nmrObj.deassertControlSignal(nmrObj.PSU_15V_TX_P_EN_msk
| nmrObj.PSU_15V_TX_N_EN_msk
| nmrObj.PSU_5V_TX_N_EN_msk
| nmrObj.PSU_5V_ADC_EN_msk
| nmrObj.PSU_5V_ANA_P_EN_msk
| nmrObj.PSU_5V_ANA_N_EN_msk)
if (process_data):
# compute the generated data
if en_remote_computing: # copy remote files to local directory
cp_rmt_file(nmrObj.scp, nmrObj.server_data_folder,
nmrObj.client_data_folder, "current_folder.txt")
meas_folder = parse_simple_info(nmrObj.data_folder, 'current_folder.txt')
if en_remote_computing: # copy remote folder to local directory
cp_rmt_folder(nmrObj.scp, nmrObj.server_data_folder,
nmrObj.client_data_folder, meas_folder[0])
exec_rmt_ssh_cmd_in_datadir(
nmrObj.ssh, "rm -rf " + meas_folder[0],
nmrObj.server_data_folder) # delete the file in the server
(a, a_integ, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df,
t_echospace) = compute_iterate(nmrObj, nmrObj.data_folder, meas_folder[0],
0, 0, 0, direct_read, datain, en_fig,
dconv_lpf_ord, dconv_lpf_cutoff_kHz)
if (meas_time):
elapsed_time = time.time() - start_time
print("data processing time: %.3f" % (elapsed_time))
start_time = time.time()
cpmg_freq_ste = 10 # number of steps
cpmg_freq_sw = np.linspace(cpmg_freq_sta, cpmg_freq_sto, cpmg_freq_ste)
ainteg_tbl = np.zeros(cpmg_freq_ste)
for i in range(0, cpmg_freq_ste):
cpmg_freq = cpmg_freq_sw[i]
nmrObj.cpmgSequence(cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl,
pulse2_dtcl, echo_spacing_us, scan_spacing_us,
samples_per_echo, echoes_per_scan,
init_adc_delay_compensation, number_of_iteration,
ph_cycl_en, pulse180_t1_int, delay180_t1_int)
datain = [
] # set datain to 0 because the data will be read from file instead
meas_folder = parse_simple_info(data_folder, 'current_folder.txt')
(a, a_integ, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df,
t_echospace) = compute_iterate(data_folder, meas_folder[0], 0, 0, 0,
direct_read, datain, en_scan_fig)
ainteg_tbl[i] = a_integ
if en_fig:
plt.ion()
fig = plt.figure(fig_num)
fig.clf()
ax = fig.add_subplot(1, 1, 1)
line1, = ax.plot(cpmg_freq_sw[0:i + 1], ainteg_tbl[0:i + 1], 'r-')
# ax.set_ylim(-50, 0)
# ax.set_xlabel('Frequency [MHz]')
# ax.set_ylabel('S11 [dB]')
# ax.set_title("Reflection Measurement (S11) Parameter")
ax.grid()
fig.canvas.draw()
# fig.canvas.flush_events()
def nmr_t2_auto ( cpmg_freq, pulse1_us, pulse2_us, echo_spacing_us, scan_spacing_us, samples_per_echo, echoes_per_scan, init_adc_delay_compensation, number_of_iteration, ph_cycl_en, dconv_lpf_ord, dconv_lpf_cutoff_Hz, client_data_folder ):
# configurations
en_fig = 1 # enable figure
direct_read = 0 # perform direct read from SDRAM. use with caution above!
process_data = 1 # process data within the SoC
en_remote_dbg = False
en_remote_computing = True
pulse1_dtcl = 0.5 # useless with current code
pulse2_dtcl = 0.5 # useless with current code
pulse180_t1_int = 0
delay180_t1_int = 0
tx_sd_msk = 1 # 1 to shutdown tx opamp during reception, or 0 to keep it powered up during reception
en_dconv = 0 # enable downconversion in the fpga
dconv_fact = 4 # downconversion factor. minimum of 4.
