','C'} + fprintf('You chose custom pixel option.\n'); + method = 'custom'; + % --- call your custom pixel picker here -- + + otherwise + fprintf('Invalid input. Must be b or c.\n') + end + end + + case 'brightest' + [ok, b1_peak] = rf2d_create.attempt_brightest(image_in, flip_angle, amp, phase, tp, x_axis, y_axis); + if ok + done = true; + else + % fallback: brightest → center → custom + resp = input('B1 Calibration based on brightest voxel failed. Select the center pixel (b) or a custom pixel (c) to perform the b1 peak calculation: ', 's'); + switch resp + case {'b','B'} + fprintf('You chose brightest pixel option.\n'); + method = 'brightest'; + % --- call your brightest pixel routine here --- + case {'c','C'} + fprintf('You chose center pixel option.\n'); + method = 'center'; + otherwise + fprintf('Invalid input. Must be b or c.\n') + end + end + + case 'custom' + [ok, b1_peak] = rf2d_create.attempt_custom(image_in, flip_angle, amp, phase, tp, x_axis, y_axis); + if ok + done = true; + else + % rule: custom failure ⇒ custom error (no more fallbacks) + error('B1Peak:CustomFailed', ... + 'Custom pixel B1 peak calculation failed as the selected point has no excitation. Retry again with a different excitation shape or select a different point.'); + end + end + + % If we just tried center or brightest and it failed twice (A↔B), drop to custom: + if ~done && loops == 2 && ~strcmp(method,'custom') + method = 'custom'; + end + end +else + b1_peak = 2.45e-6; % fallback +end +waveform = []; +waveform(:,1) = amp_data; +waveform(:,2) = phase_data; +waveform(:,3) = zeros(length(amp_data(:,1)), 1); +all_gradients = []; +all_gradients(:,1) = g_x; +all_gradients(:,2) = g_y; +all_gradients(:,3) = zeros(length(g_x(:,1)), 1); + +rf2d = struct(); +rf2d.waveform = waveform; +rf2d.type = '2drf'; +rf2d.gradients = all_gradients; +rf2d.b1_peak = b1_peak; +rf2d.flip_angle = flip_angle; +rf2d.tp = tp; +save('rf2d.mat', 'rf2d'); % write to disk +elapsed = toc; +fprintf('Elapsed time: %.3f seconds\n', elapsed); +%---------------- ANIMATION -------------------------------------- + + end + + + end +end \ No newline at end of file diff --git a/rfPulseTools/2drfPulseTools/rf2d_getRFPeakPower.m b/rfPulseTools/2drfPulseTools/rf2d_getRFPeakPower.m new file mode 100644 index 00000000..25a89fc3 --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_getRFPeakPower.m @@ -0,0 +1,59 @@ +% rf2d_getRFPeakPower.m +% Jamie Near, 2025. +% +% USAGE: +% [rfPeakPower, rfPeakB1] = rf2d_getRFPeakPower(rf2d,params,TxAmpPwrRating,sysB1max) +% +% DESCRIPTION: +% DESCRIPTION: +% Calculate the instantaneous peak RF power of a given RF waveform given +% its duration, and some properties of the MR system transmitter: the +% transmitter amplifier power rating (TxAmpPwrRating, in kilowatts), and the +% system peak B1 amplitude (sysB1max, in microtesla). This function first +% calculates the required peak B1 amplitude (rfPeakB1) for the desired RF +% pulse and flip angle. The function then determines what fraction of the +% system peak B1 strength (f_B1) this represents. Finally, the function +% calculates the instantaneous peak power (rfPeakPower) by multiplying the system +% transmitter amplifier power rating by the square of the peak B1 fraction, +% f_B1. For example, the body coil of a Siemens Prisma scanner is