Fluorescence tasks

How to use

These tasks come from ewoksfluo. It can be installed with

pip install ewoksfluo

ℹ️ These tasks are used at the following ESRF beamlines: ID16b, ID21

MeshSingleScanSingleDetector

XRF test data of one scan with one detector

Identifier:

ewoksfluo.tasks.example_data.tasks.MeshSingleScanSingleDetector

Task type:

class

Required inputs:

output_filename

Optional inputs:

counting_noise, emission_line_groups, rois, expo_time, integral_type, shape, flux, ndetectors, energy

Outputs:

scan_number, monitor_normalization_template, monitor_name, detector_name, expo_time, detector_normalization_template, filename, config

MeshSingleScanMultiDetector

XRF test data of one scan with multiple detectors

Identifier:

ewoksfluo.tasks.example_data.tasks.MeshSingleScanMultiDetector

Task type:

class

Required inputs:

output_filename

Optional inputs:

counting_noise, emission_line_groups, rois, expo_time, integral_type, shape, flux, ndetectors, energy

Outputs:

scan_number, detector_names, monitor_normalization_template, monitor_name, expo_time, detector_normalization_template, configs, filename, config

MeshMultiScanSingleDetector

XRF test data of multiple scans with one detector

Identifier:

ewoksfluo.tasks.example_data.tasks.MeshMultiScanSingleDetector

Task type:

class

Required inputs:

output_filename

Optional inputs:

counting_noise, emission_line_groups, nscans, rois, expo_time, integral_type, shape, flux, energy

Outputs:

scan_ranges, filenames, monitor_normalization_template, monitor_name, detector_name, expo_time, detector_normalization_template, config

MeshMultiScanMultiDetector

XRF test data of multiple scans with multiple detectors

Identifier:

ewoksfluo.tasks.example_data.tasks.MeshMultiScanMultiDetector

Task type:

class

Required inputs:

output_filename

Optional inputs:

counting_noise, emission_line_groups, nscans, rois, expo_time, integral_type, shape, flux, ndetectors, energy

Outputs:

detector_names, scan_ranges, filenames, monitor_normalization_template, monitor_name, expo_time, detector_normalization_template, configs, config

FitSingleScanSingleDetector

XRF fit of one scan with one detector

Identifier:

ewoksfluo.tasks.fit.tasks.FitSingleScanSingleDetector

Task type:

class

Required inputs:

bliss_scan_uri, detector_name, config, output_root_uri

Optional inputs:

energy_multiplier, diagnostics, energy_name, xrf_spectra_uri_template, fast_fitting, energy_uri_template, process_uri_template, figuresofmerit, quantification

Outputs:

bliss_scan_uri, detector_name, xrf_results_uri, output_root_uri

FitSingleScanMultiDetector

XRF fit of one scan with multiple detectors

Identifier:

ewoksfluo.tasks.fit.tasks.FitSingleScanMultiDetector

Task type:

class

Required inputs:

bliss_scan_uri, configs, output_root_uri, detector_names

Optional inputs:

energy_multiplier, diagnostics, energy_name, xrf_spectra_uri_template, fast_fitting, energy_uri_template, process_uri_template, figuresofmerit, quantification

Outputs:

bliss_scan_uri, xrf_results_uris, output_root_uri, detector_names

FitMultiScanSingleDetector

XRF fit of multiple scans with one detector

Identifier:

ewoksfluo.tasks.fit.tasks.FitMultiScanSingleDetector

Task type:

class

Required inputs:

detector_name, bliss_scan_uris, config, output_root_uri

Optional inputs:

energy_multiplier, diagnostics, energy_name, xrf_spectra_uri_template, fast_fitting, energy_uri_template, process_uri_template, figuresofmerit, quantification

Outputs:

detector_name, bliss_scan_uris, xrf_results_uri, output_root_uri

FitMultiScanMultiDetector

XRF fit of multiple scans with multiple detectors

Identifier:

ewoksfluo.tasks.fit.tasks.FitMultiScanMultiDetector

Task type:

class

Required inputs:

configs, output_root_uri, bliss_scan_uris, detector_names

Optional inputs:

energy_multiplier, diagnostics, energy_name, xrf_spectra_uri_template, fast_fitting, energy_uri_template, process_uri_template, figuresofmerit, quantification

Outputs:

xrf_results_uris, output_root_uri, bliss_scan_uris, detector_names

PickScan

Identifier:

ewoksfluo.tasks.input.pick_scan.PickScan

Task type:

class

Required inputs:

scan_number, filename

Optional inputs:

Outputs:

bliss_scan_uri

PickScans

Identifier:

ewoksfluo.tasks.input.pick_scans.PickScans

Task type:

class

Required inputs:

scan_ranges, filenames

Optional inputs:

exclude_scans

Outputs:

bliss_scan_uris

SpecToBliss

Identifier:

ewoksfluo.tasks.input.spec_to_bliss.SpecToBliss

Task type:

class

Required inputs:

input_filename, output_filename

Optional inputs:

scan_numbers, subscan_numbers

Outputs:

output_filename

NormalizeXrfResults

Normalize multi-scan XRF results with raw scan counters.

Typical normalizers are beam monitors and measurement (live) time.