echo_skip = 1 # echo skip factor. set to 1 for the ADC to capture all echoes
# instantiate nmr object
nmrObj = tunable_nmr_system_2018( client_data_folder, en_remote_dbg, en_remote_computing )
# system setup
nmrObj.initNmrSystem() # necessary to set the GPIO initial setting. Also fix the
nmrObj.assertControlSignal( nmrObj.PSU_15V_TX_P_EN_msk | nmrObj.PSU_15V_TX_N_EN_msk | nmrObj.PSU_5V_TX_N_EN_msk |
nmrObj.PSU_5V_ADC_EN_msk | nmrObj.PSU_5V_ANA_P_EN_msk |
nmrObj.PSU_5V_ANA_N_EN_msk )
# nmrObj.deassertControlSignal(
# nmrObj.PSU_15V_TX_P_EN_msk | nmrObj.PSU_15V_TX_N_EN_msk)
Vbias, Vvarac = find_Vbias_Vvarac_from_table ( nmrObj.client_path , cpmg_freq, nmrObj.S21_table )
nmrObj.setPreampTuning( Vbias, Vvarac )
Cpar, Cser = find_Cpar_Cser_from_table ( nmrObj.client_path , cpmg_freq, nmrObj.S11_table )
nmrObj.setMatchingNetwork( Cpar, Cser )
nmrObj.setMatchingNetwork( Cpar, Cser )
# setting for WMP
nmrObj.assertControlSignal(
nmrObj.RX1_1L_msk | nmrObj.RX1_1H_msk | nmrObj.RX2_L_msk | nmrObj.RX2_H_msk | nmrObj.RX_SEL1_msk | nmrObj.RX_FL_msk | nmrObj.RX_FH_msk | nmrObj.PAMP_IN_SEL2_msk )
nmrObj.deassertControlSignal( nmrObj.RX1_1H_msk | nmrObj.RX_FH_msk ) # setting for UF
# nmrObj.deassertControlSignal( nmrObj.RX_FL_msk ) # setting for WMP
if ( direct_read ):
datain = nmrObj.cpmgSequenceDirectRead( cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, samples_per_echo,
echoes_per_scan, init_adc_delay_compensation, number_of_iteration, ph_cycl_en,
pulse180_t1_int, delay180_t1_int, tx_sd_msk )
else:
nmrObj.cpmgSequence( cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, samples_per_echo,
echoes_per_scan, init_adc_delay_compensation, number_of_iteration,
ph_cycl_en, pulse180_t1_int, delay180_t1_int, tx_sd_msk, en_dconv, dconv_fact, echo_skip )
datain = [] # set datain to 0 because the data will be read from file instead
nmrObj.deassertControlSignal(
nmrObj.RX1_1H_msk | nmrObj.RX1_1L_msk | nmrObj.RX2_L_msk | nmrObj.RX2_H_msk | nmrObj.RX_SEL1_msk | nmrObj.RX_FL_msk | nmrObj.RX_FH_msk | nmrObj.PAMP_IN_SEL2_msk )
nmrObj.setMatchingNetwork( 0, 0 )
nmrObj.setPreampTuning( 0, 0 )
nmrObj.deassertControlSignal( nmrObj.PSU_15V_TX_P_EN_msk | nmrObj.PSU_15V_TX_N_EN_msk | nmrObj.PSU_5V_TX_N_EN_msk |
nmrObj.PSU_5V_ADC_EN_msk | nmrObj.PSU_5V_ANA_P_EN_msk | nmrObj.PSU_5V_ANA_N_EN_msk )
if ( process_data ):
# compute the generated data
if en_remote_computing: # copy remote files to local directory
cp_rmt_file( nmrObj.scp, nmrObj.server_data_folder, nmrObj.client_data_folder, "current_folder.txt" )
meas_folder = parse_simple_info( nmrObj.data_folder, 'current_folder.txt' )
if en_remote_computing: # copy remote folder to local directory
cp_rmt_folder( nmrObj.scp, nmrObj.server_data_folder, nmrObj.client_data_folder, meas_folder[0] )
exec_rmt_ssh_cmd_in_datadir( nmrObj.ssh, "rm -rf " + meas_folder[0], nmrObj.server_data_folder ) # delete the file in the server
( a, a_integ, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df, t_echospace ) = compute_iterate( nmrObj,
nmrObj.data_folder, meas_folder[0], 0, 0, 0, direct_read, datain, en_fig , dconv_lpf_ord, dconv_lpf_cutoff_Hz )