driven +% with a 50kW amplifier, and delivers a peak B1 intensity of 26 microtesla. +% If a pulse requires a peak B1 intensity of 13 microtesla, the instantaneous +% peak power of the RF pulse will be 50 kW x (1/2)^2 = 12.5 kW. +% +% +% FORMULA: +% rfPeakPower = (rfPeakB1 / sysB1max)^2 * TxAmpPwrRating +% +% INPUTS: +% rf2d - Structure with fields: +% • flip_angle : flip angle [rad] +% • tp : pulse duration [ms] +% (In this implementation, hardware constants are +% hard-coded; see NOTES to externalize them.) +% +% OUTPUTS: +% rfPeakPower - Instantaneous peak transmit power [kW]. +% rfPeakB1 - Echo of input b1_peak [T]. +% +% WARNINGS: +% Prints a warning if rfPeakB1/sysB1max > 1 (required B1 exceeds system). + +function [rfPeakPower,rfPeakB1]=rf2d_getRFPeakPower(rf2d) +tp = rf2d.tp; +rfPeakB1 = rf2d.b1_peak; +flipAngle = rf2d.flip_angle; +%Gyromagnetic ratio +gamma=42577000; %[Hz/T].... assuming Proton + +rfPeakB1=rfPeakB1*(rad2deg(flipAngle)/90); +%Find out the required peak B1 for the input RF pulse: +%Calculate the fraction of available system B1 amplitude: +f_B1=rfPeakB1/sysB1max; + +%Warning if pulse exceeds B1 requirements: +if f_B1>1 + disp('WARNING: Pulse exceeds system B1 amplitude limit!! Calculating anyway.'); +end + +%Calculate the instantaneous peak power of the RF pulse: +rfPeakPower = (f_B1^2)*TxAmpPwrRating; \ No newline at end of file diff --git a/rfPulseTools/2drfPulseTools/rf2d_getRFPulseEnergy.m b/rfPulseTools/2drfPulseTools/rf2d_getRFPulseEnergy.m new file mode 100644 index 00000000..708a7bba --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_getRFPulseEnergy.m @@ -0,0 +1,42 @@ +% rf2d_getRFPulseEnergy.m +% Jamie Near, 2025. +% +% USAGE: +% E = rf2d_getRFPulseEnergy(rf2d, peakPower) +% +% DESCRIPTION: +% Compute the total energy [kJ] delivered by a 2D RF pulse by integrating +% the instantaneous transmit power over the pulse duration. The power +% waveform is taken proportional to |B1(t)|^2 and normalized to the peak +% of the provided B1 waveform. If the instantaneous peak transmit power +% at max |B1| is unknown, estimate it with rf2d_getRFPeakPower. +% Useful for comparing total energy (and SAR proxies for equal durations) +% across different RF pulse waveforms. +% +% INPUTS: +% rf2d - 2D RF pulse structure with field: +% • waveform : B1(t) samples (real or complex). +% • tp : total pulse duration [s]. +% peakPower - Instantaneous peak transmit power [kW] at max |B1|. +% +% OUTPUTS: +% E - Total pulse energy [kJ]. +% +% NOTES: +% • The waveform is internally normalized by max |B1|. +% • See also: rf2d_getRFPeakPower + + +function [E]=rf2d_getRFPulseEnergy(rf2d,peakPower) + +%Calculate the power waveform as the square of the normalized B1 waveform, +%multiplied by the peak power of the pulse. +powerWaveform = peakPower*(rf2d.waveform.^2)/max(rf2d.waveform.