Class: Processing
Set of parameters describing the data processing
URI: https://w3id.org/osc-em/oscem-schemas-spa/:Processing
erDiagram
Processing {
}
Volumes {
    string volume_type  
    integer vol_number_particles  
    integerList size  
}
Descriptors {
    string descriptor_name  
}
QuantityValue {
    string unit  
    float value  
}
IsosurfaceImages {
    string front_view  
    string side_view  
    string top_view  
}
OrthogonalSlices {
    string orthogonal_slices_X  
    string orthogonal_slices_Y  
    string orthogonal_slices_Z  
}
Classes3D {
    integerList particles_per_3Dclass  
    string images_classes_3D  
}
Volume {
}
Classes2D {
    integerList particles_per_2Dclass  
    string images_classes_2D  
}
Coordinates {
    integer number_particles  
    float particles_per_micrograph  
    integer num_source_micrographs  
    string particles_histogram  
    string micrograph_examples  
}
CTFs {
    float amplitude_contrast  
}
Astigmatism {
    string astigmatism_histogram  
}
Resolution {
    string resolution_histogram  
}
Defocus {
    string defocus_histogram  
    string defocus_micrograph_examples  
}
Micrographs {
    float number_micrographs  
}
Movies {
    string gain_image  
    string dark_image  
}
Processing ||--|o Movies : "movies"
Processing ||--|o Micrographs : "micrographs"
Processing ||--|o CTFs : "ctfs"
Processing ||--|o Coordinates : "coordinates"
Processing ||--|o Classes2D : "classes2D"
Processing ||--|o Classes3D : "classes3D"
Processing ||--}o Volumes : "volumes"
Volumes ||--|o OrthogonalSlices : "orthogonal_slices"
Volumes ||--|o IsosurfaceImages : "isosurface_images"
Volumes ||--|o QuantityValue : "vol_resolution"
Volumes ||--}o Descriptors : "descriptors"
Descriptors ||--|o Any : "descriptor_thing"
Classes3D ||--}o Volume : "volume"
Classes3D ||--|o QuantityValue : "resolution_classes_3D"
Classes3D ||--}o Descriptors : "descriptors"
Volume ||--|o OrthogonalSlices : "orthogonal_slices"
Volume ||--|o IsosurfaceImages : "isosurface_images"
Classes2D ||--|o QuantityValue : "resolution_classes_2D"
Classes2D ||--}o Descriptors : "descriptors"
Coordinates ||--}o Descriptors : "descriptors"
CTFs ||--|o Defocus : "defocus"
CTFs ||--|o Resolution : "resolution"
CTFs ||--|o Astigmatism : "astigmatism"
CTFs ||--}o Descriptors : "descriptors"
Resolution ||--|o QuantityValue : "output_min_resolution"
Resolution ||--|o QuantityValue : "output_max_resolution"
Resolution ||--|o QuantityValue : "output_avg_resolution"
Defocus ||--|o QuantityValue : "output_min_defocus"
Defocus ||--|o QuantityValue : "output_max_defocus"
Defocus ||--|o QuantityValue : "output_avg_defocus"
Micrographs ||--}o Descriptors : "descriptors"
Movies ||--|o QuantityValue : "dose_per_image"
Movies ||--|o QuantityValue : "initial_dose"
Movies ||--}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/osc-em/oscem-schemas-spa
Mappings
| Mapping Type | Mapped Value | 
|---|---|
| self | https://w3id.org/osc-em/oscem-schemas-spa/:Processing | 
| native | https://w3id.org/osc-em/oscem-schemas-spa/:Processing | 
LinkML Source
Direct
name: Processing
description: Set of parameters describing the data processing
from_schema: https://w3id.org/osc-em/oscem-schemas-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/osc-em/oscem-schemas-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/osc-em/oscem-schemas-spa
    rank: 1000
    alias: movies
    owner: Processing
    domain_of:
    - Processing
    range: Movies
    required: false
  micrographs:
    name: micrographs
    description: Micrographs metadata
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: micrographs
    owner: Processing
    domain_of:
    - Processing
    range: Micrographs
    required: false
  ctfs:
    name: ctfs
    description: CTFs metadata
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: ctfs
    owner: Processing
    domain_of:
    - Processing
    range: CTFs
    required: false
  coordinates:
    name: coordinates
    description: Coordinates metadata
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: coordinates
    owner: Processing
    domain_of:
    - Processing
    range: Coordinates
    required: false
  classes2D:
    name: classes2D
    description: Classes 2D metadata
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: classes2D
    owner: Processing
    domain_of:
    - Processing
    range: Classes2D
    required: false
  classes3D:
    name: classes3D
    description: Classes 3D metadata
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: classes3D
    owner: Processing
    domain_of:
    - Processing
    range: Classes3D
    required: false
  volumes:
    name: volumes
    description: Volume metadata
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: volumes
    owner: Processing
    domain_of:
    - Processing
    range: Volumes
    required: false
    multivalued: true