SAXS/WAXS tasks

How to use

These tasks come from ewokspdf ewoksxrpd. It can be installed with

pip install ewokspdf ewoksxrpd

ℹ️ These tasks are used at the following ESRF beamlines: BM02, ID06, ID09, ID11, ID13, ID16B, ID31

SaveAsciiPattern1D

Save single diffractogram in ASCII format

Identifier:

ewoksxrpd.tasks.ascii.SaveAsciiPattern1D

Task type:

class

Inputs:

filename*

x*

xunits*

y*

header

metadata

yerror

Outputs:

saved

SaveAsciiMultiPattern1D

Identifier:

ewoksxrpd.tasks.ascii.SaveAsciiMultiPattern1D

Task type:

class

Inputs:

filenames*

x_list*

xunits_list*

y_list*

header_list

metadata_list

yerror_list

Outputs:

saved

SaveNexusPatternsAsAscii

Convert azimuthal integration results from NeXus to ASCII files

One ASCII file is created for each integration pattern in nxdata_url. ASCII files are named from the output_filename_template and the pattern index.

If output_archive_filename is provided, all ASCII files are stored in a single ZIP file. In this case, output_filename_template is the template path of ASCII files inside the ZIP file.

Required inputs:

• nxdata_url (str): The url of the NXData group storing the azimuthal integration results

• output_filename_template (str): A string template containing one ‘%d’ field. It is used to generate the filename from the frame number.

Optional inputs:

• header (dict): Information to store in ASCII file header (default: {})

• enabled (bool): True to enable saving as ASCII files, False to skip task (default: True)

• output_archive_filename (str): Filename of the ZIP file containing all ASCII files. If this is None (default) or the empty string, ZIP compression is disabled.

• overwrite (bool): True to allow overwriting existing ASCII/ZIP files (default: False)

• sector_suffix_template (str): A string template containing one ‘%d’ field. Used to generate the string appended at the end of the filename showing the sector number. Defaults to “sector%04d”. Only used if 2D integrated patterns are present.

• counter_urls (list[str]): Urls to datasets with counter values to save in the file header. The dataset should be scalar or have a length equal to the number of integrated frames from the nxdata_url. If this is None (default), no counter value is added to the header.

Outputs:

• filenames (tuple[str]): The names of the created ASCII files or ZIP file

Identifier:

ewoksxrpd.tasks.ascii.SaveNexusPatternsAsAscii

Task type:

class

Inputs:

nxdata_url*

output_filename_template*

counter_urls

enabled

header

lima_url_template

lima_url_template_args

output_archive_filename

overwrite

prioritize_non_native_h5items

retry_period

retry_timeout

sector_suffix_template

Outputs:

filenames

SubtractBackground

Background removal with normalization

.. code:

Icor = I  - B / Bmon * Imon

Identifier:

ewoksxrpd.tasks.background.SubtractBackground

Task type:

class

Inputs:

background*

background_monitor*

image*

monitor*

lima_url_template

lima_url_template_args

prioritize_non_native_h5items

retry_period

retry_timeout

Outputs:

image

monitor

LastLimaImage

Get the last Lima image from Redis

Identifier:

ewoksxrpd.tasks.bliss.LastLimaImage

Task type:

class

Inputs:

db_name*

demo

Outputs:

image

CalibrateSingle

Single distance and energy calibration. Accepts multiple values for max_rings for sequential refinement.

Identifier:

ewoksxrpd.tasks.calibrate.CalibrateSingle

Task type:

class

Inputs:

calibrant*

detector*

energy*

geometry*

image*

detector_config

fixed

lima_url_template

lima_url_template_args

max_rings

prioritize_non_native_h5items

retry_period

retry_timeout

ring_detector

robust

Outputs:

chi2

detector

detector_config

energy

geometry

rings

CalibrateMulti

Single energy, multi distance calibration with 1 distance motor.

The images and positions are the diffraction patterns and the motor positions at which those were measured.

The reference_position is the detector position that corresponds to geometry (positions[0] by default).

The sample_position is the position where sample and detector would theoretically coincide (0 by default).

The output energy and geometry correspond to sample_position.

The units of positions, sample_position and reference_position are defined by positionunits_in_meter (1e-3 by default which means the unit is in millimeter).

The parametrization allow deriving energy+geometry from the detector position.

