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stephen-riggsstephen-riggs
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Add db components from ispyb
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‎src/murfey/util/db.py‎

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@@ -9,6 +9,17 @@
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import sqlalchemy
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from sqlmodel import Field, Relationship, SQLModel, create_engine
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from murfey.util.processing_db import (
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CTF,
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Atlas,
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MotionCorrection,
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Movie as ProcessingMovie,
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ParticleClassificationGroup,
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ParticlePicker,
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RelativeIceThickness,
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Tomogram,
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)
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"""
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GENERAL
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"""
@@ -429,6 +440,7 @@ class DataCollectionGroup(SQLModel, table=True): # type: ignore
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sa_relationship_kwargs={"cascade": "delete"},
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)
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)
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Atlas: List["Atlas"] = Relationship(back_populates="DataCollectionGroup")
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class NotificationParameter(SQLModel, table=True): # type: ignore
@@ -468,6 +480,11 @@ class DataCollection(SQLModel, table=True): # type: ignore
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processing_jobs: List["ProcessingJob"] = Relationship(
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back_populates="data_collection", sa_relationship_kwargs={"cascade": "delete"}
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)
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Movie: List["ProcessingMovie"] = Relationship(back_populates="DataCollection")
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MotionCorrection: List["MotionCorrection"] = Relationship(
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back_populates="DataCollection"
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)
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Tomogram: List["Tomogram"] = Relationship(back_populates="DataCollection")
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class ProcessingJob(SQLModel, table=True): # type: ignore
@@ -569,6 +586,20 @@ class AutoProcProgram(SQLModel, table=True): # type: ignore
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murfey_ids: List["MurfeyLedger"] = Relationship(
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back_populates="auto_proc_program", sa_relationship_kwargs={"cascade": "delete"}
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)
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MotionCorrection: List["MotionCorrection"] = Relationship(
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back_populates="DataCollection"
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)
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Tomogram: List["Tomogram"] = Relationship(back_populates="AutoProcProgram")
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CTF: List["CTF"] = Relationship(back_populates="AutoProcProgram")
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ParticlePicker: List["ParticlePicker"] = Relationship(
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back_populates="AutoProcProgram"
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)
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RelativeIceThickness: List["RelativeIceThickness"] = Relationship(
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back_populates="AutoProcProgram"
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)
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ParticleClassificationGroup: List["ParticleClassificationGroup"] = Relationship(
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back_populates="AutoProcProgram"
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)
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class MurfeyLedger(SQLModel, table=True): # type: ignore

‎src/murfey/util/processing_db.py‎

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import datetime
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from typing import List, Optional
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from sqlmodel import Enum, Field, Relationship, SQLModel
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from murfey.util.db import AutoProcProgram, DataCollection, DataCollectionGroup
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class Atlas(SQLModel, table=True): # type: ignore
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atlasId: int = Field(primary_key=True, unique=True)
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dataCollectionGroupId: int = Field(foreign_key="DataCollectionGroup.id")
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atlasImage: str
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pixelSize: float
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cassetteSlot: Optional[int] = None
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DataCollectionGroup: Optional["DataCollectionGroup"] = Relationship(
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back_populates="Atlas"
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)
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GridSquare: List["GridSquare"] = Relationship(back_populates="Atlas")
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class GridSquare(SQLModel, table=True): # type: ignore
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gridSquareId: int = Field(primary_key=True, unique=True)
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atlasId: int = Field(foreign_key="Atlas.atlasId")
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gridSquareLabel: Optional[int] = None
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gridSquareImage: Optional[str] = None
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pixelLocationX: Optional[int] = None
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pixelLocationY: Optional[int] = None
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height: Optional[int] = None
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width: Optional[int] = None
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angle: Optional[float] = None
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stageLocationX: Optional[float] = None
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stageLocationY: Optional[float] = None
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qualityIndicator: Optional[float] = None
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pixelSize: Optional[float] = None
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Atlas: Optional["Atlas"] = Relationship(back_populates="Atlas")
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FoilHole: List["FoilHole"] = Relationship(back_populates="GridSquare")
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Tomogram: List["Tomogram"] = Relationship(back_populates="GridSquare")
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class FoilHole(SQLModel, table=True): # type: ignore
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foilHoleId: int = Field(primary_key=True, unique=True)
