dir = "" insysfile = dir + "gsh_test.sys" inpulse180file = dir + "bjs180_1.txt" outfile = dir + "gsh_spinecho_realpulses_pytest.txt" out_name = "test_lines" h1 = "Spin Echo Simulation Test With Real 180 Pulse" h2 = "using input sys file: " + insysfile h3 = "and input 180 pulse file: " + inpulse180file header = (h1, h2, h3) sys = pg.spin_system() t1 = 0.025 t2 = 0.025 pulsestep = 0.00001 sys.read(insysfile) specfreq = sys.Omega() # read_pulse replaces ReadPulse() and is a static member of row_vector pulse = pg.row_vector.read_pulse(inpulse180file, pg.row_vector.ASCII_MT_DEG) ptime = pg.row_vector(pulse.size()) #need to use pg.complex() so it can find correct function to call. for j in range(pulse.size()):
def pygamma_spectra(metabolite_names,
pulse_sequence='megapress',
omega=OMEGA,
linewidth=1.0,
npts=4096,
adc_dt=4e-4,
concentrations=None,
testing=False):
# by having multiple linewidths it allows the use of the same 'mx' object to run the binning over,
# rather than have to recalcualte the pulse sequence again. it would be more efficient to save the mx table
# but this functionality is currently (Sept-2018) broken in PyGamma
import pygamma as pg
linewidth = float(linewidth)
to_sim = list(metabolite_names)
basis = Basis.Basis()
for metabolite_name in metabolite_names:
if not testing:
cache_name = pulse_sequence + '_' + str(omega) + '_' + str(
linewidth) + '_' + str(npts) + '_' + str(adc_dt)
spectra_cache_dir = './cache/pygamma/' + cache_name + '/'
if os.path.isdir(spectra_cache_dir):
for file in os.listdir(spectra_cache_dir):
if file == metabolite_name + '.dill':
# print('Cache hit, already simulated '+pulse_sequence+' for ' + metabolite_name +'.')
with open(os.path.join(spectra_cache_dir, file),
'rb') as load_file:
for spectra in dill.load(load_file):
basis.add_spectra(spectra)
to_sim.remove(metabolite_name)
else:
os.makedirs(spectra_cache_dir)
for metabolite_name in to_sim:
id = hash(datetime.now().strftime('%f%S%H%M%a%d%b%Y'))
mol_spectra = []
print('Cache miss. Simulating ' + metabolite_name + ' : ' +
pulse_sequence)
infile = os.path.join('./Simulators/PyGamma/metabolite models',
metabolite_name.lower() + '.sys')
spin_system = pg.spin_system()
spin_system.read(infile)
spin_system.OmegaAdjust(omega)
if pulse_sequence.lower() == 'fid':
mx = [fid(spin_system)]
elif pulse_sequence.lower() == 'press':
mx = [press(spin_system)]
elif pulse_sequence.lower() == 'steam':
mx = [steam(spin_system)]
elif pulse_sequence.lower() == 'megapress':
mx = megapress(spin_system, omega=omega)
else:
raise Exception('Unrecognised PyGamma pulse sequence: ' +
pulse_sequence)
for count, acq in enumerate(mx):
spectra = Spectra()
spectra.source = 'pygamma'
spectra.type = 'simulated'
spectra.id = id
spectra.pulse_sequence = pulse_sequence.lower()
spectra.metabolite_names = [metabolite_name]
spectra.concentrations = [1]
spectra.omega = omega
spectra.npts = npts
spectra.dt = adc_dt
spectra.linewidth = linewidth
spectra._raw_adc = binning(acq,
linewidth=linewidth,
dt=adc_dt,
npts=npts)
spectra.pulse_sequence = pulse_sequence
spectra.center_ppm = 0
spectra.acquisition = count
if pulse_sequence.lower() == 'megapress':
if count == 0:
spectra.spectra_type = 'edit off'
elif count == 1:
spectra.spectra_type = 'edit on'
else:
raise Exception(
'More than 2 mx objects for megapress? Something is wrong here...'