nmrObj.deassertAll()
nmrObj.exit()
echoes_per_scan = 64 # number of echos
init_adc_delay_compensation = 10 # acquisition shift microseconds
number_of_iteration = 4 # number of averaging
ph_cycl_en = 1
pulse180_t1_int = 0
delay180_t1_int = 0
# measure initial T2
nmrObj.cpmgSequence(cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl,
echo_spacing_us, scan_spacing_us, samples_per_echo,
echoes_per_scan, init_adc_delay_compensation,
number_of_iteration, ph_cycl_en, pulse180_t1_int,
delay180_t1_int)
meas_folder = parse_simple_info(data_folder, 'current_folder.txt')
(a, a0, snr, T2, noise, res, theta, data_filt, echo_avg,
Df) = compute_iterate(data_folder, meas_folder[0], en_fig)
print('T2 = ' + '{0:.4f}'.format(T2 * 1e6) + ' usec' + ', t_exp = ' +
'{0:.4f}'.format(echoes_per_scan * echo_spacing_us) + ' usec')
while (T2 * 1e6) > (echoes_per_scan * echo_spacing_us):
print('T2 = ' + '{0:.4f}'.format(T2 * 1e6) + ' usec' + ', t_exp = ' +
'{0:.4f}'.format(echoes_per_scan * echo_spacing_us) + ' usec')
echoes_per_scan = round(
(T2 * 1e6) / echo_spacing_us * T2_mult) # number of echos
if echoes_per_scan > max_fifo_data / samples_per_echo:
break
# do NMR measurement
nmrObj.cpmgSequence(cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl,
def cpmgT1( self, cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, samples_per_echo, echoes_per_scan, init_adc_delay_compensation, number_of_iteration, ph_cycl_en, pulse180_t1_us, logsw, delay180_sta, delay180_sto, delay180_ste, ref_number_of_iteration, ref_twait_mult, data_folder, en_scan_fig, en_fig ):
# create t1 measurement folder
t1_meas_folder = datetime.now().strftime( '%Y_%m_%d_%H_%M_%S' ) + '_t1_meas'
os.mkdir( t1_meas_folder )
t1_meas_hist = 't1_meas_hist.txt' # the history file name for t1 measurement
self.fig_num = 1
self.fcpmg_to_fsys_mult = 16 # system_frequency/cpmg_frequency,set by fpga
self.t1_opt_mult = 1.6
# compute period for the system clock (which is multiplication of the cpmg
# freq)
t_sys = ( 1 / cpmg_freq ) / self.fcpmg_to_fsys_mult
# compute pulse180_t1 in integer values and round it to
# fcpmg_to_fsys_mult multiplication
pulse180_t1_int = np.round(
( pulse180_t1_us / t_sys ) / self.fcpmg_to_fsys_mult ) * self.fcpmg_to_fsys_mult
# process delay
if logsw:
delay180_t1_sw = np.logspace(
np.log10( delay180_sta ), np.log10( delay180_sto ), delay180_ste )
else:
delay180_t1_sw = np.linspace(
delay180_sta, delay180_sto, delay180_ste )
# make delay to be multiplication of fcpmg_to_fsys_mult
delay180_t1_sw_int = np.round( ( delay180_t1_sw / t_sys ) /
self.fcpmg_to_fsys_mult ) * self.fcpmg_to_fsys_mult
# compute the reference and do cpmg
ref_twait = ref_twait_mult * delay180_t1_sw_int[delay180_ste - 1]
ref_twait_int = np.round(
( ref_twait ) / self.fcpmg_to_fsys_mult ) * self.fcpmg_to_fsys_mult
self.cpmgSequence( cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, samples_per_echo,
echoes_per_scan, init_adc_delay_compensation, ref_number_of_iteration, ph_cycl_en, pulse180_t1_int, ref_twait_int )
