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Class: XASInstrumentData

Raw XAS sweep file (.0001, .0002, ...) produced at acquisition time.

Stores file pointer metadata and key per-sweep scan header fields.

URI: basalt_schema:XASInstrumentData

 classDiagram
    class XASInstrumentData
    click XASInstrumentData href "../XASInstrumentData/"
      InstrumentData <|-- XASInstrumentData
        click InstrumentData href "../InstrumentData/"

      XASInstrumentData : alternative_identifiers

      XASInstrumentData : amplifiers





        XASInstrumentData --> "*" XASAmplifier : amplifiers
        click XASAmplifier href "../XASAmplifier/"



      XASInstrumentData : compression_type

      XASInstrumentData : core_section





        XASInstrumentData --> "0..1" CoreSectionEnum : core_section
        click CoreSectionEnum href "../CoreSectionEnum/"



      XASInstrumentData : data_rows





        XASInstrumentData --> "*" XASDataRow : data_rows
        click XASDataRow href "../XASDataRow/"



      XASInstrumentData : description

      XASInstrumentData : e0_ev

      XASInstrumentData : file_curie

      XASInstrumentData : file_type





        XASInstrumentData --> "0..1" FileTypeEnum : file_type
        click FileTypeEnum href "../FileTypeEnum/"



      XASInstrumentData : filesize

      XASInstrumentData : fy_element

      XASInstrumentData : fy_transition

      XASInstrumentData : id

      XASInstrumentData : integration_times

      XASInstrumentData : ion_chambers





        XASInstrumentData --> "*" XASIonChamber : ion_chambers
        click XASIonChamber href "../XASIonChamber/"



      XASInstrumentData : kwgt

      XASInstrumentData : md5checksum

      XASInstrumentData : motors





        XASInstrumentData --> "*" XASMotorPosition : motors
        click XASMotorPosition href "../XASMotorPosition/"



      XASInstrumentData : n_data_rows

      XASInstrumentData : n_points

      XASInstrumentData : name

      XASInstrumentData : positioner

      XASInstrumentData : produced_by_xas_run





        XASInstrumentData --> "0..1" XASDataGenerationActivity : produced_by_xas_run
        click XASDataGenerationActivity href "../XASDataGenerationActivity/"



      XASInstrumentData : project

      XASInstrumentData : s3_base_url

      XASInstrumentData : s3_bucket

      XASInstrumentData : s3_key

      XASInstrumentData : sample_name

      XASInstrumentData : sampling_set

      XASInstrumentData : scan_bounds

      XASInstrumentData : scan_datetime

      XASInstrumentData : scan_steps

      XASInstrumentData : scan_subtype





        XASInstrumentData --> "0..1" XASScanSubtype : scan_subtype
        click XASScanSubtype href "../XASScanSubtype/"



      XASInstrumentData : scan_time_sec

      XASInstrumentData : signal_columns





        XASInstrumentData --> "*" XASSignalColumn : signal_columns
        click XASSignalColumn href "../XASSignalColumn/"



      XASInstrumentData : software_version

      XASInstrumentData : sweep_number

      XASInstrumentData : x_first

      XASInstrumentData : x_last

Inheritance

Slots

Name Cardinality and Range Description Inheritance
produced_by_xas_run 0..1
XASDataGenerationActivity		 Reference to the XAS data generation activity that produced this raw file direct
sweep_number 0..1
Integer		 1-based sweep index within the measurement session direct
scan_datetime 0..1
Datetime		 Date and time at scan start direct
scan_time_sec 0..1
Integer		 Total scan duration in seconds direct
scan_subtype 0..1
XASScanSubtype		 Scan type, energy (XAS) or motor (alignment) direct
positioner 0..1
String		 Primary positioner name (e direct
e0_ev 0..1
Float		 Absorption edge energy E0 in eV direct
n_points 0..1
Integer		 Number of scan points direct
n_data_rows 0..1
Integer		 Number of data rows in the file direct
x_first 0..1
Float		 First positioner value in the scan (eV or mm) direct
x_last 0..1
Float		 Last positioner value in the scan (eV or mm) direct
scan_bounds 0..1
String		 Scan boundary string as written in file header direct
scan_steps 0..1
String		 Step sizes string as written in file header direct
integration_times 0..1
String		 Integration times string as written in file header direct
kwgt 0..1
Float		 k-weighting exponent used in EXAFS region direct
fy_element 0..1
String		 Target element detected by fluorescence detector (e direct
fy_transition 0..1
String		 X-ray transition detected (e direct
amplifiers *
XASAmplifier		 Amplifier sensitivity entries (one per signal channel) direct
motors *
XASMotorPosition		 Motor positions recorded at scan start direct
signal_columns *
XASSignalColumn		 Detector signal name / EPICS PV pairs direct
data_rows *
XASDataRow		 Per-energy-point representative fluorescence or transmission values direct
ion_chambers *
XASIonChamber		 Ion chamber gas mixture components parsed from user comment direct
file_curie 0..1
String		 an identifier for a file that resolves to the file's accessible location InstrumentData
alternative_identifiers 0..1
String		 InstrumentData
compression_type 0..1
String		 InstrumentData
file_type 0..1
FileTypeEnum		 InstrumentData
software_version 0..1
String		 InstrumentData
name 1
String		 Human-readable name for the entity or activity DataProduct
description 1
String		 Human-readable description for the entity or activity DataProduct
project 0..1
Integer		 Identifier for the user project associated with the entity or activity DataProduct
sampling_set 0..1
Integer		 Sampling set number for grouping related samples collected together DataProduct
core_section 0..1
CoreSectionEnum		 The section of the core DataProduct
sample_name 0..1
String		 The name or label that is present on the shipped sample DataProduct
s3_base_url 0..1
String		 DataProduct
s3_bucket 0..1
String		 DataProduct
s3_key 1
String		 MinIO/S3 object key; required for all data products DataProduct
filesize 0..1
Integer		 Size of the file in bytes DataProduct
md5checksum 0..1
String		 DataProduct
id 1
Uuid		 DataProduct