.. code-block:: python

energy, geometry = parametrization(parameters, position)

Identifier:

ewoksxrpd.tasks.calibrate.CalibrateMulti

Task type:

class

Inputs:

calibrant*

detector*

energy*

geometry*

images*

positions*

detector_config

fixed

lima_url_template

lima_url_template_args

max_rings

positionunits_in_meter

prioritize_non_native_h5items

reference_position

retry_period

retry_timeout

robust

sample_position

Outputs:

chi2

detector

detector_config

energy

geometry

parameters

parametrization

rings

CalculateGeometry

Calculate energy and geometry from pyFAI parametrization

Identifier:

ewoksxrpd.tasks.calibrate.CalculateGeometry

Task type:

class

Inputs:

parameters*

parametrization*

position*

lima_url_template

lima_url_template_args

prioritize_non_native_h5items

retry_period

retry_timeout

Outputs:

energy

geometry

DiagnoseCalibrateSingleResults

Quality of a single-distance pyFAI calibration

Identifier:

ewoksxrpd.tasks.diagnostics.DiagnoseCalibrateSingleResults

Task type:

class

Inputs:

calibrant*

detector*

energy*

geometry*

image*

detector_config

dpi

figsize

filename

fontsize

lima_url_template

lima_url_template_args

pause

prioritize_non_native_h5items

retry_period

retry_timeout

rings

scaling

show

Outputs:

saved

DiagnoseCalibrateMultiResults

Quality of a multi-distance pyFAI calibration

Identifier:

ewoksxrpd.tasks.diagnostics.DiagnoseCalibrateMultiResults

Task type:

class

Inputs:

calibrant*

detector*

images*

parameters*

parametrization*

positions*

detector_config

dpi

figsize

filename

fontsize

lima_url_template

lima_url_template_args

pause

prioritize_non_native_h5items

retry_period

retry_timeout

rings

scaling

show

Outputs:

saved

DiagnoseIntegrate1D

Quality of a pyFAI integration

Identifier:

ewoksxrpd.tasks.diagnostics.DiagnoseIntegrate1D

Task type:

class

Inputs:

x*

xunits*

y*

calibrant

dpi

energy

figsize

filename

fontsize

lima_url_template

lima_url_template_args

pause

prioritize_non_native_h5items

retry_period

retry_timeout

scaling

show

yerror

Outputs:

saved

IntegrateSinglePattern

1D or 2D integration of a single diffraction pattern.

Identifier:

ewoksxrpd.tasks.integrate.IntegrateSinglePattern

Task type:

class

Inputs:

detector*

energy*

geometry*

image*

darkcurrent

demo

detector_config

fixed_integration_options

flatfield

frame_band_index

integration_options

lima_url_template

lima_url_template_args

mask

maximum_persistent_workers

monitor

monitors

prioritize_non_native_h5items

reference

references

retry_period

retry_timeout

Outputs:

azimuthal

azimuthal_units

info

intensity

intensity_error

radial

radial_units

Integrate1D

DEPRECATED. Use IntegrateSinglePattern instead.

Identifier:

ewoksxrpd.tasks.integrate.Integrate1D

Task type:

class

Inputs:

detector*

energy*

geometry*

image*

darkcurrent

demo

detector_config

fixed_integration_options

flatfield

frame_band_index

integration_options

lima_url_template

lima_url_template_args

mask

maximum_persistent_workers

monitor

monitors

prioritize_non_native_h5items

reference

references

retry_period

retry_timeout

Outputs:

azimuthal

azimuthal_units

info

intensity

intensity_error

radial

radial_units

x

xunits

y

yerror

Integrate1DList

1D integration of a list of diffraction patterns.

Identifier:

ewoksxrpd.tasks.integrate.Integrate1DList

Task type:

class

Inputs:

detector*

energy*

geometry*

images*

output_file*

darkcurrent

demo

detector_config

entry_name

fixed_integration_options

flatfield

flush_period

frame_band_index

integration_options

lima_url_template

lima_url_template_args

mask

maximum_persistent_workers

monitors

prioritize_non_native_h5items

reference

retry_period

retry_timeout

Outputs:

output_uri

IntegrateBlissScan

1D or 2D integration of a single detector in a single Bliss scan with saving.

Identifier:

ewoksxrpd.tasks.integrate.IntegrateBlissScan

Task type:

class

Inputs:

detector*

detector_name*

energy*

filename*

geometry*

output_filename*

scan*

counter_names

darkcurrent

demo

detector_config

external_output_filename

fixed_integration_options

flatfield

flush_period

frame_band_index

integration_options

lima_url_template

lima_url_template_args

mask

maximum_persistent_workers

monitor_name

monitors

nxmeasurement_name

nxprocess_as_default

nxprocess_name

overwrite

prioritize_non_native_h5items

reference

references

retry_period

retry_timeout

scan_memory_url

subscan

Outputs:

info

nxdata_url

IntegrateBlissScanWithoutSaving

1D or 2D integration of a single detector in a single Bliss scan without saving.