^2); + +%calculate the step size of the RF pulse +deltaT=rf2d.tp/length(rf2d.waveform); + +%Calculate the total pulse energy as the sum of the power waveform, +%multiplied by the step size: +E=sum(powerWaveform)*deltaT; + diff --git a/rfPulseTools/2drfPulseTools/rf2d_plotWaveform.m b/rfPulseTools/2drfPulseTools/rf2d_plotWaveform.m new file mode 100644 index 00000000..9f578c61 --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_plotWaveform.m @@ -0,0 +1,97 @@ +% rf2d_plotWaveform.m +% Jamie Near, 2025. +% +% USAGE: +% out=rf2d_plotWaveform(rf,mode); +% +% DESCRIPTION: +% Plot the 2DRF pulse waveforms in the time domain. +% +% INPUTS: +% rf2d = RF pulse in FID-A structure format. +% mode = Which waveform to plot: 'ph', 'amp', 'gm' or 'all' (optional. Default = all). +% +% OUTPUTS: +% out = Figure handle. + +function out=rf2d_plotWaveform(rf2d,mode) +cond = 7; +[amp, phase, g_x, g_y, g_z] = rf2d_pulse_readin.read_pulse_for_bloch(cond); + + +%First make the time vector to use for all plots: +t=linspace(0, rf2d.tp * 1000, length(rf2d.waveform(:,2))); +tgrad = linspace(0, rf2d.tp * 1000, length(g_x)); + +%Check the mode and plot accordingly: +if strcmp(mode,'ph'); + out=figure; + set(gcf,'color','w'); + plot(t,rf2d.waveform(:,2),'LineWidth',1.2); + set(gca,'FontSize',16); + xlabel('Time (ms)','FontSize',20); + ylabel('Phase (rad)','FontSize',20); + title('2DRF Pulse Phase'); +elseif strcmp(mode,'amp'); + out=figure; + set(gcf,'color','w'); + plot(t,rf2d.waveform(:,1),'LineWidth',1.2); + set(gca,'FontSize',16); + xlabel('Time (ms)','FontSize',20); + ylabel('Amplitude (arb units)','FontSize',20); + title('2DRF Pulse Amplitude'); +elseif strcmp(mode,'gm') + out1=figure; + set(gcf,'color','w'); + plot(tgrad,g_x,'LineWidth',1.2,'DisplayName','Gradient in X'); + hold on; + plot(tgrad,g_y,'LineWidth',1.2,'DisplayName','Gradient in Y'); + set(gca,'FontSize',16); + xlabel('Time (ms)','FontSize',20); + ylabel('Gradient Amplitude (mT/m)','FontSize',20); + legend; + title('2DRF Pulse Gradients'); +elseif strcmp(mode,'all'); + out1=figure; + set(gcf,'color','w'); + plot(tgrad,g_x,'LineWidth',1.2,'DisplayName','Gradient in X'); + hold on; + plot(tgrad,g_y,'LineWidth',1.2,'DisplayName','Gradient in Y'); + set(gca,'FontSize',16); + xlabel('Time (ms)','FontSize',20); + ylabel('Gradient Amplitude (mT/m)','FontSize',20); + legend; + title('2DRF Pulse Gradients'); + + hold off; + + out2=figure; + set(gcf,'color','w'); + plot(t,rf2d.waveform(:,1),'LineWidth',1.2); + set(gca,'FontSize',16); + xlabel('Time (ms)','FontSize',20); + ylabel('Amplitude (arb units)','FontSize',20); + title('2DRF Pulse Amplitude'); + + hold off; + + out3=figure; + set(gcf,'color','w'); + plot(t,rf2d.waveform(:,2),'LineWidth',1.2); + set(gca,'FontSize',16); + xlabel('Time (ms)','FontSize',20); + ylabel('Phase (rad)','FontSize',20); + title('2DRF Pulse Phase'); +else + error('ERROR: mode not recognized. Choose ''ph'', ''amp'', ''gm'', or ''all''. ABORTING!!'); +end +end + + + + + + + + + diff --git a/rfPulseTools/2drfPulseTools/rf2d_pulse_readin.m b/rfPulseTools/2drfPulseTools/rf2d_pulse_readin.m new file mode 100644 index 00000000..5fd3834f --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_pulse_readin.m @@ -0,0 +1,291 @@ +% rf2d_pulse_readin.m +% Jason Rock, Elena Osipyan and Jamie Near, 2025. +% +% USAGE: +% [amp, phase, g_x, g_y, g_z] = rf2d_pulse_readin.read_pulse_for_bloch(cond) +% +% DESCRIPTION: +% This class provides utility functions for reading in 2D RF pulse and gradient +% waveforms from different file formats. It supports multiple input conditions +% corresponding to pulse formats from various sources (e.g., Vespa, McGill, +% Peyshan, Pauly, custom B1_maker). The output waveforms can then be used in +% Bloch simulations or other MR sequence modeling