# process the data
meas_folder = parse_simple_info( data_folder, 'current_folder.txt' )
( a_ref, _, a0_ref, snr_ref, T2_ref, noise_ref, res_ref, theta_ref, data_filt_ref, echo_avg_ref, Df, _ ) = compute_iterate(
data_folder, meas_folder[0], 0, 0, 0, en_scan_fig )
# move the folder to t1 measurement folder and write history
shutil.move( meas_folder[0], t1_meas_folder )
write_text_append( t1_meas_folder, t1_meas_hist, meas_folder[0] )
# make the loop
a0_table = np.zeros( delay180_ste ) # normal format
a0_table_decay = np.zeros( delay180_ste ) # decay format
asum_table = np.zeros( delay180_ste ) # normal format
asum_table_decay = np.zeros( delay180_ste ) # decay format
for i in range( 0, delay180_ste ):
delay180_t1_int = delay180_t1_sw_int[i]
# do cpmg scan
self.cpmgSequence( cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, samples_per_echo,
echoes_per_scan, init_adc_delay_compensation, number_of_iteration, ph_cycl_en, pulse180_t1_int, delay180_t1_int )
# process the data (note that a0 and T2 is based on single
# exponential fit)
meas_folder = parse_simple_info( data_folder, 'current_folder.txt' )
( a, _, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df, _ ) = compute_iterate(
data_folder, meas_folder[0], 1, theta_ref, echo_avg_ref, en_scan_fig )
# move the folder to t1 measurement folder and write history
shutil.move( meas_folder[0], t1_meas_folder )
write_text_append( t1_meas_folder, t1_meas_hist, meas_folder[0] )
# interscan data store
a0_table[i] = a0
a0_table_decay[i] = a0_ref - a0
asum_table[i] = np.mean( np.real( a ) )
asum_table_decay[i] = np.mean( np.real( a_ref ) ) - np.mean( np.real( a ) )
if en_fig:
print( 'Loading Figure' )
plt.ion()
fig = plt.figure( self.fig_num )
fig.clf()
ax = fig.add_subplot( 3, 1, 1 )
if logsw:
line1, = ax.semilogx(
delay180_t1_sw[0:i + 1] / 1000, asum_table[0:i + 1], 'r-' )
else:
line1, = ax.plot(
delay180_t1_sw[0:i + 1] / 1000, asum_table[0:i + 1], 'r-' )
# ax.set_xlim(-50, 0)
# ax.set_ylim(-50, 0)
ax.set_ylabel( 'Initial amplitude [a.u.]' )
ax.set_title( "T1 inversion recovery" )
ax.grid()
ax = fig.add_subplot( 3, 1, 2 )
if logsw:
line1, = ax.semilogx(
delay180_t1_sw[0:i + 1] / 1000, asum_table_decay[0:i + 1], 'r-' )
else:
line1, = ax.plot(
delay180_t1_sw[0:i + 1] / 1000, asum_table_decay[0:i + 1], 'r-' )
# ax.set_xlim(-50, 0)
# ax.set_ylim(-50, 0)
# ax.set_xlabel('Wait time [ms]')
ax.set_ylabel( 'Initial amplitude [a.u.]' )
ax.grid()
ax = fig.add_subplot( 3, 1, 3 )
ax.set_ylabel( 'Amplitude [a.u.]' )
ax.set_xlabel( 'Wait time [ms]' )
ax.grid()
fig.canvas.draw()
fig.canvas.flush_events()
print( 'Figure Loaded' )
# save t1 data to csv file to be processed
f = open( t1_meas_folder + '/' + 't1heel_in.csv', "w+" )
for i in range( 0, delay180_ste ):
f.write( "%f," % ( delay180_t1_sw[i] / 1000 ) ) # in milisecond
f.write( "%f\n" % ( a0_table_decay[i] ) )
f.close()
# process t1 data
self.doLaplaceInversion( t1_meas_folder + '/' + 't1heel_in.csv',
t1_meas_folder )
tvect, data = parse_csv_float2col(
t1_meas_folder, 't1heel_out.csv' )
