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Migration guide

v0.4.0 was a major release and a complete rewrite of the code-generation part of the library: ome-types is now generated using xsdata.

Much effort has been made to keep all existing APIs working, but you may encounter a number of deprecation warnings. This guide will help you migrate your code to the new version.

General Changes

👀 Read these first

  • All IDs are no longer subclasses of LSID, but are now simply str type with a pydantic regex validator.

  • Many plural names have been updated, such as annotation_ref -> annotation_refs. The old names still work in __init__ methods and as attributes on instances, but will emit a deprecation warning.

    List of plural name changes

    These fields appear in many different classes:

    • annotation_ref -> annotation_refs
    • bin_data -> bin_data_blocks
    • dataset_ref -> dataset_refs
    • emission_filter_ref -> emission_filters
    • excitation_filter_ref -> excitation_filters
    • experimenter_ref -> experimenter_refs
    • folder_ref -> folder_refs
    • image_ref -> image_refs
    • leader -> leaders
    • light_source_settings -> light_source_settings_combinations
    • m -> ms
    • microbeam_manipulation_ref -> microbeam_manipulation_refs
    • plate_ref -> plate_refs
    • roi_ref -> roi_refs
    • well_sample_ref -> well_sample_refs

  • Fields types PositiveInt, PositiveFloat, NonNegativeInt, and NonNegativeFloat are no longer typed with subclasses of pydantic ConstrainedInt and ConstrainedFloat, but are now simply int or float type with field validators.

  • Many local Type enums have been renamed to globally unique names. For example model.detector.Type is now model.Detector_Type. For backwards compatibility, the old names are still available as aliases in the corresponding modules. For example, Detector_Type is aliased as Type in the model.detector module.
  • The kind fields that were present on Shape and LightSourceGroup subclasses have been removed from the models. The kind key may still be included in a dict when instantiating a subclass, but the name will not be available on the model. (This was not an OME field to begin with, it was a workaround for serialization/deserialization to dict.)
  • Many fields that take an Enum and have a default value have had their types changed from Optional[EnumType] to EnumType. For example fields typed asOptional[UnitsLength] for which a default value is specified are now typed as UnitsLength.
  • The ome_types.model.simple_types module is deprecated and should not be used (import directly from model instead). Names that were previously there are still aliased in simple_types for backwards compatibility, but code should be updated and a deprecation warning will soon be added.

Changes to ome_types.model

Added classes

Removed classes

  • LightSourceGroup
  • ShapeGroup

Class Field Changes

Annotation

  • annotation_ref - name changed to annotation_refs
  • annotator - type changed from Optional[ExperimenterID] to Optional[ConstrainedStrValue]

Arc

  • type - type changed from Optional[Type] to Optional[Arc_Type]

BinData

  • compression - type changed from Optional[Compression] to BinData_Compression
  • length - type changed from int to ConstrainedIntValue
  • value - type changed from str to bytes

BinaryFile

  • size - type changed from NonNegativeLong to ConstrainedIntValue

OME.BinaryOnly

  • uuid - type changed from UniversallyUniqueIdentifier to ConstrainedStrValue

Channel

  • annotation_ref - name changed to annotation_refs
  • acquisition_mode - type changed from Optional[AcquisitionMode] to Optional[Channel_AcquisitionMode]
  • color - type changed from Optional[Color] to Color
  • contrast_method - type changed from Optional[ContrastMethod] to Optional[Channel_ContrastMethod]
  • emission_wavelength_unit - type changed from Optional[UnitsLength] to UnitsLength
  • excitation_wavelength_unit - type changed from Optional[UnitsLength] to UnitsLength
  • illumination_type - type changed from Optional[IlluminationType] to Optional[Channel_IlluminationType]
  • pinhole_size_unit - type changed from Optional[UnitsLength] to UnitsLength

Dataset

  • annotation_ref - name changed to annotation_refs
  • image_ref - name changed to image_refs

Detector

  • annotation_ref - name changed to annotation_refs
  • type - type changed from Optional[Type] to Optional[Detector_Type]
  • voltage_unit - type changed from Optional[UnitsElectricPotential] to UnitsElectricPotential

DetectorSettings

  • read_out_rate_unit - type changed from Optional[UnitsFrequency] to UnitsFrequency
  • voltage_unit - type changed from Optional[UnitsElectricPotential] to UnitsElectricPotential