)
basis.add_spectra(spectra)
mol_spectra.append(spectra)
# and force gc to try and delete the C++ PyGamma mx object
for acq in mx:
acq.disown()
del acq
del mx
# finally we cache the spectra
if not testing:
cache(spectra_cache_dir, mol_spectra)
basis.setup()
if pulse_sequence.lower() == 'megapress':
basis.add_difference_spectra()
basis.update_spectra_scale(concentrations=concentrations)
return basis
insysfile = dir + "gsh_test.sys" inpulse180file = dir + "bjs180_1.txt" outfile = dir + "gsh_spinecho_realpulses_pytest.txt"; out_name = "test_lines"; h1 = "Spin Echo Simulation Test With Real 180 Pulse" h2 = "using input sys file: " + insysfile h3 = "and input 180 pulse file: " + inpulse180file header = (h1, h2, h3) sys = pg.spin_system() t1 = 0.025 t2 = 0.025 pulsestep = 0.00001 sys.read(insysfile) specfreq = sys.Omega() # read_pulse replaces ReadPulse() and is a static member of row_vector pulse = pg.row_vector.read_pulse(inpulse180file, pg.row_vector.ASCII_MT_DEG) ptime = pg.row_vector(pulse.size()) #need to use pg.complex() so it can find correct function to call. for j in range(pulse.size()):
def load_sys(infile):
sys = pg.spin_system()
sys.read(infile)
return sys
def simulate(self):
self.postToConsole.emit(' | Simulating ... ' + self.insysfile)
print(' | Simulating ...' + self.insysfile)
metab_name = self.insysfile.replace('.sys', '')
if self.sim_experiment.b0 == 123.3:
self.insysfile = 'pints/metabolites/3T_' + self.insysfile
elif self.sim_experiment.b0 == 297.2:
self.insysfile = 'pints/metabolites/7T_' + self.insysfile
elif self.sim_experiment.b0 == 400.2:
self.insysfile = 'pints/metabolites/9.4T_' + self.insysfile
if self.sim_experiment.name == "semi-LASER (Bruker)":
spin_system = pg.spin_system()
spin_system.read(self.insysfile)
for i in range(spin_system.spins()):
spin_system.PPM(
i,
spin_system.PPM(i) - self.sim_experiment.RF_OFFSET)
TE = self.sim_experiment.TE * 1E-3
TE1 = self.sim_experiment.TE1 * 1E-3
TE2 = self.sim_experiment.TE2 * 1E-3
# build 90 degree pulse
inpulse90file = self.sim_experiment.inpulse90file
A_90 = self.sim_experiment.A_90
PULSE_90_LENGTH = self.sim_experiment.PULSE_90_LENGTH
gyratio = self.sim_experiment.getGyratio()
pulse90 = Pulse(inpulse90file, PULSE_90_LENGTH, 'bruker')
n_old = np.linspace(0, PULSE_90_LENGTH, sp.size(pulse90.waveform))
n_new = np.linspace(0, PULSE_90_LENGTH,
sp.size(pulse90.waveform) + 1)
waveform_real = sp.interpolate.InterpolatedUnivariateSpline(
n_old,
np.real(pulse90.waveform) * A_90)(n_new)
waveform_imag = sp.interpolate.InterpolatedUnivariateSpline(
n_old,
np.imag(pulse90.waveform) * A_90)(n_new)
pulse90.waveform = waveform_real + 1j * (waveform_imag)
ampl_arr = np.abs(pulse90.waveform)
phas_arr = np.unwrap(np.angle(pulse90.waveform)) * 180.0 / math.pi
pulse = pg.row_vector(len(pulse90.waveform))
ptime = pg.row_vector(len(pulse90.waveform))
for j, val in enumerate(zip(ampl_arr, phas_arr)):
pulse.put(pg.complex(val[0], val[1]), j)
ptime.put(pg.complex(pulse90.pulsestep, 0), j)
pulse_dur_90 = pulse.size() * pulse90.pulsestep
