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

Outputs:

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

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

Outputs:

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

MosaicMeshSingleDetector

XRF test data of a mosaic scan with one detector

Identifier:

ewoksfluo.tasks.example_data.tasks.MosaicMeshSingleDetector

Task type:

class

Required inputs:

output_filename

Optional inputs:

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

Outputs:

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

MosaicMeshMultiDetector

XRF test data of a mosaic scan with multiple detectors

Identifier:

ewoksfluo.tasks.example_data.tasks.MosaicMeshMultiDetector

Task type:

class

Required inputs:

output_filename

Optional inputs:

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

Outputs:

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

MeshStackSingleDetector

XRF test data of a stack of identical scans with one detector

Identifier:

ewoksfluo.tasks.example_data.tasks.MeshStackSingleDetector

Task type:

class

Required inputs:

output_filename

Optional inputs:

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

Outputs:

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

MeshStackMultiDetector

XRF test data of a stack of identical scans with multiple detectors

Identifier:

ewoksfluo.tasks.example_data.tasks.MeshStackMultiDetector

Task type:

class

Required inputs:

output_filename

Optional inputs:

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

Outputs:

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

FitSingleScanSingleDetector

XRF fit of one scan with one detector

Identifier:

ewoksfluo.tasks.fit.tasks.FitSingleScanSingleDetector

Task type:

class

Required inputs:

bliss_scan_uri, config, detector_name, output_root_uri

Optional inputs:

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

Outputs:

bliss_scan_uri, detector_name, output_root_uri, xrf_results_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, detector_names, output_root_uri

Optional inputs:

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

Outputs:

bliss_scan_uri, detector_names, output_root_uri, xrf_results_uris

FitStackSingleDetector

XRF fit of a stack of identical scan with one detector

Identifier:

ewoksfluo.tasks.fit.tasks.FitStackSingleDetector

Task type:

class

Required inputs:

bliss_scan_uris, config, detector_name, output_root_uri

Optional inputs:

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

Outputs:

bliss_scan_uris, detector_name, output_root_uri, xrf_results_uri

FitStackMultiDetector

XRF fit of a stack of identical scan with multiple detectors

Identifier:

ewoksfluo.tasks.fit.tasks.FitStackMultiDetector

Task type:

class

Required inputs:

bliss_scan_uris, configs, detector_names, output_root_uri

Optional inputs:

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

Outputs:

bliss_scan_uris, detector_names, output_root_uri, xrf_results_uris

ConcatBliss

Concatenate Bliss scans.

Identifier:

ewoksfluo.tasks.input.concat_bliss.ConcatBliss

Task type:

class

Required inputs:

bliss_scan_uri, bliss_scan_uris

Optional inputs:

axes_units, virtual_axes

Outputs:

bliss_scan_uri

PickScan

Select a single Bliss scan.

Identifier:

ewoksfluo.tasks.input.pick_scan.PickScan

Task type:

class

Required inputs:

filename, scan_number

Optional inputs:

Outputs:

bliss_scan_uri

PickScans

Select a multiple Bliss scan from multiple files.

Identifier:

ewoksfluo.tasks.input.pick_scans.PickScans

Task type:

class

Required inputs:

filenames, scan_ranges

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 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, output_root_uri, xrf_results_uri

Optional inputs:

counter_name, counter_normalization_template, detector_name, detector_normalization_template, normalization_expression

Outputs:

bliss_scan_uri, output_root_uri, xrf_results_uri

NormalizeXrfResultsStack

Normalize XRF stack 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, output_root_uri, xrf_results_uri

Optional inputs:

counter_name, counter_normalization_template, detector_name, detector_normalization_template, normalization_expression

Outputs:

bliss_scan_uris, output_root_uri, xrf_results_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, output_root_uri, xrf_results_uri

ExtractRawCountersStack

Extract raw stack 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, output_root_uri, xrf_results_uri

RegridXrfResults

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

Identifier:

ewoksfluo.tasks.regrid.regrid.RegridXrfResults

Task type:

class

Required inputs:

bliss_scan_uri, output_root_uri, xrf_results_uri

Optional inputs:

axes_units, ignore_positioners, interpolate, positioner_uri_template, positioners, resolution

Outputs:

bliss_scan_uri, output_root_uri, xrf_results_uri

RegridXrfResultsStack

Regrid XRF stack results on a regular grid by interpolation.

Identifier:

ewoksfluo.tasks.regrid.regrid_stack.RegridXrfResultsStack

Task type:

class

Required inputs:

bliss_scan_uris, output_root_uri, xrf_results_uri

Optional inputs:

axes_units, ignore_positioners, interpolate, positioner_uri_template, positioners, resolution, stack_positioner

Outputs:

bliss_scan_uris, output_root_uri, xrf_results_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, detector_names, output_root_uri, xrf_results_uris

Optional inputs:

detector_normalization_template

Outputs:

bliss_scan_uri, output_root_uri, xrf_results_uri

SumXrfResultsStack

Add XRF stack results of multiple detectors

Identifier:

ewoksfluo.tasks.sum_detectors.sum_results_stack.SumXrfResultsStack

Task type:

class

Required inputs:

bliss_scan_uris, detector_names, output_root_uri, xrf_results_uris

Optional inputs:

detector_normalization_template

Outputs:

bliss_scan_uris, output_root_uri, xrf_results_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, detector_names, output_root_uri

Optional inputs:

detector_normalization_template, xrf_spectra_uri_template

Outputs:

bliss_scan_uri, detector_name, output_root_uri, xrf_spectra_uri_template