i_peaks = signal.find_peaks_cwt( data, np.arange( 1, 10 ) )
t1_opt = tvect[max( i_peaks )]
'''
a_peaks = np.zeros(len(i_peaks))
for i in range(0, len(i_peaks)):
a_peaks[i] = data[i_peaks[i]]
# find tvect in which the largest peak is found
t1_opt = tvect[i_peaks[np.where(max(a_peaks))[0][0]]] # in second
'''
if en_fig:
ax = fig.add_subplot( 3, 1, 3 )
if logsw:
line1, = ax.semilogx( np.multiply( tvect, 1000 ), data, 'r-' )
else:
line1, = ax.plot( np.multiply( tvect, 1000 ), data, 'r-' )
ax.set_ylabel( 'Amplitude [a.u.]' )
ax.set_xlabel( 'Wait time [ms]' )
ax.grid()
fig.canvas.draw()
# copy the measurement history script
shutil.copy( 'measurement_history_matlab_script.txt', t1_meas_folder )
return delay180_t1_sw, a0_table, a0_ref, asum_table, t1_opt, t1_meas_folder
Vvarac = 2.8
nmrObj.setPreampTuning(Vbias, Vvarac)
# nmrObj.setMatchingNetwork(255, 76) # 4.05 MHz
nmrObj.setMatchingNetwork(Cpar, Cser)
nmrObj.assertControlSignal(
nmrObj.RX1_1H_msk | nmrObj.RX1_1L_msk | nmrObj.RX2_L_msk | nmrObj.RX2_H_msk | nmrObj.RX_SEL1_msk | nmrObj.RX_FL_msk | nmrObj.RX_FH_msk | nmrObj.PAMP_IN_SEL2_msk)
nmrObj.cpmgSequence( cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, samples_per_echo,
echoes_per_scan, init_adc_delay_compensation, number_of_iteration,
ph_cycl_en, pulse180_t1_int, delay180_t1_int , tx_sd_msk, en_dconv, dconv_fact )
datain = [] # set datain to 0 because the data will be read from file instead
meas_folder = parse_simple_info(data_folder, 'current_folder.txt')
#(a, a_integ, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df, t_echospace) = compute_iterate(
# data_folder, meas_folder[0], 0, 0, 0, direct_read, datain, en_scan_fig)
(a, a_integ, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df, t_echospace ) = compute_iterate(
nmrObj, data_folder, meas_folder[0], 0, 0, 0, direct_read, datain, en_scan_fig )
ainteg_tbl[i] = a_integ
if en_fig:
plt.ion()
fig = plt.figure(fig_num)
fig.clf()
ax = fig.add_subplot(1, 1, 1)
line1, = ax.plot(cpmg_freq_sw[0:i + 1], ainteg_tbl[0:i + 1], 'r-')
# ax.set_ylim(-50, 0)
# ax.set_xlabel('Frequency [MHz]')
# ax.set_ylabel('S11 [dB]')
# ax.set_title("Reflection Measurement (S11) Parameter")
ax.grid()
fig.canvas.draw()
# fig.canvas.flush_events()
import matplotlib.pyplot as plt
from nmr_std_function.data_parser import parse_csv_float2col
from nmr_std_function.data_parser import parse_simple_info
from nmr_std_function.nmr_class import tunable_nmr_system_2018
from nmr_std_function.nmr_functions import compute_iterate
# variables
data_folder = "D:\\NMR_Data"
en_fig = True
en_remote_dbg = False
use_latest_folder = False # use latest experiment, otherwise specify the folder below
from nmr_std_function.sys_configs import UF_black_holder_brown_coil_PCB04 as conf
dconv_lpf_ord = conf.dconv_lpf_ord # downconversion order
dconv_lpf_cutoff_kHz = conf.meas_bw_kHz # downconversion lpf cutoff
nmrObj = tunable_nmr_system_2018( data_folder, en_remote_dbg, 1 )
datain = [] # set datain to 0 because the data will be read from file instead
direct_read = 0 # perform direct read from SDRAM. use with caution above!
