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pypulseq/SAR/SAR_calc.py
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SAR_calc.py
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# Copyright of the Board of Trustees of Columbia University in the City of New York
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import numpy.matlib
import scipy.io as sio
from scipy import interpolate
from pypulseq.Sequence.sequence import Sequence
from pypulseq.calc_duration import calc_duration
def calc_SAR(Q, I):
"""
Compute the SAR output for a given Q matrix and I current values.
Parameters
----------
Q : numpy.ndarray
I : numpy.ndarray
Returns
-------
SAR : numpy.ndarray
contains the SAR value for a particular Q matrix
"""
if len(I.shape) == 1: # Just to fit the multi-transmit case for now, ToDo
I = np.matlib.repmat(I, Q.shape[0], 1) # Nc x Nt
Ifact = np.divide(np.matmul(I, np.matrix(I).getH()), I.shape[1])
SAR_temp = np.multiply(Q, Ifact)
SAR = np.abs(np.sum(SAR_temp[:]))
return SAR
def loadQ():
"""
Load Q matrix that is precomputed based on the VHM model for 8 channels.
Returns
-------
Qtmf, Qhmf : numpy.ndarray
Contains the Q-matrix, GSAR head and body for now.
"""
# Load relevant Q matrices computed from the model - this code will be integrated later - starting from E fields
Qpath = str(Path(__file__).parent / 'QGlobal.mat')
Qmat = sio.loadmat(
Qpath)
Q = Qmat['Q']
val = Q[0, 0]
Qtmf = val['Qtmf']
Qhmf = val['Qhmf']
return Qtmf, Qhmf
def SARfromseq(seq, Qtmf, Qhmf):
"""
Compute global whole body and head only SAR values.
Parameters
----------
seq : Sequence
Qtmf : numpy.ndarray
Qhmf : numpy.ndarray
Returns
-------
SARwbg_vec : numpy.ndarray
SARhg_vec : numpy.ndarray
t_vec : numpy.ndarray
Contains the Q-matrix, GSAR head and body for now.
"""
# Identify rf blocks and compute SAR - 10 seconds must be less than twice and 6 minutes must be less than 4 (WB) and 3.2 (head-20)
blockEvents = seq.block_events
numEvents = len(blockEvents)
t_vec = np.zeros(numEvents)
SARwbg_vec = np.zeros(t_vec.shape)
SARhg_vec = np.zeros(t_vec.shape)
t_prev = 0
for iB in blockEvents:
block = seq.get_block(iB)
block_dur = calc_duration(block)
t_vec[iB - 1] = t_prev + block_dur
t_prev = t_vec[iB - 1]
if ('rf' in block): # has rf
rf = block['rf']
t = rf.t
signal = rf.signal
# This rf could be parallel transmit as well
SARwbg_vec[iB] = calc_SAR(Qtmf, signal)
SARhg_vec[iB] = calc_SAR(Qhmf, signal)
return SARwbg_vec, SARhg_vec, t_vec
def SARinterp(SAR, t):
"""
Interpolate SAR values for one second resolution.
Parameters
----------
SAR : numpy.ndarray
t : numpy.ndarray
Returns
-------
SARinterp : numpy.ndarray
tsec : numpy.ndarray
Interpolated values of SAR for a temporal resolution of 1 second
"""
tsec = np.arange(1, np.floor(t[-1]) + 1, 1)
f = interpolate.interp1d(t, SAR)
SARinterp = f(tsec)
return SARinterp, tsec
def SARlimscheck(SARwbg_lim_s, SARhg_lim_s, tsec):
"""
Check for SAR violations as compared to IEC 10 second and 6 minute averages;
returns SAR values that are interpolated for the fixed IEC time intervals.
