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feat: modulo[wip] #222

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7ebc806
feat: modulo[wip]
tlambert03 Sep 24, 2023
5e9f6f8
Merge branch 'main' into modulo
tlambert03 Dec 28, 2023
194acdd
fix file
tlambert03 Dec 28, 2023
b3912e5
fix for field name
tlambert03 Dec 28, 2023
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3 changes: 1 addition & 2 deletions src/ome_types/_mixins/_base_type.py
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Expand Up @@ -156,8 +156,7 @@ def __getattr__(self, key: str) -> Any:
stacklevel=2,
)
return getattr(self, new_key)

return super().__getattr__(key) # type: ignore
return object.__getattribute__(self, key)

def to_xml(self, **kwargs: Any) -> str:
"""Serialize this object to XML.
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12 changes: 11 additions & 1 deletion src/ome_types/_mixins/_collections.py
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Expand Up @@ -105,8 +105,18 @@
raise TypeError( # pragma: no cover
f"Expected an instance of {AnnotationInstances}, got {item!r}"
)

item_type = type(item)
# where 10 is the length of "Annotation"
return item.__class__.__name__[:-10].lower() + "_annotations"
field_name = item_type.__name__[:-10].lower() + "_annotations"
if hasattr(cls, field_name):
return field_name

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for annotation_type in AnnotationInstances:
if issubclass(item_type, annotation_type):
return annotation_type.__name__[:-10].lower() + "_annotations"
raise TypeError( # pragma: no cover
f"Could not find field name for {item_type.__name__}"
)


ShapeType = Union[Rectangle, Mask, Point, Ellipse, Line, Polyline, Polygon, Label]
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145 changes: 145 additions & 0 deletions src/ome_types/model/modulo.py
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@@ -0,0 +1,145 @@
from enum import Enum
from typing import List, Optional, Union

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from pydantic_compat import model_validator

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from ome_types._autogenerated.ome_2016_06 import XMLAnnotation
from ome_types._mixins._base_type import OMEType
from xsdata_pydantic_basemodel.pydantic_compat import Field

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MODULO_NS = "openmicroscopy.org/omero/dimension/modulo"
ADDITIONS_NS = "http://www.openmicroscopy.org/Schemas/Additions/2011-09"

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class ModuloType(Enum):

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"""The dimension represented by this modulo."""

ANGLE = "angle"
PHASE = "phase"
TILE = "tile"
LIFETIME = "lifetime"
LAMBDA = "lambda"
OTHER = "other"

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class Label(OMEType):
value: int = Field(

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metadata={
"required": True,
"format": "base64",
}
)


class Modulo(OMEType):
class Meta:
namespace = MODULO_NS

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type: ModuloType = Field(

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metadata={
"name": "Type",
"type": "Attribute",
"required": True,
},
)
labels: List[Label] = Field(

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default_factory=list,
metadata={
"name": "Label",
"type": "Element",
},
)
type_description: Optional[str] = Field(

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default=None,
metadata={
"name": "TypeDescription",
"type": "Attribute",
},
)
unit: Optional[str] = Field(

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default=None,
metadata={
"name": "Unit",
"type": "Attribute",
},
)
start: Union[int, float, None] = Field(

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default=None,
metadata={
"name": "Start",
"type": "Attribute",
},
)
step: Union[int, float, None] = Field(

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default=None,
metadata={
"name": "Step",
"type": "Attribute",
},
)
end: Union[int, float, None] = Field(

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default=None,
metadata={
"name": "End",
"type": "Attribute",
},
)

@model_validator(mode="after")
def _vroot(cls, v: "Modulo") -> "Modulo":
if not v.labels and (v.start is None or v.end is None):
raise ValueError("Must specify either labels or start/end")
return v

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class ModuloContainer(OMEType):
class Meta:
namespace = ADDITIONS_NS

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modulo_along_c: Optional[Modulo] = Field(

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default=None,
metadata={
"type": "Element",
"name": "ModuloAlongC",
},
)
modulo_along_z: Optional[Modulo] = Field(

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default=None,
metadata={
"type": "Element",
"name": "ModuloAlongZ",
},
)
modulo_along_t: Optional[Modulo] = Field(

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default=None,
metadata={
"type": "Element",
"name": "ModuloAlongT",
},
)


class ModuloValue(XMLAnnotation.Value):
class Meta:
namespace = "http://www.openmicroscopy.org/Schemas/OME/2016-06"

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modulos: ModuloContainer = Field(