Identifier:

ewoksxrpd.tasks.integrate.IntegrateBlissScanWithoutSaving

Task type:

class

Inputs:

detector*

detector_name*

energy*

filename*

geometry*

scan*

counter_names

darkcurrent

demo

detector_config

fixed_integration_options

flatfield

frame_band_index

integration_options

lima_url_template

lima_url_template_args

mask

maximum_persistent_workers

monitor_name

monitors

prioritize_non_native_h5items

reference

references

retry_period

retry_timeout

scan_memory_url

subscan

Outputs:

azimuthal

azimuthal_units

info

intensity

intensity_error

radial

radial_units

MultiConfigIntegrateSinglePattern

Multiple integrations of a single diffraction pattern with different configurations

Identifier:

ewoksxrpd.tasks.integrate.MultiConfigIntegrateSinglePattern

Task type:

class

Inputs:

configs*

detector*

energy*

geometry*

image*

darkcurrent

demo

detector_config

fixed_integration_options

flatfield

frame_band_index

integration_options

lima_url_template

lima_url_template_args

mask

maximum_persistent_workers

monitor

monitors

prioritize_non_native_h5items

reference

references

retry_period

retry_timeout

Outputs:

azimuthal

azimuthal_units

info

intensity

intensity_error

radial

radial_units

MultiConfigIntegrate1D

DEPRECATED. Use MultiConfigIntegrateSinglePattern instead.

Identifier:

ewoksxrpd.tasks.integrate.MultiConfigIntegrate1D

Task type:

class

Inputs:

configs*

detector*

energy*

geometry*

image*

darkcurrent

demo

detector_config

fixed_integration_options

flatfield

frame_band_index

integration_options

lima_url_template

lima_url_template_args

mask

maximum_persistent_workers

monitor

monitors

prioritize_non_native_h5items

reference

references

retry_period

retry_timeout

Outputs:

azimuthal

azimuthal_units

info

intensity

intensity_error

radial

radial_units

x

xunits

y

yerror

MaskDetection

The pixels with the same ratio as the monitor ratio within an error margin are considered “good pixels”. The others are masked off.

The error margin monitor_ratio_margin is a fraction of the monitor ratio (0.1 by default).

Masked pixels have value 1. The mask can be smoothed with smooth > 0 to avoid border effects.

.. code:

monitor_ratio = monitor_high / monitor_low
image_ratio = image_high / image_low

bad = abs(image_ratio - monitor_ratio) > monitor_ratio * monitor_ratio_margin

Identifier:

ewoksxrpd.tasks.mask.MaskDetection

Task type:

class

Inputs:

image1*

image2*

monitor1*

monitor2*

lima_url_template

lima_url_template_args

monitor_ratio_margin

prioritize_non_native_h5items

retry_period

retry_timeout

smooth

Outputs:

mask

Integrate2DMultiGeometry

Identifier:

ewoksxrpd.tasks.multi_geometry_integrate.Integrate2DMultiGeometry

Task type:

class

Inputs:

goniometer_file*

images*

positions*

darkcurrent

fixed_integration_options

flatfield

integration_options

lima_url_template

lima_url_template_args

mask

prioritize_non_native_h5items

retry_period

retry_timeout

Outputs:

azimuthal

azimuthal_units

info

intensity

intensity_error

radial

radial_units

SaveNexusPattern1D

Save single diffractogram in HDF5/NeXus format

Identifier:

ewoksxrpd.tasks.nexus.SaveNexusPattern1D

Task type:

class

Inputs:

url*

x*

xunits*

y*

bliss_scan_url

external_url

header

lima_url_template

lima_url_template_args

metadata

nxmeasurement_name

nxprocess_as_default

nxprocess_name

prioritize_non_native_h5items

retry_period

retry_timeout

yerror

Outputs:

saved

SaveNexusIntegrated

Save 1D or 2D integration diffraction patterns in HDF5/NeXus format

Identifier:

ewoksxrpd.tasks.nexus.SaveNexusIntegrated

Task type:

class

Inputs:

intensity*

radial*

radial_units*

url*

azimuthal

azimuthal_units

bliss_scan_url

external_url

info

intensity_error

lima_url_template

lima_url_template_args

metadata

nxmeasurement_name

nxprocess_as_default

nxprocess_name

prioritize_non_native_h5items

retry_period

retry_timeout

Outputs:

saved

SaveNexusMultiPattern1D

Identifier:

ewoksxrpd.tasks.nexus.SaveNexusMultiPattern1D

Task type:

class

Inputs:

url*

x_list*

xunits*

y_list*

bliss_scan_url

external_url

header_list

lima_url_template

lima_url_template_args

metadata

nxmeasurement_name

nxprocess_as_default

nxprocess_name

prioritize_non_native_h5items

retry_period

retry_timeout

yerror_list

Outputs:

saved

PyFaiConfig

Parse pyFAI calibration and integration parameters.

Optional inputs:

• energy (float|None): Energy in KeV (priority 1)

• geometry (dict|None): pyFAI geometry information (priority 1)

• detector (str|None): Name of the detector (priority 1)

• detector_config (dict|None): Configuration of the detector (priority 1)

• mask (str|numpy.ndarray|None): Filename or data of the detector mask (priority 1)

• flatfield (str|numpy.ndarray|None): Filename or data of the detector flat-field (priority 1)

• darkcurrent (str|numpy.ndarray|None): Filename or data of the detector dark-current (priority 1)

• integration_options (dict|None): Extra pyFAI worker or integration parameters (priority 2)

• filenames (Sequence[str]|None): PyFAI poni or json file name (priority 3, last file has highest priority)

• filename (str|None): PyFAI poni or json file name (priority 4)

• calibrant (str|None): Calibrant name

• darkflatmethod (str|None): Dark and flat-field correction method

Outputs:

• energy (float): Energy in KeV

• geometry (dict): pyFAI geometry information

• detector (str): Name of the detector

• detector_config (dict): Configuration of the detector

• mask (str|numpy.ndarray|None): Filename or data of the detector mask

• flatfield (str|numpy.ndarray|None): Filename or data of the detector flat-field

• darkcurrent (str|numpy.ndarray|None): Filename or data of the detector dark-current

• integration_options (dict): Extra pyFAI worker or integration parameters

• calibrant (str|None): Calibrant name

Identifier:

ewoksxrpd.tasks.pyfaiconfig.PyFaiConfig

Task type:

class

Inputs:

calibrant

darkcurrent

darkflatmethod

detector

detector_config

energy

filename

filenames

flatfield

geometry

integration_options

mask

show_merge_warnings

Outputs:

calibrant

darkcurrent

detector

detector_config

energy

flatfield

geometry

integration_options

mask

SavePyFaiConfig

Save inputs as pyFAI calibration and integration configuration file (.json)

The configuration is saved as a JSON file following pyFAI configuration format.

Required inputs:

• output_filename (str): Name of the file where to save pyFAI configuration. Must include the extension

• energy (float): Energy in KeV

• geometry (dict): pyFAI geometry information (poni)

• detector (str): Name of the detector

Optional inputs:

• mask (str): Filename of the mask to used

• detector_config (dict): Configuration of the detector

• integration_options (dict): Extra configuration fields

Outputs:

• filename (str): Saved filename, same as output_filename

Identifier:

ewoksxrpd.tasks.pyfaiconfig.SavePyFaiConfig

Task type:

class

Inputs:

detector*

energy*

geometry*

output_filename*

detector_config

integration_options

mask

Outputs:

filename

SavePyFaiPoniFile

Save inputs as pyFAI PONI file

Required inputs:

• output_filename (str): Name of the file where to save pyFAI PONI. Must include extension.

• energy (float): Energy in KeV

• geometry (dict): pyFAI geometry information (poni)

• detector (str): Name of the detector

Optional inputs:

• detector_config (dict): Configuration of the detector

Outputs:

• filename (str): Saved filename, same as output_filename

Identifier:

ewoksxrpd.tasks.pyfaiconfig.SavePyFaiPoniFile

Task type:

class

Inputs:

detector*

energy*

geometry*

output_filename*

detector_config

Outputs:

filename

SaveImages

Save images with monitor and other metadata

Identifier:

ewoksxrpd.tasks.save_images.SaveImages

Task type:

class

Inputs:

image_uris*

output_dir*

ext

Outputs:

output_paths

SubtractBackgroundPattern

Subtract an integrated pattern from patterns stored in NeXus and saves the result in a new NeXus process group

.. code:

I_pattern_corrected = I_pattern - (I_background_pattern * background_factor)

If errors are available in the background and in the input data, errors are propagated and saved as well.

