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Class: Processing

Set of parameters describing the data processing

URI: https://w3id.org/oscem-schemas/latest/spa/Processing

erDiagram Astigmatism { string astigmatism_histogram } CTFs { float amplitude_contrast } Classes2D { string images_classes_2D integerList particles_per_2Dclass } Classes3D { string images_classes_3D integerList particles_per_3Dclass } Coordinates { string micrograph_examples integer num_source_micrographs integer number_particles string particles_histogram float particles_per_micrograph } Defocus { string defocus_histogram string defocus_micrograph_examples } Descriptors { string descriptor_name } IsosurfaceImages { string front_view string side_view string top_view } Micrographs { float number_micrographs } Movies { string dark_image string gain_image } OrthogonalSlices { string orthogonal_slices_X string orthogonal_slices_Y string orthogonal_slices_Z } Processing { } QuantityValue { string unit float value } Resolution { string resolution_histogram } Volume { } Volumes { integerList size integer vol_number_particles string volume_type } CTFs ||--|o Astigmatism : "astigmatism" CTFs ||--|o Defocus : "defocus" CTFs ||--|o Resolution : "resolution" CTFs ||--}o Descriptors : "descriptors" Classes2D ||--|o QuantityValue : "resolution_classes_2D" Classes2D ||--}o Descriptors : "descriptors" Classes3D ||--|o QuantityValue : "resolution_classes_3D" Classes3D ||--}o Descriptors : "descriptors" Classes3D ||--}o Volume : "volume" Coordinates ||--}o Descriptors : "descriptors" Defocus ||--|o QuantityValue : "output_avg_defocus, output_max_defocus, output_min_defocus" Descriptors ||--|o Any : "descriptor_thing" Micrographs ||--}o Descriptors : "descriptors" Movies ||--|o QuantityValue : "dose_per_image, initial_dose" Movies ||--}o Descriptors : "descriptors" Processing ||--|o CTFs : "ctfs" Processing ||--|o Classes2D : "classes2D" Processing ||--|o Classes3D : "classes3D" Processing ||--|o Coordinates : "coordinates" Processing ||--|o Micrographs : "micrographs" Processing ||--|o Movies : "movies" Processing ||--}o Volumes : "volumes" Resolution ||--|o QuantityValue : "output_avg_resolution, output_max_resolution, output_min_resolution" Volume ||--|o IsosurfaceImages : "isosurface_images" Volume ||--|o OrthogonalSlices : "orthogonal_slices" Volumes ||--|o IsosurfaceImages : "isosurface_images" Volumes ||--|o OrthogonalSlices : "orthogonal_slices" Volumes ||--|o QuantityValue : "vol_resolution" Volumes ||--}o Descriptors : "descriptors"

Slots

Name Cardinality and Range Description Inheritance
movies 0..1
Movies		 Movies metadata direct
micrographs 0..1
Micrographs		 Micrographs metadata direct
ctfs 0..1
CTFs		 CTFs metadata direct
coordinates 0..1
Coordinates		 Coordinates metadata direct
classes2D 0..1
Classes2D		 Classes 2D metadata direct
classes3D 0..1
Classes3D		 Classes 3D metadata direct
volumes *
Volumes		 Volume metadata direct

Usages

used by used in type used
EMDatasetSpa processing range Processing

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/oscem-schemas/latest/spa

Mappings

Mapping Type Mapped Value
self https://w3id.org/oscem-schemas/latest/spa/Processing
native https://w3id.org/oscem-schemas/latest/spa/Processing

LinkML Source

Direct

name: Processing
description: Set of parameters describing the data processing
from_schema: https://w3id.org/oscem-schemas/latest/spa
slots:
- movies
- micrographs
- ctfs
- coordinates
- classes2D
- classes3D
- volumes
slot_usage:
  movies:
    name: movies
    required: false
  micrographs:
    name: micrographs
    required: false
  ctfs:
    name: ctfs
    required: false
  coordinates:
    name: coordinates
    required: false
  classes2D:
    name: classes2D
    required: false
  classes3D:
    name: classes3D
    required: false
  volumes:
    name: volumes
    required: false

Induced

name: Processing
description: Set of parameters describing the data processing
from_schema: https://w3id.org/oscem-schemas/latest/spa
slot_usage:
  movies:
    name: movies
    required: false
  micrographs:
    name: micrographs
    required: false
  ctfs:
    name: ctfs
    required: false
  coordinates:
    name: coordinates
    required: false
  classes2D:
    name: classes2D
    required: false
  classes3D:
    name: classes3D
    required: false
  volumes:
    name: volumes
    required: false
attributes:
  movies:
    name: movies
    description: Movies metadata
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Processing
    domain_of:
    - Processing
    range: Movies
    required: false
  micrographs:
    name: micrographs
    description: Micrographs metadata
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Processing
    domain_of:
    - Processing
    range: Micrographs
    required: false
  ctfs:
    name: ctfs
    description: CTFs metadata
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Processing
    domain_of:
    - Processing
    range: CTFs
    required: false
  coordinates:
    name: coordinates
    description: Coordinates metadata
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Processing
    domain_of:
    - Processing
    range: Coordinates
    required: false
  classes2D:
    name: classes2D
    description: Classes 2D metadata
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Processing
    domain_of:
    - Processing
    range: Classes2D
    required: false
  classes3D:
    name: classes3D
    description: Classes 3D metadata
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Processing
    domain_of:
    - Processing
    range: Classes3D
    required: false
  volumes:
    name: volumes
    description: Volume metadata
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Processing
    domain_of:
    - Processing
    range: Volumes
    required: false
    multivalued: true