Class: XASLCFDataProcessingActivity

Athena or Larch Linear Combination Fitting (LCF) processing activity for

XAS data. One instance represents a single .lcf fit run.

URI: basalt_schema:XASLCFDataProcessingActivity

 classDiagram
    class XASLCFDataProcessingActivity
    click XASLCFDataProcessingActivity href "../XASLCFDataProcessingActivity/"
      DataProcessingActivity <|-- XASLCFDataProcessingActivity
        click DataProcessingActivity href "../DataProcessingActivity/"

      XASLCFDataProcessingActivity : analysis_code

      XASLCFDataProcessingActivity : chi_square

      XASLCFDataProcessingActivity : description

      XASLCFDataProcessingActivity : e0_shift_used

      XASLCFDataProcessingActivity : ended_at_time

      XASLCFDataProcessingActivity : execution_resource





        XASLCFDataProcessingActivity --> "0..1" ExecutionResourceEnum : execution_resource
        click ExecutionResourceEnum href "../ExecutionResourceEnum/"



      XASLCFDataProcessingActivity : fit_label

      XASLCFDataProcessingActivity : fit_range_max

      XASLCFDataProcessingActivity : fit_range_min

      XASLCFDataProcessingActivity : fit_range_unit

      XASLCFDataProcessingActivity : id

      XASLCFDataProcessingActivity : lcf_type





        XASLCFDataProcessingActivity --> "0..1" XASLCFType : lcf_type
        click XASLCFType href "../XASLCFType/"



      XASLCFDataProcessingActivity : n_data_points

      XASLCFDataProcessingActivity : n_standards

      XASLCFDataProcessingActivity : n_variables

      XASLCFDataProcessingActivity : noise_added

      XASLCFDataProcessingActivity : parent_workflow_id





        XASLCFDataProcessingActivity --> "0..1" DataProcessingActivity : parent_workflow_id
        click DataProcessingActivity href "../DataProcessingActivity/"



      XASLCFDataProcessingActivity : r_factor

      XASLCFDataProcessingActivity : reduced_chi_square

      XASLCFDataProcessingActivity : run_label

      XASLCFDataProcessingActivity : sample_nor_file

      XASLCFDataProcessingActivity : software_poc

      XASLCFDataProcessingActivity : software_url

      XASLCFDataProcessingActivity : software_version

      XASLCFDataProcessingActivity : started_at_time

      XASLCFDataProcessingActivity : uses_xas_raw_data





        XASLCFDataProcessingActivity --> "*" XASInstrumentData : uses_xas_raw_data
        click XASInstrumentData href "../XASInstrumentData/"



