aind-data-schema-models 0.1.0__py3-none-any.whl

aind_data_schema_models/__init__.py

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+"""Init package"""
+
+__version__ = "0.1.0"

aind_data_schema_models/harp_types.py

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+"""Module for Harp Device Types"""
+
+from typing import Literal, Union
+
+from pydantic import BaseModel, ConfigDict, Field
+from typing_extensions import Annotated
+
+
+class _HarpDeviceType(BaseModel):
+    """Base model config"""
+
+    model_config = ConfigDict(frozen=True)
+    name: str
+    whoami: int
+
+
+class Behavior(_HarpDeviceType):
+    """Behavior"""
+
+    name: Literal["Behavior"] = "Behavior"
+    whoami: Literal[1216] = 1216
+
+
+class CameraController(_HarpDeviceType):
+    """Camera Controller"""
+
+    name: Literal["Camera Controller"] = "Camera Controller"
+    whoami: Literal[1168] = 1168
+
+
+class ClockSynchronizer(_HarpDeviceType):
+    """Clock Synchronizer"""
+
+    name: Literal["Clock Synchronizer"] = "Clock Synchronizer"
+    whoami: Literal[1152] = 1152
+
+
+class GenericHarpDevice(_HarpDeviceType):
+    """Generic Harp Device"""
+
+    name: Literal["Generic Harp Device"] = "Generic Harp Device"
+    whoami: int = Field(default=0, ge=0, le=9999, title="WhoAmI")
+
+
+class InputExpander(_HarpDeviceType):
+    """Input Expander"""
+
+    name: Literal["Input Expander"] = "Input Expander"
+    whoami: Literal[1106] = 1106
+
+
+class LoadCells(_HarpDeviceType):
+    """Load Cells"""
+
+    name: Literal["Load Cells"] = "Load Cells"
+    whoami: Literal[1232] = 1232
+
+
+class Olfactometer(_HarpDeviceType):
+    """Olfactometer"""
+
+    name: Literal["Olfactometer"] = "Olfactometer"
+    whoami: Literal[1140] = 1140
+
+
+class SoundCard(_HarpDeviceType):
+    """Sound Card"""
+
+    name: Literal["Sound Card"] = "Sound Card"
+    whoami: Literal[1280] = 1280
+
+
+class Synchronizer(_HarpDeviceType):
+    """Synchronizer"""
+
+    name: Literal["Synchronizer"] = "Synchronizer"
+    whoami: Literal[1104] = 1104
+
+
+class TimestampGeneratorGen1(_HarpDeviceType):
+    """Timestamp Generator Gen 1"""
+
+    name: Literal["Timestamp Generator Gen 1"] = "Timestamp Generator Gen 1"
+    whoami: Literal[1154] = 1154
+
+
+class TimestampGeneratorGen3(_HarpDeviceType):
+    """Timestamp Generator Gen 3"""
+
+    name: Literal["Timestamp Generator Gen 3"] = "Timestamp Generator Gen 3"
+    whoami: Literal[1158] = 1158
+
+
+class LicketySplit(_HarpDeviceType):
+    """Lickety Split"""
+
+    name: Literal["Lickety Split"] = "Lickety Split"
+    whoami: Literal[1400] = 1400
+
+
+class SniffDetector(_HarpDeviceType):
+    """Sniff Detector"""
+
+    name: Literal["Sniff Detector"] = "Sniff Detector"
+    whoami: Literal[1401] = 1401
+
+
+class Treadmill(_HarpDeviceType):
+    """Treadmill"""
+
+    name: Literal["Treadmill"] = "Treadmill"
+    whoami: Literal[1402] = 1402
+
+
+class Cuttlefish(_HarpDeviceType):
+    """Cuttlefish"""
+
+    name: Literal["Cuttlefish"] = "Cuttlefish"
+    whoami: Literal[1403] = 1403
+
+
+class StepperDriver(_HarpDeviceType):
+    """Stepper Driver"""
+
+    name: Literal["Stepper Driver"] = "Stepper Driver"
+    whoami: Literal[1130] = 1130
+
+
+class HarpDeviceType:
+    """Harp device type definitions"""
+
+    BEHAVIOR = Behavior()
+    GENERIC_HARP_DEVICE = GenericHarpDevice()
+    CAMERA_CONTROLLER = CameraController()
+    CLOCK_SYNCHRONIZER = ClockSynchronizer()
+    INPUT_EXPANDER = InputExpander()
+    LOAD_CELLS = LoadCells()
+    OLFACTOMETER = Olfactometer()
+    SOUND_CARD = SoundCard()
+    SYNCHRONIZER = Synchronizer()
+    TIMESTAMP_GENERATOR_1 = TimestampGeneratorGen1()
+    TIMESTAMP_GENERATOR_3 = TimestampGeneratorGen3()
+    LICKETY_SPLIT = LicketySplit()
+    SNIFF_DETECTOR = SniffDetector()
+    TREADMILL = Treadmill()
+    CUTTLEFISH = Cuttlefish()
+    STEPPER_DRIVER = StepperDriver()
+
+    _ALL = tuple(_HarpDeviceType.__subclasses__())
+    ONE_OF = Annotated[Union[_ALL], Field(discriminator="name")]

