panalytical: For Panalytical XRD data

Extractors for various exports of Panalytical X-ray diffractograms.

yadg.extractors.panalytical.common module

yadg.extractors.panalytical.common.panalytical_comment(line: str) → dict

Processes a comments from the file header into a dictionary.

Parameters:: line – A line containing the comment.
Returns:: A dictionary containing the processed comment.
Return type:: dict

yadg.extractors.panalytical.common.snake_case(s: str) → str

Converts Sentence case. and camelCase strings to snake_case.

From https://stackoverflow.com/a/1176023

Parameters:: s – The input string to be converted.
Returns:: The corresponding snake_case string.
Return type:: str

yadg.extractors.panalytical.csv module

Handles processing of csv exports of Panalytical XRD files.

Usage

Available since yadg-4.2.

pydantic model dgbowl_schemas.yadg.dataschema_6_0.filetype.Panalytical_csv

Config:

extra: str = forbid

Validators:

field filetype: Literal['panalytical.csv'] [Required]

Schema

xarray.DataTree:
  coords:
    uts:            !!float               # Unix timestamp
    angle:          !!float               # 2θ angle
  data_vars:
    intensity:      (uts, angle)          # Measured intensity

Metadata

With the exception of the comment, the metadata present in the csv file is extracted from the file header without post-processing.

Notes on file structure

These files are split into a [Measurement conditions] and a [Scan points] section. The former stores the metadata and the latter all the datapoints.

Uncertainties

The uncertainties of "angle" are taken from the number of significant figures.

The uncertainties of "intensity" are taken from the number of significant figures.

Code author: Nicolas Vetsch, Peter Kraus

yadg.extractors.panalytical.csv.extract(*, fn: str, encoding: str, timezone: str, **kwargs: dict) → DataTree

yadg.extractors.panalytical.xrdml module

Handles processing of Panalytical XRDML files.

Usage

Available since yadg-4.2.

pydantic model dgbowl_schemas.yadg.dataschema_6_0.filetype.Panalytical_xrdml

Config:

extra: str = forbid

Validators:

field filetype: Literal['panalytical.xrdml'] [Required]

Schema

xarray.DataTree:
  coords:
    uts:            !!float               # Unix timestamp
    angle:          !!float               # 2θ angle
  data_vars:
    intensity:      (uts, angle)          # Measured intensity

Metadata

The following metadata is extracted:

sample: Metadata information about the sample.

wavelength: Measurement wavelength.

comment: A free-form description of the experiment.

incident_beam_path

diffracted_beam_path

counting_time

Note

The returned metadata contain only a subset of the available metadata in the XML file. If something important is missing, please contact us!

Notes on file structure

These are xml-formatted files, which we here parse using the xml.etree library into a Python dict.

The angle returned from this parser is based on a linear interpolation of the start and end point of the scan, and is the \(2\theta\). The values of \(\omega\) are discarded.

Uncertainties

The uncertainties of in "angle" are taken as the step-width of the linearly spaced \(2\theta\) values.

The uncertainties of of "intensity" are currently set to a constant value of 1.0 count as all the supported files seem to produce integer values.

Code author: Nicolas Vetsch, Peter Kraus

yadg.extractors.panalytical.xrdml.etree_to_dict(e: Element) → dict

Recursively converts an ElementTree.Element into a dictionary.

Element attributes are stored into “@”-prefixed attribute keys. Element text is stored into “#text” for all nodes.

From https://stackoverflow.com/a/10076823.

yadg.extractors.panalytical.xrdml.extract(*, fn: str, timezone: str, **kwargs: dict) → DataTree

yadg.extractors.panalytical.xy module

Handles processing of xy exports of Panalytical XRD files. When possible, the xrdml or csv files should be used instead.

Usage

Available since yadg-4.2.

pydantic model dgbowl_schemas.yadg.dataschema_6_0.filetype.Panalytical_xy

Config:

extra: str = forbid

Validators:

field filetype: Literal['panalytical.xy'] [Required]

Schema

xarray.DataTree:
  coords:
    angle:          !!float               # 2θ angle
  data_vars:
    intensity:      (angle)          # Measured intensity

Metadata

No metadata is present in files.

Notes on file structure

These files basically just contain the [Scan points] part of Panalytical csv files. As a consequence, no metadata is recorded, and the format does not have an associated timestamp.

Code author: Nicolas Vetsch, Peter Kraus

yadg.extractors.panalytical.xy.extract(*, fn: str, encoding: str, **kwargs: dict) → DataTree