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default_factory=list,
metadata={
"name": "Modulo",
"type": "Element",
},
)


class ModuloAnnotation(XMLAnnotation):
class Meta:
namespace = MODULO_NS

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value: ModuloValue = Field(

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default_factory=ModuloValue,
metadata={
"name": "Value",
"type": "Element",
},
)
3 changes: 3 additions & 0 deletions tests/data/FLIM-ModuloAlongC.ome.xml
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<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.0-m4" UUID="urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="FLIM"><AcquisitionDate>2011-10-03T14:34:07</AcquisitionDate><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="16" SizeT="1" SizeX="180" SizeY="150" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:3" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:4" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:5" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:6" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:7" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:8" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:9" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:10" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:11" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:12" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:13" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:14" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:15" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="3" FirstT="0" FirstZ="0" IFD="3" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="4" FirstT="0" FirstZ="0" IFD="4" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="5" FirstT="0" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="6" FirstT="0" FirstZ="0" IFD="6" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="7" FirstT="0" FirstZ="0" IFD="7" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="8" FirstT="0" FirstZ="0" IFD="8" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="9" FirstT="0" FirstZ="0" IFD="9" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="10" FirstT="0" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="11" FirstT="0" FirstZ="0" IFD="11" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="12" FirstT="0" FirstZ="0" IFD="12" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="13" FirstT="0" FirstZ="0" IFD="13" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="14" FirstT="0" FirstZ="0" IFD="14" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><TiffData FirstC="15" FirstT="0" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongC.ome.tiff">urn:uuid:51fb5d8e-7ae1-437f-96bc-ed67b8d14822</UUID></TiffData><Plane TheC="0" TheT="0" TheZ="0"/><Plane TheC="1" TheT="0" TheZ="0"/><Plane TheC="2" TheT="0" TheZ="0"/><Plane TheC="3" TheT="0" TheZ="0"/><Plane TheC="4" TheT="0" TheZ="0"/><Plane TheC="5" TheT="0" TheZ="0"/><Plane TheC="6" TheT="0" TheZ="0"/><Plane TheC="7" TheT="0" TheZ="0"/><Plane TheC="8" TheT="0" TheZ="0"/><Plane TheC="9" TheT="0" TheZ="0"/><Plane TheC="10" TheT="0" TheZ="0"/><Plane TheC="11" TheT="0" TheZ="0"/><Plane TheC="12" TheT="0" TheZ="0"/><Plane TheC="13" TheT="0" TheZ="0"/><Plane TheC="14" TheT="0" TheZ="0"/><Plane TheC="15" TheT="0" TheZ="0"/></Pixels><AnnotationRef ID="Annotation:3"/></Image><StructuredAnnotations><XMLAnnotation ID="Annotation:3" Namespace="openmicroscopy.org/omero/dimension/modulo"><Value><Modulo namespace="http://www.openmicroscopy.org/Schemas/Additions/2011-09">
<ModuloAlongC End="8" Start="1" Step="1" Type="lifetime" Unit="ps"/>
</Modulo></Value></XMLAnnotation></StructuredAnnotations></OME>
6 changes: 6 additions & 0 deletions tests/data/FLIM-ModuloAlongT-TSCPC.ome.xml
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<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.0-m4" UUID="urn:uuid:4bd6aecd-1da8-47b3-8271-b02240bfcd1e" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="FLIM"><AcquisitionDate>2013-07-11T15:56:06</AcquisitionDate><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="2" SizeT="16" SizeX="180" SizeY="200" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongT-TSCPC.ome.tiff">urn:uuid:4bd6aecd-1da8-47b3-8271-b02240bfcd1e</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongT-TSCPC.ome.tiff">urn:uuid:4bd6aecd-1da8-47b3-8271-b02240bfcd1e</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongT-TSCPC.ome.tiff">urn:uuid:4bd6aecd-1da8-47b3-8271-b02240bfcd1e</UUID></TiffData><TiffData FirstC="1" FirstT="1" FirstZ="0" IFD="3" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongT-TSCPC.ome.tiff">urn:uuid:4bd6aecd-1da8-47b3-8271-b02240bfcd1e</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="4" PlaneCount="1"><UUID FileName="FLIM-ModuloAlongT-TSCPC.ome.tiff">urn:uuid:4bd6aecd-1da8-47b3-8271-b02240bfcd1e</UUID></TiffData><TiffData FirstC="1" FirstT="2" FirstZ="0" IFD="5" PlaneCount="1"><UUID 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