pwf_90 = pg.PulWaveform(pulse, ptime, "90excite")
pulc_90 = pg.PulComposite(pwf_90, spin_system,
self.sim_experiment.obs_iso)
Ureal90 = pulc_90.GetUsum(-1)
# build 180 degree pulse
inpulse180file = self.sim_experiment.inpulse180file
A_180 = self.sim_experiment.A_180
PULSE_180_LENGTH = self.sim_experiment.PULSE_180_LENGTH
gyratio = self.sim_experiment.getGyratio()
pulse180 = Pulse(inpulse180file, PULSE_180_LENGTH, 'bruker')
n_old = np.linspace(0, PULSE_180_LENGTH,
sp.size(pulse180.waveform))
n_new = np.linspace(0, PULSE_180_LENGTH,
sp.size(pulse180.waveform) + 1)
waveform_real = sp.interpolate.InterpolatedUnivariateSpline(
n_old,
np.real(pulse180.waveform) * A_180)(n_new)
waveform_imag = sp.interpolate.InterpolatedUnivariateSpline(
n_old,
np.imag(pulse180.waveform) * A_180)(n_new)
pulse180.waveform = waveform_real + 1j * (waveform_imag)
ampl_arr = np.abs(pulse180.waveform)
phas_arr = np.unwrap(np.angle(pulse180.waveform)) * 180.0 / math.pi
freq_arr = np.gradient(phas_arr)
pulse = pg.row_vector(len(pulse180.waveform))
ptime = pg.row_vector(len(pulse180.waveform))
for j, val in enumerate(zip(ampl_arr, phas_arr)):
pulse.put(pg.complex(val[0], val[1]), j)
ptime.put(pg.complex(n_new[1], 0), j)
pulse_dur_180 = pulse.size() * pulse180.pulsestep
pwf_180 = pg.PulWaveform(pulse, ptime, "180afp")
pulc_180 = pg.PulComposite(pwf_180, spin_system,
self.sim_experiment.obs_iso)
Ureal180 = pulc_180.GetUsum(-1)
H = pg.Hcs(spin_system) + pg.HJ(spin_system)
D = pg.Fm(spin_system, self.sim_experiment.obs_iso)
ac = pg.acquire1D(pg.gen_op(D), H, self.sim_experiment.dwell_time)
ACQ = ac
delay1 = TE1 / 2.0 - pulse_dur_90 / 2.0 - pulse_dur_180 / 2.0
delay2 = TE1 / 2.0 + TE2 / 2.0 - pulse_dur_180
delay3 = TE2 - pulse_dur_180
delay4 = delay2
delay5 = TE1 / 2.0 - pulse_dur_180 + self.sim_experiment.DigShift
Udelay1 = pg.prop(H, delay1)
Udelay2 = pg.prop(H, delay2)
Udelay3 = pg.prop(H, delay3)
Udelay4 = pg.prop(H, delay4)
Udelay5 = pg.prop(H, delay5)
sigma0 = pg.sigma_eq(spin_system) # init
sigma1 = Ureal90.evolve(sigma0) # apply 90-degree pulse
sigma0 = pg.evolve(sigma1, Udelay1)
sigma1 = Ureal180.evolve(sigma0) # apply AFP1
sigma0 = pg.evolve(sigma1, Udelay2)
sigma1 = Ureal180.evolve(sigma0) # apply AFP2
sigma0 = pg.evolve(sigma1, Udelay3)
sigma1 = Ureal180.evolve(sigma0) # apply AFP3
sigma0 = pg.evolve(sigma1, Udelay4)
sigma1 = Ureal180.evolve(sigma0) # apply AFP4
sigma0 = pg.evolve(sigma1, Udelay5)
elif self.sim_experiment.name == "semi-LASER":
spin_system = pg.spin_system()
spin_system.read(self.insysfile)
for i in range(spin_system.spins()):
spin_system.PPM(
i,
spin_system.PPM(i) - self.sim_experiment.RF_OFFSET)
TE = self.sim_experiment.TE
TE1 = float((TE * 0.31) / 1000.0)
TE3 = float((TE * 0.31) / 1000.0)
TE2 = float(TE / 1000.0 - TE1 - TE3)
TE_fill = TE / 1000.0 - TE1 - TE2 - TE3
# build 90 degree pulse
inpulse90file = self.sim_experiment.inpulse90file
A_90 = self.sim_experiment.A_90
PULSE_90_LENGTH = self.sim_experiment.PULSE_90_LENGTH
gyratio = self.sim_experiment.getGyratio()