workflows. +% +% INPUTS: +% cond = integer specifying which input case to use: +% 1 - Vespa format text file ("MAO_vespaFormat.txt") +% 2 - Jamie’s RF pulse (loaded from "RFpulse.mat") +% 3 - Peyshan’s pulse (RF: "MAO_vespaFormat.txt", Gradients: "2DGpulse.txt") +% 4 - McGill EPI pulse (RF: "RF_EPI_McGill.txt", Gradients: "grad_EPI_McGill.txt") +% 5 - Custom RF + gradient (RF: "2DRFpulse.txt", Gradients: "2DGpulse.txt") +% 6 - Pauly analytical pulse (generated internally, no files required) +% 7 - Peyshan’s sequence-compatible RF + gradient files +% +% FILE FORMATS: +% - RF text files: contain amplitude and phase (in degrees or radians). +% - Gradient text files: contain x, y, (optionally z) gradient values per line. +% - .mat file: should contain struct/array "RFpulse" with phase and amplitude columns. +% +% OUTPUTS: +% amp = RF amplitude waveform +% phase = RF phase waveform +% g_x = Gradient waveform in X direction +% g_y = Gradient waveform in Y direction +% g_z = Gradient waveform in Z direction (may be zero if not provided) + + +classdef rf2d_pulse_readin + methods(Static) + function lines = readfiles(f) + lines = {}; + tline = fgetl(f); + while ischar(tline) + lines{end+1} = tline; + tline = fgetl(f); % <- use 'f' here instead of 'fid' + end + fclose(f); + end + function [amp, phase, g_x, g_y, g_z] = read_pulse_for_bloch(cond) + amp = []; + phase = []; + + g_x = []; + g_y = []; + g_z = []; + if(cond == 1) + f = fopen('MAO_vespaFormat.txt', 'r'); + lines = rf2d_pulse_readin.readfiles(f); + for i = 1:length(lines) + tokens = str2double(strsplit(lines{i})); + amp(end+1) = tokens(1); + phase(end+1) = tokens(2); + end + end + if(cond == 2) % Jamie's pulse + data = load('RFpulse.mat'); % Loads struct + RFpulse = data.RFpulse; % Extract the variable + + % Assuming RFpulse is an Nx2 array: column 1 = phase, column 2 = amp + phase = RFpulse(:, 1); + amp = RFpulse(:, 2); + end + + + if(cond == 3) %Peyshan's pulse + f = fopen('MAO_vespaFormat.txt', 'r'); + lines = rf2d_pulse_readin.readfiles(f); + for i = 1:length(lines) + if i > 0 + tokens = str2double(strsplit(lines{i})); + amp(end+1) = tokens(1); + phase(end+1) = tokens(2); + end + end + + f2 = fopen('2DGpulse.txt', 'r'); + lines = rf2d_pulse_readin.readfiles(f2); + + for i = 1:length(lines) + if i > 0 + tokens = str2double(strsplit(lines{i})); + g_x(end+1) = 20 * tokens(1); + g_y(end+1) = 20 * tokens(2); + g_z(end+1) = 10 * tokens(3); + end + end + end + if(cond == 4) %for Jamie McGill pulse + f = fopen('RF_EPI_McGill.txt', 'r'); + lines = rf2d_pulse_readin.readfiles(f); + for i = 1:length(lines) + tokens = str2double(strsplit(strtrim(lines{i}), ',')); + if ~isempty(tokens) && ~any(isnan(tokens)) + amp(end+1) = tokens(1); + phase(end+1) = tokens(2); + end + end + + f2 = fopen('grad_EPI_McGill.txt', 'r'); + lines = rf2d_pulse_readin.readfiles(f2); + for i = 1:length(lines) + tokens = str2double(strsplit(lines{i}, ',')); + if ~isempty(tokens) && ~all(isnan(tokens)) + g_x(end+1) = 9.63 * tokens(1); + g_y(end+1) = 2.10 * tokens(2); + g_z(end+1) = 0 * tokens(3); % or just g_z(end+1) = 0; + end + end + end + if cond == 5 % My custom RF from B1_maker + Gx_max = 0; + Gy_max = 0; + + % --- Read RF pulse file --- + data = readmatrix('2DRFpulse.txt'); + amp = data(:, 1); % Extract column 1 + phase = data(:, 2); % Extract column 