Absorption

Functions to load and process x-ray absorption data.

load_absorption(scan, source[, positioner, ...])	Load the x-ray absorption from one scan.
load_dichro(scan, source[, positioner, ...])	Load the x-ray magnetic dichroism from one scan taken in non-lock-in mode ('dichro').
load_lockin(scan, source[, positioner, ...])	Load the x-ray magnetic dichroism from one scan taken in lock-in mode.
load_multi_xas(scans, source[, return_mean, ...])	Load multiple x-ray absorption energy scans.
load_multi_dichro(scans, source[, ...])	Load multiple x-ray magnetic dichroism energy "dichro" scans.
load_multi_lockin(scans, source[, ...])	Load multiple x-ray magnetic dichroism energy "lockin" scans.
normalize_absorption(energy, mu, *[, e0, ...])	Extract pre- and post-edge normalization curves by fitting polynomials.
pre_edge_background(energy, mu[, e0, pre1, ...])	Extracts the pre-edge background by fitting a polynomial.
post_edge_background(energy, mu[, preedge, ...])	Extracts the post-edge background by fitting a polynomial.
post_edge_flatten(energy, norm[, ...])	Flattens the normalized absorption.
fluo_corr(norm, formula, elem, edge, line, ...)	Correct over-absorption (self-absorption) for fluorescene XAFS using the based on the larch implementation of the FLUO alogrithm of D.
process_xmcd(scans_plus, scans_minus, source)	Process the XMCD scans of +/- magnetic fields.
plot_xmcd(plus, minus)	Plots a new figure with the combined XMCD of plus and minus fields.
save_xmcd(plus, minus, file_name[, header, fmt])	Saves processed XANES/XMCD data into a file.

polartools.absorption.fluo_corr(norm, formula, elem, edge, line, anginp, angout)

Correct over-absorption (self-absorption) for fluorescene XAFS using the based on the larch implementation of the FLUO alogrithm of D. Haskel. See FLUO manual for details.

Parameters:

normiter

Normalized fluorescence

formulastr

Chemical formula of the compound. For example: ‘EuO’.

elemstr

Element of interest. For example: ‘Eu’.

edgestr

Absorption edge of interest. For example: ‘L3’.

linestr

Fluorescence line measured. For example: ‘La’.

anginpfloat

Input angle with respect to the sample surface. See FLUO manual.

anginpfloat

Output angle with respect to the sample surface. See FLUO manual.

Returns:

norm_corrnumpy.array

Corrected normalized fluorescence.

polartools.absorption.load_absorption(scan, source, positioner=None, detector=None, monitor=None, transmission=True, **kwargs)

Load the x-ray absorption from one scan.

Parameters:

scanint

Scan_id our uid. If scan_id is passed, it will load the last scan with that scan_id. See kwargs for search options.

sourcedatabroker database, name of the spec file, or ‘csv’

Note that applicable kwargs depend on this selection.

positionerstring, optional

Name of the positioner, this needs to be the same as defined in Bluesky or SPEC. If None is passed, it defauts to the x-ray energy.

detectorstring, optional

Detector to be read from this scan, again it needs to be the same name as in Bluesky. If None is passed, it defaults to the ion chamber 5.

monitorstring, optional

Name of the monitor detector. If None is passed, it defaults to the ion chamber 4.

transmissionbool, optional

Flag to select between transmission mode -> ln(monitor/detector) or fluorescence mode -> detector/monitor

kwargs

The necessary kwargs are passed to the loading functions defined by the source argument:

• csv -> possible kwargs: folder, name_format.

• spec -> possible kwargs: folder.

• databroker -> possible kwargs: stream, query, use_db_v1.

Note that a warning will be printed if the an unnecessary kwarg is passed.

Returns:

xnumpy.array

Positioner data.

ynumpy.array

X-ray absorption.

See also

polartools.load_data.load_table()

polartools.absorption.load_dichro(scan, source, positioner=None, detector=None, monitor=None, transmission=True, **kwargs)

Load the x-ray magnetic dichroism from one scan taken in non-lock-in mode (‘dichro’).

Parameters:

scanint

Scan_id our uid. If scan_id is passed, it will load the last scan with that scan_id. See kwargs for search options.

sourcedatabroker database, name of the spec file, or ‘csv’

Note that applicable kwargs depend on this selection.

positionerstring, optional

Name of the positioner, this needs to be the same as defined in Bluesky. Defauts to the x-ray energy.

detectorstring, optional

Detector to be read from this scan, again it needs to be the same name as in Bluesky. Defaults to the ion chamber 5.

monitorstring, optional

Name of the monitor detector. Defaults to the ion chamber 4.

transmission: bool, optional

Flag to select between transmission mode -> ln(monitor/detector) or fluorescence mode -> detector/monitor.

kwargs

The necessary kwargs are passed to the loading functions defined by the source argument:

• csv -> possible kwargs: folder, name_format.

