`CHAP.edd.reader`¶

Module Contents¶

Classes¶

`EddMapReader`	Reader for taking an EDD-style .par file and returning a `MapConfig` representing one of the datasets in the file. Independent dimensions are determined automatically, and a specific set of items to use for extra scalar datasets to include are hard-coded in. The raw data is read if detector_names are specified.
`EddMPIMapReader`	Reader for taking an EDD-style .par file and returning a representing one of the datasets in the file as a NeXus NXentry object. Independent dimensions are determined automatically, and a specific set of items to use for extra scalar datasets to include are hard-coded in.
`ScanToMapReader`	Reader for turning a single SPEC scan into a MapConfig.
`SetupNXdataReader`	Reader for converting the SPEC input .txt file for EDD dataset collection to an approporiate input argument for `CHAP.common.SetupNXdataProcessor`.
`UpdateNXdataReader`	Companion to `edd.SetupNXdataReader` and `common.UpdateNXDataProcessor`. Constructs a list of data points to pass as pipeline data to `common.UpdateNXDataProcessor` so that an `NXdata` constructed by `edd.SetupNXdataReader` and `common.SetupNXdataProcessor` can be updated live as individual scans in an EDD dataset are completed.
`NXdataSliceReader`	Reader for returning a sliced verison of an `NXdata` (which represents a full EDD dataset) that contains data from just a single SPEC scan.

API¶

class CHAP.edd.reader.EddMapReader¶

Bases: CHAP.reader.Reader

Reader for taking an EDD-style .par file and returning a MapConfig representing one of the datasets in the file. Independent dimensions are determined automatically, and a specific set of items to use for extra scalar datasets to include are hard-coded in. The raw data is read if detector_names are specified.

Initialization

Constructor of PipelineItem class

read(parfile, dataset_id, detector_names=None)¶

Return a validated MapConfig object representing an EDD dataset.

Parameters:

parfile (str) – Name of the EDD-style .par file containing the dataset.
dataset_id (int) – Number of the dataset in the .par file to return as a map.
detector_names (list[str], optional) – Detector prefixes for the raw data.

Returns:

Map configuration packaged with the appropriate value for ‘schema’.

Return type:

PipelineData

class CHAP.edd.reader.EddMPIMapReader¶

Bases: CHAP.reader.Reader

Reader for taking an EDD-style .par file and returning a representing one of the datasets in the file as a NeXus NXentry object. Independent dimensions are determined automatically, and a specific set of items to use for extra scalar datasets to include are hard-coded in.

Initialization

Constructor of PipelineItem class

read(parfile, dataset_id, detector_names)¶

Return a NeXus NXentry object after validating the MapConfig object representing an EDD dataset.

Parameters:

parfile (str) – Name of the EDD-style .par file containing the dataset.
dataset_id (int) – Number of the dataset in the .par file to return as a map.
detector_names (list[str]) – Detector prefixes for the raw data.

Returns:

The EDD map including the raw data packaged with the appropriate value for ‘schema’.

Return type:

PipelineData

class CHAP.edd.reader.ScanToMapReader¶

Bases: CHAP.reader.Reader

Reader for turning a single SPEC scan into a MapConfig.

Initialization

Constructor of PipelineItem class

read(spec_file, scan_number)¶

Return a dictionary representing a valid map configuration consisting of the single SPEC scan specified.

Parameters:

spec_file (str) – Name of the SPEC file.
scan_number (int) – Number of the SPEC scan.

Returns:

Map configuration dictionary

Return type:

dict

class CHAP.edd.reader.SetupNXdataReader¶

Bases: CHAP.reader.Reader

Reader for converting the SPEC input .txt file for EDD dataset collection to an approporiate input argument for CHAP.common.SetupNXdataProcessor.