:param xrf_results_uri: URI to the group containing the XRF results to be corrected. Format: /path/to/file.h5::/path/to/results/group.
:param bliss_scan_uri: URIs to the datasets to normalize the data with. Format: /path/to/file.h5::/path/to/normalizer/dataset.
:param expression: Arithmetic expression to be used for normalization.
:param counter_normalization_template: Arithmetic expression to be used for normalization.
:param counter_name: To be used in :math:`counter_normalization_template`.
:param detector_normalization_template: Arithmetic expression to be used for normalization
:param detector_name: To be used in :math:`detector_normalization_template`.
:param output_root_uri: URI to the HDF5 group where the results must be saved. Format: /path/to/file.h5::/entry
:returns xrf_results_uri: URI to the nexus collection where the results were saved.

Identifier:

ewoksfluo.tasks.normalization.norm_results.NormalizeXrfResults

Task type:

class

Required inputs:

bliss_scan_uri, xrf_results_uri, output_root_uri

Optional inputs:

detector_name, counter_normalization_template, counter_name, normalization_expression, detector_normalization_template

Outputs:

bliss_scan_uri, xrf_results_uri, output_root_uri

NormalizeXrfResultsStack

Normalize single-scan XRF results with raw scan counters.

Typical normalizers are beam monitors and measurement (live) time.

:param xrf_results_uri: URI to the group containing the XRF results to be corrected. Format: /path/to/file.h5::/path/to/results/group.
:param bliss_scan_uris: URIs to the datasets to normalize the data with. Format: [/path/to/file.h5::/path/to/normalizer/dataset].
:param expression: Arithmetic expression to be used for normalization.
:param counter_normalization_template: Arithmetic expression to be used for normalization.
:param counter_name: To be used in :math:`counter_normalization_template`.
:param detector_normalization_template: Arithmetic expression to be used for normalization
:param detector_name: To be used in :math:`detector_normalization_template`.
:param output_root_uri: URI to the HDF5 group where the results must be saved. Format: /path/to/file.h5::/entry
:returns xrf_results_uri: URI to the nexus collection where the results were saved.

Identifier:

ewoksfluo.tasks.normalization.norm_results_stack.NormalizeXrfResultsStack

Task type:

class

Required inputs:

bliss_scan_uris, xrf_results_uri, output_root_uri

Optional inputs:

detector_name, counter_normalization_template, counter_name, normalization_expression, detector_normalization_template

Outputs:

bliss_scan_uris, xrf_results_uri, output_root_uri

ExtractRawCounters

Extract raw single-scan counters and save them like XRF results.

Identifier:

ewoksfluo.tasks.raw_counters.extract_counters.ExtractRawCounters

Task type:

class

Required inputs:

bliss_scan_uri, output_root_uri

Optional inputs:

xrf_results_uri

Outputs:

bliss_scan_uri, xrf_results_uri, output_root_uri

ExtractRawCountersStack

Extract raw multi-scan counters and save them like XRF results.

Identifier:

ewoksfluo.tasks.raw_counters.extract_counters_stack.ExtractRawCountersStack

Task type:

class

Required inputs:

bliss_scan_uris, output_root_uri

Optional inputs:

xrf_results_uri

Outputs:

bliss_scan_uris, xrf_results_uri, output_root_uri

RegridXrfResults

Regrid single-scan XRF results on a regular grid by interpolation or reshaping.

Identifier:

ewoksfluo.tasks.regrid.regrid.RegridXrfResults

Task type:

class

Required inputs:

bliss_scan_uri, xrf_results_uri, output_root_uri

Optional inputs:

interpolate, positioners, positioner_uri_template, flatten

Outputs:

bliss_scan_uri, xrf_results_uri, output_root_uri

RegridXrfResultsStack

Regrid multi-scan XRF results on a regular grid by interpolation or reshaping.

Identifier:

ewoksfluo.tasks.regrid.regrid_stack.RegridXrfResultsStack

Task type:

class

Required inputs:

bliss_scan_uris, xrf_results_uri, output_root_uri

Optional inputs:

interpolate, positioners, stack_positioner, positioner_uri_template

Outputs:

bliss_scan_uris, xrf_results_uri, output_root_uri

SumXrfResults

Add single-scan XRF results of multiple detectors

Identifier:

ewoksfluo.tasks.sum_detectors.sum_results.SumXrfResults

Task type:

class

Required inputs:

bliss_scan_uri, xrf_results_uris, output_root_uri, detector_names

Optional inputs:

detector_normalization_template

Outputs:

bliss_scan_uri, xrf_results_uri, output_root_uri

SumXrfResultsStack

Add multi-scan XRF results of multiple detectors

Identifier:

ewoksfluo.tasks.sum_detectors.sum_results_stack.SumXrfResultsStack

Task type:

class

Required inputs:

xrf_results_uris, output_root_uri, bliss_scan_uris, detector_names

Optional inputs:

detector_normalization_template

Outputs:

bliss_scan_uris, xrf_results_uri, output_root_uri

SumXrfSpectra

Add single-scan XRF spectra from multiple detectors

Identifier:

ewoksfluo.tasks.sum_detectors.sum_spectra.SumXrfSpectra

Task type:

class

Required inputs:

bliss_scan_uri, output_root_uri, detector_names

Optional inputs:

xrf_spectra_uri_template, detector_normalization_template

Outputs:

xrf_spectra_uri_template, bliss_scan_uri, detector_name, output_root_uri