JupyLabBook @ SIRIUS¶

In [1]:

%%latex
\tableofcontents
\newpage

\tableofcontents \newpage

In [2]:

__version__ = '2.10.3'
print("JupyLabBook version: %s"%__version__)
print("More info on: %s"%"https://gitlab.com/soleil-data-treatment/soleil-beamlines/soleil-beamline-sirius/JupyLabBook")

#import useful libraries
import numpy as np
import matplotlib.pyplot as plt
from IPython.display import set_matplotlib_formats, Javascript, display

# import custom libraries
import lib.frontend as FE
from lib.extraction.common import PyNexus as PN
from lib.extraction import GIXD
from lib.extraction import GIXS
from lib.extraction import DetectorSum
from lib.extraction import Isotherm
from lib.extraction import Sensors1D
from lib.extraction import XRF
from lib.extraction import XRR

# necessary for plotting in the notebook
%matplotlib inline

# pdf images for the final pdf report
try:
    import matplotlib_inline.backend_inline
    matplotlib_inline.backend_inline.set_matplotlib_formats('png', 'pdf')
except:
    #for IPython<7.23
    set_matplotlib_formats('png', 'pdf')

# to have all the cells expanded (not collapsed)
display(Javascript('IPython.OutputArea.prototype._should_scroll = function(lines) {return false;}'))
        
# define the class experiment
class Experiment:
    """
    Class Experiment is used to pass arguments concerning the current experiment only.
    """
    def __init__(self):
        pass

# test if the expt already exists (avoid loosing info when reloading this cell)
if not 'expt' in locals():
    expt = Experiment() 

# necessary for saving in pdf
expt.notebook_name = 'Example.ipynb'

# directory where the data will be saved
expt.working_dir = "working/"

# directory where the nexus files are 
expt.recording_dir = "recording/"

# directory where the logs are
expt.logs_dir = "logs/"   

FE.Action.Check_and_init(expt)

JupyLabBook version: 2.10.3
More info on: https://gitlab.com/soleil-data-treatment/soleil-beamlines/soleil-beamline-sirius/JupyLabBook

Data reduction will be saved in the folder:
working/

The original nexus files should be in the folder:
recording/

The log files should be in the folder:
logs/

Experimental setup¶

$\LARGE \textbf{SIRIUS Beamline}:\textbf{Experiment 1234}$

$\Large \color{red}{\bf Example\ }$

Type: Proposal
Safety: Yellow
Date: 11/06/21-12/06/21

Main proposer: Hemmerle
Local contact: Arnaud
Users (on site): Person 1, Person 2, Person 3, Person 4

Machine:
- Current: 450 mA
- Mode: Top-up

Optics:
- DCM: Si111
- MGM: Not used
- M1: M1-A Pt Track
- M2: M2 Pt Track
- M3: No M3
- M4: M4 Pt Track

Beam:
- Fixed/Variable energy: Fixed
- Energy (keV): 8
- Wavelength (nm): 0.155
- Harmonic: 12
- Polarisation: LH
- Phase (deg): 0
- Horizontal focalisation: False
- Vertical focalisation: True
- Horizontal beamsize (mm): 2
- Vertical beamsize (mm): 0.5

Monitors and XBPM:
- mon1:
- mon2:
- mon3:
- mon4: thick diamond
- Detectors: None

Remarks: This is an example.

Beamline alignment¶

Here we show functions used during beamline alignment.

LaTeX formula can be used in the text:
$$\frac{786-558}{2 \times 2069} \times 0.0355 = 1.9mrad$$

Subsection¶

Fit with erf function.

SIRIUS_2020_03_11_0744: dscan basez -.2 .2 50 .1¶

In [3]:

xData, yData, yFit = \
Sensors1D.GaussianRepartitionFit(nxs_filename='SIRIUS_2020_03_11_0744.nxs', recording_dir = expt.recording_dir, \
xLabel='basez', yLabel='camxdeflected', verbose=False)

Fit with Gaussian function.