      XASLCFDataProcessingActivity : weights_bounded

      XASLCFDataProcessingActivity : weights_sum

      XASLCFDataProcessingActivity : weights_sum_to_1

      XASLCFDataProcessingActivity : workflow_steps

      XASLCFDataProcessingActivity : xas_filename

Inheritance

DataProcessingActivity
- XASLCFDataProcessingActivity

Slots

Name	Cardinality and Range	Description	Inheritance
uses_xas_raw_data	* XASInstrumentData	Raw XAS instrument data inputs consumed by this LCF processing activity	direct
xas_filename	0..1 String	Measurement filename stem linking LCF results to source XAS data	direct
lcf_type	0..1 XASLCFType	LCF analysis subtype, XANES or EXAFS	direct
run_label	0..1 String	Analysis run variant label extracted from filename	direct
fit_label	0..1 String	Iteration label for EXAFS fits extracted from filename	direct
analysis_code	0..1 String	Athena or Larch internal code from the	direct
sample_nor_file	0..1 String	Normalised spectrum filename recorded in the LCF header	direct
fit_range_min	0..1 Float	Lower bound of fit range (eV for XANES, A^-1 for EXAFS)	direct
fit_range_max	0..1 Float	Upper bound of fit range (eV for XANES, A^-1 for EXAFS)	direct
fit_range_unit	0..1 String	Unit of fit range (eV for XANES, A^-1 for EXAFS)	direct
n_data_points	0..1 Integer	Number of data points included in the fit	direct
n_variables	0..1 Integer	Number of free variables in the fit	direct
n_standards	0..1 Integer	Number of reference standards used in the linear combination	direct
weights_sum_to_1	0..1 String	Whether component weights were constrained to sum to 1	direct
weights_bounded	0..1 String	Whether component weights were bounded between 0 and 1	direct
e0_shift_used	0..1 String	Whether an overall E0 energy shift was applied	direct
noise_added	0..1 Float	Statistical noise added to data before fitting (0 if none)	direct
r_factor	0..1 Float	R-factor goodness-of-fit statistic	direct
chi_square	0..1 Float	Chi-square statistic from the LCF fit	direct
reduced_chi_square	0..1 Float	Reduced chi-square statistic	direct
weights_sum	0..1 Float	Actual sum of fitted component weights	direct
parent_workflow_id	0..1 DataProcessingActivity	Self-referential FK to the preceding DataProcessingActivity in a chain	DataProcessingActivity
workflow_steps	0..1 String	Per-run workflow parameters	DataProcessingActivity
description	0..1 String	A human-readable description of the data analysis workflow	DataProcessingActivity
id	1 Uuid		DataProcessingActivity
started_at_time	1 Datetime		DataProcessingActivity
ended_at_time	0..1 Datetime		DataProcessingActivity
software_url	0..1 String		DataProcessingActivity
software_version	0..1 String		DataProcessingActivity
software_poc	0..1 String		DataProcessingActivity
execution_resource	0..1 ExecutionResourceEnum		DataProcessingActivity

Usages

used by	used in	type	used
XASLCFProduct	results_from_xas_processing	range	XASLCFDataProcessingActivity

Identifier and Mapping Information

Schema Source

from schema: https://emsl-computing.github.io/BASALT-Schema

Mappings

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

LinkML Source

Direct

name: XASLCFDataProcessingActivity
description: 'Athena or Larch Linear Combination Fitting (LCF) processing activity
  for

  XAS data. One instance represents a single .lcf fit run.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: DataProcessingActivity
slots:
- uses_xas_raw_data
- xas_filename
- lcf_type
- run_label
- fit_label
- analysis_code
- sample_nor_file
- fit_range_min
- fit_range_max
- fit_range_unit
- n_data_points
- n_variables
- n_standards
- weights_sum_to_1
- weights_bounded
- e0_shift_used
- noise_added
- r_factor
- chi_square
- reduced_chi_square
- weights_sum

Induced

name: XASLCFDataProcessingActivity
description: 'Athena or Larch Linear Combination Fitting (LCF) processing activity
  for