pulse90 = Pulse(inpulse90file, PULSE_90_LENGTH)
n_old = np.linspace(0, PULSE_90_LENGTH, sp.size(pulse90.waveform))
n_new = np.linspace(0, PULSE_90_LENGTH,
sp.size(pulse90.waveform) + 1)
waveform_real = sp.interpolate.InterpolatedUnivariateSpline(
n_old,
np.real(pulse90.waveform) * A_90)(n_new)
waveform_imag = sp.interpolate.InterpolatedUnivariateSpline(
n_old,
np.imag(pulse90.waveform) * A_90)(n_new)
pulse90.waveform = waveform_real + 1j * (waveform_imag)
ampl_arr = np.abs(pulse90.waveform) * gyratio
phas_arr = np.unwrap(np.angle(pulse90.waveform)) * 180.0 / math.pi
pulse = pg.row_vector(len(pulse90.waveform))
ptime = pg.row_vector(len(pulse90.waveform))
for j, val in enumerate(zip(ampl_arr, phas_arr)):
pulse.put(pg.complex(val[0], val[1]), j)
ptime.put(pg.complex(pulse90.pulsestep, 0), j)
pulse_dur_90 = pulse.size() * pulse90.pulsestep
peak_to_end_90 = pulse_dur_90 - (
209 + self.sim_experiment.fudge_factor) * pulse90.pulsestep
pwf_90 = pg.PulWaveform(pulse, ptime, "90excite")
pulc_90 = pg.PulComposite(pwf_90, spin_system,
self.sim_experiment.obs_iso)
Ureal90 = pulc_90.GetUsum(-1)
# build 180 degree pulse
inpulse180file = self.sim_experiment.inpulse180file
A_180 = self.sim_experiment.A_180
PULSE_180_LENGTH = self.sim_experiment.PULSE_180_LENGTH
gyratio = self.sim_experiment.getGyratio()
pulse180 = Pulse(inpulse180file, PULSE_180_LENGTH)
n_old = np.linspace(0, PULSE_180_LENGTH,
sp.size(pulse180.waveform))
n_new = np.linspace(0, PULSE_180_LENGTH,
sp.size(pulse180.waveform) + 1)
waveform_real = sp.interpolate.InterpolatedUnivariateSpline(
n_old,
np.real(pulse180.waveform) * A_180)(n_new)
waveform_imag = sp.interpolate.InterpolatedUnivariateSpline(
n_old,
np.imag(pulse180.waveform) * A_180)(n_new)
pulse180.waveform = waveform_real + 1j * (waveform_imag)
ampl_arr = np.abs(pulse180.waveform) * gyratio
phas_arr = np.unwrap(np.angle(pulse180.waveform)) * 180.0 / math.pi
freq_arr = np.gradient(phas_arr)
pulse = pg.row_vector(len(pulse180.waveform))
ptime = pg.row_vector(len(pulse180.waveform))
for j, val in enumerate(zip(ampl_arr, phas_arr)):
pulse.put(pg.complex(val[0], val[1]), j)
ptime.put(pg.complex(n_new[1], 0), j)
pulse_dur_180 = pulse.size() * pulse180.pulsestep
pwf_180 = pg.PulWaveform(pulse, ptime, "180afp")
pulc_180 = pg.PulComposite(pwf_180, spin_system,
self.sim_experiment.obs_iso)
Ureal180 = pulc_180.GetUsum(-1)
H = pg.Hcs(spin_system) + pg.HJ(spin_system)
D = pg.Fm(spin_system, self.sim_experiment.obs_iso)
ac = pg.acquire1D(pg.gen_op(D), H, self.sim_experiment.dwell_time)
ACQ = ac
delay1 = TE1 / 2.0 + TE_fill / 8.0 - pulse_dur_180 / 2.0 - peak_to_end_90
delay2 = TE1 / 2.0 + TE_fill / 8.0 + TE2 / 4.0 + TE_fill / 8.0 - pulse_dur_180
delay3 = TE2 / 4.0 + TE_fill / 8.0 + TE2 / 4.0 + TE_fill / 8.0 - pulse_dur_180
delay4 = TE2 / 4.0 + TE_fill / 8.0 + TE3 / 2.0 + TE_fill / 8.0 - pulse_dur_180
delay5 = TE3 / 2.0 + TE_fill / 8.0 - pulse_dur_180 / 2.0
Udelay1 = pg.prop(H, delay1)
Udelay2 = pg.prop(H, delay2)
Udelay3 = pg.prop(H, delay3)
Udelay4 = pg.prop(H, delay4)
Udelay5 = pg.prop(H, delay5)