aind_data_schema_models/modalities.py

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+"""Module for Modality definitions"""
+
+from typing import Literal, Union
+
+from pydantic import ConfigDict, Field
+from typing_extensions import Annotated
+
+from aind_data_schema_models.pid_names import BaseName
+
+
+class _Modality(BaseName):
+    """Base model config"""
+
+    model_config = ConfigDict(frozen=True)
+
+
+class Behavior(_Modality):
+    """Behavior"""
+
+    name: Literal["Behavior"] = "Behavior"
+    abbreviation: Literal["behavior"] = "behavior"
+
+
+class BehaviorVideos(_Modality):
+    """BehaviorVideos"""
+
+    name: Literal["Behavior videos"] = "Behavior videos"
+    abbreviation: Literal["behavior-videos"] = "behavior-videos"
+
+
+class Confocal(_Modality):
+    """Confocal"""
+
+    name: Literal["Confocal microscopy"] = "Confocal microscopy"
+    abbreviation: Literal["confocal"] = "confocal"
+
+
+class Ecephys(_Modality):
+    """Ecephys"""
+
+    name: Literal["Extracellular electrophysiology"] = "Extracellular electrophysiology"
+    abbreviation: Literal["ecephys"] = "ecephys"
+
+
+class Electromyography(_Modality):
+    """Electromyography"""
+
+    name: Literal["Electromyography"] = "Electromyography"
+    abbreviation: Literal["EMG"] = "EMG"
+
+
+class Fmost(_Modality):
+    """Fmost"""
+
+    name: Literal["Fluorescence micro-optical sectioning tomography"] = (
+        "Fluorescence micro-optical sectioning tomography"
+    )
+    abbreviation: Literal["fMOST"] = "fMOST"
+
+
+class Icephys(_Modality):
+    """Icephys"""
+
+    name: Literal["Intracellular electrophysiology"] = "Intracellular electrophysiology"
+    abbreviation: Literal["icephys"] = "icephys"
+
+
+class Isi(_Modality):
+    """Intrinsic signal imaging"""
+
+    name: Literal["Intrinsic signal imaging"] = "Intrinsic signal imaging"
+    abbreviation: Literal["ISI"] = "ISI"
+
+
+class Fib(_Modality):
+    """Fib"""
+
+    name: Literal["Fiber photometry"] = "Fiber photometry"
+    abbreviation: Literal["fib"] = "fib"
+
+
+class Merfish(_Modality):
+    """Merfish"""
+
+    name: Literal["Multiplexed error-robust fluorescence in situ hybridization"] = (
+        "Multiplexed error-robust fluorescence in situ hybridization"
+    )
+    abbreviation: Literal["merfish"] = "merfish"
+
+
+class Mri(_Modality):
+    """Mri"""
+
+    name: Literal["Magnetic resonance imaging"] = "Magnetic resonance imaging"
+    abbreviation: Literal["MRI"] = "MRI"
+
+
+class POphys(_Modality):
+    """POphys"""
+
+    name: Literal["Planar optical physiology"] = "Planar optical physiology"
+    abbreviation: Literal["ophys"] = "ophys"
+
+
+class Slap(_Modality):
+    """Slap"""
+
+    name: Literal["Scanned line projection imaging"] = "Scanned line projection imaging"
+    abbreviation: Literal["slap"] = "slap"
+
+
+class Spim(_Modality):
+    """Spim"""
+
+    name: Literal["Selective plane illumination microscopy"] = "Selective plane illumination microscopy"
+    abbreviation: Literal["SPIM"] = "SPIM"
+
+
+class Modality:
+    """Modality classes"""
+
+    BEHAVIOR = Behavior()
+    BEHAVIOR_VIDEOS = BehaviorVideos()
+    CONFOCAL = Confocal()
+    ECEPHYS = Ecephys()
+    EMG = Electromyography()
+    FMOST = Fmost()
+    ICEPHYS = Icephys()
+    FIB = Fib()
+    ISI = Isi()
+    MERFISH = Merfish()
+    MRI = Mri()
+    POPHYS = POphys()
+    SLAP = Slap()
+    SPIM = Spim()
+    _ALL = tuple(_Modality.__subclasses__())
+    ONE_OF = Annotated[Union[_ALL], Field(discriminator="name")]
+
+    _abbreviation_map = {m().abbreviation: m() for m in _ALL}
+
+    @classmethod
+    def from_abbreviation(cls, abbreviation: str):
+        """Get class from abbreviation"""
+        return cls._abbreviation_map[abbreviation]