Usages

used by used in type used
XASLCFDataProcessingActivity uses_xas_raw_data range XASInstrumentData

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self basalt_schema:XASInstrumentData
native basalt_schema:XASInstrumentData

LinkML Source

Direct

name: XASInstrumentData
description: 'Raw XAS sweep file (.0001, .0002, ...) produced at acquisition time.

  Stores file pointer metadata and key per-sweep scan header fields.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: InstrumentData
slots:
- produced_by_xas_run
- sweep_number
- scan_datetime
- scan_time_sec
- scan_subtype
- positioner
- e0_ev
- n_points
- n_data_rows
- x_first
- x_last
- scan_bounds
- scan_steps
- integration_times
- kwgt
- fy_element
- fy_transition
attributes:
  amplifiers:
    name: amplifiers
    description: Amplifier sensitivity entries (one per signal channel)
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - XASInstrumentData
    range: XASAmplifier
    multivalued: true
    inlined: true
    inlined_as_list: true
  motors:
    name: motors
    description: Motor positions recorded at scan start
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - XASInstrumentData
    range: XASMotorPosition
    multivalued: true
    inlined: true
    inlined_as_list: true
  signal_columns:
    name: signal_columns
    description: Detector signal name / EPICS PV pairs
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - XASInstrumentData
    range: XASSignalColumn
    multivalued: true
    inlined: true
    inlined_as_list: true
  data_rows:
    name: data_rows
    description: Per-energy-point representative fluorescence or transmission values
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - XASInstrumentData
    range: XASDataRow
    multivalued: true
    inlined: true
    inlined_as_list: true
  ion_chambers:
    name: ion_chambers
    description: Ion chamber gas mixture components parsed from user comment
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - XASInstrumentData
    range: XASIonChamber
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: XASInstrumentData
description: 'Raw XAS sweep file (.0001, .0002, ...) produced at acquisition time.