SIRIUS_2020_03_11_0752: continuous_ascan delta -.15 .15 100 1¶

In [4]:

xData, yData, yFit = \
Sensors1D.GaussianFit(nxs_filename='SIRIUS_2020_03_11_0752.nxs', recording_dir = expt.recording_dir, \
xLabel='delta', yLabel='pilatusroi1', verbose=False)

Calibration thetaz¶

In [5]:

calib_thetaz_data = np.array([
# gamma  channel
[0,      970],
[-1,     899],
[-2,     827],
[-3,     755],
[-4,     683],
[-5,     611],
[-6,     539],
])
expt.thetazfactor=GIXD.Calib_thetaz(calib_thetaz_data)

GIXD¶

Extraction of the Yoneda-Vineyard peak.

SIRIUS_2020_03_12_0756: continuous_ascan delta -24 -19 100 5¶

In [6]:

expt.channel0 = \
GIXD.Extract_channel0(nxs_filename='SIRIUS_2020_03_12_0756.nxs', recording_dir=expt.recording_dir, \
binsize=10, logx=False, logy=False, logz=False, nblevels=50, cmap='jet', \
force_gamma=False, fgamma=0., show_data_stamps = True, verbose=True)

 - Open Nexus Data File :
	recording/SIRIUS_2020_03_12_0756.nxs
	. Number of data points: 101
	. Available Counters:
		0  -------> delta
		1  -------> zs
		2  -------> gamma
		3  -------> hu36energy
		4  -------> xs
		5  -------> energydcm
		6  -------> current
		7  -------> mon2
		8  -------> surfacepressure
		9  -------> areapermolecule
		10  -------> qxy
		11  -------> pilatus
		12  -------> pilatusroi1
		13  -------> integration_time
		14  -------> sensorsRelTimestamps
		15  -------> sensorsTimestamps
	. Pilatus data found, (column 11, alias pilatus)
	. qxy data found, (column 10, alias qxy)
	. Valid data between points 0 and 100
	. Surface pressure data found, mean value 19.74 ± 0.006119 mN/m
	. Area per molecule data found, mean value 0.3557 ± 3.944e-05 nm2 per molecule
	. Gamma motor data found, mean value -0.0004471 deg

Data not saved. To save data, run a GIXD on the scan.
Channel0: 607

SIRIUS_2020_03_12_0756: continuous_ascan delta -24 -19 100 5¶

In [7]:

x, y, daty, datyTop, datyBottom, datyFirstQuarter, mat, mat_binned, ch_binned, mean_pi, mean_area, mean_gamma = \
GIXD.Treat(nxs_filename='SIRIUS_2020_03_12_0756.nxs', recording_dir=expt.recording_dir, channel0=607.0, \
thetazfactor=0.00024318628377198605, wavelength=0.155, thetac=0.0028, binsize=10, computeqz=True, \
force_gamma=False, fgamma=0.0, absorbers='29 - Vide', logx=False, logy=False, logz=False, \
nblevels=50, cmap='jet', working_dir=expt.working_dir, \
moytocreate=[10, 20, 40], show_data_stamps=True, plot=True, save=True, verbose=True)

 - Open Nexus Data File :
	recording/SIRIUS_2020_03_12_0756.nxs
	. Number of data points: 101
	. Available Counters:
		0  -------> delta
		1  -------> zs
		2  -------> gamma
		3  -------> hu36energy
		4  -------> xs
		5  -------> energydcm
		6  -------> current
		7  -------> mon2
		8  -------> surfacepressure
		9  -------> areapermolecule
		10  -------> qxy
		11  -------> pilatus
		12  -------> pilatusroi1
		13  -------> integration_time
		14  -------> sensorsRelTimestamps
		15  -------> sensorsTimestamps
	. Pilatus data found, (column 11, alias pilatus)
	. qxy data found, (column 10, alias qxy)
	. Valid data between points 0 and 100
	. Surface pressure data found, mean value 19.74 ± 0.006119 mN/m
	. Area per molecule data found, mean value 0.3557 ± 3.944e-05 nm2 per molecule
	. Gamma motor data found, mean value -0.0004471 deg
Absorbers: 29 - Vide

