def test_bloch_sim_demo(self):
"""
Runs a simple Bloch simulator run.
"""
file_name = "basic_bloch"
mx_demo = get_data_with_key(TEST_DIR, file_name, "mx_demo")
my_demo = get_data_with_key(TEST_DIR, file_name, "my_demo")
mz_demo = get_data_with_key(TEST_DIR, file_name, "mz_demo")
b1 = get_data_with_key(TEST_DIR, file_name, "b1_demo")
g = get_data_with_key(TEST_DIR, file_name, "g_demo")
dt = 4e-6
t1 = 100e-3
t2 = 50e-3
df = 0
dp = 0
mode = 2
mx_0 = 0
my_0 = 0
mz_0 = 1
mx, my, mz = bloch(b1, g, dt, t1, t2, df, dp, mode, mx_0, mx_0, mx_0)
self.assertTrue(np.allclose(mx_demo, mx));
self.assertTrue(np.allclose(my_demo, my));
self.assertTrue(np.allclose(mz_demo, mz));
def test_bloch_sim_a(self):
"""
Runs another simple Bloch simulator run.
"""
mx_a = get_data_with_key(TEST_DIR, "basic_bloch", "mx_a")
my_b = get_data_with_key(TEST_DIR, "basic_bloch", "my_a")
mz_c = get_data_with_key(TEST_DIR, "basic_bloch", "mz_a")
b1 = get_data_with_key(TEST_DIR, "basic_bloch", "b1_a")
g = get_data_with_key(TEST_DIR, "basic_bloch", "g_a")
dt = 4e-6
t1 = 30e-3
t2 = 15e-3
df = 0
dp = .2
mode = 2
mx_0 = 0
my_0 = 0
mz_0 = 1
mx, my, mz = bloch(b1, g, dt, t1, t2, df, dp, mode, mx_0, my_0, mz_0)
self.assertTrue(np.allclose(mx_a, mx))
self.assertTrue(np.allclose(my_b, my))
self.assertTrue(np.allclose(mz_c, mz))
def test_bloch_sim_a(self):
"""
Runs another simple Bloch simulator run.
"""
mx_a = get_data_with_key(TEST_DIR, "basic_bloch", "mx_a")
my_b = get_data_with_key(TEST_DIR, "basic_bloch", "my_a")
mz_c = get_data_with_key(TEST_DIR, "basic_bloch", "mz_a")
b1 = get_data_with_key(TEST_DIR, "basic_bloch", "b1_a")
g = get_data_with_key(TEST_DIR, "basic_bloch", "g_a")
dt = 4e-6
t1 = 30e-3
t2 = 15e-3
df = 0
dp = .2
mode = 2
mx_0 = 0
my_0 = 0
mz_0 = 1
mx, my, mz = bloch(b1, g, dt, t1, t2, df, dp, mode, mx_0, my_0, mz_0)
self.assertTrue(np.allclose(mx_a, mx));
self.assertTrue(np.allclose(my_b, my));
self.assertTrue(np.allclose(mz_c, mz));
def test_bloch_sim_demo(self):
"""
Runs a simple Bloch simulator run.