Example of use in a Pipeline configuration:

config:
  inputdir: /rawdata/samplename
  outputdir: /reduceddata/samplename
pipeline:
  - edd.SetupNXdataReader:
      filename: SpecInput.txt
      dataset_id: 1
  - common.SetupNXdataProcessor:
      nxname: samplename_dataset_1
  - common.NexusWriter:
      filename: data.nxs

Initialization

Constructor of PipelineItem class

read(filename, dataset_id)¶

Return a dictionary containing the coords, signals, and attrs arguments appropriate for use with CHAP.common.SetupNXdataProcessor.process to set up an initial NXdata object representing a complete and organized structured EDD dataset.

Parameters:

filename (str) – Name of the input .txt file provided to SPEC for EDD dataset collection.
dataset_id (int) – Number of the dataset in the .txt file to return CHAP.common.SetupNXdataProcessor.process arguments for.

Returns:

The dataset’s coordinate names, values, attributes, and signal names, shapes, and attributes.

Return type:

dict

class CHAP.edd.reader.UpdateNXdataReader¶

Bases: CHAP.reader.Reader

Companion to edd.SetupNXdataReader and common.UpdateNXDataProcessor. Constructs a list of data points to pass as pipeline data to common.UpdateNXDataProcessor so that an NXdata constructed by edd.SetupNXdataReader and common.SetupNXdataProcessor can be updated live as individual scans in an EDD dataset are completed.

Example of use in a Pipeline configuration:

config:
  inputdir: /rawdata/samplename
pipeline:
  - edd.UpdateNXdataReader:
      spec_file: spec.log
      scan_number: 1
  - common.SetupNXdataProcessor:
      nxfilename: /reduceddata/samplename/data.nxs
      nxdata_path: /entry/samplename_dataset_1

Initialization

Constructor of PipelineItem class

read(spec_file, scan_number, inputdir='.')¶

Return a list of data points containing raw data values for a single EDD spec scan. The returned values can be passed along to common.UpdateNXdataProcessor to fill in an existing NXdata set up with common.SetupNXdataProcessor.

Parameters:

spec_file (str) – Name of the spec file containing the spec scan (a relative or absolute path).
scan_number (int) – Number of the spec scan.
inputdir (str) – Parent directory of spec_file, used only if spec_file is a relative path. Will be ignored if spec_file is an absolute path. Defaults to '.'.

Returs:

List of data points appropriate for input to common.UpdateNXdataProcessor.

Return type:

list[dict[str, object]]

class CHAP.edd.reader.NXdataSliceReader¶

Bases: CHAP.reader.Reader

Reader for returning a sliced verison of an NXdata (which represents a full EDD dataset) that contains data from just a single SPEC scan.

Example of use in a Pipeline configuration:

config:
  inputdir: /rawdata/samplename
  outputdir: /reduceddata/samplename
pipeline:
  - edd.NXdataSliceReader:
      filename: /reduceddata/samplename/data.nxs
      nxpath: /path/to/nxdata
      spec_file: spec.log
      scan_number: 1
  - common.NexusWriter:
      filename: scan_1.nxs

Initialization

Constructor of PipelineItem class

read(filename, nxpath, spec_file, scan_number, inputdir='.')¶

Return a “slice” of an EDD dataset’s NXdata that represents just the data from one scan in the dataset.

Parameters:

filename (str) – Name of the NeXus file in which the existing full EDD dataset’s NXdata resides.
nxpath (str) – Path to the existing full EDD dataset’s NXdata group in filename.
spec_file (str) – Name of the spec file containing whose data will be the only contents of the returned NXdata.
scan_number (int) – Number of the spec scan whose data will be the only contents of the returned NXdata.
inputdir (str, optional) – Directory containing filename and/or spec_file, if either one / both of them are not absolute paths. Defaults to '.'.

Returns:

An NXdata similar to the one at nxpath in filename, but containing only the data collected by the specified spec scan.

Return type:

nexusformat.nexus.NXdata

`CHAP.edd.reader`¶

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API¶

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Module Contents¶

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`CHAP.edd.reader`¶