if ( use_latest_folder ):
meas_folder = parse_simple_info( data_folder, 'current_folder.txt' )
( a, a_integ, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df, t_echospace ) = compute_iterate(
nmrObj, data_folder, meas_folder[0], 0, 0, 0, direct_read, datain, en_fig )
else:
meas_folder = '2021_10_19_00_33_22_cpmg_001' # with scope probe placed at W45
# meas_folder = '2019_05_26_21_24_41_cpmg' # no scope probe placed at W45
( a, a_integ, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df, t_echospace ) = compute_iterate(
nmrObj, data_folder, meas_folder, 0, 0, 0, direct_read, datain, en_fig , dconv_lpf_ord, dconv_lpf_cutoff_kHz )
pulse1_us_sto = 20 # in microsecond
pulse1_us_ste = 40 # number of steps
pulse1_us_sw = np.linspace(pulse1_us_sta, pulse1_us_sto, pulse1_us_ste)
a0_table = np.zeros(pulse1_us_ste)
for i in range(0, pulse1_us_ste):
pulse1_us = 8 # pulse pi/2 length
pulse2_us = pulse1_us_sw[i] # pulse pi length
nmrObj.cpmgSequence(cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl,
pulse2_dtcl, echo_spacing_us, scan_spacing_us,
samples_per_echo, echoes_per_scan,
init_adc_delay_compensation, number_of_iteration,
ph_cycl_en, pulse180_t1_int, delay180_t1_int)
meas_folder = parse_simple_info(data_folder, 'current_folder.txt')
(a, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df,
t_echospace) = compute_iterate(data_folder, meas_folder[0], 0, 0, 0,
en_scan_fig)
a0_table[i] = a0
if en_fig:
plt.ion()
fig = plt.figure(fig_num)
fig.clf()
ax = fig.add_subplot(1, 1, 1)
line1, = ax.plot(pulse1_us_sw[0:i + 1], a0_table[0:i + 1], 'r-')
# ax.set_ylim(-50, 0)
# ax.set_xlabel('Frequency [MHz]')
# ax.set_ylabel('S11 [dB]')
# ax.set_title("Reflection Measurement (S11) Parameter")
ax.grid()
fig.canvas.draw()
# fig.canvas.flush_events()
delay180_t1_sw = np.linspace(delay180_sta, delay180_sto, delay180_ste)
# make delay to be multiplication of 16
delay180_t1_sw_int = np.round(
(delay180_t1_sw / t_sys) / fcpmg_to_fsys_mult) * fcpmg_to_fsys_mult
# compute the reference
# do cpmg scan
nmrObj.cpmgSequence(cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl,
echo_spacing_us, scan_spacing_us, samples_per_echo,
echoes_per_scan, init_adc_delay_compensation,
ref_number_of_iteration, ph_cycl_en, pulse180_t1_int,
delay180_t1_sw_int[delay180_ste - 1])
# process the data
meas_folder = parse_simple_info(data_folder, 'current_folder.txt')
(a_ref, a0_ref, snr_ref, T2_ref, noise_ref, res_ref, theta_ref, data_filt_ref,
echo_avg_ref, Df, _) = compute_iterate(data_folder, meas_folder[0], 0, 0, 0,
en_scan_fig)
# make the loop
snr_table = np.zeros(delay180_ste)
a0_table = np.zeros(delay180_ste)
for i in range(0, delay180_ste):
# do cpmg scan
nmrObj.cpmgSequence(cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl,
pulse2_dtcl, echo_spacing_us, scan_spacing_us,
samples_per_echo, echoes_per_scan,
init_adc_delay_compensation, number_of_iteration,
ph_cycl_en, pulse180_t1_int, delay180_t1_sw_int[i])
# process the data
meas_folder = parse_simple_info(data_folder, 'current_folder.txt')
(a, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df,
_) = compute_iterate(data_folder, meas_folder[0], 1, theta_ref,
def nmr_t2_multifreq_auto ( cpmg_freq_list, pulse1_us, pulse2_us, echo_spacing_us, scan_spacing_us, multiscan_spacing_us, samples_per_echo, echoes_per_scan, init_adc_delay_compensation, number_of_iteration, ph_cycl_en, dconv_lpf_ord, dconv_lpf_cutoff_Hz, client_data_folder ):
# configurations
en_fig = 0 # enable figure
direct_read = 0 # perform direct read from SDRAM. use with caution above!