"""
file_name = "basic_bloch"
mx_demo = get_data_with_key(TEST_DIR, file_name, "mx_demo")
my_demo = get_data_with_key(TEST_DIR, file_name, "my_demo")
mz_demo = get_data_with_key(TEST_DIR, file_name, "mz_demo")
b1 = get_data_with_key(TEST_DIR, file_name, "b1_demo")
g = get_data_with_key(TEST_DIR, file_name, "g_demo")
dt = 4e-6
t1 = 100e-3
t2 = 50e-3
df = 0
dp = 0
mode = 2
mx_0 = 0
my_0 = 0
mz_0 = 1
mx, my, mz = bloch(b1, g, dt, t1, t2, df, dp, mode, mx_0, mx_0, mx_0)
self.assertTrue(np.allclose(mx_demo, mx));
self.assertTrue(np.allclose(my_demo, my));
self.assertTrue(np.allclose(mz_demo, mz));
def test_hw5_bloch_sim_first_part(self):
matlab = sio.loadmat(TEST_DIR.format("hw5", "hw5_img"))
dp = matlab["dp"]
mx_0 = matlab["mx"].ravel()
my_0 = matlab["my"].ravel()
mz_0 = matlab["mz"].ravel()
expected_mx1 = sio.loadmat(TEST_DIR.format("hw5", "mxa.mat"))["mx1"].ravel()
expected_my1 = sio.loadmat(TEST_DIR.format("hw5", "mya.mat"))["my1"].ravel()
expected_mz1 = sio.loadmat(TEST_DIR.format("hw5", "mza.mat"))["mz1"].ravel()
expected_mx2 = np.transpose(sio.loadmat(TEST_DIR.format("hw5", "mxb.mat"))["mx1"])
expected_my2= np.transpose(sio.loadmat(TEST_DIR.format("hw5", "myb.mat"))["my1"])
expected_mz2= np.transpose(sio.loadmat(TEST_DIR.format("hw5", "mzb.mat"))["mz1"])
Nf = 64
Np = 32
Nrf = 92
Fov_r = 14
Fov_p = 7
g_max = 4
s_max = 15000
dt = 4e-6
bwpp = 1862.4
gamma = 4257
flip = 90
gx, rowin = genReadoutGradient(Nf, Fov_r, bwpp, g_max, s_max, dt)
gpe, petable = genPEGradient(Np, Fov_p, g_max, s_max, dt)
rf_90 = np.ones(Nrf) * (flip/360) / (Nrf * dt * gamma)
gy = np.zeros(gx.size)
gy[:gpe.size] = gpe
g = np.asarray([gx, gy * -petable[0]])
mx1, my1, mz1 = bloch(rf_90, rf_90 * 0, dt, 100, 100, 0, dp, 0, mx_0, my_0, mz_0)
mx2, my2, mz2 = bloch(gx * 0, g, dt, 100, 100, 0, dp, 2, mx1, my1, mz1)
self.assertTrue(np.allclose(expected_mx1, mx1))
self.assertTrue(np.allclose(expected_my1, my1))
self.assertTrue(np.allclose(expected_mz1, mz1))
self.assertTrue(np.allclose(expected_mx2, mx2))
self.assertTrue(np.allclose(expected_my2, my2))
self.assertTrue(np.allclose(expected_mz2, mz2))
def test_ssfptransiest(self):
"""
Runs an SSFP response calculation using bloch.m
"""
expected_mxss = get_data_with_key(TEST_DIR, "ssfptransient", "mxss")
expected_myss = get_data_with_key(TEST_DIR, "ssfptransient", "myss")
expected_mzss = get_data_with_key(TEST_DIR, "ssfptransient", "mzss")
expected_mx = get_data_with_key(TEST_DIR, "ssfptransient", "mx")
expected_my = get_data_with_key(TEST_DIR, "ssfptransient", "my")
expected_mz = get_data_with_key(TEST_DIR, "ssfptransient", "mz")
TR = .005 #Seconds
Trf = 0.0001 #100 us "hard" RF pulse
