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‎pyproject.toml‎

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@@ -24,6 +24,7 @@ dependencies = [
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"numpy",
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"protobuf>=3.0.0",
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"pybids==0.17.0",
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"pydantic",
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"pydicom",
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"python-dateutil",
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"scikit-learn",
@@ -45,6 +46,7 @@ Homepage = "https://github.com/aces/loris-mri"
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[tool.hatch.build.targets.wheel]
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packages = [
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"python/lib",
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"python/loris_bids_reader",
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"python/loris_eeg_chunker",
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"python/tests",
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]
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preview = true
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[tool.ruff.lint]
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ignore = ["E202", "E203", "E221", "E241", "E251", "E272"]
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ignore = ["E202", "E203", "E221", "E241", "E251", "E271", "E272"]
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select = ["E", "EXE", "F", "I", "N", "RUF", "UP", "W"]
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[tool.ruff.per-file-ignores]
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# Ignore line length in ORM models.
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"python/lib/db/models/*.py" = ["E501"]
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# The strict type checking configuration is used to type check only the modern (typed) modules. An
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# additional basic type checking configuration to type check legacy modules can be found in the
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# `test` directory.
@@ -76,6 +82,7 @@ include = [
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"python/lib/get_session_info.py",
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"python/lib/logging.py",
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"python/lib/make_env.py",
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"python/loris_bids_reader",
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"python/scripts/import_bids_dataset.py",
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"python/scripts/import_dicom_study.py",
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"python/scripts/summarize_dicom_study.py",

‎python/lib/db/models/bids_event_dataset_mapping.py‎

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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column
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from lib.db.base import Base
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from lib.db.decorators.int_bool import IntBool
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class DbBidsEventDatasetMapping(Base):
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__tablename__ = 'bids_event_dataset_mapping'
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id : Mapped[int] = mapped_column('ID', primary_key=True)
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project_id : Mapped[int] = mapped_column('ProjectID', ForeignKey('Project.ProjectID'))
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property_name : Mapped[str] = mapped_column('PropertyName')
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property_value : Mapped[str] = mapped_column('PropertyValue')
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hed_tag_id : Mapped[int | None] = mapped_column('HEDTagID', ForeignKey('hed_schema_nodes.ID'))
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tag_value : Mapped[str | None] = mapped_column('TagValue')
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description : Mapped[str | None] = mapped_column('Description')
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has_pairing : Mapped[bool | None] = mapped_column('HasPairing', IntBool)
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pair_rel_id : Mapped[int | None] = mapped_column('PairRelID')
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additional_members : Mapped[int | None] = mapped_column('AdditionalMembers')
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tagged_by : Mapped[int | None] = mapped_column('TaggedBy', ForeignKey('users.ID'))

‎python/lib/db/models/bids_event_file_mapping.py‎

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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column
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from lib.db.base import Base
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from lib.db.decorators.int_bool import IntBool
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class DbBidsEventFileMapping(Base):
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__tablename__ = 'bids_event_file_mapping'
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id : Mapped[int] = mapped_column('ID', primary_key=True)
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event_file_id : Mapped[int] = mapped_column('EventFileID', ForeignKey('physiological_event_file.EventFileID'))
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property_name : Mapped[str] = mapped_column('PropertyName')
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property_value : Mapped[str] = mapped_column('PropertyValue')
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hed_tag_id : Mapped[int | None] = mapped_column('HEDTagID', ForeignKey('hed_schema_nodes.ID'))
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tag_value : Mapped[str | None] = mapped_column('TagValue')
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description : Mapped[str | None] = mapped_column('Description')
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has_pairing : Mapped[bool | None] = mapped_column('HasPairing', IntBool)
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pair_rel_id : Mapped[int | None] = mapped_column('PairRelID')
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additional_members : Mapped[int | None] = mapped_column('AdditionalMembers')
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tagged_by : Mapped[int | None] = mapped_column('TaggedBy', ForeignKey('users.ID'))

‎python/lib/db/models/hed_schema.py‎

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from sqlalchemy.orm import Mapped, mapped_column
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from lib.db.base import Base
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class DbHedSchema(Base):
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__tablename__ = 'hed_schema'
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id : Mapped[int] = mapped_column('ID', primary_key=True)
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name : Mapped[str] = mapped_column('Name')
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version : Mapped[str] = mapped_column('Version')
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description : Mapped[str | None] = mapped_column('Description')
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url : Mapped[str] = mapped_column('URL')

‎python/lib/db/models/hed_schema_node.py‎

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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column
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from lib.db.base import Base
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class DbHedSchemaNode(Base):
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__tablename__ = 'hed_schema_nodes'
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id : Mapped[int] = mapped_column('ID', primary_key=True)
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parent_id : Mapped[int | None] = mapped_column('ParentID', ForeignKey('hed_schema_nodes.ID'))
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schema_id : Mapped[int] = mapped_column('SchemaID', ForeignKey('hed_schema.ID'))
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name : Mapped[str] = mapped_column('Name')
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long_name : Mapped[str] = mapped_column('LongName')
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description : Mapped[str] = mapped_column('Description')