2 + % fid = fopen(filename, 'r'); + % if fid == -1 + % error('Could not open file: %s', filename); + % end + % try + % fgetl(fid); % Skip header + % line_count = 0; + % while ~feof(fid) + % line = fgetl(fid); + % if ischar(line) && ~isempty(strtrim(line)) + % line_data = str2num(line); %#ok + % if length(line_data) >= 2 + % amp(end+1) = line_data(1); + % phase(end+1) = line_data(2); + % end + % end + % end + % catch ME + % fclose(fid); + % rethrow(ME); + % end + % fclose(fid); + + % --- Read gradient pulse file --- + gradfile = '2DGpulse.txt'; + f2 = fopen(gradfile, 'r'); + if f2 == -1 + error('Could not open file: %s', gradfile); + end + + lines1 = {}; + tline = fgetl(f2); + while ischar(tline) + lines1{end+1} = tline; + tline = fgetl(f2); + end + fclose(f2); + + % Process gradient file + for i = 1:length(lines1) + tokens = str2double(split(strtrim(lines1{i}))); + if i == 2 + Gx_max = tokens(1); + Gy_max = tokens(2); + elseif i > 2 && length(tokens) >= 2 + g_x(end+1) = Gx_max * tokens(1); + g_y(end+1) = Gy_max * tokens(2); + end + end + end + + if cond == 7 % Peyshan's sequence compatible pulse + Gx_max = 0; + Gy_max = 0; + + % --- Read RF pulse file --- + filename = '2DRFpulse.txt'; + fid = fopen(filename, 'r'); + if fid == -1 + error('Could not open file: %s', filename); + end + + try + % Read all lines first + lines = rf2d_pulse_readin.readfiles(fid); + + % Process RF data (skip header if present) + start_idx = 1; + if ~isempty(lines) && isempty(str2num(lines{1})) + start_idx = 2; % Skip header + end + + for i = start_idx:length(lines) + line = strtrim(lines{i}); + if ~isempty(line) + line_data = str2num(line); %#ok + if length(line_data) >= 2 + amp(end+1) = line_data(1); + phase(end+1) = line_data(2); + end + end + end + + catch ME + if fid ~= -1 + fclose(fid); + end + rethrow(ME); + end + + % --- Read gradient pulse file --- + gradfile = '2DGpulse.txt'; + f2 = fopen(gradfile, 'r'); + if f2 == -1 + error('Could not open file: %s', gradfile); + end + + try + lines1 = rf2d_pulse_readin.readfiles(f2); + + % Process gradient file + for i = 1:length(lines1) + line = strtrim(lines1{i}); + if ~isempty(line) + tokens = str2double(split(line)); + tokens = tokens(~isnan(tokens)); % Remove NaN values + + if i == 2 && length(tokens) >= 2 + Gx_max = tokens(1); + Gy_max = tokens(2); + elseif i > 2 && length(tokens) >= 2 + g_x(end+1) = Gx_max * tokens(1); + g_y(end+1) = Gy_max * tokens(2); + end + end + end + + catch ME + if f2 ~= -1 + fclose(f2); + end + rethrow(ME); + end + + % Data validation and debugging + fprintf('RF Data: %d amplitude points, %d phase points\n', length(amp), length(phase)); + fprintf('Gradient Data: %d Gx points, %d Gy points\n', length(g_x), length(g_y)); + fprintf('Amplitude range: [%.4f, %.4f]\n', min(amp), max(amp)); + fprintf('Phase range: [%.4f, %.4f]\n', min(phase), max(phase)); + + % Convert phase from degrees to radians if needed + if max(abs(phase)) > 10 % Likely in degrees + fprintf('Converting phase from degrees to radians\n'); + phase = phase * pi / 180; + end + end + + + if(cond == 6) %pauly pulse exact + gamma = 267.522*10^6; + T = 8; %ms + Gmax = 6; %mT/m + alpha = 1; %90 degree flip + beta = 2; + n = 8; + t_i = linspace(0, T, 1000); + for i = 1:1000 + b1_temp = alpha * gamma / T * exp(-beta^2 * (1 - t_i(i)/T)^2) * sqrt((2 * pi * n * (1 - t_i(i)/T))^2); + amp(i) = b1_temp; + phase(i) = 0; + end + + for i = 1:length(t_i) + gx_val = -1 * (2*pi*n * (1 - t_i(i)/T) * sin(2*pi*n*t_i(i)/T) + cos(2*pi*n*t_i(i)/T)); + gy_val = (2*pi*n * (1 - t_i(i)/T) * cos(2*pi*n*t_i(i)/T) - sin(2*pi*n*t_i(i)/T)); + g_x(end+1) = gx_val; + g_y(end+1) = gy_val; + end + g_x = g_x / max(g_y) * 6; + g_y = g_y / max(g_y) * 6; + end + end + end +end + diff --git a/rfPulseTools/2drfPulseTools/rf2d_resample.m b/rfPulseTools/2drfPulseTools/rf2d_resample.m new file mode 100644 index 00000000..308ccb92 --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_resample.m @@ -0,0 +1,58 @@ +% rf2d_resample.m +% Jamie Near, 2025. +% tl-edit: edited by Thomas Lange, University of Freiburg +% +% USAGE: +% RF_out=rf2d_resample(RF_in,N); +% +% DESCRIPTION: +% Resample the input RF pulse into a new waveform with N discrete points. +% +% INPUTS: +% rf2d = Input RF pulse definition structure +% N = Number of points in new RF waveform +% +% OUTPUTS: +% RF_out = Output rf waveform following resampling. + +function RF_out=rf2d_resample(rf2d,N) + +if ~isstruct(rf2d) + error('ERROR: the input RF pulse must be in structure format. Aborting. '); +end + +P=N; +Q=length(rf2d.waveform(:,2)); + +%Find out if the pulse is phase modulated. Whether or not it is phase +%modulated will determine how we go about resampling the phase function +a=(round(rf2d.waveform(:,2))==0)|(round(rf2d.waveform(:,2))==6*pi); + +if sum(a)=1; 1 = fully sampled; higher = faster/aliasing trade-offs) + +% Flip angle and frequency offset +params.flip_angle = 0.174533; % [rad] Nominal small-tip flip angle (10°); used in B1 peak calibration +params.ppm = 0; % [ppm] Off-resonance/chemical-shift for simulation (0 = on-resonance) + +% Discretization for design/simulation +params.voxels = 128; % [-] Number of spatial samples per axis for design/Bloch sim grid (power-of-two convenient) + +% B1 calibration policy for setting rf2d.b1_peak (affects small-tip scaling and validation) +params.calibration = 'center';% {'center','brightest','custom'} method for B1 peak estimation (with black-pixel guard checks) + + +save('params.mat', 'params'); +load params + +rf2d_create.makepulse(params); % Creates the 2DRF pulse + +load rf2d +rf2d_plotWaveform(rf2d,'all'); % Sample use of function to plot amplitude, phase and gradients + + +rf2d_bloch_sim.runblochsim(rf2d); % Runs the Bloch simulator with the 2DRF pulse + + diff --git a/rfPulseTools/2drfPulseTools/rf2d_scaleGrad.m b/rfPulseTools/2drfPulseTools/rf2d_scaleGrad.m new file mode 100644 index 00000000..d754c830 --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_scaleGrad.m @@ -0,0 +1,31 @@ +% rf2d_scaleGrad.m +% Jamie Near, 2025. +% +% USAGE: +% RF_out=rf2d_scaleGrad(2drf,scale); +% +% DESCRIPTION: +% Scale the gradient amplitude of a gradient modulated 2DRF pulse by a fixed factor. +% +% INPUTS: +% 2drf = Input 2DRF pulse definition structure. Must be a gradient +% modulated pulse. +% scale = Scaling factor by which you would like to multiply the +% existing gradient waveform. +% +% OUTPUTS: +% RF_out = Output rf waveform following the scaling of gradient +% waveform. + +function RF_out=rf2d_scaleGrad(rf2d,scale) + +if ~isstruct(rf2d) + error('ERROR: the input 2DRF pulse must be in structure format. Try using rf2d_create() to