  Stores file pointer metadata and key per-sweep scan header fields.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: InstrumentData
attributes:
  amplifiers:
    name: amplifiers
    description: Amplifier sensitivity entries (one per signal channel)
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: amplifiers
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: XASAmplifier
    multivalued: true
    inlined: true
    inlined_as_list: true
  motors:
    name: motors
    description: Motor positions recorded at scan start
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: motors
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: XASMotorPosition
    multivalued: true
    inlined: true
    inlined_as_list: true
  signal_columns:
    name: signal_columns
    description: Detector signal name / EPICS PV pairs
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: signal_columns
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: XASSignalColumn
    multivalued: true
    inlined: true
    inlined_as_list: true
  data_rows:
    name: data_rows
    description: Per-energy-point representative fluorescence or transmission values
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: data_rows
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: XASDataRow
    multivalued: true
    inlined: true
    inlined_as_list: true
  ion_chambers:
    name: ion_chambers
    description: Ion chamber gas mixture components parsed from user comment
    from_schema: https://emsl-computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: ion_chambers
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: XASIonChamber
    multivalued: true
    inlined: true
    inlined_as_list: true
  produced_by_xas_run:
    name: produced_by_xas_run
    description: Reference to the XAS data generation activity that produced this
      raw file
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: produced_by_xas_run
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: XASDataGenerationActivity
  sweep_number:
    name: sweep_number
    description: 1-based sweep index within the measurement session
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sweep_number
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: integer
  scan_datetime:
    name: scan_datetime
    description: Date and time at scan start
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: scan_datetime
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: datetime
  scan_time_sec:
    name: scan_time_sec
    description: Total scan duration in seconds
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: scan_time_sec
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: integer
  scan_subtype:
    name: scan_subtype
    description: Scan type, energy (XAS) or motor (alignment)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: scan_subtype
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: XASScanSubtype
  positioner:
    name: positioner
    description: Primary positioner name (e.g. Mono Energy)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: positioner
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: string
  e0_ev:
    name: e0_ev
    description: Absorption edge energy E0 in eV
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: e0_ev
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: float
  n_points:
    name: n_points
    description: Number of scan points
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: n_points
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: integer
  n_data_rows:
    name: n_data_rows
    description: Number of data rows in the file
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: n_data_rows
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: integer
  x_first:
    name: x_first
    description: First positioner value in the scan (eV or mm)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: x_first
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: float
  x_last:
    name: x_last
    description: Last positioner value in the scan (eV or mm)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: x_last
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: float
  scan_bounds:
    name: scan_bounds
    description: Scan boundary string as written in file header
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: scan_bounds
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: string
  scan_steps:
    name: scan_steps
    description: Step sizes string as written in file header
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: scan_steps
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: string
  integration_times:
    name: integration_times
    description: Integration times string as written in file header
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: integration_times
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: string
  kwgt:
    name: kwgt
    description: k-weighting exponent used in EXAFS region
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: kwgt
    owner: XASInstrumentData
    domain_of:
    - XASInstrumentData
    range: float
  fy_element:
    name: fy_element
    description: Target element detected by fluorescence detector (e.g. Fe)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: fy_element
    owner: XASInstrumentData
    domain_of:
    - XASDataGenerationActivity
    - XASInstrumentData
    range: string
  fy_transition:
    name: fy_transition
    description: X-ray transition detected (e.g. Ka, Kb)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: fy_transition
    owner: XASInstrumentData
    domain_of:
    - XASDataGenerationActivity
    - XASInstrumentData
    range: string
  file_curie:
    name: file_curie
    description: an identifier for a file that resolves to the file's accessible location
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: file_curie
    owner: XASInstrumentData
    domain_of:
    - InstrumentData
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: alternative_identifiers
    owner: XASInstrumentData
    domain_of:
    - InstrumentData
    - OntologyClass
    range: string
  compression_type:
    name: compression_type
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: compression_type
    owner: XASInstrumentData
    domain_of:
    - InstrumentData
    range: string
  file_type:
    name: file_type
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: file_type
    owner: XASInstrumentData
    domain_of:
    - InstrumentData
    range: FileTypeEnum
  software_version:
    name: software_version
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: software_version
    owner: XASInstrumentData
    domain_of:
    - InstrumentData
    - DataProcessingActivity
    range: string
  name:
    name: name
    description: Human-readable name for the entity or activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: name
    owner: XASInstrumentData
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - SampleProcessing
    - Configuration
    - CalibrationStandardRun
    - PurchasedMaterial
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - Study
    - SoftwareControlledTermValue
    range: string
    required: true
  description:
    name: description
    description: Human-readable description for the entity or activity
    title: description
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: description
    owner: XASInstrumentData
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - SampleProcessing
    - Configuration
    - CalibrationStandardRun
    - PurchasedMaterial
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
    required: true
  project:
    name: project
    description: 'Identifier for the user project associated with the entity or activity. '
    title: Project
    todos:
    - should this be an ID? CURIE can use the one NMDC has https://bioregistry.io/reference/emsl.project:60141
      where emsl.project is the CURIE prefix
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    aliases:
    - study
    - study_id
    - project_id
    - proposal
    - proposal_id
    rank: 1000
    alias: project
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - SamplingActivity
    range: integer
  sampling_set:
    name: sampling_set
    description: 'Sampling set number for grouping related samples collected together.

      This is a user-defined sequential integer that can be used to link samples collected

      in the same sampling event or campaign.'
    title: sampling set
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sampling_set
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    - MonetSoilSample
    range: integer
  core_section:
    name: core_section
    description: The section of the core.
    title: core section
    examples:
    - value: TOP
    - value: MID
    - value: BTM
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: core_section
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    - CoreSection
    range: CoreSectionEnum
  sample_name:
    name: sample_name
    description: 'The name or label that is present on the shipped sample. This should

      be a human readable name.'
    title: sample name
    notes:
    - This is typically an alias for the inherited 'name' slot on Sample classes.
      Defined separately for compatibility with source data files using 'sample_name'
      column headers.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    aliases:
    - samp_name
    rank: 1000
    alias: sample_name
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: string
  s3_base_url:
    name: s3_base_url
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_base_url
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    range: string
  s3_bucket:
    name: s3_bucket
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_bucket
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    range: string
  s3_key:
    name: s3_key
    description: MinIO/S3 object key; required for all data products
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_key
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    range: string
    required: true
  filesize:
    name: filesize
    description: Size of the file in bytes
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: filesize
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    range: integer
  md5checksum:
    name: md5checksum
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: md5checksum
    owner: XASInstrumentData
    domain_of:
    - DataProduct
    range: string
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: XASInstrumentData
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MobilePhase
    - MobilePhaseSubstance
    - CalibrationStandardRun
    - PurchasedMaterial
    - MAOMProduct
    - WEOMProduct
    - organism
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - SubstancesUsedLink
    - SampleProcessingSubstance
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true