Overlay
The overlay implementation is an extension of the abstract copick API implementation that adds methods to seamlessly overlay data from two
different sources. Each overlay implementation is a subclass of the corresponding abstract data entity and implements
methods to overlay data from two sources. The overlay implementations are defined in the copick.impl.overlay module.
One source is considered read-only ('static'), while the other source is considered read-write ('overlay').
copick.impl.overlay.CopickRunOverlay
Bases: CopickRun
CopickRun class that queries two different storage locations for runs. The first location is read-only (static) and the second location is writable (overlay).
_query_static_voxel_spacings() -> List[CopickVoxelSpacingOverlay]
Override to query the static source for the voxel spacings. All returned voxel spacings must be read-only.
Returns:
-
List[CopickVoxelSpacingOverlay]–List[CopickVoxelSpacingOverlay]: List of read-only voxel spacings.
_query_overlay_voxel_spacings() -> List[CopickVoxelSpacingOverlay]
Override to query the overlay source for the voxel spacings.
Returns:
-
List[CopickVoxelSpacingOverlay]–List[CopickVoxelSpacingOverlay]: List of writable voxel spacings.
query_voxelspacings() -> List[CopickVoxelSpacingOverlay]
Query all voxel spacings.
Returns:
-
List[CopickVoxelSpacingOverlay]–List[CopickVoxelSpacingOverlay]: List of voxel spacings from both sources.
_query_static_picks() -> List[CopickPicksOverlay]
Override to query the static source for the picks. All returned picks must be read-only.
Returns:
-
List[CopickPicksOverlay]–List[CopickPicksOverlay]: List of read-only picks.
_query_overlay_picks() -> List[CopickPicksOverlay]
Override to query the overlay source for the picks.
Returns:
-
List[CopickPicksOverlay]–List[CopickPicksOverlay]: List of writable picks.
query_picks() -> List[CopickPicksOverlay]
Query all picks.
Returns:
-
List[CopickPicksOverlay]–List[CopickPicksOverlay]: List of picks from both sources.
_query_static_meshes() -> List[CopickMeshOverlay]
Override to query the static source for the meshes. All returned meshes must be read-only.
Returns:
-
List[CopickMeshOverlay]–List[CopickMeshOverlay]: List of read-only meshes.
_query_overlay_meshes() -> List[CopickMeshOverlay]
Override to query the overlay source for the meshes.
Returns:
-
List[CopickMeshOverlay]–List[CopickMeshOverlay]: List of writable meshes.
query_meshes() -> List[CopickMeshOverlay]
Query all meshes.
Returns:
-
List[CopickMeshOverlay]–List[CopickMeshOverlay]: List of meshes from both sources.
_query_static_segmentations() -> List[CopickSegmentationOverlay]
Override to query the static source for the segmentations. All returned segmentations must be read-only.
Returns:
-
List[CopickSegmentationOverlay]–List[CopickSegmentationOverlay]: List of read-only segmentations.
_query_overlay_segmentations() -> List[CopickSegmentationOverlay]
Override to query the overlay source for the segmentations.
Returns:
-
List[CopickSegmentationOverlay]–List[CopickSegmentationOverlay]: List of writable segmentations.
query_segmentations() -> List[CopickSegmentationOverlay]
Query all segmentations.
Returns:
-
List[CopickSegmentationOverlay]–List[CopickSegmentationOverlay]: List of segmentations from both sources.
copick.impl.overlay.CopickObjectOverlay
Bases: CopickObject
CopickObject class that keeps track of whether the object is read-only.
Attributes:
-
read_only(bool) –Whether the object is read-only.
copick.impl.overlay.CopickPicksOverlay
Bases: CopickPicks
CopickPicks class that keeps track of whether the picks are read-only.
Attributes:
-
read_only(bool) –Whether the picks are read-only.
store()
Store the picks, making sure the source is writable.
copick.impl.overlay.CopickMeshOverlay
Bases: CopickMesh
CopickMesh class that keeps track of whether the mesh is read-only.
Attributes:
-
read_only(bool) –Whether the mesh is read-only.
store()
Store the mesh, making sure the source is writable.
copick.impl.overlay.CopickSegmentationOverlay
Bases: CopickSegmentation
CopickSegmentation class that keeps track of whether the segmentation is read-only.
Attributes:
-
read_only(bool) –Whether the segmentation is read-only.
copick.impl.overlay.CopickVoxelSpacingOverlay
Bases: CopickVoxelSpacing
CopickVoxelSpacing class that queries two different storage locations for voxel spacings. The first location is read-only (static) and the second location is writable (overlay).
_query_static_tomograms() -> List[CopickTomogramOverlay]
Override to query the static source for the tomograms. All returned tomograms must be read-only.
Returns:
-
List[CopickTomogramOverlay]–List[CopickTomogramOverlay]: List of read-only tomograms.
_query_overlay_tomograms() -> List[CopickTomogramOverlay]
Override to query the overlay source for the tomograms.
Returns:
-
List[CopickTomogramOverlay]–List[CopickTomogramOverlay]: List of writable tomograms.
query_tomograms() -> List[CopickTomogramOverlay]
Query all tomograms.
Returns:
-
List[CopickTomogramOverlay]–List[CopickTomogramOverlay]: List of tomograms from both sources.
copick.impl.overlay.CopickTomogramOverlay
Bases: CopickTomogram
CopickTomogram class that keeps track of whether the tomogram is read-only and queries two different storage locations for tomograms. The first location is read-only (static) and the second location is writable (overlay).
Attributes:
-
read_only(bool) –Whether the tomogram is read-only.
_query_static_features() -> List[CopickFeaturesOverlay]
Override to query the static source for the features. All returned features must be read-only.
Returns:
-
List[CopickFeaturesOverlay]–List[CopickFeaturesOverlay]: List of read-only features.
_query_overlay_features() -> List[CopickFeaturesOverlay]
Override to query the overlay source for the features.
Returns:
-
List[CopickFeaturesOverlay]–List[CopickFeaturesOverlay]: List of writable features.
query_features() -> List[CopickFeaturesOverlay]
Query all features.
Returns:
-
List[CopickFeaturesOverlay]–List[CopickFeaturesOverlay]: List of features from both sources.
copick.impl.overlay.CopickFeaturesOverlay
Bases: CopickFeatures
CopickFeatures class that keeps track of whether the features are read-only.
Attributes:
-
read_only(bool) –Whether the features are read-only.