sigma0 = pg.sigma_eq(spin_system) # init
sigma1 = Ureal90.evolve(sigma0) # apply 90-degree pulse
sigma0 = pg.evolve(sigma1, Udelay1)
sigma1 = Ureal180.evolve(sigma0) # apply AFP1
sigma0 = pg.evolve(sigma1, Udelay2)
sigma1 = Ureal180.evolve(sigma0) # apply AFP2
sigma0 = pg.evolve(sigma1, Udelay3)
sigma1 = Ureal180.evolve(sigma0) # apply AFP3
sigma0 = pg.evolve(sigma1, Udelay4)
sigma1 = Ureal180.evolve(sigma0) # apply AFP4
sigma0 = pg.evolve(sigma1, Udelay5)
elif self.sim_experiment.name == "LASER":
spin_system = pg.spin_system()
spin_system.read(self.insysfile)
for i in range(spin_system.spins()):
spin_system.PPM(
i,
spin_system.PPM(i) - self.sim_experiment.RF_OFFSET)
# build 90 degree AHP pulse
inpulse90file = self.sim_experiment.inpulse90file
A_90 = self.sim_experiment.A_90
PULSE_90_LENGTH = self.sim_experiment.PULSE_90_LENGTH
gyratio = self.sim_experiment.getGyratio()
pulse90 = Pulse(inpulse90file, PULSE_90_LENGTH, 'varian')
n_new = np.linspace(0, PULSE_90_LENGTH, 256)
waveform_real = np.real(pulse90.waveform) * A_90
waveform_imag = np.imag(pulse90.waveform) * A_90
pulse90.waveform = waveform_real + 1j * (waveform_imag)
ampl_arr = np.abs(pulse90.waveform) * gyratio
phas_arr = np.unwrap(np.angle(pulse90.waveform)) * 180.0 / math.pi
pulse = pg.row_vector(len(pulse90.waveform))
ptime = pg.row_vector(len(pulse90.waveform))
for j, val in enumerate(zip(ampl_arr, phas_arr)):
pulse.put(pg.complex(val[0], val[1]), j)
ptime.put(pg.complex(pulse90.pulsestep, 0), j)
pulse_dur_90 = pulse.size() * pulse90.pulsestep
pwf_90 = pg.PulWaveform(pulse, ptime, "90excite")
pulc_90 = pg.PulComposite(pwf_90, spin_system,
self.sim_experiment.obs_iso)
Ureal90 = pulc_90.GetUsum(-1)
# build 180 degree pulse
inpulse180file = self.sim_experiment.inpulse180file
A_180 = self.sim_experiment.A_180
PULSE_180_LENGTH = self.sim_experiment.PULSE_180_LENGTH
gyratio = self.sim_experiment.getGyratio()
pulse180 = Pulse(inpulse180file, PULSE_180_LENGTH, 'varian')
n_new = np.linspace(0, PULSE_180_LENGTH, 512)
waveform_real = np.real(pulse180.waveform) * A_180
waveform_imag = np.imag(pulse180.waveform) * A_180
pulse180.waveform = waveform_real + 1j * (waveform_imag)
ampl_arr = np.abs(pulse180.waveform) * gyratio
phas_arr = np.unwrap(np.angle(pulse180.waveform)) * 180.0 / math.pi
freq_arr = np.gradient(phas_arr)
pulse = pg.row_vector(len(pulse180.waveform))
ptime = pg.row_vector(len(pulse180.waveform))
for j, val in enumerate(zip(ampl_arr, phas_arr)):
pulse.put(pg.complex(val[0], val[1]), j)
ptime.put(pg.complex(n_new[1], 0), j)
pulse_dur_180 = pulse.size() * pulse180.pulsestep
pwf_180 = pg.PulWaveform(pulse, ptime, "180afp")
pulc_180 = pg.PulComposite(pwf_180, spin_system,
self.sim_experiment.obs_iso)
Ureal180 = pulc_180.GetUsum(-1)
# calculate pulse timings
ROF1 = 100E-6 #sec
ROF2 = 10E-6 #sec
TCRUSH1 = 0.0008 #sec
TCRUSH2 = 0.0008 #sec
ss_grad_rfDelayFront = 0 #TCRUSH1 - ROF1
ss_grad_rfDelayBack = 0 #TCRUSH2 - ROF2
ro_grad_atDelayFront = 0
ro_grad_atDelayBack = 0
TE = self.sim_experiment.TE / 1000.