• spec -> possible kwargs: folder.

• databroker -> possible kwargs: stream, query, use_db_v1.

Note that a warning will be printed if the an unnecessary kwarg is passed.

Returns:

xnumpy.array

Positioner data.

xanesnumpy.array

X-ray absorption.

xmcdnumpy.array

X-ray magnetic dichroism.

See also

polartools.load_data.load_absorption()

polartools.load_data.load_table()

polartools.absorption.load_lockin(scan, source, positioner=None, dc_col=None, ac_col=None, acoff_col=None, **kwargs)

Load the x-ray magnetic dichroism from one scan taken in lock-in mode.

Parameters:

scanint

Scan_id our uid. If scan_id is passed, it will load the last scan with that scan_id. See kwargs for search options.

sourcedatabroker database, name of the spec file, or ‘csv’

Note that applicable kwargs depend on this selection.

positionerstring, optional

Name of the positioner, this needs to be the same as defined in Bluesky or SPEC. If None is passed, it defaults to the x-ray energy.

dc_colstring, optional

Name of the DC scaler, again it needs to be the same name as in Bluesky or SPEC. If None is passed, it defaults to ‘Lock DC’.

ac_colstring, optional

Name of the AC scaler. If None is passed, it defaults to ‘Lock AC’.

acoff_colstring, optional

Name of the AC offset scaler. If None is passed, it defaults to ‘Lock AC off’.

kwargs

The necessary kwargs are passed to the loading functions defined by the source argument:

• csv -> possible kwargs: folder, name_format.

• spec -> possible kwargs: folder.

• databroker -> possible kwargs: stream, query, use_db_v1.

Note that a warning will be printed if the an unnecessary kwarg is passed.

Returns:

xnumpy.array

Positioner data.

dcnumpy.array

DC response, normally corresponds to the x-ray absorption.

ac-ac_offnumpy.array

AC response minus the offset, normally corresponds to the x-ray magnetic dichroism.

See also

polartools.load_data.load_table()

polartools.absorption.load_multi_dichro(scans, source, return_mean=True, positioner=None, detector=None, monitor=None, transmission=True, **kwargs)

Load multiple x-ray magnetic dichroism energy “dichro” scans.

Parameters:

scansiterable

Sequence of scan_ids our uids. If scan_id is passed, it will load the last scan with that scan_id. Use kwargs for search options.

sourcedatabroker database, name of the spec file, or ‘csv’

Note that applicable kwargs depend on this selection.

return_meanboolean, optional

Flag to indicate if the averaging of multiple scans will be performed. Note that if True three outputs are generated, otherwise two.

positionerstring, optional

Name of the positioner, this needs to be the same as defined in Bluesky or SPEC. If None is passed, it defauts to the x-ray energy.

detectorstring, optional

Detector to be read from this scan, again it needs to be the same name as in Bluesky. If None is passed, it defaults to the ion chamber 5.

monitorstring, optional

Name of the monitor detector. If None is passed, it defaults to the ion chamber 4.

transmission: bool, optional

Flag to select between transmission mode -> ln(monitor/detector) or fluorescence mode -> detector/monitor

kwargs

The necessary kwargs are passed to the loading functions defined by the source argument:

• csv -> possible kwargs: folder, name_format.

• spec -> possible kwargs: folder.

• databroker -> possible kwargs: stream, query, use_db_v1.

Note that a warning will be printed if the an unnecessary kwarg is passed.

Returns:

energynumpy.array

X-ray energy.

xanesnumpy.array

X-ray absorption. If return_mean = True: xanes.shape = (len(scans), len(energy)), otherwise: xanes.shape = (len(energy))

xmcdnumpy.array

X-ray magnetic dichroism. It has the same shape as the xanes.

xanes_stdnumpy.array, optional

Error of the mean of x-ray absorption. This will only be returned if return_mean = True.

xmcd_stdnumpy.array, optional

Error of the mean of x-ray magnetic dichroism. This will only be returned if return_mean = True.

See also

polartools.load_data.load_dichro()

polartools.absorption.load_multi_lockin(scans, source, return_mean=True, positioner=None, dc_col=None, ac_col=None, acoff_col=None, **kwargs)

Load multiple x-ray magnetic dichroism energy “lockin” scans.