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gridSquareId: int = Field(foreign_key="GridSquare.gridSquareId")
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foilHoleLabel: str
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foilHoleImage: Optional[str] = None
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pixelLocationX: Optional[int] = None
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pixelLocationY: Optional[int] = None
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diameter: Optional[int] = None
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stageLocationX: Optional[float] = None
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stageLocationY: Optional[float] = None
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qualityIndicator: Optional[float] = None
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pixelSize: Optional[float] = None
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GridSquare: Optional["GridSquare"] = Relationship(back_populates="FoilHole")
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Movie: List["Movie"] = Relationship(back_populates="FoilHole")
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class Movie(SQLModel, table=True): # type: ignore
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movieId: int = Field(primary_key=True, unique=True)
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createdTimeStamp: datetime.datetime
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dataCollectionId: Optional[int] = Field(foreign_key="DataCollection.id")
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movieNumber: Optional[int] = None
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movieFullPath: Optional[str] = None
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positionX: Optional[float] = None
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positionY: Optional[float] = None
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nominalDefocus: Optional[float] = None
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angle: Optional[float] = None
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fluence: Optional[float] = None
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numberOfFrames: Optional[int] = None
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foilHoleId: Optional[int] = Field(foreign_key="FoilHole.foilHoleId")
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templateLabel: Optional[int] = None
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DataCollection: Optional["DataCollection"] = Relationship(back_populates="Movie")
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FoilHole: Optional["FoilHole"] = Relationship(back_populates="Movie")
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MotionCorrection: List["MotionCorrection"] = Relationship(back_populates="Movie")
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TiltImageAlignment: List["TiltImageAlignment"] = Relationship(
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back_populates="Movie"
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)
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class MotionCorrection(SQLModel, table=True): # type: ignore
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motionCorrectionId: int = Field(primary_key=True, unique=True)
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dataCollectionId: Optional[int] = Field(foreign_key="DataCollection.id")
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autoProcProgramId: Optional[int] = Field(foreign_key="AutoProcProgram.id")
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imageNumber: Optional[int] = None
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firstFrame: Optional[int] = None
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lastFrame: Optional[int] = None
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dosePerFrame: Optional[float] = None
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doseWeight: Optional[float] = None
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totalMotion: Optional[float] = None
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averageMotionPerFrame: Optional[float] = None
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driftPlotFullPath: Optional[str] = None
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micrographFullPath: Optional[str] = None
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micrographSnapshotFullPath: Optional[str] = None
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patchesUsedX: Optional[int] = None
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patchesUsedY: Optional[int] = None
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fftFullPath: Optional[str] = None
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fftCorrectedFullPath: Optional[str] = None
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comments: Optional[str] = None
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movieId: Optional[int] = Field(foreign_key="Movie.movieId")
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AutoProcProgram: Optional["AutoProcProgram"] = Relationship(
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back_populates="MotionCorrection"
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)
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DataCollection: Optional["DataCollection"] = Relationship(
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back_populates="MotionCorrection"
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)
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Movie: Optional["Movie"] = Relationship(back_populates="MotionCorrection")
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CTF: List["CTF"] = Relationship(back_populates="MotionCorrection")
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ParticlePicker: List["ParticlePicker"] = Relationship(
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back_populates="MotionCorrection"
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)
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RelativeIceThickness: List["RelativeIceThickness"] = Relationship(
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back_populates="MotionCorrection"
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)
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class Tomogram(SQLModel, table=True): # type: ignore
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tomogramId: int = Field(primary_key=True, unique=True)
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dataCollectionId: Optional[int] = Field(foreign_key="DataCollection.id")
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autoProcProgramId: Optional[int] = Field(foreign_key="AutoProcProgram.id")
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volumeFile: Optional[str] = None
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stackFile: Optional[str] = None
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sizeX: Optional[int] = None
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sizeY: Optional[int] = None
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sizeZ: Optional[int] = None
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pixelSpacing: Optional[float] = None
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residualErrorMean: Optional[float] = None
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residualErrorSD: Optional[float] = None
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xAxisCorrection: Optional[float] = None
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tiltAngleOffset: Optional[float] = None
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zShift: Optional[float] = None
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fileDirectory: Optional[str] = None
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centralSliceImage: Optional[str] = None
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tomogramMovie: Optional[str] = None