	. Original, non binned, matrix saved in:
	working/SIRIUS_2020_03_12_0756_1D.mat
	. Scalar data saved in:
	working/SIRIUS_2020_03_12_0756_1D.dat
	. qz values saved in:
	working/SIRIUS_2020_03_12_0756_1D_qz.dat10
	. Binned matrix saved in:
	working/SIRIUS_2020_03_12_0756_1D.mat10
	. XYZ data saved in:
	working/SIRIUS_2020_03_12_0756_1D.moy10
	. qz values saved in:
	working/SIRIUS_2020_03_12_0756_1D_qz.dat20
	. Binned matrix saved in:
	working/SIRIUS_2020_03_12_0756_1D.mat20
	. XYZ data saved in:
	working/SIRIUS_2020_03_12_0756_1D.moy20
	. qz values saved in:
	working/SIRIUS_2020_03_12_0756_1D_qz.dat40
	. Binned matrix saved in:
	working/SIRIUS_2020_03_12_0756_1D.mat40
	. XYZ data saved in:
	working/SIRIUS_2020_03_12_0756_1D.moy40
	. Figure saved in:
	working/SIRIUS_2020_03_12_0756_1D.pdf

Classic GIXD with: $$q_{xy} = \frac{4\pi}{\lambda}\sin{\left(\frac{2\theta}{2}\right)}$$

Generates:

SIRIUS_2020_03_12_0756_1D_qz.dat for each binning
SIRIUS_2020_03_12_0756_1D.dat
SIRIUS_2020_03_12_0756_1D.mat for each binning
SIRIUS_2020_03_12_0756_1D.moy for each binning

Isotherm¶

SIRIUS_Isotherm_2019_02_17_01544: isotherm 1.97 46 35000 1¶

In [8]:

area, pressure, time = \
Isotherm.Treat(nxs_filename='SIRIUS_Isotherm_2019_02_17_01544.nxs', recording_dir=expt.recording_dir, \
working_dir=expt.working_dir, fast=True, show_data_stamps=False, plot=True, save=True, verbose=False)

1D plot¶

Add a 1D plot by clicking on Add plot to report. Generates SIRIUS_2020_03_12_0760.dat

SIRIUS_2020_03_12_0760: run cont_regh.ipy¶

In [9]:

xData, yData = \
Sensors1D.Treat(nxs_filename='SIRIUS_2020_03_12_0760.nxs', recording_dir=expt.recording_dir, \
xLabel='zs', yLabel='camxreflected', working_dir=expt.working_dir, show_data_stamps=False, \
plot=True, save=True, verbose=False)

GIXS¶

WAXS on Ag Behenate for calibration. Use the GIXS command with thetai forced to 0.

GIXS: $q_z$ vs $q_{xy}$.
Image and profiles with the approximation $q_{xy} = \frac{4\pi}{\lambda}\sin{\left(\frac{2\theta}{2}\right)}$.
Generates:

SIRIUS_2021_11_26_6088_pilatus_sum.tiff
SIRIUS_2021_11_26_6088_pilatus_sum.mat
SIRIUS_2021_11_26_6088_integrated_qz.dat
SIRIUS_2021_11_26_6088_integrated_qxy.dat

SIRIUS_2021_11_26_6088: tscan 5 5¶

In [10]:

images_sum, integrated_qxy, integrated_qz, qxy_array, qz_array = \
GIXS.Treat(nxs_filename='SIRIUS_2021_11_26_6088.nxs', recording_dir=expt.recording_dir, \
wavelength=0.12398, distance=335.5, pixel_PONI_x=572.1, pixel_PONI_y=1016.0, pixel_size=0.172, \
force_gamma=False, force_delta=False, force_thetai=True, fgamma=0.0, fdelta=0.0, fthetai=0.0, \
qxymin=-22.0, qxymax=0.0, qzmin=0.0, qzmax=22.0, \
absorbers='29 - Vide', logz=True, cmap='viridis', working_dir=expt.working_dir, \
show_data_stamps=False, plot=True, save=True, verbose=False)

Absorbers: 29 - Vide          
gamma found: gamma = -0.9997 deg
delta found: delta = -8.875 deg
thetai is forced to the value: thetai =   0 deg

GIWAXS on a P3HT film.