‎python/lib/db/models/physio_channel.py‎

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from datetime import datetime
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from decimal import Decimal
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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column, relationship
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import lib.db.models.physio_channel_type as db_physio_channel_type
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import lib.db.models.physio_file as db_physio_file
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import lib.db.models.physio_status_type as db_physio_status_type
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from lib.db.base import Base
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class DbPhysioChannel(Base):
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__tablename__ = 'physiological_channel'
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id : Mapped[int] = mapped_column('PhysiologicalChannelID', primary_key=True)
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physio_file_id : Mapped[int] = mapped_column('PhysiologicalFileID', ForeignKey('physiological_file.PhysiologicalFileID'))
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channel_type_id : Mapped[int] = mapped_column('PhysiologicalChannelTypeID', ForeignKey('physiological_channel_type.PhysiologicalChannelTypeID'))
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status_type_id : Mapped[int | None] = mapped_column('PhysiologicalStatusTypeID', ForeignKey('physiological_status_type.PhysiologicalStatusTypeID'))
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insert_time : Mapped[datetime] = mapped_column('InsertTime', default=datetime.now)
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name : Mapped[str] = mapped_column('Name')
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description : Mapped[str | None] = mapped_column('Description')
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sampling_frequency : Mapped[int | None] = mapped_column('SamplingFrequency')
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low_cutoff : Mapped[Decimal | None] = mapped_column('LowCutoff')
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high_cutoff : Mapped[Decimal | None] = mapped_column('HighCutoff')
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manual_flag : Mapped[Decimal | None] = mapped_column('ManualFlag')
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notch : Mapped[int | None] = mapped_column('Notch')
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reference : Mapped[str | None] = mapped_column('Reference')
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status_description : Mapped[str | None] = mapped_column('StatusDescription')
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unit : Mapped[str | None] = mapped_column('Unit')
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file_path : Mapped[str | None] = mapped_column('FilePath')
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physio_file : Mapped['db_physio_file.DbPhysioFile'] = relationship(back_populates='channels')
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channel_type : Mapped['db_physio_channel_type.DbPhysioChannelType'] = relationship()
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status_type : Mapped['db_physio_status_type.DbPhysioStatusType'] = relationship()

‎python/lib/db/models/physio_channel_type.py‎

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from sqlalchemy.orm import Mapped, mapped_column
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from lib.db.base import Base
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class DbPhysioChannelType(Base):
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__tablename__ = 'physiological_channel_type'
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id : Mapped[int] = mapped_column('PhysiologicalChannelTypeID', primary_key=True)
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channel_type_name : Mapped[str] = mapped_column('ChannelTypeName')
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channel_description : Mapped[str | None] = mapped_column('ChannelDescription')

‎python/lib/db/models/physio_coord_system.py‎

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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column, relationship
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import lib.db.models.physio_coord_system_name as db_physio_coord_system_name
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import lib.db.models.physio_coord_system_type as db_physio_coord_system_type
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import lib.db.models.physio_coord_system_unit as db_physio_coord_system_unit
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import lib.db.models.physio_modality as db_physio_modality
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from lib.db.base import Base
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class DbPhysioCoordSystem(Base):
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__tablename__ = 'physiological_coord_system'
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id : Mapped[int] = mapped_column('PhysiologicalCoordSystemID', primary_key=True)
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name_id : Mapped[int] = mapped_column('NameID', ForeignKey('physiological_coord_system_name.PhysiologicalCoordSystemNameID'))
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type_id : Mapped[int] = mapped_column('TypeID', ForeignKey('physiological_coord_system_type.PhysiologicalCoordSystemTypeID'))
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unit_id : Mapped[int] = mapped_column('UnitID', ForeignKey('physiological_coord_system_unit.PhysiologicalCoordSystemUnitID'))
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modality_id : Mapped[int] = mapped_column('ModalityID', ForeignKey('physiological_modality.PhysiologicalModalityID'))
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file_path : Mapped[str | None] = mapped_column('FilePath')
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name : Mapped['db_physio_coord_system_name.DbPhysioCoordSystemName'] = relationship()
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type : Mapped['db_physio_coord_system_type.DbPhysioCoordSystemType'] = relationship()
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unit : Mapped['db_physio_coord_system_unit.DbPhysioCoordSystemUnit'] = relationship()
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modality : Mapped['db_physio_modality.DbPhysioModality'] = relationship()

‎python/lib/db/models/physio_coord_system_name.py‎

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from sqlalchemy.orm import Mapped, mapped_column
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from lib.db.base import Base
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class DbPhysioCoordSystemName(Base):
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__tablename__ = 'physiological_coord_system_name'
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id : Mapped[int] = mapped_column('PhysiologicalCoordSystemNameID', primary_key=True)
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name : Mapped[str] = mapped_column('Name')
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orientation : Mapped[str | None] = mapped_column('Orientation')
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origin : Mapped[str | None] = mapped_column('Origin')

‎python/lib/db/models/physio_coord_system_type.py‎

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from sqlalchemy.orm import Mapped, mapped_column
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from lib.db.base import Base
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class DbPhysioCoordSystemType(Base):
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__tablename__ = 'physiological_coord_system_type'
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id : Mapped[int] = mapped_column('PhysiologicalCoordSystemTypeID', primary_key=True)
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name : Mapped[str] = mapped_column('Name')

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