create it! Aborting. '); +end + +newgrads = rf2d.gradients; +newgrads(:,1)=newgrads(:,1)*scale; +newgrads(:,2)=newgrads(:,2)*scale; + +RF_out=rf2d; +RF_out.gradients=newgrads; diff --git a/rfPulseTools/2drfPulseTools/rf2d_shapes.m b/rfPulseTools/2drfPulseTools/rf2d_shapes.m new file mode 100644 index 00000000..7401423b --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_shapes.m @@ -0,0 +1,154 @@ + +% rf2d_shapes.m +% Jason Rock, Jamie Near, Elena Osipyan, 2025. +% +% USAGE: +% img = rf2d_shapes(instance) +% +% DESCRIPTION: +% Generate a synthetic 2-D target pattern (binary or grayscale) for +% 2DRF excitation testing/visualization. The pattern is selected by +% 'instance' (enumerated below). Except for the Gaussian (case 3, +% 1024×1024), all outputs are 256×256. Outputs are of class double; +% most cases are in [0,1]. +% +% INSTANCES: +% 1 Square (64×64 block centered in 256×256; value = 1 inside). +% 2 External image 'triangle.png' → grayscale → rescaled to [0,1] → +% resized to 256×256. triangle.png can be changed to any desired +% excitation image. + +% 3 2-D isotropic Gaussian (σ = 120 px) on a 1024×1024 grid with peak +% ≈ 1/(2πσ^2). +% 4 Isosceles triangle (binary) blurred with imgaussfilt(·, 4). +% 5 Filled circle (radius = 256/6) centered at (128,128). +% 6 Annular “lipid layer”: r ∈ (r0, 2r0), r0 = 256/6, blurred σ = 4. +% 7 External mask 'mask_only.png' → grayscale in [0,1]. +% 9 Shifted square: case 1 translated by (+30, +30) px. +% 10 Square cross: orthogonal bars with arm_length = 64, arm_width = 32. +% +% INPUTS: +% instance - Integer selector ∈ {1,2,3,4,5,6,7,9,10}. +% +% OUTPUTS: +% image - Double matrix: +% • 256×256 for all cases except instance = 3 +% • 1024×1024 for instance = 3 (Gaussian) +% Values are binary or grayscale as described above. +% +% DEPENDENCIES: +% Requires Image Processing Toolbox functions: imgaussfilt, imresize. +% Files required on path for certain cases: +% • 'circle.png' (instance 2) +% • 'mask_only.png' (instance 7) +% +% NOTES: +% • Unsupported instance values trigger: error('Invalid case_id'). + +function[image] = rf2d_shapes(instance) + + if instance == 3 % Gaussian + image = zeros(1024, 1024); + sig = 120; + for i = 1:1024 + for j = 1:1024 + image(i, j) = 1/(2*pi*sig^2) * exp(-((i - 512)^2 + (j - 512)^2) / (2 * sig^2)); + end + end + end + + if instance == 1 % Square + image = zeros(256, 256); + for i = 96:160 + for j = 96:160 + image(i, j) = 1; + end + end + end + + if instance == 2 % Load and resize image + image_filename = 'star.png'; % Change this to your desired image + img = imread(image_filename); + if size(img, 3) == 3 + img = mean(img, 3); % Convert RGB to grayscale + img = (img - min(img(:)))/(max(img(:)) - min(img(:))); + %img = img/max(abs(img)); + end + image = imresize(img, [256, 256]); + end + if instance== 4 % Triangle + image = zeros(256, 256); + counter = 1; + for i = 101:154 + for j = 1:(2*counter) + col = 128 - counter + j; + if col >= 1 && col <= 256 + image(i, col) = 1; + end + end + counter = counter + 1; + end + image = imgaussfilt(image, 4); + end + if instance == 5 % Circle + image = zeros(256, 256); + radius = 256 / 6; + for i = 1:256 + for j = 1:256 + if (i - 128)^2 + (j - 128)^2 < radius^2 + image(i, j) = 1; + end + end + end + end + if instance == 6 % Lipid layer + image = zeros(256, 256); + radius = 256 / 6; + radius2 = 2 * radius; + for i = 1:256 + for j = 1:256 + r2 = (i - 128)^2 + (j - 128)^2; + if r2 > radius^2 && r2 < radius2^2 + image(i, j) = 1; + end + end + end + image = imgaussfilt(image, 4); + end + if instance == 7 % Mask image + image_filename = 'mask_only.png'; + img = imread(image_filename); + if size(img, 3) == 3 + img = mean(img, 3); + end + image = double(img) / max(img(:)); + end + + if instance == 9 % Shifted square + image = zeros(256, 256); + shift_sq_x = 30; + shift_sq_y = 30; + for i = (96 - shift_sq_x):(160 - shift_sq_x) + for j = (96 - shift_sq_y):(160 - shift_sq_y) + new_i = i; + new_j = j; + if new_i >= 1 && new_j >= 1 && new_i <= 256 && new_j <= 256 + image(new_i, new_j) = 1; + end + end + end + end + + if instance == 10 % Square cross + image = zeros(256, 256); + arm_length = 64; + arm_width = 32; + center = 128; + image(center - arm_width/2 + 1:center + arm_width/2, center - arm_length + 1:center + arm_length) = 1; + image(center - arm_length + 1:center + arm_length, center - arm_width/2 + 1:center + arm_width/2) = 1; + end + if ~ismember(instance, [1,2,3,4,5,6,7,9,10]) + error('Invalid case_id'); + end + +end \ No newline at end of file diff --git a/rfPulseTools/2drfPulseTools/rf2d_timeReverse.m b/rfPulseTools/2drfPulseTools/rf2d_timeReverse.m new file mode 100644 index 00000000..297afcde --- /dev/null +++ b/rfPulseTools/2drfPulseTools/rf2d_timeReverse.m @@ -0,0 +1,39 @@ +% rf_2dtimeReverse.m +% Jamie Near, Sunnybrook Research Institute 2022. +% +% USAGE: +% RF_out=rf_2dtimeReverse(rf2d); +% +% DESCRIPTION: +% Time-reverse the 2DRF pulse. +% +% INPUTS: +% rf2d = Input RF pulse definition structure. +% +% OUTPUTS: +% RF_out = Time-reversed version of the input RF pulse. +% +% NOTES: Pulses put into this function CANNOT have a ramp! Remove ramp in rf2d_create() through +% setting 'withRamp = False'. + +function RF_out = rf2d_timeReverse(rf2d) + + if ~isstruct(rf2d) + error('ERROR: input RF pulse must be a struct. Use rf2d_create() to generate the waveform.'); + end + + amp = rf2d.waveform(:,1); + + % Count leading and trailing zeros only + leadingZeros = find(amp,1,'first') - 1; + counter = leadingZeros; + + if counter > 2 + error(['ERROR!! Cannot reverse a ramped pulse. ' ... + 'Set withRamp = False in rf2d_create() and try remaking the pulse again.']); + else + RF_out = rf2d; + RF_out.waveform = rf2d.waveform(end:-1:1,:); + RF_out.gradients = rf2d.gradients(end:-1:1,:); + end +end diff --git a/rfPulseTools/2drfPulseTools/sample pulses/Gpulse_circle.txt b/rfPulseTools/2drfPulseTools/sample pulses/Gpulse_circle.txt new file mode 100644 index 00000000..62212e91 --- /dev/null +++ b/rfPulseTools/2drfPulseTools/sample pulses/Gpulse_circle.txt @@ -0,0 +1,1030 @@ +1028 +9.335000 9.568000 0.000000 +-0.006720 0.002654 0.000000 +0.001342 0.053978 0.000000 +-0.000689 0.116820 0.000000 +0.000439 0.176736 0.000000 +-0.000305 0.237429 0.000000 +0.000222 0.296429 0.000000 +-0.000164 0.355029 0.000000 +0.000120 0.411849 0.000000 +-0.000084 0.467575 0.000000 +0.000054 0.521232 0.000000 +-0.000028 0.573244 0.000000 +0.000003 0.622848 0.000000 +0.000021 0.670335 0.000000 +-0.000045 0.715074 0.000000 +0.000070 0.757281 0.000000 +-0.000098 0.796423 0.000000 +0.000129 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