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xyShiftPlot: Optional[str] = None
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projXY: Optional[str] = None
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projXZ: Optional[str] = None
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recordTimeStamp: Optional[datetime.datetime] = None
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globalAlignmentQuality: Optional[float] = None
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gridSquareId: Optional[int] = Field(foreign_key="GridSquare.gridSquareId")
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pixelLocationX: Optional[int] = None
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pixelLocationY: Optional[int] = None
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AutoProcProgram: Optional["AutoProcProgram"] = Relationship(
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back_populates="Tomogram"
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)
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DataCollection: Optional["DataCollection"] = Relationship(back_populates="Tomogram")
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GridSquare: Optional["GridSquare"] = Relationship(back_populates="Tomogram")
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ProcessedTomogram: List["ProcessedTomogram"] = Relationship(
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back_populates="Tomogram"
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)
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TiltImageAlignment: List["TiltImageAlignment"] = Relationship(
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back_populates="Tomogram"
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)
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class CTF(SQLModel, table=True): # type: ignore
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ctfId: int = Field(primary_key=True, unique=True)
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motionCorrectionId: Optional[int] = Field(
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foreign_key="MotionCorrection.motionCorrectionId"
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)
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autoProcProgramId: Optional[int] = Field(foreign_key="AutoProcProgram.id")
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boxSizeX: Optional[float] = None
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boxSizeY: Optional[float] = None
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minResolution: Optional[float] = None
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maxResolution: Optional[float] = None
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minDefocus: Optional[float] = None
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maxDefocus: Optional[float] = None
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defocusStepSize: Optional[float] = None
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astigmatism: Optional[float] = None
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astigmatismAngle: Optional[float] = None
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estimatedResolution: Optional[float] = None
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estimatedDefocus: Optional[float] = None
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amplitudeContrast: Optional[float] = None
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ccValue: Optional[float] = None
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fftTheoreticalFullPath: Optional[str] = None
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comments: Optional[str] = None
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AutoProcProgram: Optional["AutoProcProgram"] = Relationship(back_populates="CTF")
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MotionCorrection: Optional["MotionCorrection"] = Relationship(back_populates="CTF")
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class ParticlePicker(SQLModel, table=True): # type: ignore
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particlePickerId: int = Field(primary_key=True, unique=True)
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programId: Optional[int] = Field(foreign_key="AutoProcProgram.autoProcProgramId")
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firstMotionCorrectionId: Optional[int] = Field(
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foreign_key="MotionCorrection.motionCorrectionId"
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)
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particlePickingTemplate: Optional[str] = None
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particleDiameter: Optional[float] = None
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numberOfParticles: Optional[int] = None
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summaryImageFullPath: Optional[str] = None
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MotionCorrection: Optional["MotionCorrection"] = Relationship(
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back_populates="ParticlePicker"
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)
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AutoProcProgram: Optional["AutoProcProgram"] = Relationship(
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back_populates="ParticlePicker"
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)
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ParticleClassificationGroup: List["ParticleClassificationGroup"] = Relationship(
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back_populates="ParticlePicker"
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)
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class ProcessedTomogram(SQLModel, table=True): # type: ignore
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processedTomogramId: int = Field(primary_key=True, unique=True)
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tomogramId: int = Field(foreign_key="Tomogram.tomogramId")
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filePath: Optional[str] = None
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processingType: Optional[str] = None
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Tomogram: Optional["Tomogram"] = Relationship(back_populates="ProcessedTomogram")
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class RelativeIceThickness(SQLModel, table=True): # type: ignore
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relativeIceThicknessId: int = Field(primary_key=True, unique=True)
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motionCorrectionId: Optional[int] = Field(
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foreign_key="MotionCorrection.motionCorrectionId"
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)
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autoProcProgramId: Optional[int] = Field(
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foreign_key="AutoProcProgram.autoProcProgramId"
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)
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minimum: Optional[float] = None
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q1: Optional[float] = None
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median: Optional[float] = None
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q3: Optional[float] = None
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maximum: Optional[float] = None
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AutoProcProgram: Optional["AutoProcProgram"] = Relationship(
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back_populates="RelativeIceThickness"
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)
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MotionCorrection: Optional["MotionCorrection"] = Relationship(
