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