process_data = 1 # process data within the SoC
en_remote_dbg = False
en_remote_computing = True
pulse1_dtcl = 0.5 # useless with current code
pulse2_dtcl = 0.5 # useless with current code
pulse180_t1_int = 0
delay180_t1_int = 0
tx_sd_msk = 1 # 1 to shutdown tx opamp during reception, or 0 to keep it powered up during reception
en_dconv = 0 # enable downconversion in the fpga
dconv_fact = 4 # downconversion factor. minimum of 4.
echo_skip = 1 # echo skip factor. set to 1 for the ADC to capture all echoes
# additional configurations
timeObj = time_meas( True )
# error checker
if ( not ( len( cpmg_freq_list ) % 2 ) ):
print( "ERROR: please use odd n number for total different frequencies used inside cpmg_freq_list to ensure phase cycling works correctly." )
quit()
# instantiate nmr object
nmrObj = tunable_nmr_system_2018( client_data_folder, en_remote_dbg, en_remote_computing )
# system setup
nmrObj.initNmrSystem() # necessary to set the GPIO initial setting. Also fix the
nmrObj.assertControlSignal( nmrObj.PSU_15V_TX_P_EN_msk | nmrObj.PSU_15V_TX_N_EN_msk | nmrObj.PSU_5V_TX_N_EN_msk |
nmrObj.PSU_5V_ADC_EN_msk | nmrObj.PSU_5V_ANA_P_EN_msk |
nmrObj.PSU_5V_ANA_N_EN_msk )
# nmrObj.deassertControlSignal(
# nmrObj.PSU_15V_TX_P_EN_msk | nmrObj.PSU_15V_TX_N_EN_msk)
Vbias, Vvarac = find_Vbias_Vvarac_from_table ( nmrObj.client_path , cpmg_freq_list[0], nmrObj.S21_table )
nmrObj.setPreampTuning( Vbias, Vvarac )
Cpar, Cser = find_Cpar_Cser_from_table ( nmrObj.client_path , cpmg_freq_list[0], nmrObj.S11_table )
nmrObj.setMatchingNetwork( Cpar, Cser )
nmrObj.setMatchingNetwork( Cpar, Cser )
vbias_list = np.zeros( len( cpmg_freq_list ), dtype = float )
vvarac_list = np.zeros( len( cpmg_freq_list ), dtype = float )
c_series_list = np.zeros( len( cpmg_freq_list ), dtype = int )
c_shunt_list = np.zeros( len( cpmg_freq_list ), dtype = int )
for i in range ( 0, len( cpmg_freq_list ) ):
Vbias, Vvarac = find_Vbias_Vvarac_from_table ( nmrObj.client_path , cpmg_freq_list[i], nmrObj.S21_table )
Cpar, Cser = find_Cpar_Cser_from_table ( nmrObj.client_path , cpmg_freq_list[i], nmrObj.S11_table )
vbias_list[i] = Vbias
vvarac_list[i] = Vvarac
c_series_list[i] = Cser
c_shunt_list[i] = Cpar
# setting for WMP
nmrObj.assertControlSignal(
nmrObj.RX1_1L_msk | nmrObj.RX1_1H_msk | nmrObj.RX2_L_msk | nmrObj.RX2_H_msk | nmrObj.RX_SEL1_msk | nmrObj.RX_FL_msk | nmrObj.RX_FH_msk | nmrObj.PAMP_IN_SEL2_msk )
nmrObj.deassertControlSignal( nmrObj.RX1_1H_msk | nmrObj.RX_FH_msk ) # setting for UF
# nmrObj.deassertControlSignal( nmrObj.RX_FL_msk ) # setting for WMP
timeObj.setTimeSta()
