Analysis of Viking spectrometer data¶

The Viking spectrometer is typically used with an Andor Newton CCD to record the transmitted FEL spectrum. The Viking class of the SCS ToolBox contains all the details about the experiment, but no data. It allows the calculation of an absorption spectrum based on averaged spectra with and without sample (reference).

All the parameters need to be carefully calibrated whenever the spectrometer is moved, usually at the beginning of a beamtime.

[1]:

%load_ext autoreload
%autoreload 2

[2]:

import numpy as np
import xarray as xr
import matplotlib.pyplot as plt
plt.rcParams['figure.constrained_layout.use'] = True
#%matplotlib notebook
import toolbox_scs as tb

Setting the stage¶

[3]:

proposal = 2953
runNB = 321  # run containing the data with sample
refNB = 322  # run containing the data without sample
darkNB = 375  # dark run

[4]:

v = tb.Viking(proposal)
v.FIELDS += ['XTD10_SA3']  # add the pulse energy measured by XGM in the XTD10 tunnel
v.X_RANGE = slice(0, 1500) # define the dispersive axis range of interest (in pixels)
v.Y_RANGE = slice(29, 82) # define the non-dispersive axis range of interest (in pixels)
v.ENERGY_CALIB = [1.47802667e-06, 2.30600328e-02, 5.15884589e+02] # energy calibration, see further below
v.BL_POLY_DEG = 1 # define the polynomial degree for baseline subtraction
v.BL_SIGNAL_RANGE = [500, 545] # define the range containing the signal, to be excluded for baseline subtraction

v.load_dark(darkNB)  # load a dark image (averaged over the dark run number)

Plotting baseline subtracted spectrum¶

There is often a broad spectral background added to the SASE spectra that needs to be removed. To do so, a polynomial of degree BL_POLY_DEG is fitted to the baseline. The ranges where the actual SASE signal is present are avoided by setting the BL_SIGNAL_RANGE parameter.

[6]:

plt.figure()
ds_ref['spectrum'].mean(dim='trainId').plot(label='spectrum')
ds_ref['spectrum_nobl'].mean(dim='trainId').plot(label='spectrum_nobl')
plt.legend()
plt.xlabel('Energy [eV]')
plt.grid()

_images/Analysis_of_Viking_spectrometer_data_9_0.png

Beam size measurement with knife-edge¶

[8]:

proposal = 2953
fields = ['newton', 'chem_X']  # chem_X is the manipulator used to move a blade through the beam.

runNB = 405

v.set_params(fields=fields)
v.X_RANGE = slice(0, 1550)
v.Y_RANGE = slice(15, 90)
ds = v.from_run(runNB)

[9]:

plt.figure()
ds['newton'].mean(dim='trainId').plot(vmax=1000)

[9]:

<matplotlib.collections.QuadMesh at 0x2aeb0cbfb828>

_images/Analysis_of_Viking_spectrometer_data_15_1.png

[10]:

roi1 = [30, 430]
roi2 = [960, 1540]
ds['sum1'] = ds['newton'].isel(newt_x=slice(*roi1)).sum(dim=['newt_x', 'newt_y'])
ds['sum2'] = ds['newton'].isel(newt_x=slice(*roi2)).sum(dim=['newt_x', 'newt_y'])
tb.knife_edge(ds, axisKey='chem_X', signalKey='sum1', plot=True) # color 1
tb.knife_edge(ds, axisKey='chem_X', signalKey='sum2', plot=True) # color 2

fitting function: a*erfc(np.sqrt(2)*(x-x0)/w0) + b
w0 = (25.6 +/- 0.4) um
x0 = (-30.598 +/- 0.000) mm
a = 8.038647e+06 +/- 1.638269e+04
b = 9.109166e+06 +/- 2.041594e+04
fitting function: a*erfc(np.sqrt(2)*(x-x0)/w0) + b
w0 = (27.5 +/- 0.4) um
x0 = (-30.598 +/- 0.000) mm
a = 3.405624e+07 +/- 8.242170e+04
b = 1.331917e+07 +/- 1.025471e+05

[10]:

(0.02746726107164219, 0.0004455003530353428)

_images/Analysis_of_Viking_spectrometer_data_16_2.png

_images/Analysis_of_Viking_spectrometer_data_16_3.png

Energy calibration¶

The calibrate method determines the calibration coefficients to translate the camera pixels into energy in eV. The Viking spectrometer is calibrated using the beamline monochromator: runs with various monochromatized photon energy are recorded and their peak position on the detector are determined by Gaussian fitting. The energy vs. position data is then fitted to a second degree polynomial.

[11]:

proposal = 2593
v = tb.Viking(proposal)
v.X_RANGE = slice(0, 1900)
v.Y_RANGE = slice(30, 75)

print('energy calibration before:', v.ENERGY_CALIB)
runs = list(range(118,125))

v.calibrate(runs, plot=True)
plt.xlim(750, 1250)

print('energy calibration after:', v.ENERGY_CALIB)

energy calibration before: [0, 1, 0]
118
119
120
121
122
123
124
energy calibration after: [1.18294370e-05 8.08628533e-02 8.63298212e+02]

_images/Analysis_of_Viking_spectrometer_data_18_1.png

Analysis of Viking spectrometer data¶

Setting the stage¶

Loading data¶

Plotting baseline subtracted spectrum¶

Calculating and plotting XAS spectrum¶

Beam size measurement with knife-edge¶

Energy calibration¶