ipd = (TE - pulse_dur_90 \
- 6*(ss_grad_rfDelayFront + pulse_dur_180 + ss_grad_rfDelayBack) \
- ro_grad_atDelayFront) / 12
delay1 = ipd + ss_grad_rfDelayFront
delay2 = ss_grad_rfDelayBack + 2 * ipd + ss_grad_rfDelayFront
delay3 = ss_grad_rfDelayBack + 2 * ipd + ss_grad_rfDelayFront
delay4 = ss_grad_rfDelayBack + 2 * ipd + ss_grad_rfDelayFront
delay5 = ss_grad_rfDelayBack + 2 * ipd + ss_grad_rfDelayFront
delay6 = ss_grad_rfDelayBack + 2 * ipd + ss_grad_rfDelayFront
delay7 = ss_grad_rfDelayBack + ipd + ro_grad_atDelayFront
# print A_90, A_180, pulse_dur_90, pulse_dur_180
# print TE, ipd, pulse_dur_90+6*pulse_dur_180, delay1+delay2+delay3+delay4+delay5+delay6+delay7, pulse_dur_90+6*pulse_dur_180+delay1+delay2+delay3+delay4+delay5+delay6+delay7
# print ''
# initialize acquisition
H = pg.Hcs(spin_system) + pg.HJ(spin_system)
D = pg.Fm(spin_system, self.sim_experiment.obs_iso)
ac = pg.acquire1D(pg.gen_op(D), H, self.sim_experiment.dwell_time)
ACQ = ac
Udelay1 = pg.prop(H, delay1)
Udelay2 = pg.prop(H, delay2)
Udelay3 = pg.prop(H, delay3)
Udelay4 = pg.prop(H, delay4)
Udelay5 = pg.prop(H, delay5)
Udelay6 = pg.prop(H, delay6)
Udelay7 = pg.prop(H, delay7)
sigma0 = pg.sigma_eq(spin_system) # init
sigma1 = Ureal90.evolve(sigma0) # apply 90-degree pulse
sigma0 = pg.evolve(sigma1, Udelay1)
sigma1 = Ureal180.evolve(sigma0) # apply AFP1
sigma0 = pg.evolve(sigma1, Udelay2)
sigma1 = Ureal180.evolve(sigma0) # apply AFP2
sigma0 = pg.evolve(sigma1, Udelay3)
sigma1 = Ureal180.evolve(sigma0) # apply AFP3
sigma0 = pg.evolve(sigma1, Udelay4)
sigma1 = Ureal180.evolve(sigma0) # apply AFP4
sigma0 = pg.evolve(sigma1, Udelay5)
sigma1 = Ureal180.evolve(sigma0) # apply AFP5
sigma0 = pg.evolve(sigma1, Udelay6)
sigma1 = Ureal180.evolve(sigma0) # apply AFP6
sigma0 = pg.evolve(sigma1, Udelay7)
# acquire
mx = pg.TTable1D(ACQ.table(sigma0))
