Add additional columns to the 'ImagingSite' table to keep track of stage position, image field of view, and rotation

Author: tieneupin

src/murfey/util/db.py

@@ -107,9 +107,6 @@ class ImagingSite(SQLModel, table=True):  # type: ignore
         foreign_key="session.id", default=None, unique=False
     )
 
-    # Type of data (atlas/overview or grid square)
-    data_type: Optional[str] = Field(default=None)  # "atlas" or "grid_square"
-
     # Link to data collection group
     data_collection_group: Optional["DataCollectionGroup"] = Relationship(
         back_populates="imaging_sites"
@@ -123,20 +120,38 @@ class ImagingSite(SQLModel, table=True):  # type: ignore
     grid_square: Optional["GridSquare"] = Relationship(back_populates="imaging_sites")
     grid_square_id: Optional[int] = Field(foreign_key="gridsquare.id", default=None)
 
+    # Type of data (atlas/overview or grid square)
+    data_type: Optional[str] = Field(default=None)  # "atlas" or "grid_square"
+
+    # Stage position (image centre) and rotation
+    stage_x: Optional[float] = Field(default=None)
+    stage_y: Optional[float] = Field(default=None)
+    stage_z: Optional[float] = Field(default=None)
+    rotation: Optional[float] = Field(default=None)
+    tilt_alpha: Optional[float] = Field(default=None)
+    tilt_beta: Optional[float] = Field(default=None)
+
+    # Field and depth of view
+    length_x: Optional[float] = Field(default=None)
+    length_y: Optional[float] = Field(default=None)
+    length_z: Optional[float] = Field(default=None)
+
+    # Extent of the imaged area in real space
+    x0: Optional[float] = Field(default=None)
+    x1: Optional[float] = Field(default=None)
+    y0: Optional[float] = Field(default=None)
+    y1: Optional[float] = Field(default=None)
+
     # Shape and resolution information
     image_pixels_x: Optional[int] = Field(default=None)
     image_pixels_y: Optional[int] = Field(default=None)
     image_pixel_size: Optional[float] = Field(default=None)
     thumbnail_pixels_x: Optional[int] = Field(default=None)
     thumbnail_pixels_y: Optional[int] = Field(default=None)
     thumbnail_pixel_size: Optional[float] = Field(default=None)
-    units: Optional[str] = Field(default=None)
 
-    # Extent of the imaged area in real space
-    x0: Optional[float] = Field(default=None)
-    x1: Optional[float] = Field(default=None)
-    y0: Optional[float] = Field(default=None)
-    y1: Optional[float] = Field(default=None)
+    # Spatial units
+    units: Optional[str] = Field(default=None)
 
     # Colour channel-related fields
     number_of_members: Optional[int] = Field(default=None)