Parameters
----------
SARwbg_lim_s : numpy.ndarray
SARhg_lim_s : numpy.ndarray
tsec : numpy.ndarray
Returns
-------
SAR_wbg_tensec : numpy.ndarray
SAR_wbg_sixmin : numpy.ndarray
SAR_hg_tensec : numpy.ndarray
SAR_hg_sixmin : numpy.ndarray
SAR_wbg_sixmin_peak : numpy.ndarray
SAR_hg_sixmin_peak : numpy.ndarray
SAR_wbg_tensec_peak : numpy.ndarray
SAR_hg_tensec_peak : numpy.ndarray
"""
if (tsec[-1] > 10):
SixMinThresh_wbg = 4
TenSecThresh_wbg = 8
SixMinThresh_hg = 3.2
TenSecThresh_hg = 6.4
SARwbg_lim_app = np.concatenate((np.zeros(5), SARwbg_lim_s, np.zeros(5)), axis=0)
SARhg_lim_app = np.concatenate((np.zeros(5), SARhg_lim_s, np.zeros(5)), axis=0)
SAR_wbg_tensec = do_sw_sar(SARwbg_lim_app, tsec, 10) # < 2 SARmax
SAR_hg_tensec = do_sw_sar(SARhg_lim_app, tsec, 10) # < 2 SARmax
SAR_wbg_tensec_peak = np.round(np.max(SAR_wbg_tensec), 2)
SAR_hg_tensec_peak = np.round(np.max(SAR_hg_tensec), 2)
if ((np.max(SAR_wbg_tensec) > TenSecThresh_wbg) or (np.max(SAR_hg_tensec) > TenSecThresh_hg)):
print('Pulse exceeding 10 second Global SAR limits, increase TR')
SAR_wbg_sixmin = 'NA'
SAR_hg_sixmin = 'NA'
SAR_wbg_sixmin_peak = 'NA'
SAR_hg_sixmin_peak = 'NA'
if (tsec[-1] > 600):
SARwbg_lim_app = np.concatenate((np.zeros(300), SARwbg_lim_s, np.zeros(300)), axis=0)
SARhg_lim_app = np.concatenate((np.zeros(300), SARhg_lim_s, np.zeros(300)), axis=0)
SAR_hg_sixmin = do_sw_sar(SARhg_lim_app, tsec, 600)
SAR_wbg_sixmin = do_sw_sar(SARwbg_lim_app, tsec, 600)
SAR_wbg_sixmin_peak = np.round(np.max(SAR_wbg_sixmin), 2)
SAR_hg_sixmin_peak = np.round(np.max(SAR_hg_sixmin), 2)
if ((np.max(SAR_hg_sixmin) > SixMinThresh_wbg) or (np.max(SAR_hg_sixmin) > SixMinThresh_hg)):
print('Pulse exceeding 10 second Global SAR limits, increase TR')
else:
print('Need at least 10 seconds worth of sequence to calculate SAR')
SAR_wbg_tensec = 'NA'
SAR_wbg_sixmin = 'NA'
SAR_hg_tensec = "NA"
SAR_hg_sixmin = "NA"
SAR_wbg_sixmin_peak = 'NA'
SAR_hg_sixmin_peak = 'NA'
SAR_wbg_tensec_peak = 'NA'
SAR_hg_tensec_peak = 'NA'
return SAR_wbg_tensec, SAR_wbg_sixmin, SAR_hg_tensec, SAR_hg_sixmin, SAR_wbg_sixmin_peak, SAR_hg_sixmin_peak, SAR_wbg_tensec_peak, SAR_hg_tensec_peak
def do_sw_sar(SAR, tsec, t):
"""
Compute a sliding window average of SAR values.
Parameters
----------
SAR : numpy.ndarray
tsec : numpy.ndarray
t : numpy.ndarray
Returns
-------
SAR_timeavag : numpy.ndarray
Sliding window time average of SAR values
"""
SAR_timeavg = np.zeros(len(tsec) + int(t))
for instant in range(int(t / 2), int(t / 2) + (int(tsec[-1]))): # better to go from -sw / 2: sw / 2
SAR_timeavg[instant] = sum(SAR[range(instant - int(t / 2), instant + int(t / 2) - 1)]) / t
SAR_timeavg = SAR_timeavg[int(t / 2):int(t / 2) + (int(tsec[-1]))]
return SAR_timeavg
def payload_process(seq: Sequence):
"""
Compute Global SAR values on the `seq` object for head and whole body over the specified time averages.
Parameters
----------
seq : Sequence
pypulseq `Sequence` object for which global SAR values will be computed.
"""
if not isinstance(seq, Sequence):
raise TypeError(f'Sequence object expected. You passed: {type(seq)}')
Qtmf, Qhmf = loadQ()
SARwbg, SARhg, t_vec = SARfromseq(seq, Qtmf, Qhmf)
SARwbg_lim, tsec = SARinterp(SARwbg, t_vec)
SARhg_lim, tsec = SARinterp(SARhg, t_vec)
SAR_wbg_tensec, SAR_wbg_sixmin, SAR_hg_tensec, SAR_hg_sixmin, SAR_wbg_sixmin_peak, SAR_hg_sixmin_peak, SAR_wbg_tensec_peak, SAR_hg_tensec_peak = SARlimscheck(
SARwbg_lim, SARhg_lim, tsec)
# Plot 10 sec average SAR
if (tsec[-1] > 10):
plt.plot(tsec, SAR_wbg_tensec, label='Whole Body: 10sec')
plt.plot(tsec, SAR_hg_tensec, label='Head only: 10sec')
# plt.plot(t_vec, SARwbg, label='Whole Body - instant')
# plt.plot(t_vec, SARhg, label='Whole Body - instant')
plt.xlabel('Time (s)')
plt.ylabel('SAR (W/kg)')
plt.title('Global SAR - Mass Normalized - Whole body and head only')
ax = plt.subplot(111)
# ax.legend()
plt.grid(True)
plt.show()
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