Parameters:

scansiterable

Sequence of scan_ids our uids. If scan_id is passed, it will load the last scan with that scan_id. Use kwargs for search options.

sourcedatabroker database, name of the spec file, or ‘csv’

Note that applicable kwargs depend on this selection.

return_meanboolean, optional

Flag to indicate if the averaging of multiple scans will be performed. Note that if True three outputs are generated, otherwise two.

positionerstring, optional

Name of the positioner, this needs to be the same as defined in Bluesky or SPEC. If None is passed, it defauts to the x-ray energy.

dc_colstring, optional

Name of the DC scaler, again it needs to be the same name as in Bluesky or SPEC. If None is passed, it defaults to ‘Lock DC’.

ac_colstring, optional

Name of the AC scaler. If None is passed, it defaults to ‘Lock AC’.

acoff_colstring, optional

Name of the AC offset scaler. If None is passed, it defaults to ‘Lock AC off’.

kwargs

The necessary kwargs are passed to the loading functions defined by the source argument:

• csv -> possible kwargs: folder, name_format.

• spec -> possible kwargs: folder.

• databroker -> possible kwargs: stream, query, use_db_v1.

Note that a warning will be printed if the an unnecessary kwarg is passed.

Returns:

energynumpy.array

X-ray energy.

xanesnumpy.array

X-ray absorption. If return_mean = True: xanes.shape = (len(scans), len(energy)), otherwise: xanes.shape = (len(energy))

xmcdnumpy.array

X-ray magnetic dichroism. It has the same shape as the xanes.

xanes_stdnumpy.array, optional

Error of the mean of x-ray absorption. This will only be returned if return_mean = True.

xmcd_stdnumpy.array, optional

Error of the mean of x-ray magnetic dichroism. This will only be returned if return_mean = True.

See also

polartools.load_data.load_lockin()

polartools.absorption.load_multi_xas(scans, source, return_mean=True, positioner=None, detector=None, monitor=None, transmission=True, **kwargs)

Load multiple x-ray absorption energy scans.

Parameters:

scansiterable

Sequence of scan_ids our uids. If scan_id is passed, it will load the last scan with that scan_id. Use kwargs for search options.

sourcedatabroker database, name of the spec file, or ‘csv’

Note that applicable kwargs depend on this selection.

return_meanboolean, optional

Flag to indicate if the averaging of multiple scans will be performed. Note that if True three outputs are generated, otherwise two.

positionerstring, optional

Name of the positioner, this needs to be the same as defined in Bluesky or SPEC. If None is passed, it defauts to the x-ray energy.

detectorstring, optional

Detector to be read from this scan, again it needs to be the same name as in Bluesky. If None is passed, it defaults to the ion chamber 5.

monitorstring, optional

Name of the monitor detector. If None is passed, it defaults to the ion chamber 4.

transmission: bool, optional

Flag to select between transmission mode -> ln(monitor/detector) or fluorescence mode -> detector/monitor

kwargs

The necessary kwargs are passed to the loading functions defined by the source argument:

• csv -> possible kwargs: folder, name_format.

• spec -> possible kwargs: folder.

• databroker -> possible kwargs: stream, query, use_db_v1.

Note that a warning will be printed if the an unnecessary kwarg is passed.

Returns:

energynumpy.array

X-ray energy.

xanesnumpy.array

X-ray absorption. If return_mean = True: xanes.shape = (len(scans), len(energy)), otherwise: xanes.shape = (len(energy))

xanes_stdnumpy.array, optional

Error of the mean of x-ray absorption. This will only be returned if return_mean = True.

See also

polartools.load_data.load_absorption()

polartools.absorption.normalize_absorption(energy, mu, *, e0=None, edge_step=None, pre_range=None, pre_order=1, nvict=0, post_range=None, post_order=None, flat_range=None, flat_order=None, pre_pars=None, post_pars=None, flat_pars=None)

Extract pre- and post-edge normalization curves by fitting polynomials.

This is a wrapper of for the pre_edge_background, post_edge_background, and post_edge_flatten. The overall process is largely based on larch.xafs.preedge, but it was modified so that a polynomial of any order can be applied to the pre-edge, and the initial parameters for the pre- and post-edge polynomials can be given by the user.

Parameters:

energyiterable

Incident energy. Must be in eV. It will raise an error if it notices the maximum of this list is below 100.

muiterable

Raw x-ray absorption.

e0float or int, optional

Absorption edge energy. If None, it is extracted from the data.

edge_stepfloat, optional

Size of edge step of the raw data. If None, it is calculated based by postedge[e0] - preedge[e0].

pre_rangelist, optional

List with the energy ranges [initial, final] of the pre-edge region relative to the absorption edge. If None is passed to either pre_range or one of the elements, a guessed value will be used. For example:

• pre_range = None -> guess initial and final points.