Dichroic

  • annotation_ref - name changed to annotation_refs

Experiment

  • type - type changed from List[Type] to List[Experiment_value]

Experimenter

  • annotation_ref - name changed to annotation_refs

ExperimenterGroup

  • annotation_ref - name changed to annotation_refs
  • experimenter_ref - name changed to experimenter_refs
  • leader - name changed to leaders

External

  • compression - type changed from Optional[Compression] to External_Compression
  • sha1 - type changed from Hex40 to bytes

Filament

  • type - type changed from Optional[Type] to Optional[Filament_Type]

Filter

  • annotation_ref - name changed to annotation_refs
  • type - type changed from Optional[Type] to Optional[Filter_Type]

FilterSet

  • emission_filter_ref - name changed to emission_filters
  • excitation_filter_ref - name changed to excitation_filters

Folder

  • annotation_ref - name changed to annotation_refs
  • folder_ref - name changed to folder_refs
  • image_ref - name changed to image_refs
  • roi_ref - name changed to roi_refs

Image

  • annotation_ref - name changed to annotation_refs
  • microbeam_manipulation_ref - name changed to microbeam_manipulation_refs
  • roi_ref - name changed to roi_refs

ImagingEnvironment

  • air_pressure_unit - type changed from Optional[UnitsPressure] to UnitsPressure
  • co2_percent - type changed from Optional[PercentFraction] to Optional[ConstrainedFloatValue]
  • humidity - type changed from Optional[PercentFraction] to Optional[ConstrainedFloatValue]
  • temperature_unit - type changed from Optional[UnitsTemperature] to UnitsTemperature

Instrument

  • light_source_group - name removed
  • arcs - name added
  • filaments - name added
  • generic_excitation_sources - name added
  • lasers - name added
  • light_emitting_diodes - name added
  • annotation_ref - name changed to annotation_refs

Laser

  • laser_medium - type changed from Optional[LaserMedium] to Optional[Laser_LaserMedium]
  • pulse - type changed from Optional[Pulse] to Optional[Laser_Pulse]
  • repetition_rate_unit - type changed from Optional[UnitsFrequency] to UnitsFrequency
  • type - type changed from Optional[Type] to Optional[Laser_Type]
  • wavelength_unit - type changed from Optional[UnitsLength] to UnitsLength

LightPath

  • annotation_ref - name changed to annotation_refs
  • emission_filter_ref - name changed to emission_filters
  • excitation_filter_ref - name changed to excitation_filters

LightSource

  • annotation_ref - name changed to annotation_refs
  • power_unit - type changed from Optional[UnitsPower] to UnitsPower

LightSourceSettings

  • attenuation - type changed from Optional[PercentFraction] to Optional[ConstrainedFloatValue]
  • wavelength_unit - type changed from Optional[UnitsLength] to UnitsLength

Map.M

  • k - type changed from str to Optional[str]

Map

  • m - name changed to ms

MicrobeamManipulation

  • light_source_settings - name changed to light_source_settings_combinations
  • roi_ref - name changed to roi_refs
  • type - type changed from List[Type] to List[MicrobeamManipulation_value]

Microscope

  • type - type changed from Optional[Type] to Optional[Microscope_Type]

OME

  • structured_annotations - type changed from List[Annotation] to StructuredAnnotations
  • uuid - type changed from Optional[UniversallyUniqueIdentifier] to Optional[ConstrainedStrValue]

Objective

  • annotation_ref - name changed to annotation_refs
  • correction - type changed from Optional[Correction] to Optional[Objective_Correction]
  • immersion - type changed from Optional[Immersion] to Optional[Objective_Immersion]
  • working_distance_unit - type changed from Optional[UnitsLength] to UnitsLength

ObjectiveSettings

  • medium - type changed from Optional[Medium] to Optional[ObjectiveSettings_Medium]

Pixels

  • bin_data - name changed to bin_data_blocks
  • dimension_order - type changed from DimensionOrder to Pixels_DimensionOrder
  • metadata_only - type changed from bool to Optional[MetadataOnly]
  • physical_size_x_unit - type changed from Optional[UnitsLength] to UnitsLength
  • physical_size_y_unit - type changed from Optional[UnitsLength] to UnitsLength
  • physical_size_z_unit - type changed from Optional[UnitsLength] to UnitsLength
  • time_increment_unit - type changed from Optional[UnitsTime] to UnitsTime

