replace=False)
vb_epos = epos_s[vb_idxs]
tof_sing_corr, p_volt, p_bowl = do_voltage_and_bowl(vb_epos, p_volt, p_bowl)
tof_vcorr_fac = voltage_and_bowl.mod_full_voltage_correction(
p_volt, np.ones_like(epos['tof']), epos['v_dc'])
tof_bcorr_fac = voltage_and_bowl.mod_geometric_bowl_correction(
p_bowl, np.ones_like(epos['tof']), epos['x_det'], epos['y_det'])
# find the voltage and bowl coefficients for the doubles data
tof_vcorr_fac_d = tof_vcorr_fac[doub_idxs]
tof_bcorr_fac_d = tof_bcorr_fac[doub_idxs]
# Find transform to m/z space
m2q_corr, p_m2q = m2q_calib.align_m2q_to_ref_m2q(epos_s['m2q'], tof_sing_corr)
epos['m2q'] = m2q_calib.mod_physics_m2q_calibration(
p_m2q, mod_full_vb_correction(epos, p_volt, p_bowl))
plotting_stuff.plot_histo(epos['m2q'],
fig_idx=1,
user_xlim=[0, 250],
user_bin_width=0.03)
import GaN_fun
pk_data = GaN_type_peak_assignments.GaN_with_H()
bg_rois = [[0.4, 0.9]]
pk_params, glob_bg_param, Ga1p_idxs, Ga2p_idxs = GaN_fun.fit_spectrum(
epos=epos, pk_data=pk_data, peak_height_fraction=0.05, bg_rois=bg_rois)
# Compute some extra information from epos information
wall_time = np.cumsum(epos['pslep']) / 10000.0
pulse_idx = np.arange(0, epos.size)
isSingle = np.nonzero(epos['ipp'] == 1)
# Voltage and bowl correct ToF data
p_volt = np.array([])
p_bowl = np.array([])
t_i = time.time()
tof_corr, p_volt, p_bowl = do_voltage_and_bowl(epos, p_volt, p_bowl)
print("time to voltage and bowl correct: " + str(time.time() - t_i) +
" seconds")
# Find c and t0 for ToF data based on aligning to reference spectrum
m2q_corr, p_m2q = m2q_calib.align_m2q_to_ref_m2q(ref_epos['m2q'], tof_corr)
#
import sel_align_m2q_log_xcorr
pointwise_scales, piecewise_scales = sel_align_m2q_log_xcorr.get_all_scale_coeffs(
m2q_corr, m2q_roi=[0.5, 75], cts_per_slice=2**8, max_scale=1.15)
# Compute corrected data
m2q_corr_q = m2q_corr / pointwise_scales
# Convert back to tof
tof_corr_q = np.sqrt(m2q_corr_q / (p_m2q[0] * 1e-4)) + p_m2q[1]
# Plot TOF vs event index with voltage overlaid to show if voltage corr went ok
ax = plotting_stuff.plot_TOF_vs_time(tof_corr_q, epos, 2)
ax.set_title('voltage and bowl corrected')
# Plot slices from the detector to show if bowl corr went ok
ax = fig.gca()
ax.scatter(epos['x_det'][idxs],
epos['y_det'][idxs],
alpha=0.1,
s=0.1,
c=epos['v_dc'][idxs] / epos['v_dc'].max())
ax.axis('equal')
ax.axis('square')
ax.set_xlabel('x')
ax.set_ylabel('y')
vc = np.sqrt(5000) / np.sqrt(epos['v_dc'])
plotting_stuff.plot_TOF_vs_time(epos['tof'] / vc, epos, 1, user_ylim=[0, 5000])
# Find transform to m/z space
epos_R44['m2q'], p_m2q_R44 = m2q_calib.align_m2q_to_ref_m2q(
ref_epos['m2q'], mod_full_vb_correction(epos_R44, p_volt_R44, p_bowl_R44))
epos_R20['m2q'], p_m2q_R20 = m2q_calib.align_m2q_to_ref_m2q(
ref_epos['m2q'], mod_full_vb_correction(epos_R20, p_volt_R20, p_bowl_R20))
plotting_stuff.plot_histo(epos_R44['m2q'],
fig_idx=1,
user_label='R44',
scale_factor=1 / epos_R44.size)
plotting_stuff.plot_histo(epos_R20['m2q'],
fig_idx=1,
user_label='R20',
clearFigure=False,
scale_factor=1 / epos_R20.size)
# Make a correlation histogram of doubles
epos_vb_R44 = epos_R44.copy()
#fn = r"Q:\NIST_Projects\EUV_APT_IMS\BWC\GaN epos files\R20_07250-v01.epos"
epos = apt_fileio.read_epos_numpy(fn)
#epos = epos[1450000:-1]
# Voltage and bowl correct ToF data
p_volt = np.array([])
p_bowl = np.array([])
t_i = time.time()
tof_corr, p_volt, p_bowl = do_voltage_and_bowl(epos, p_volt, p_bowl)
print("time to voltage and bowl correct: " + str(time.time() - t_i) +
" seconds")
# Find c and t0 for ToF data based on aligning to reference spectrum
m2q_corr, p_m2q = m2q_calib.align_m2q_to_ref_m2q(ref_epos['m2q'],
tof_corr,
nom_voltage=np.mean(
epos['v_dc']))
print(p_m2q)
plotting_stuff.plot_histo(ref_epos['m2q'], 4, user_label='ref')
plotting_stuff.plot_histo(m2q_corr[m2q_corr.size // 2:-1],
4,
clearFigure=False,
user_label='[c,t0] corr')
xs, ys = bin_dat(tof_corr, isDensity=True, bin_width=0.25)
bg_lvl = np.mean(ys[(xs > 1000) & (xs < 3500)])
idxs = np.nonzero((xs > 200) & (xs < 1000))
np.ones_like(sub_epos['tof']),
sub_epos['v_dc'])\
*voltage_and_bowl.mod_geometric_bowl_correction(p_bowl,
np.ones_like(sub_epos['tof']),
sub_epos['x_det'],
sub_epos['y_det'])
# for the moment we are working with doubles only for simplicity
idxs = np.where(epos['ipp'] == 2)[0]
idxs = sorted(np.concatenate((idxs, idxs + 1)))
epos_d = epos[idxs]
ref_fn = r"C:\Users\capli\Google Drive\NIST\pos_and_epos_files\GaN_manuscript\R20_07094-v03.epos"
ref_epos = apt_fileio.read_epos_numpy(ref_fn)
m2q_corr, p_m2q = m2q_calib.align_m2q_to_ref_m2q(ref_epos['m2q'],
tof_singles_corr)
# Verify the alignment worked
m2q_corr = 1e-4*p_m2q[0]*np.square(epos['tof']\
*voltage_and_bowl.mod_full_voltage_correction(p_volt,
np.ones_like(epos['tof']),
epos['v_dc'])\
*voltage_and_bowl.mod_geometric_bowl_correction(p_bowl,
np.ones_like(epos['tof']),
epos['x_det'],
epos['y_det'])
-p_m2q[1])
plotting_stuff.plot_histo(ref_epos['m2q'], 33211233, clearFigure=True)
plotting_stuff.plot_histo(m2q_corr, 33211233, clearFigure=False)