# nmrObj.cpmgSequence( cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, samples_per_echo, echoes_per_scan, init_adc_delay_compensation, number_of_iteration, ph_cycl_en, pulse180_t1_int, delay180_t1_int, tx_sd_msk, en_dconv, dconv_fact, echo_skip )
# nmrObj.cpmgSequence( cpmg_freq, pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, samples_per_echo, echoes_per_scan, init_adc_delay_compensation, number_of_iteration, ph_cycl_en, pulse180_t1_int, delay180_t1_int, tx_sd_msk, en_dconv, dconv_fact, echo_skip )
nmrObj.cpmgSequenceMultifreq( pulse1_us, pulse2_us, pulse1_dtcl, pulse2_dtcl, echo_spacing_us, scan_spacing_us, multiscan_spacing_us, samples_per_echo, echoes_per_scan, init_adc_delay_compensation, number_of_iteration, ph_cycl_en, pulse180_t1_int, delay180_t1_int, tx_sd_msk, en_dconv, dconv_fact, echo_skip, cpmg_freq_list, c_series_list, c_shunt_list, vbias_list, vvarac_list )
datain = [] # set datain to 0 because the data will be read from file instead
timeObj.setTimeSto()
timeObj.reportTimeRel( "cpmgSequenceMultifreq" )
nmrObj.deassertControlSignal(
nmrObj.RX1_1H_msk | nmrObj.RX1_1L_msk | nmrObj.RX2_L_msk | nmrObj.RX2_H_msk | nmrObj.RX_SEL1_msk | nmrObj.RX_FL_msk | nmrObj.RX_FH_msk | nmrObj.PAMP_IN_SEL2_msk )
nmrObj.setMatchingNetwork( 0, 0 )
nmrObj.setPreampTuning( 0, 0 )
nmrObj.deassertControlSignal( nmrObj.PSU_15V_TX_P_EN_msk | nmrObj.PSU_15V_TX_N_EN_msk | nmrObj.PSU_5V_TX_N_EN_msk |
nmrObj.PSU_5V_ADC_EN_msk | nmrObj.PSU_5V_ANA_P_EN_msk | nmrObj.PSU_5V_ANA_N_EN_msk )
if ( process_data ):
# compute the generated data
if en_remote_computing: # copy remote files to local directory
cp_rmt_file( nmrObj.scp, nmrObj.server_data_folder, nmrObj.client_data_folder, "current_folder.txt" )
meas_folder = parse_simple_info( nmrObj.data_folder, 'current_folder.txt' )
for i in range ( 0, len( cpmg_freq_list ) ):
meas_folder[0] = meas_folder[0][:len( meas_folder[0] ) - 3] + "%03d" % i # change the meas_folder name to different folder names generated by the C programming. 25 is the character count before the last 3 digit number.
if en_remote_computing: # copy remote folder to local directory
cp_rmt_folder( nmrObj.scp, nmrObj.server_data_folder, nmrObj.client_data_folder, meas_folder[0] )
exec_rmt_ssh_cmd_in_datadir( nmrObj.ssh, "rm -rf " + meas_folder[0], nmrObj.server_data_folder ) # delete the file in the server
( a, a_integ, a0, snr, T2, noise, res, theta, data_filt, echo_avg, Df, t_echospace ) = compute_iterate( nmrObj,
nmrObj.data_folder, meas_folder[0], 0, 0, 0, direct_read, datain, en_fig , dconv_lpf_ord, dconv_lpf_cutoff_Hz )
