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 )