• pre_range = [None, -20] -> guess only initial point.

• pre_range = [-40, None] -> guess only final point.

• pre_range = [-40, -20] -> guess neither.

pre_orderint, optional

Order of the polynomial to be used in the pre-edge. Defaults to 1.

nvictint, optional

Energy exponent to use. The pre-edge background is modelled by a line that is fit to xanes(energy)*energy**pre_exponent. Defaults to 0.

post_rangelist, optional

List with the energy ranges [initial, final] of the post-edge region relative to the absorption edge.

post_orderint, optional

Order of the polynomial to be used in the post-edge. If None, it will be determined by larch.xafs.preedge:

• If post_range[1]-post_range[0]>350 -> post_order = 2;

• if 50 < post_range[1]-post_range[0] < 350 -> post_order = 1;

• otherwise -> post_order = 0

flat_rangelist, optional

List with the energy ranges [initial, final] of the post-edge region relative to the absorption edge. If None, it will be set as the same as post_range.

flat_orderint, optional

Order of the polynomial to be used in the post-edge. If None, it will be set as the same as post_order.

pre_pars, post_pars, flat_parslmfit.Parameters, optional

Option to input the initial parameters to the polynomial used in the data flattening. These will be labelled ‘c0’, ‘c1’, …, depending on post_order. See lmfit.models.PolynomialModel for details.

Returns:

resultsdict

Dictionary with the results and parameters of the normalization and flattening. The most important items are:

• ‘energy’ -> incident energy.

• ‘mu’ -> raw xanes.

• ‘norm’ -> normalized xanes.

• ‘flat’ -> flattened xanes.

See also

larch.xafs.preedge()

polartools.absorption.pre_edge_background()

polartools.absorption.post_edge_background()

polartools.absorption.post_edge_flatten()

polartools.absorption.plot_xmcd(plus, minus)

Plots a new figure with the combined XMCD of plus and minus fields.

Parameters:

plusdictionary

XANES/XMCD taken using the “plus” magnetic field. Output of the normalize_absorption function.

minusdictionary

XANES/XMCD taken using the “minus” magnetic field. Output of the normalize_absorption function.

Returns:

figmatplotlib.pyplot.figure

Figure instance.

axslist

List of the figure axes.

See also

polartools.absorption.process_xmcd()

polartools.absorption.normalize_absorption()

polartools.absorption.post_edge_background(energy, mu, preedge=None, e0=None, edge_step=None, post1=None, post2=None, post_order=None, post_pars=None)

Extracts the post-edge background by fitting a polynomial.

Based on larch.xafs.preedge. Modified so that a polynomial of any order can be applied to the post-edge, and its initial parameters can be given by the user.

Parameters:

energyiterable

Incident energy. Must be in eV. It will raise an error if it notices the maximum of this list is below 100.

muiterable

Raw x-ray absorption.

e0float or int, optional

Absorption edge energy.

edge_stepfloat, optional

Size of edge step of the raw data. If None, it is calculated based by postedge[e0] - preedge[e0].

preedgeiterable, optional

Pre-edge polynomial. If None, it will be set to zero.

post1, post2float, optional

Low, high energy limit of post-edge range with respect to e0. If None,

it will try to guess it based on mu(energy).

post_orderint, optional

Order of the polynomial to be used in the post-edge. If None, it will be determined using:

• If post2-post1>350 -> post_order = 2;

• if 50 < post2-post1 < 350 -> post_order = 1;

• otherwise -> post_order = 0

post_parslmfit.Parameters, optional

Option to input the initial parameters to the polynomial used in the data flattening. These will be labelled ‘c0’, ‘c1’, …, depending on post_order. See lmfit.models.PolynomialModel for details.

Returns:

resultsdict

Dictionary with the results and parameters of the normalization and flattening. The most important items are:

• ‘energy’ -> incident energy.

• ‘mu’ -> raw xanes.

• ‘norm’ -> normalized XAS.

• ‘post-edge’ -> post-edge background.

• ‘edge-step’ -> Absorption jump size.

See also

larch.xafs.preedge()

larch.absorption.normalize_absorption()

polartools.absorption.post_edge_flatten(energy, norm, bkg_results=None, e0=None, flat1=None, flat2=None, flat_order=None, flat_pars=None)

Flattens the normalized absorption.

This is a slightly modified version from that in the larch package.

The energies inputs must have the same units.