  XAS data. One instance represents a single .lcf fit run.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: DataProcessingActivity
attributes:
  uses_xas_raw_data:
    name: uses_xas_raw_data
    description: Raw XAS instrument data inputs consumed by this LCF processing activity
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: uses_xas_raw_data
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    range: XASInstrumentData
    multivalued: true
    inlined: false
  xas_filename:
    name: xas_filename
    description: Measurement filename stem linking LCF results to source XAS data
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: xas_filename
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  lcf_type:
    name: lcf_type
    description: LCF analysis subtype, XANES or EXAFS
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: lcf_type
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: XASLCFType
  run_label:
    name: run_label
    description: Analysis run variant label extracted from filename
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: run_label
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  fit_label:
    name: fit_label
    description: Iteration label for EXAFS fits extracted from filename
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: fit_label
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  analysis_code:
    name: analysis_code
    description: Athena or Larch internal code from the .lcf filename
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: analysis_code
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  sample_nor_file:
    name: sample_nor_file
    description: Normalised spectrum filename recorded in the LCF header
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sample_nor_file
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  fit_range_min:
    name: fit_range_min
    description: Lower bound of fit range (eV for XANES, A^-1 for EXAFS)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: fit_range_min
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: float
  fit_range_max:
    name: fit_range_max
    description: Upper bound of fit range (eV for XANES, A^-1 for EXAFS)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: fit_range_max
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: float
  fit_range_unit:
    name: fit_range_unit
    description: Unit of fit range (eV for XANES, A^-1 for EXAFS)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: fit_range_unit
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  n_data_points:
    name: n_data_points
    description: Number of data points included in the fit
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: n_data_points
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: integer
  n_variables:
    name: n_variables
    description: Number of free variables in the fit
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: n_variables
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: integer
  n_standards:
    name: n_standards
    description: Number of reference standards used in the linear combination
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: n_standards
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: integer
  weights_sum_to_1:
    name: weights_sum_to_1
    description: Whether component weights were constrained to sum to 1.0
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: weights_sum_to_1
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  weights_bounded:
    name: weights_bounded
    description: Whether component weights were bounded between 0 and 1
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: weights_bounded
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  e0_shift_used:
    name: e0_shift_used
    description: Whether an overall E0 energy shift was applied
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: e0_shift_used
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: string
  noise_added:
    name: noise_added
    description: Statistical noise added to data before fitting (0 if none)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: noise_added
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: float
  r_factor:
    name: r_factor
    description: R-factor goodness-of-fit statistic
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: r_factor
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: float
  chi_square:
    name: chi_square
    description: Chi-square statistic from the LCF fit
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: chi_square
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: float
  reduced_chi_square:
    name: reduced_chi_square
    description: Reduced chi-square statistic
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: reduced_chi_square
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: float
  weights_sum:
    name: weights_sum
    description: Actual sum of fitted component weights
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: weights_sum
    owner: XASLCFDataProcessingActivity
    domain_of:
    - XASLCFDataProcessingActivity
    - XASLCFProduct
    range: float
  parent_workflow_id:
    name: parent_workflow_id
    description: "Self-referential FK to the preceding DataProcessingActivity in a\
      \ chain.\nNULL -> first (or standalone) step.\nNon-null -> this execution directly\
      \ follows parent_workflow_id.\nEnables single-hop chaining queries; full traversal\
      \ via linkage_cache.\n\nDDL: ALTER TABLE \"DataProcessingActivity\"\n      \
      \ ADD COLUMN parent_workflow_id UUID\n       REFERENCES \"DataProcessingActivity\"\
      (id);"
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: parent_workflow_id
    owner: XASLCFDataProcessingActivity
    domain_of:
    - DataProcessingActivity
    range: DataProcessingActivity
    required: false
  workflow_steps:
    name: workflow_steps
    description: 'Per-run workflow parameters. Previously annotated TODO JSONB in
      schema.

      Direction: structured key-value pairs keyed by workflow type.

      Schema for allowed keys TBD per workflow type before full implementation.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: workflow_steps
    owner: XASLCFDataProcessingActivity
    domain_of:
    - DataProcessingActivity
    range: string
    required: false
  description:
    name: description
    description: A human-readable description of the data analysis workflow. May  include
      details such as the purpose, output, and/or main steps of  the workflow.
    title: description
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: description
    owner: XASLCFDataProcessingActivity
    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
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: XASLCFDataProcessingActivity
    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
  started_at_time:
    name: started_at_time
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    alias: started_at_time
    owner: XASLCFDataProcessingActivity
    domain_of:
    - Activity
    - DataProcessingActivity
    range: datetime
    required: true
  ended_at_time:
    name: ended_at_time
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    alias: ended_at_time
    owner: XASLCFDataProcessingActivity
    domain_of:
    - Activity
    - DataProcessingActivity
    range: datetime
  software_url:
    name: software_url
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: software_url
    owner: XASLCFDataProcessingActivity
    domain_of:
    - DataProcessingActivity
    range: string
  software_version:
    name: software_version
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    alias: software_version
    owner: XASLCFDataProcessingActivity
    domain_of:
    - InstrumentData
    - DataProcessingActivity
    range: string
  software_poc:
    name: software_poc
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: software_poc
    owner: XASLCFDataProcessingActivity
    domain_of:
    - DataProcessingActivity
    range: string
  execution_resource:
    name: execution_resource
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: execution_resource
    owner: XASLCFDataProcessingActivity
    domain_of:
    - DataProcessingActivity
    range: ExecutionResourceEnum