shared_libraries.models

Pydantic models of ScanHub.

Copyright (C) 2023, BRAIN-LINK UG (haftungsbeschränkt). All Rights Reserved. SPDX-License-Identifier: GPL-3.0-only OR LicenseRef-ScanHub-Commercial

Classes

XYZ	Pydantic definition of coordinates.
Gender	Pydantic definition of genders.
DeviceStatus	Pydantic definition of a commands.
CalibrationType	Pydantic definition of calibration methods.
ItemStatus	Task status enum.
TaskType	Task type enum.
ResultType	Result type enum.
UserRole	User role enum.
DeviceCreationRequest	Device registration request pydantic model.
DeviceDetails	Device creation request pydantic model.
DeviceOut	Device pydantic output model.
BaseMRISequence	Base model for MRI sequence.
MRISequenceOut	Output model for MRI sequence.
BaseResult	Result model.
SetResult	Update result model.
ResultOut	Result output model.
BaseTask	Task base model.
TaskOut	Task output model.
AcquisitionParameter	Pydantic definition of acquisition parameters.
BaseAcquisitionTask	Represents a task for data acquisition in the system.
AcquisitionLimits	Pydantic definition of AcquisitionLimits.
AcquisitionTaskOut	Acquisition Task output model.
AcquisitionPayload	Acquisition Task payload model.
BaseProtocol	Protocol base model.
ProtocolOut	Protocol output model.
User	Authenticated user, as returned to callers after login.
PasswordUpdateRequest	Request payload to change a user's password.
BasePatient	Patient pydantic base model.
PatientOut	Patient pydantic output model.
MRDAcquisitionInfo	ISMRM raw data / (ISMR)MRD acquisition info.
MRDMetaResponse	ISMRM raw data / (ISMR)MRD meta data response.

Module Contents

class shared_libraries.models.XYZ

Bases: pydantic.BaseModel

Pydantic definition of coordinates.

x: float

y: float

z: float

class shared_libraries.models.Gender

Bases: str, enum.Enum

Pydantic definition of genders.

MALE = 'MALE'

FEMALE = 'FEMALE'

OTHER = 'OTHER'

NOT_GIVEN = 'NOT_GIVEN'

class shared_libraries.models.DeviceStatus

Bases: str, enum.Enum

Pydantic definition of a commands.

ONLINE = 'ONLINE'

OFFLINE = 'OFFLINE'

BUSY = 'BUSY'

ERROR = 'ERROR'

class shared_libraries.models.CalibrationType

Bases: str, enum.Enum

Pydantic definition of calibration methods.

FLIPANGLE = 'flip-angle'

FREQUENCY = 'frequency'

SHIMS = 'shims'

class shared_libraries.models.ItemStatus

Bases: str, enum.Enum

Task status enum.

NEW = 'NEW'

UPDATED = 'UPDATED'

STARTED = 'STARTED'

INPROGRESS = 'INPROGRESS'

ACQUIRED = 'ACQUIRED'

FINISHED = 'FINISHED'

ERROR = 'ERROR'

FAILED = 'FAILED'

CANCELLED = 'CANCELLED'

class shared_libraries.models.TaskType

Bases: str, enum.Enum

Task type enum.

ACQUISITION = 'ACQUISITION'

class shared_libraries.models.ResultType

Bases: str, enum.Enum

Result type enum.

DICOM = 'DICOM'

MRD = 'MRD'

NPY = 'NUMPY'

CALIBRATION = 'CALIBRATION'

NOT_SET = 'NOT_SET'

class shared_libraries.models.UserRole

Bases: enum.Enum

User role enum.

admin = 'admin'

medical = 'medical'

scientist = 'scientist'

engineer = 'engineer'

class shared_libraries.models.DeviceCreationRequest

Bases: pydantic.BaseModel

Device registration request pydantic model.

(to be sent by user first adding the device to the platform).

model_config

name: str

description: str

status: DeviceStatus | None = None

class shared_libraries.models.DeviceDetails

Bases: pydantic.BaseModel

Device creation request pydantic model.

model_config

device_name: str | None = None

serial_number: str | None = None

manufacturer: str | None = None

modality: str | None = None

status: DeviceStatus | None = None

site: str | None = None

parameter: dict | None = None

class shared_libraries.models.DeviceOut

Bases: DeviceCreationRequest, DeviceDetails

Device pydantic output model.

id: uuid.UUID

datetime_created: datetime.datetime

datetime_updated: datetime.datetime | None = None

class shared_libraries.models.BaseMRISequence

Bases: pydantic.BaseModel

Base model for MRI sequence.