alpha = 60 #Degrees
gamma = 4258 #Hz/G
T1 = 1 #Seconds
T2 = .2 #Seconds
freq = np.arange(-200, 201) #Hz
N = 100
Tpad = (TR - Trf) / 2 #Seconds
t = np.asarray([Tpad, Trf, Tpad])
b1 = np.concatenate(
(np.zeros(1),
np.asarray([np.pi / 180 * alpha / Trf / gamma / 2 / np.pi]),
np.zeros(1)))
mxss, myss, mzss = bloch(b1, 0 * b1, t, T1, T2, freq, 0, 1)
mx, my, mz = bloch(1.0j * np.max(b1) / 2, 0, Trf, T1, T2, freq, 0, 0)
for _ in range(N):
mx, my, mz = bloch(b1, 0 * b1, t, T1, T2, freq, 0, 0, mx, my, mz)
self.assertTrue(np.allclose(expected_mxss, mxss))
self.assertTrue(np.allclose(expected_myss, myss))
self.assertTrue(np.allclose(expected_mzss, mzss))
self.assertTrue(np.allclose(expected_mx, mx))
self.assertTrue(np.allclose(expected_my, my))
self.assertTrue(np.allclose(expected_mz, mz))
def test_ssfptransiest(self):
"""
Runs an SSFP response calculation using bloch.m
"""
expected_mxss = get_data_with_key(TEST_DIR, "ssfptransient", "mxss")
expected_myss = get_data_with_key(TEST_DIR, "ssfptransient", "myss")
expected_mzss = get_data_with_key(TEST_DIR, "ssfptransient", "mzss")
expected_mx = get_data_with_key(TEST_DIR, "ssfptransient", "mx")
expected_my = get_data_with_key(TEST_DIR, "ssfptransient", "my")
expected_mz = get_data_with_key(TEST_DIR, "ssfptransient", "mz")
TR = .005 #Seconds
Trf = 0.0001 #100 us "hard" RF pulse
alpha = 60 #Degrees
gamma = 4258 #Hz/G
T1 = 1 #Seconds
T2 = .2 #Seconds
freq = np.arange(-200, 201) #Hz
N = 100
Tpad = (TR - Trf)/2 #Seconds
t = np.asarray([Tpad, Trf, Tpad])
b1 = np.concatenate((np.zeros(1), np.asarray([np.pi/180*alpha/Trf/gamma/2/np.pi]), np.zeros(1)))
mxss, myss, mzss = bloch(b1, 0*b1, t, T1, T2, freq, 0, 1)
mx, my, mz = bloch(1.0j * np.max(b1)/2, 0, Trf, T1, T2, freq, 0, 0)
for _ in range(N):
mx, my, mz = bloch(b1, 0*b1, t, T1, T2, freq, 0, 0, mx, my, mz)
self.assertTrue(np.allclose(expected_mxss, mxss))
self.assertTrue(np.allclose(expected_myss, myss))
self.assertTrue(np.allclose(expected_mzss, mzss))
self.assertTrue(np.allclose(expected_mx, mx))
self.assertTrue(np.allclose(expected_my, my))
self.assertTrue(np.allclose(expected_mz, mz))
def test_sinc_pulse(self):
"""
Tests generation of sinc pulse.
"""
expected_mxy = get_data_with_key(TEST_DIR, "rf_test", "mxy")
duration = 3.2e-3
dt = duration / 256
flip = np.pi / 2
tbw = 8
rf = sinc_pulse(tbw, flip, duration, dt)
g = np.ones(rf.size) * .6
dp = np.linspace(-2, 2, 512)
mx0 = np.zeros(512)
my0 = np.zeros(512)
mz0 = np.ones(512)
mx, my, mz = bloch(rf, g, dt, 100, 100, 0, dp, 0, mx0, my0, mz0)
mxy = mx + 1.0j * my
np.allclose(expected_mxy, mxy)
def test_sinc_pulse(self):
"""
Tests generation of sinc pulse.