Parameters:

energyiterable

Incident energy in eV.

normiterable

Normalized x-ray absorption.

bkg_resultsdict, optional

Results of the data processing done by post_edge_background. If None, the remaining keyword arguments will be ignored.

e0float or int

Absorption edge energy.

flat1, flat2float or int

Low, high energy limit of flattening range with respect to e0.

flat_orderint, optional

Degree of polynomial to be used. If None, it will be determined using:

• If post2-post1>350 -> post_order = 2;

• if 50 < post2-post1 < 350 -> post_order = 1;

• otherwise -> post_order = 0

fparslmfit.Parameters, optional

Option to input the initial parameters. These will be labelled ‘c0’, ‘c1’, …, depending on nnorm. See lmfit.models.PolynomialModel for details.

Returns:

flatnumpy.array

Flattened x-ray absorption.

See also

larch.xafs.pre_edge()

lmfit.models.PolynomialModel()

polartools.absorption.pre_edge_background(energy, mu, e0=None, pre1=None, pre2=None, pre_order=1, nvict=0, pre_pars=None)

Extracts the pre-edge background by fitting a polynomial.

Based on larch.xafs.preedge. Modified so that a polynomial of any order can be applied to the pre-edge, and its initial parameters can be given by the user.

Parameters:

energyiterable

Incident energy. Must be in eV. It will raise an error if it notices the maximum of this list is below 100.

muiterable

Raw x-ray absorption.

e0float or int, optional

Absorption edge energy.

pre1, pre2float, optional

Low, high energy limit of pre-edge range with respect to e0. If None,

it will try to guess it based on mu(energy).

pre_orderint, optional

Order of the polynomial to be used in the pre-edge. Defaults to 1.

nvictint, optional

Energy exponent to use. The pre-edge background is modelled by a line that is fit to xanes(energy)*energy**pre_exponent. Defaults to 0.

pre_parslmfit.Parameters, optional

Option to input the initial parameters to the polynomial used in the data flattening. These will be labelled ‘c0’, ‘c1’, …, depending on post_order. See lmfit.models.PolynomialModel for details.

Returns:

resultsdict

Dictionary with the results and parameters of the normalization and flattening. The most important items are:

• ‘energy’ -> incident energy.

• ‘mu’ -> raw xanes.

• ‘preedge’ -> preedge polynomial.

See also

larch.xafs.preedge()

larch.absorption.normalize_absorption()

polartools.absorption.process_xmcd(scans_plus, scans_minus, source, xmcd_kind='dichro', load_parameters={}, normalization_parameters={}, normalization_parameters_minus=None)

Process the XMCD scans of +/- magnetic fields.

Parameters:

scans_plusiterable

List of scan number or scan_id of XMCD taken using the “plus” magnetic field.

scans_minusiterable

List of scan number or scan_id of XMCD taken using the “minus” magnetic field.

sourcedatabroker database, name of the spec file, or ‘csv’

Note that applicable load_parameters depend on this selection.

xmcd_kind“dichro” or “lockin”, optional

Type of XMCD scan used, defaults to “dichro”.

load_parametersdictionary

Parameters used to load data. Passed as kwargs to polartools.absorption.load_multi_dichro or polartools.absorption.load_multi_lockin.

normalization_parametersdictionary

Parameters used to normalize the “plus” data (and the “minus” data when normalization_parameters_minus is None). Passed as kwargs to polartools.absorption.normalize_absorption.

normalization_parameters_minusdictionary, optional

If provided, used to normalize the “minus” data independently. When None (default), the “minus” data is normalized with the same parameters as the “plus” data.

Returns:

plusdictionary

XANES/XMCD taken using the “plus” magnetic field. Output of polartools.absorption.normalize_absorption with the XMCD data added.

minusdictionary

XANES/XMCD taken using the “minus” magnetic field. Output of polartools.absorption.normalize_absorption with the XMCD data added.

See also

polartools.absorption.load_multi_dichro()

polartools.absorption.load_multi_lockin()

polartools.absorption.normalize_absorption()

polartools.absorption.save_xmcd(plus, minus, file_name, header='XMCD\n', fmt='%0.5e')

Saves processed XANES/XMCD data into a file.

Parameters:

plusdictionary

XMCD taken using the “plus” magnetic field. It needs at least three keys: “energy”, “norm”, and “xmcd”.

minusdictionary

XMCD taken using the “minus” magnetic field. It needs at least three keys: “energy”, “norm”, and “xmcd”.

file_namestring

File name (including folder if not current).

headerstring, optional

File header. Note that each line has to be finished with the newline character.

fmtstring, optional

Format of the data, defaults to %0.5e

See also

polartools.absorption.process_xmcd()

polartools.absorption.normalize_absorption()