.. code:

E_I_pattern_corrected = \sqrt{E_I_pattern^2 + (E_I_background_pattern * background_factor)^2}

Identifier:

ewoksxrpd.tasks.subtract_pattern.SubtractBackgroundPattern

Task type:

class

Inputs:

background_nxdata_url*

nxdata_url*

output_nxprocess_url*

background_factor

enabled

external_nxprocess_url

lima_url_template

lima_url_template_args

prioritize_non_native_h5items

retry_period

retry_timeout

Outputs:

nxdata_url

SumBlissScanImages

Sum images of a single camera of a single Bliss scan

Identifier:

ewoksxrpd.tasks.sum.SumBlissScanImages

Task type:

class

Inputs:

detector_name*

filename*

output_filename*

scan*

background_step

lima_url_template

lima_url_template_args

monitor_name

output_process

prioritize_non_native_h5items

retry_period

retry_timeout

scan_memory_url

subscan

Outputs:

monitor

output_uri

SumImages

Sum images of a single camera from a Bliss scan file

For each scan, images are added in blocks of block_size images (one block with all images by default).

The result contains: * the block sums when sum_type=per_scan or sum_type=both * the sum of the block sums when sum_type=all_scans or sum_type=both

Identifier:

ewoksxrpd.tasks.sum.SumImages

Task type:

class

Inputs:

detector_name*

filename*

output_filename*

block_size

end_image

end_scan

monitor_name

output_entry

output_process

start_image

start_scan

sum_type

Outputs:

monitor_uris

output_uris

PdfGetXAverage

Average a list of 1D XRPD patterns from provided output of IntegrateBlissScan

Inputs: - nxdata_url: .h5 path with NXData url - average_every: how many rows to average over; - ‘all’ for all rows, - ‘1’ for no averaging, - or any integer divisor of the total number of rows Outputs: - radial: 1D array - intensity: 1D or 2D array based on average_every - info: dict with radial_units and wavelength

Identifier:

ewokspdf.tasks.average.PdfGetXAverage

Task type:

class

Inputs:

nxdata_url*

average_every

Outputs:

info

intensity

radial

PdfGetXConfig

Parse pdfgetx config parameters

Identifier:

ewokspdf.tasks.config.PdfGetXConfig

Task type:

class

Inputs:

filename

pdfgetx_options_dict

Outputs:

pdfgetx_options

PdfGetXProcessor

Extracts the PDF signal from provided intensities and radial

Inputs: - radial: 1D array - intensity: 1D or 2D array - info: dict with unit, wavelength, and nb_avg - pdfgetx_options: PDFConfig object Outputs: - results: List od PDFGetter object with attributes defined by outputtype. Attributes are tuples with [0] X (radial) and [1] Y (intensity) - info: dict with unit, wavelength, and nb_avg - pdfgetx_options: PDFConfig object

Identifier:

ewokspdf.tasks.processor.PdfGetXProcessor

Task type:

class

Inputs:

info*

intensity*

pdfgetx_options*

radial*

Outputs:

info

pdfgetx_options

results

PdfGetXSaveAscii

Saves the PDF result (iq, sq, fq, gr) in separate ASCII files

Inputs: - filename: Path to the base file used to save data. - results: List of PDFGetter objects with attributes for output types. - info: dict with unit, wavelength, and nb_avg Outputs: - saved: True if files are saved successfully. - filenames: List of saved filenames.

Identifier:

ewokspdf.tasks.save_ascii.PdfGetXSaveAscii

Task type:

class

Inputs:

filename*

info*

results*

Outputs:

filenames

saved

PdfGetXSaveNexus

Saves the PDF results (iq, sq, fq, gr) in a NeXus file

Inputs: - nxdata_url: .h5 path with NXData url in which the data will be saved - results: List of PDFGetter object with attributes defined by outputtype. Attributes are tuples with [0] X (radial) and [1] Y (intensity) Outputs: - pdfgetx_options: pdfgetx.PDFConfig object containing the configuration

Identifier:

ewokspdf.tasks.save_nexus.PdfGetXSaveNexus

Task type:

class

Inputs:

info*

nxdata_url*

pdfgetx_options*

results*

lima_url_template

lima_url_template_args

prioritize_non_native_h5items

retry_period

retry_timeout

subscan

Outputs:

output_url