# binning to remove degenerate peaks
# BINNING
# Note: Metabolite Peak Normalization and Blending
# The transition tables calculated by the GAMMA density matrix simulations frequently contain a
# large number of transitions caused by degenerate splittings and other processes. At the
# conclusion of each simulation run a routine is called to extract lines from the transition table.
# These lines are then normalized using a closed form calculation based on the number of spins.
# To reduce the number of lines required for display, multiple lines are blended by binning them
# together based on their PPM locations and phases. The following parameters are used to
# customize these procedures:
# Peak Search Range -- Low/High (PPM): the range in PPM that is searched for lines from the
# metabolite simulation.
# Peak Blending Tolerance (PPM and Degrees): the width of the bins (+/- in PPM and +/- in
# PhaseDegrees) that are used to blend the lines in the simulation. Lines that are included in the
# same bin are summed using complex addition based on Amplitude and Phase.
b0 = self.sim_experiment.b0
obs_iso = self.sim_experiment.obs_iso
tolppm = self.sim_experiment.tolppm
tolpha = self.sim_experiment.tolpha
ppmlo = self.sim_experiment.ppmlo
ppmhi = self.sim_experiment.ppmhi
rf_off = self.sim_experiment.RF_OFFSET
field = b0
nspins = spin_system.spins()
nlines = mx.size()
tmp = pg.Isotope(obs_iso)
obs_qn = tmp.qn()
qnscale = 1.0
for i in range(nspins):
qnscale *= 2 * spin_system.qn(i) + 1
qnscale = qnscale / (2.0 * (2.0 * obs_qn + 1))
freqs = []
outf = []
outa = []
outp = []
nbin = 0
found = False
PI = 3.14159265358979323846
RAD2DEG = 180.0 / PI
indx = mx.Sort(0, -1, 0)
for i in range(nlines):
freqs.append(-1 * mx.Fr(indx[i]) / (2.0 * PI * field))
for i in range(nlines):
freq = freqs[i]
if (freq > ppmlo) and (freq < ppmhi):
val = mx.I(indx[i])
tmpa = np.sqrt(val.real()**2 + val.imag()**2) / qnscale
tmpp = -RAD2DEG * np.angle(val.real() + 1j * val.imag())
if nbin == 0:
outf.append(freq)
outa.append(tmpa)
outp.append(tmpp)
nbin += 1
else:
for k in range(nbin):
if (freq >= outf[k] - tolppm) and (freq <=
outf[k] + tolppm):
if (tmpp >= outp[k] - tolpha) and (tmpp <=
outp[k] + tolpha):
ampsum = outa[k] + tmpa
outf[k] = (outa[k] * outf[k] +
tmpa * freq) / ampsum
outp[k] = (outa[k] * outp[k] +
tmpa * tmpp) / ampsum
outa[k] += tmpa
found = True
if not found:
outf.append(freq)
outa.append(tmpa)
outp.append(tmpp)
nbin += 1
found = False
for i, item in enumerate(outf):
outf[i] = item + rf_off
outp[i] = outp[i] - 90.0
metab = Metabolite()
metab.name = metab_name
metab.var = 0.0
for i in range(sp.size(outf)):
if outf[i] <= 5:
metab.ppm.append(outf[i])
metab.area.append(outa[i])
metab.phase.append(-1.0 * outp[i])
insysfile = self.insysfile.replace('pints/metabolites/3T_', '')
insysfile = self.insysfile.replace('pints/metabolites/7T_', '')
insysfile = self.insysfile.replace('pints/metabolites/9.4T_', '')
if insysfile == 'alanine.sys': #
metab.A_m = 0.078
metab.T2 = (87E-3)
elif insysfile == 'aspartate.sys':
metab.A_m = 0.117
metab.T2 = (87E-3)
elif insysfile == 'choline_1-CH2_2-CH2.sys': #
metab.A_m = 0.165
metab.T2 = (87E-3)