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back_populates="RelativeIceThickness"
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)
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class TiltImageAlignment(SQLModel, table=True): # type: ignore
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movieId: int = Field(foreign_key="Movie.movieId", primary_key=True)
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tomogramId: int = Field(foreign_key="Tomogram.tomogramId", primary_key=True)
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defocusU: Optional[float] = None
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defocusV: Optional[float] = None
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psdFile: Optional[str] = None
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resolution: Optional[float] = None
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fitQuality: Optional[float] = None
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refinedMagnification: Optional[float] = None
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refinedTiltAngle: Optional[float] = None
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refinedTiltAxis: Optional[float] = None
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residualError: Optional[float] = None
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Movie: Optional["Movie"] = Relationship(back_populates="TiltImageAlignment")
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Tomogram: Optional["Tomogram"] = Relationship(back_populates="TiltImageAlignment")
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class ParticleClassificationGroup(SQLModel, table=True): # type: ignore
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particleClassificationGroupId: int = Field(primary_key=True, unique=True)
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particlePickerId: Optional[int] = Field(
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foreign_key="ParticlePicker.particlePickerId"
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)
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programId: Optional[int] = Field(foreign_key="AutoProcProgram.autoProcProgramId")
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type: Optional[str] = Enum("2D", "3D")
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batchNumber: Optional[int] = None
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numberOfParticlesPerBatch: Optional[int] = None
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numberOfClassesPerBatch: Optional[int] = None
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symmetry: Optional[str] = None
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binnedPixelSize: Optional[float] = None
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ParticlePicker: Optional["ParticlePicker"] = Relationship(
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back_populates="ParticleClassificationGroup"
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)
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AutoProcProgram: Optional["AutoProcProgram"] = Relationship(
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back_populates="ParticleClassificationGroup"
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)
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ParticleClassification: List["ParticleClassification"] = Relationship(
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back_populates="ParticleClassificationGroup"
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)
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class ParticleClassification(SQLModel, table=True): # type: ignore
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particleClassificationId: int = Field(primary_key=True, unique=True)
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classNumber: Optional[int] = None
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classImageFullPath: Optional[str] = None
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particlesPerClass: Optional[int] = None
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rotationAccuracy: Optional[float] = None
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translationAccuracy: Optional[float] = None
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estimatedResolution: Optional[float] = None
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overallFourierCompleteness: Optional[float] = None
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particleClassificationGroupId: Optional[int] = Field(
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foreign_key="ParticleClassificationGroup.particleClassificationGroupId"
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)
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classDistribution: Optional[float] = None
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selected: Optional[int] = None
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bFactorFitIntercept: Optional[float] = None
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bFactorFitLinear: Optional[float] = None
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bFactorFitQuadratic: Optional[float] = None
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angularEfficiency: Optional[float] = None
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suggestedTilt: Optional[float] = None
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CryoemInitialModel: List["CryoemInitialModel"] = Relationship(
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back_populates="ParticleClassification"
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)
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ParticleClassificationGroup: Optional["ParticleClassificationGroup"] = Relationship(
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back_populates="ParticleClassification"
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)
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BFactorFit: List["BFactorFit"] = Relationship(
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back_populates="ParticleClassification"
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)
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class BFactorFit(SQLModel, table=True): # type: ignore
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bFactorFitId: int = Field(primary_key=True, unique=True)
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particleClassificationId: int = Field(
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foreign_key="ParticleClassification.particleClassificationId"
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)
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resolution: Optional[float] = None
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numberOfParticles: Optional[int] = None
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particleBatchSize: Optional[int] = None
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ParticleClassification: Optional["ParticleClassification"] = Relationship(
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back_populates="BFactorFit"
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)
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class CryoemInitialModel(SQLModel, table=True): # type: ignore
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cryoemInitialModelId: int = Field(primary_key=True, unique=True)
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resolution: Optional[float] = None
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numberOfParticles: Optional[int] = None
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ParticleClassification: List["ParticleClassification"] = Relationship(
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back_populates="CryoemInitialModel"
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)

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