"""
expected_mxy = get_data_with_key(TEST_DIR, "rf_test", "mxy")
duration = 3.2e-3
dt = duration / 256
flip = np.pi / 2
tbw = 8
rf = sinc_pulse(tbw, flip, duration, dt)
g = np.ones(rf.size) * .6
dp = np.linspace(-2, 2, 512)
mx0 = np.zeros(512)
my0 = np.zeros(512)
mz0 = np.ones(512)
mx, my, mz = bloch(rf, g, dt, 100, 100, 0, dp, 0, mx0, my0, mz0)
mxy = mx + 1.0j*my
np.allclose(expected_mxy, mxy)
def test_hw4_bloch_sim_a(self):
mx_a = sio.loadmat(TEST_DIR.format("hw4", "mx_a"))["mx"].ravel()
my_b = sio.loadmat(TEST_DIR.format("hw4", "my_a"))["my"].ravel()
mz_c = sio.loadmat(TEST_DIR.format("hw4", "mz_a"))["mz"].ravel()
b1 = sio.loadmat(TEST_DIR.format("hw4", "B1_a"))["B1"].ravel()
g = np.transpose(sio.loadmat(TEST_DIR.format("hw4", "G_a"))["G"]).ravel()
dt = 4e-6
t1 = 30e-3
t2 = 15e-3
df = 0
dp = .2
mode = 2
mx_0 = 0
my_0 = 0
mz_0 = 1
mx, my, mz = bloch(b1, g, dt, t1, t2, df, dp, mode, mx_0, my_0, mz_0)
self.assertTrue(np.allclose(mx_a, mx));
self.assertTrue(np.allclose(my_b, my));
self.assertTrue(np.allclose(mz_c, mz));
def test_hw4_bloch_sim_demo(self):
mx_demo = sio.loadmat(TEST_DIR.format("hw4", "mx_demo"))["mx"].ravel()
my_demo = sio.loadmat(TEST_DIR.format("hw4", "my_demo"))["my"].ravel()
mz_demo = sio.loadmat(TEST_DIR.format("hw4", "mz_demo"))["mz"].ravel()
b1 = sio.loadmat(TEST_DIR.format("hw4", "b1_demo"))["b1"].ravel()
g = np.transpose(sio.loadmat(TEST_DIR.format("hw4", "g_demo"))["g"]).ravel()
dt = 4e-6
t1 = 100e-3
t2 = 50e-3
df = 0
dp = 0
mode = 2
mx_0 = 0
my_0 = 0
mz_0 = 1
mx, my, mz = bloch(b1, g, dt, t1, t2, df, dp, mode, mx_0, mx_0, mx_0)
self.assertTrue(np.allclose(mx_demo, mx));
self.assertTrue(np.allclose(my_demo, my));
self.assertTrue(np.allclose(mz_demo, mz));
flip = 180
flip_rad = flip * np.pi / 180
b2_time = flip_rad / B1max / gamma
N2 = int(np.ceil(b2_time / dt))
b2 = np.ones((N2, )) * B1max * 1j
x = 1
area = .99 / x / gamma_bar
g = minimum_time_gradient(area, Gmax, Smax, dt)
B1 = np.zeros((int(np.round(sim_time / dt)), ), dtype=np.complex)
G = np.zeros((int(np.round(sim_time / dt)), ))
B1[:N] = b1
G[N:N + len(g)] = g
B1[N + len(g):N + len(g) + N2] = b2
G[N + len(g) + N2:N + len(g) + N2 + len(g)] = g
mx, my, mz = bloch(B1,
G,
dt,
100e-4,
100e-5,
0,
np.linspace(-.5, .5, 15)[None, :],
2,
mx=1,
my=0,
mz=0)
visualize_magnetization(B1, G * x, mx, my, mz, accel=5)
# Setup parameters
b1 = np.hstack((np.zeros((500, )), msinc(250, 2), np.zeros((500, ))))
gr = np.hstack((np.zeros(375, ), - np.ones((125, )), np.ones((250, )), - np.ones((125, )), np.zeros((375, ))))
b1 = 1.56 * b1 / np.max(b1) / 4
dp = np.arange(-4, 4.1, .1)
T = 4e-6
df = np.arange(-250., 251., 5.)
tp = np.arange(1, b1.size + 1) * T
t1 = 1.
t2 = .2
# Run bloch simulation
[mx, my, mz] = bloch(b1, gr, tp, 1., .2, df, dp, 3)
#mxy = mx + 1j * my
# Display
f_c = 34
p_c = 40
pl.figure(figsize=(5, 9))
pl.subplot(3, 1, 1)
pl.plot(tp * 1e3, b1)
pl.xlabel('Time (ms)')
pl.ylabel('RF amplitude (Gauss)')
pl.title('RF pulse')
pl.subplot(3, 1, 2)
pl.plot(tp * 1e3, gr)
pl.xlabel('Time (ms)')