elif insysfile == 'choline_N(CH3)3_a.sys' or insysfile == 'choline_N(CH3)3_b.sys': #
metab.A_m = 0.165
metab.T2 = (121E-3)
elif insysfile == 'creatine_N(CH3).sys':
metab.A_m = 0.296
metab.T2 = (90E-3)
elif insysfile == 'creatine_X.sys':
metab.A_m = 0.296
metab.T2 = (81E-3)
elif insysfile == 'd-glucose-alpha.sys': #
metab.A_m = 0.049
metab.T2 = (87E-3)
elif insysfile == 'd-glucose-beta.sys': #
metab.A_m = 0.049
metab.T2 = (87E-3)
elif insysfile == 'eth.sys': #
metab.A_m = 0.320
metab.T2 = (87E-3)
elif insysfile == 'gaba.sys': #
metab.A_m = 0.155
metab.T2 = (82E-3)
elif insysfile == 'glutamate.sys':
metab.A_m = 0.898
metab.T2 = (88E-3)
elif insysfile == 'glutamine.sys':
metab.A_m = 0.427
metab.T2 = (87E-3)
elif insysfile == 'glutathione_cysteine.sys':
metab.A_m = 0.194
metab.T2 = (87E-3)
elif insysfile == 'glutathione_glutamate.sys':
metab.A_m = 0.194
metab.T2 = (87E-3)
elif insysfile == 'glutathione_glycine.sys':
metab.A_m = 0.194
metab.T2 = (87E-3)
elif insysfile == 'glycine.sys':
metab.A_m = 0.068
metab.T2 = (87E-3)
elif insysfile == 'gpc_7-CH2_8-CH2.sys': #
metab.A_m = 0.097
metab.T2 = (87E-3)
elif insysfile == 'gpc_glycerol.sys': #
metab.A_m = 0.097
metab.T2 = (87E-3)
elif insysfile == 'gpc_N(CH3)3_a.sys': #
metab.A_m = 0.097
metab.T2 = (121E-3)
elif insysfile == 'gpc_N(CH3)3_b.sys': #
metab.A_m = 0.097
metab.T2 = (121E-3)
elif insysfile == 'lactate.sys': #
metab.A_m = 0.039
metab.T2 = (87E-3)
elif insysfile == 'myoinositol.sys':
metab.A_m = 0.578
metab.T2 = (87E-3)
elif insysfile == 'naa_acetyl.sys':
metab.A_m = 1.000
metab.T2 = (130E-3)
elif insysfile == 'naa_aspartate.sys':
metab.A_m = 1.000
metab.T2 = (69E-3)
elif insysfile == 'naag_acetyl.sys':
metab.A_m = 0.160
metab.T2 = (130E-3)
elif insysfile == 'naag_aspartyl.sys':
metab.A_m = 0.160
metab.T2 = (87E-3)
elif insysfile == 'naag_glutamate.sys':
metab.A_m = 0.160
metab.T2 = (87E-3)
elif insysfile == 'pcho_N(CH3)3_a.sys': #
metab.A_m = 0.058
metab.T2 = (121E-3)
elif insysfile == 'pcho_N(CH3)3_b.sys': #
metab.A_m = 0.058
metab.T2 = (121E-3)
elif insysfile == 'pcho_X.sys': #
metab.A_m = 0.058
metab.T2 = (87E-3)
elif insysfile == 'pcr_N(CH3).sys':
metab.A_m = 0.422
metab.T2 = (90E-3)
elif insysfile == 'pcr_X.sys':
metab.A_m = 0.422
metab.T2 = (81E-3)
elif insysfile == 'peth.sys':
metab.A_m = 0.126
metab.T2 = (87E-3)
elif insysfile == 'scyllo-inositol.sys':
metab.A_m = 0.044
metab.T2 = (87E-3)
elif insysfile == 'taurine.sys':
metab.A_m = 0.117
metab.T2 = (85E-3)
elif insysfile == 'water.sys':
metab.A_m = 1.000
metab.T2 = (43.60E-3)
# Send save data signal
self.outputResults.emit(metab)
self.postToConsole.emit(' | Simulation completed for ... ' +
self.insysfile)
self.finished.emit(self.thread_num)
"""
1H Single Pulse
###############
An example of simulating a single pulse experiment using pygamma.
"""
import nmrglue as ng
import pygamma as pg
import matplotlib.pyplot as plt
sys = pg.spin_system() # define the system, read in
sys.read("cosy1.sys") # from disk
print( sys)
dt2 = 0.002 # t2 time increment
t2pts = 1024 # points on t2 axis
udic = {'ndim': 1,
0: { 'sw': 1/dt2,
'dw': dt2,
'complex': True,
'obs': 400.0,
'car': 0,
'size': t2pts,
'label': '1H',
'encoding': 'direct',