Skip to content

Class: FieldIlluminationInput

URI: microscopemetrics_schema:FieldIlluminationInput

classDiagram class FieldIlluminationInput MetricsInput <|-- FieldIlluminationInput FieldIlluminationInput : bit_depth FieldIlluminationInput : center_threshold FieldIlluminationInput : corner_fraction FieldIlluminationInput : field_illumination_image FieldIlluminationInput --|> ImageAsNumpy : field_illumination_image FieldIlluminationInput : intensity_map_size FieldIlluminationInput : saturation_threshold FieldIlluminationInput : sigma

Inheritance

Slots

Name Cardinality and Range Description Inheritance
field_illumination_image 1..1
ImageAsNumpy		 Input parameter: homogeneity image provided as a numpy array in the order direct
bit_depth 0..1
Integer		 Detector bit depth direct
saturation_threshold 1..1
Float		 Tolerated saturation threshold direct
center_threshold 1..1
Float		 Input parameter: relative threshold for what is going to be considered as the... direct
corner_fraction 1..1
Float		 Input parameter: the proportion of the image to be considered as corner or ce... direct
sigma 1..1
Float		 Input parameter: the sigma for the smoothing gaussian filter to be applied pr... direct
intensity_map_size 1..1
Integer		 Input parameter: the size of the output intensity map in pixels direct

Usages

used by used in type used
FieldIlluminationDataset input range FieldIlluminationInput

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema

Mappings

Mapping Type Mapped Value
self microscopemetrics_schema:FieldIlluminationInput
native microscopemetrics_schema:FieldIlluminationInput

LinkML Source

Direct

name: FieldIlluminationInput
from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
is_a: MetricsInput
slots:
- field_illumination_image
- bit_depth
- saturation_threshold
- center_threshold
- corner_fraction
- sigma
- intensity_map_size
slot_usage:
  saturation_threshold:
    name: saturation_threshold
    domain_of:
    - ArgolightBInput
    - ArgolightEInput
    - FieldIlluminationInput
    required: true

Induced

name: FieldIlluminationInput
from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
is_a: MetricsInput
slot_usage:
  saturation_threshold:
    name: saturation_threshold
    domain_of:
    - ArgolightBInput
    - ArgolightEInput
    - FieldIlluminationInput
    required: true
attributes:
  field_illumination_image:
    name: field_illumination_image
    description: 'Input parameter: homogeneity image provided as a numpy array in
      the order. While the analysis accepts multiple channels, the T and Z dimensions
      are expected to be 1.'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    alias: field_illumination_image
    owner: FieldIlluminationInput
    domain_of:
    - FieldIlluminationInput
    range: ImageAsNumpy
    required: true
    inlined: true
  bit_depth:
    name: bit_depth
    description: Detector bit depth
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    alias: bit_depth
    owner: FieldIlluminationInput
    domain_of:
    - ArgolightBInput
    - ArgolightEInput
    - FieldIlluminationInput
    range: integer
    minimum_value: 1
    maximum_value: 64
  saturation_threshold:
    name: saturation_threshold
    description: Tolerated saturation threshold. If the amount of saturated pixels
      is above this threshold,  the image is considered as saturated and the analysis
      is not performed.
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: float(0.01)
    alias: saturation_threshold
    owner: FieldIlluminationInput
    domain_of:
    - ArgolightBInput
    - ArgolightEInput
    - FieldIlluminationInput
    range: float
    required: true
    minimum_value: 0
    maximum_value: 1
  center_threshold:
    name: center_threshold
    description: 'Input parameter: relative threshold for what is going to be considered
      as the intensity center of the image'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: float(0.9)
    alias: center_threshold
    owner: FieldIlluminationInput
    domain_of:
    - FieldIlluminationInput
    range: float
    required: true
    minimum_value: 0
    maximum_value: 1
  corner_fraction:
    name: corner_fraction
    description: 'Input parameter: the proportion of the image to be considered as
      corner or center'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: float(0.1)
    alias: corner_fraction
    owner: FieldIlluminationInput
    domain_of:
    - FieldIlluminationInput
    range: float
    required: true
    minimum_value: 0
    maximum_value: 0
  sigma:
    name: sigma
    description: 'Input parameter: the sigma for the smoothing gaussian filter to
      be applied prior to analysis'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: float(2.0)
    alias: sigma
    owner: FieldIlluminationInput
    domain_of:
    - FieldIlluminationInput
    range: float
    required: true
    minimum_value: 0
    maximum_value: 100
  intensity_map_size:
    name: intensity_map_size
    description: 'Input parameter: the size of the output intensity map in pixels'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: int(64)
    alias: intensity_map_size
    owner: FieldIlluminationInput
    domain_of:
    - FieldIlluminationInput
    range: integer
    required: true
    minimum_value: 5
    maximum_value: 512