Plane

  • annotation_ref - name changed to annotation_refs
  • delta_t_unit - type changed from Optional[UnitsTime] to UnitsTime
  • exposure_time_unit - type changed from Optional[UnitsTime] to UnitsTime
  • hash_sha1 - type changed from Optional[Hex40] to Optional[bytes]
  • position_x_unit - type changed from Optional[UnitsLength] to UnitsLength
  • position_y_unit - type changed from Optional[UnitsLength] to UnitsLength
  • position_z_unit - type changed from Optional[UnitsLength] to UnitsLength

Plate

  • annotation_ref - name changed to annotation_refs
  • well_origin_x_unit - type changed from Optional[UnitsLength] to UnitsLength
  • well_origin_y_unit - type changed from Optional[UnitsLength] to UnitsLength

PlateAcquisition

  • annotation_ref - name changed to annotation_refs
  • well_sample_ref - name changed to well_sample_refs

Project

  • annotation_ref - name changed to annotation_refs
  • dataset_ref - name changed to dataset_refs

ROI

  • annotation_ref - name changed to annotation_refs
  • union - type changed from List[Union[Rectangle, Mask, Point, Ellipse, Line, Polyline, Polygon, Label]] to ShapeUnion

Reagent

  • annotation_ref - name changed to annotation_refs

Screen

  • annotation_ref - name changed to annotation_refs
  • plate_ref - name changed to plate_refs

Shape

  • annotation_ref - name changed to annotation_refs
  • fill_rule - type changed from Optional[FillRule] to Optional[Shape_FillRule]
  • font_family - type changed from Optional[FontFamily] to Optional[Shape_FontFamily]
  • font_size_unit - type changed from Optional[UnitsLength] to UnitsLength
  • font_style - type changed from Optional[FontStyle] to Optional[Shape_FontStyle]
  • stroke_width_unit - type changed from Optional[UnitsLength] to UnitsLength

StageLabel

  • x_unit - type changed from Optional[UnitsLength] to UnitsLength
  • y_unit - type changed from Optional[UnitsLength] to UnitsLength
  • z_unit - type changed from Optional[UnitsLength] to UnitsLength

StructuredAnnotations

  • boolean_annotations - type changed from Optional[BooleanAnnotation] to List[BooleanAnnotation]
  • comment_annotations - type changed from Optional[CommentAnnotation] to List[CommentAnnotation]
  • double_annotations - type changed from Optional[DoubleAnnotation] to List[DoubleAnnotation]
  • file_annotations - type changed from Optional[FileAnnotation] to List[FileAnnotation]
  • list_annotations - type changed from Optional[ListAnnotation] to List[ListAnnotation]
  • long_annotations - type changed from Optional[LongAnnotation] to List[LongAnnotation]
  • map_annotations - type changed from Optional[MapAnnotation] to List[MapAnnotation]
  • tag_annotations - type changed from Optional[TagAnnotation] to List[TagAnnotation]
  • term_annotations - type changed from Optional[TermAnnotation] to List[TermAnnotation]
  • timestamp_annotations - type changed from Optional[TimestampAnnotation] to List[TimestampAnnotation]
  • xml_annotations - type changed from Optional[XMLAnnotation] to List[XMLAnnotation]

TransmittanceRange

  • cut_in_tolerance_unit - type changed from Optional[UnitsLength] to UnitsLength
  • cut_in_unit - type changed from Optional[UnitsLength] to UnitsLength
  • cut_out_tolerance_unit - type changed from Optional[UnitsLength] to UnitsLength
  • cut_out_unit - type changed from Optional[UnitsLength] to UnitsLength
  • transmittance - type changed from Optional[PercentFraction] to Optional[ConstrainedFloatValue]

TiffData.UUID

  • file_name - type changed from str to Optional[str]
  • value - type changed from UniversallyUniqueIdentifier to ConstrainedStrValue

XMLAnnotation.Value

Well

  • annotation_ref - name changed to annotation_refs
  • color - type changed from Optional[Color] to Color

WellSample

  • position_x_unit - type changed from Optional[UnitsLength] to UnitsLength
  • position_y_unit - type changed from Optional[UnitsLength] to UnitsLength

XMLAnnotation

  • value - type changed from Element to Value