model_config

name: str

description: str

sequence_type: str

tags: list[str] = []

class shared_libraries.models.MRISequenceOut

Bases: BaseMRISequence

Output model for MRI sequence.

id: str

created_at: datetime.datetime

updated_at: datetime.datetime | None = None

seq_file: Any

seq_file_extension: str | None = None

xml_file: Any | None = None

xml_file_extension: str | None = None

class shared_libraries.models.BaseResult

Bases: pydantic.BaseModel

Result model.

model_config

task_id: uuid.UUID

class shared_libraries.models.SetResult

Bases: pydantic.BaseModel

Update result model.

model_config

type: ResultType

directory: str

files: list[str] = []

meta: dict | None = None

class shared_libraries.models.ResultOut

Bases: BaseResult, SetResult

Result output model.

id: uuid.UUID

datetime_created: datetime.datetime

class shared_libraries.models.BaseTask

Bases: pydantic.BaseModel

Task base model.

model_config

protocol_id: uuid.UUID | None = None

name: str

description: str

task_type: TaskType

destination: str

status: ItemStatus

progress: int

is_template: bool

position: int = 0

class shared_libraries.models.TaskOut

Bases: BaseTask

Task output model.

id: uuid.UUID

creator: str

datetime_created: datetime.datetime

datetime_updated: datetime.datetime | None = None

results: list[ResultOut]

class shared_libraries.models.AcquisitionParameter

Bases: pydantic.BaseModel

Pydantic definition of acquisition parameters.

fov_scaling: XYZ

fov_offset: XYZ

fov_rotation: XYZ

class shared_libraries.models.BaseAcquisitionTask

Bases: BaseTask

Represents a task for data acquisition in the system.

task_type: Literal[TaskType]

device_id: uuid.UUID | None = None

calibration: list[CalibrationType] = []

sequence_id: str | None = None

acquisition_parameter: AcquisitionParameter | None = None

class shared_libraries.models.AcquisitionLimits

Bases: pydantic.BaseModel

Pydantic definition of AcquisitionLimits.

patient_height: int

patient_weight: int

patient_gender: Gender

patient_age: int

class shared_libraries.models.AcquisitionTaskOut

Bases: TaskOut, BaseAcquisitionTask

Acquisition Task output model.

acquisition_limits: AcquisitionLimits | None = None

class shared_libraries.models.AcquisitionPayload

Bases: AcquisitionTaskOut

Acquisition Task payload model.

mrd_header: str | None = None

sequence: MRISequenceOut

access_token: str

device_parameter: dict

class shared_libraries.models.BaseProtocol

Bases: pydantic.BaseModel

Protocol base model.

model_config

patient_id: uuid.UUID | None = None

name: str

description: str

indication: str | None = None

comment: str | None = None

status: ItemStatus

is_template: bool

class shared_libraries.models.ProtocolOut

Bases: BaseProtocol

Protocol output model.

id: uuid.UUID

creator: str

datetime_created: datetime.datetime

datetime_updated: datetime.datetime | None = None

tasks: list[AcquisitionTaskOut]

class shared_libraries.models.User

Bases: pydantic.BaseModel

Authenticated user, as returned to callers after login.

username: str

first_name: str

last_name: str

email: str | None = None

role: UserRole

access_token: str

token_type: str

last_activity_unixtime: int | None = None

last_login_unixtime: int | None = None

class shared_libraries.models.PasswordUpdateRequest

Bases: pydantic.BaseModel

Request payload to change a user’s password.

password_of_requester: str

username_to_change_password_for: str

newpassword: str

class shared_libraries.models.BasePatient

Bases: pydantic.BaseModel

Patient pydantic base model.

model_config

first_name: str

last_name: str

birth_date: datetime.date

sex: Gender

height: float

weight: float

issuer: str

status: ItemStatus

comment: str | None = None

class shared_libraries.models.PatientOut

Bases: BasePatient

Patient pydantic output model.

patient_id: uuid.UUID

datetime_created: datetime.datetime

datetime_updated: datetime.datetime | None = None

class shared_libraries.models.MRDAcquisitionInfo

Bases: pydantic.BaseModel

ISMRM raw data / (ISMR)MRD acquisition info.

acquisition_id: int

num_samples: int

num_coils: int

dwell_time: float

class shared_libraries.models.MRDMetaResponse

Bases: pydantic.BaseModel

ISMRM raw data / (ISMR)MRD meta data response.

protocol_id: str

task_id: str

result_id: str

dtype: str = 'fc32'

acquisitions: list[MRDAcquisitionInfo] = []