SIRIUS_2021_11_26_6103: tscan 10 10¶

In [11]:

images_sum, integrated_qxy, integrated_qz, qxy_array, qz_array = \
GIXS.Treat(nxs_filename='SIRIUS_2021_11_26_6103.nxs', recording_dir=expt.recording_dir, \
wavelength=0.12398, distance=335.5, pixel_PONI_x=572.1, pixel_PONI_y=1016.0, pixel_size=0.172, \
force_gamma=False, force_delta=False, force_thetai=False, fgamma=0.0, fdelta=0.0, fthetai=0.0, \
qxymin=-21.0, qxymax=0.0, qzmin=0.0, qzmax=22.0, \
absorbers='29 - Vide', logz=True, cmap='viridis', working_dir=expt.working_dir, \
show_data_stamps=False, plot=True, save=True, verbose=False)

Absorbers: 29 - Vide          
gamma found: gamma =  -2 deg
delta found: delta = -8.875 deg
thetai (alphax) found: thetai = 0.1 deg

GISAXS image. Delta and gamma have to be forced to zero (the detector is not on the diffractometer).

SIRIUS_2021_10_16_2739: run scan_0_18.ipy¶

In [12]:

images_sum, integrated_qxy, integrated_qz, qxy_array, qz_array = \
GIXS.Treat(nxs_filename='SIRIUS_2021_10_16_2739.nxs', recording_dir=expt.recording_dir, \
wavelength=0.155, distance=4368.9, pixel_PONI_x=490.5, pixel_PONI_y=954.0, pixel_size=0.172, \
force_gamma=True, force_delta=True, force_thetai=False, fgamma=0.0, fdelta=0.0, fthetai=0.0, \
qxymin=-0.65, qxymax=0.65, qzmin=0.0, qzmax=1.3, \
absorbers='', logz=True, cmap='viridis', working_dir=expt.working_dir, \
show_data_stamps=False, plot=True, save=True, verbose=False)

gamma is forced to the value: gamma =   0 deg
delta is forced to the value: delta =   0 deg
thetai (alphax) found: thetai = 0.18 deg

Plot 2D detector¶

Plot the sum of the images from a 2D detector. Can also extract and save all the individual images if save='all'.

Here with the Pilatus.
Generates:

SIRIUS_2021_11_26_6088_pilatus_sum.tiff
SIRIUS_2021_11_26_6088_pilatus_sum.mat
SIRIUS_2021_11_26_6088_integrated_x.dat
SIRIUS_2021_11_26_6088_integrated_y.dat

SIRIUS_2021_11_26_6088: tscan 5 5¶

In [13]:

images_sum, integrated_x, integrated_y = \
DetectorSum.Treat(nxs_filename='SIRIUS_2021_11_26_6088.nxs', recording_dir=expt.recording_dir, \
xmin=0.0, xmax=980.0, ymin=0.0, ymax=1042.0, \
absorbers='', logz=True, cmap='Greys', working_dir=expt.working_dir, \
show_data_stamps=False, plot=True, save=True, verbose=False)

Works also with the detector UFXC.

SIRIUS_2021_11_11_3728: tscan 2 9¶

In [14]:

images_sum, integrated_x, integrated_y = \
DetectorSum.Treat(nxs_filename='SIRIUS_2021_11_11_3728.nxs', recording_dir=expt.recording_dir, \
xmin=150.0, xmax=170.0, ymin=150.0, ymax=200.0, \
absorbers='', logz=True, cmap='jet', working_dir=expt.working_dir, \
show_data_stamps=True, plot=True, save='all', verbose=False)

