xrdtrace: X-ray diffractogram trace file parser

This module handles the reading and processing of X-ray diffraction data.

xrdtrace loads X-ray diffraction data, determines reasonable uncertainties of the signal intensity (y-axis), and explicitly populates the angle axis (\(2\theta\)), if necessary.

Usage

Available since yadg-4.0. The parser supports the following parameters:

pydantic model dgbowl_schemas.yadg.dataschema_4_2.step.XRDTrace.Params

Show JSON schema
{
   "title": "Params",
   "type": "object",
   "properties": {
      "filetype": {
         "title": "Filetype",
         "default": "panalytical.csv",
         "enum": [
            "panalytical.xy",
            "panalytical.csv",
            "panalytical.xrdml"
         ],
         "type": "string"
      }
   },
   "additionalProperties": false
}

field filetype: Literal['panalytical.xy', 'panalytical.csv', 'panalytical.xrdml'] = 'panalytical.csv'

Formats

The filetypes currently supported by the parser are:

Provides

The raw data is stored, for each timestep, using the following format:

- raw:
    traces:
      "{{ trace_number }}":   # number of the trace
        angle:
          {n: [!!float, ...], s: [!!float, ...], u: "deg"}
        intensity:
          {n: [!!float, ...], s: [!!float, ...], u: "counts"}

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

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

Submodules

yadg.parsers.xrdtrace.common.panalytical_comment(line)

Processes a comments from the file header into a dictionary.

Parameters

line (str) – A line containing the comment.

Returns

A dictionary containing the processed comment.

Return type

dict

yadg.parsers.xrdtrace.common.snake_case(s)

Converts Sentence case. and camelCase strings to snake_case.

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

Parameters

s (str) – The input string to be converted.

Returns

The corresponding snake_case string.

Return type

str

yadg.parsers.xrdtrace.main.process(fn, encoding='utf-8', timezone='UTC', parameters=None)

Unified X-ray diffractogram data parser.

This parser processes X-ray diffractogram scans in intensity(angle) format.

Parameters

  • fn (str) – The file containing the trace(s) to parse.

  • encoding (str) – Encoding of fn, by default “utf-8”.

  • timezone (str) – A string description of the timezone. Default is “UTC”.

  • parameters (Optional[BaseModel]) – Parameters for XRDTrace.

Returns

(data, metadata, fulldate) – Tuple containing the timesteps, metadata, and full date tag. The currently implemented parsers all return full date.

Return type

tuple[list, dict, bool]

panalyticalcsv: Processing of PANalytical XRD csv files

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.

Warning

This parser is fairly new and untested. As a result, the returned metadata contain all the entries in the [Measurement conditions] section, without any additional filtering.

Structure of Parsed Timesteps

- fn:  !!str
- uts: !!float
- raw:
    traces:
      "{{ trace_number }}":  # Number of the trace.
        angle:               # Diffraction angle.
          {n: [!!float, ...], s: [!!float, ...], u: "deg"}
        intensity:           # Detector counts.
          {n: [!!float, ...], s: [!!float, ...], u: "counts"}

Code author: Nicolas Vetsch

yadg.parsers.xrdtrace.panalyticalcsv.process(fn, encoding='utf-8', timezone='UTC')

Processes a PANalytical XRD csv file. All information contained in the header of the csv file is stored in the metadata.

Parameters

  • fn (str) – The file containing the trace(s) to parse.

  • encoding (str) – Encoding of fn, by default “utf-8”.

  • timezone (str) – A string description of the timezone. Default is “UTC”.

Returns

(data, meta) – (data, metadata, fulldate) : tuple[list, dict, bool] Tuple containing the timesteps, metadata, and the full date tag. For .csv files tag is specified.

Return type

tuple[list, dict]

panalyticalxrdml: Processing of PANalytical XRD xml files

File Structure

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

Note

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.

Warning

This parser is fairly new and untested. As a result, the returned metadata contain only a subset of the available metadata in the XML file. If something important is missing, please contact us!

Structure of Parsed Timesteps

- fn:  !!str
- uts: !!float
- raw:
    traces:
      "{{ trace_number }}":  # Number of the trace.
        angle:               # Diffraction angle.
          {n: [!!float, ...], s: [!!float, ...], u: "deg"}
        intensity:           # Detector counts.
          {n: [!!float, ...], s: [!!float, ...], u: "counts"}

Code author: Nicolas Vetsch, Peter Kraus

yadg.parsers.xrdtrace.panalyticalxrdml.etree_to_dict(e)

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.

Parameters

e (Element) – The ElementTree root Element.

Returns

ElementTree parsed into a dictionary.

Return type

dict

yadg.parsers.xrdtrace.panalyticalxrdml.process(fn, encoding='utf-8', timezone='UTC')

Processes a PANalytical xrdml file.

Parameters

  • fn (str) – The file containing the trace(s) to parse.

  • encoding (str) – Encoding of fn, by default “utf-8”.

  • timezone (str) – A string description of the timezone. Default is “UTC”.

Returns

(data, metadata, fulldate) – Tuple containing the timesteps, metadata, and the full date tag. For .xrdml tag is always specified

Return type

tuple[list, dict, bool]

panalyticalxy: Processing of PANalytical XRD xy files

File Structure

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

Structure of Parsed Timesteps

- fn:  !!str
- uts: !!float
- raw:
    traces:
      "{{ trace_number }}":  # Number of the trace.
        angle:               # Diffraction angle.
          {n: [!!float, ...], s: [!!float, ...], u: "deg"}
        intensity:           # Detector counts.
          {n: [!!float, ...], s: [!!float, ...], u: "counts"}

Code author: Nicolas Vetsch

yadg.parsers.xrdtrace.panalyticalxy.process(fn, encoding='utf-8', timezone='UTC')

Processes a PANalytical XRD xy file.

Parameters

  • fn (str) – The file containing the trace(s) to parse.

  • encoding (str) – Encoding of fn, by default “utf-8”.

  • timezone (str) – A string description of the timezone. Default is “UTC”.

Returns

(data, metadata, fulldate) – Tuple containing the timesteps, metadata, and the full date tag. For .xy files tag is never specified.

Return type

tuple[list, dict, bool]