	. Available Counters:
		0  -------> delta
		1  -------> shg
		2  -------> zs
		3  -------> alphax
		4  -------> gamma
		5  -------> xs
		6  -------> energydcm
		7  -------> svg
		8  -------> current
		9  -------> mon2
		10  -------> fluoicr00
		11  -------> fluoicr01
		12  -------> fluoicr02
		13  -------> fluoicr03
		14  -------> fluospectrum00
		15  -------> fluospectrum01
		16  -------> fluospectrum02
		17  -------> fluospectrum03
		18  -------> mon4
		19  -------> ionchamber
		20  -------> fluoocr00
		21  -------> fluoocr01
		22  -------> fluoocr02
		23  -------> fluoocr03
		24  -------> commandfemtoionchamber
		25  -------> ufx
		26  -------> ufxroi2
		27  -------> integration_time
		28  -------> sensorsRelTimestamps
		29  -------> sensorsTimestamps

XRF¶

Plot XRF from the 4-elements detector, in channels and without peak identification.
Generates:

SIRIUS_2017_12_11_08042_fluospectrum.mat for each element
SIRIUS_2017_12_11_08042.dat

SIRIUS_2017_12_11_08042: run xsw7.ipy¶

In [15]:

channels, eVs, spectrums = \
XRF.Treat(nxs_filename='SIRIUS_2017_12_11_08042.nxs', recording_dir=expt.recording_dir, \
list_elems=[0, 1, 2], absorbers='Al 200micron', logz=True, first_channel=100, last_channel=800, use_eV=True, \
gain=10.0, eV0=0.0, arr_peaks=[(None, None)], working_dir=expt.working_dir, fast=True, \
show_data_stamps=False, plot_spectrogram=True, plot_sum=True, plot_first_last=True, save=True, verbose=False)

Absorbers: Al 200micron

Plot XRF from the 1-element detector, in eVs and with peak identification.
Generates:

SIRIUS_Fluo_2020_07_03_0042_fluospectrum04.mat
SIRIUS_Fluo_2020_07_03_0042.dat

SIRIUS_Fluo_2020_07_03_0042: tscan 500 30¶

In [16]:

channels, eVs, spectrums = \
XRF.Treat(nxs_filename='SIRIUS_Fluo_2020_07_03_0042.nxs', recording_dir=expt.recording_dir, \
list_elems=[4], absorbers='Al 800micron', logz=True, first_channel=170, last_channel=1250, use_eV=True, \
gain=9.89, eV0=6.0, arr_peaks=[('Elastic', '12000'), ('Compton', '11670'), ('Cl (Ka1)', '2622'), ('Fe (Ka1)', '6400'), \
 ('K (Ka1)', '3314')], working_dir=expt.working_dir, fast=True, \
show_data_stamps=False, plot_spectrogram=True, plot_sum=True, plot_first_last=True, save=True, verbose=False)

Absorbers: Al 800micron

XRR¶

To start the calibration click on Calib. XRR.

Calibration XRR¶

In [17]:

# For each line of the table:
# 1) Move m4pitch and zs to their suggested values
# 2) Move c10tablepitch and gamma to their suggested value
# 3) Adjust the attenuators
# 4) Align gamma so that the reflection is in the center of the ROI
# 5) Align c10tablepitch and zs around their suggested values
# 6) Replace the values in the table
# 
# When done, execute the cell
# Use the value of each fit in the XRR scripts
# 
calib_XRR_data = np.array([
# m4pitch  c10tablepitch gamma zs 
[-0.08, -3335, 5.6, 34.5],
[-0.31, -7935, 3.72396, 16.744],
[-0.54, -12535, 1.84793, -1.012],
[-0.77, -17135, -0.0281093, -18.768],
[-1, -21735, -1.90415, -36.524],
])
expt.distance = 435.5
XRR.Calib(calib_XRR_data, distance=expt.distance)

Scan XRR¶

Select the first scan of the XRR series and click on Plot XRR. Here we show only a few point for the example.

SIRIUS_2021_04_14_4298: No command found¶

In [18]:

m4pitch, theta, qz, bckg_R_up, bckg_R_down, bckg_R_left, bckg_R_right, bckg_R, err_R, R = \
XRR.Treat(nxs_filename='SIRIUS_2021_04_14_4298.nxs', recording_dir=expt.recording_dir, \
direct_nxs_filename='SIRIUS_2021_04_14_4297.nxs', ROIx0=550, ROIy0=905, ROIsizex=40, ROIsizey=40, \
summation_ROIsizey=7, m4pitch0=-0.0375, wavelength=0.1208, force_direct=False, fdirect=1.0, \
is_bckg_up=True, is_bckg_down=True, is_bckg_left=False, is_bckg_right=False, is_tracking=True, \
working_dir=expt.working_dir, plot_XRR_m4pitch=True, plot_XRR_qz=True, plot_pos_y=True, \
save=True, verbose=False)

Direct extracted from SIRIUS_2021_04_14_4297.nxs: direct=2.44387e+12

Insert script¶

Script inserted (with automatic scan numbering) using Insert script.

script_with_loop.ipy¶

%shopen
%amove delta -40
%run reset_motors.ipy
%continuous_ascan delta -35 -25 250 5 #123
%tscan 10 10 #124

for i in range(4):
    %amove delta -20
    %continuous_ascan delta -10 -3 175 5 #125 #127 #129 #131
    %run reset_motors.ipy
    %run cont_regh_abs.ipy #126 #128 #130 #132

for i in range(3):
    %amove delta -20
    %dscan delta -10 -3 175 5 #133 #135 #137
    %run reset_motors.ipy

    #%run cont_regh_abs.ipy
    %run cont_regh_abs.ipy #134 #136 #138

for i in range(2):
    %amove delta -20
    %tscan 10 100 #139 #140
    %slist scan add camxdirect

%continuous_ascan delta -35 -25 250 5 #141
# %tscan 10 10
%shclose

Insert positions¶

Positions extracted from the logs, using Insert positions.

wm alphax gamma¶

alphax	gamma
2.0679	4.1401

wm diffracto¶

deltacodeur	euchi	euth	euphi	kappa_h	kappa_k
	1.00196	-89.57961	90.42039	-0.00580	-0.08252
Degrees	deg	deg	deg

kappa_l	qxy	qxy0	qz	basexPoint	basexTrait
-0.18486	2.0556	23.82	-0.92	-15.7275	-15.7274
	nm-1	nm-1	nm-1

basezPlan	basezPoint	basezTrait	basepitch	baseroll	basex
71.1257	71.1257	71.1257	-0.0000	0.000	-15.727
			mrad	mrad	mm

baseyaw	basez	alphax	alphay	delta	delta0
-0.000	71.126	0.2998	0.2000	-2.9110	-34.2322
mrad	mm

deltaa	etaa	gamma	kappav	mu	kphi
0.0000	0.0000	1.2997	1.3080	-179.9997	0.0000

thetaa	thetah	komega	xs	ky	ys
0.0000	0.0185	0.0000	0.0000	-0.1000	0.0000

kz	zs	kx
0.0000	-41.9999	-0.1000

Insert commands¶

Commands extracted from the logs, using Insert commands.

Fri, 26 Nov 2021 14:13:34 ct 1 pilatus
Fri, 26 Nov 2021 14:13:56 tscan 10 10 #6109
Fri, 26 Nov 2021 14:17:29 shclose
Fri, 26 Nov 2021 14:26:40 run config_alignment.ipy
Fri, 26 Nov 2021 10:34:48 ct 1 pilatus

Convert logs¶

Human-readable logs generated in the folder /working/readable_logs/ by clicking on Convert logs.

Insert an image¶

Using the command Insert image.

Save/load state¶

Save the current state of the notebook (the variable expt) by clicking on Save state.

In [19]:

import pickle
with open('working/expt.pkl', 'wb') as f:
	pickle.dump(expt, f, pickle.HIGHEST_PROTOCOL)

Load the previous state of the notebook by clicking on Load state(for example after creating a new notebook).

In [20]:

import pickle
with open('working/expt.pkl', 'rb') as f:
	expt = pickle.load(f)

Insert text¶

Use the button Insert text to insert text into the report.

Export to pdf¶

PDF generated by clicking on Export to pdf.

In [22]:

FE.Action.Choose(expt)

Export in progress...

Notebook exported to Example.pdf