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

_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

_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

query_voxelspacings() -> List[CopickVoxelSpacingOverlay]

Query all voxel spacings.

Returns:

List[CopickVoxelSpacingOverlay] –

List[CopickVoxelSpacingOverlay]: List of voxel spacings from both sources.

_query_static_picks

_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

_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

query_picks() -> List[CopickPicksOverlay]

Query all picks.

Returns:

List[CopickPicksOverlay] –

List[CopickPicksOverlay]: List of picks from both sources.

_query_static_filaments

_query_static_filaments() -> List[CopickFilamentsOverlay]

Override to query the static source for filaments; all returned filaments must be read-only. Sources without filaments return none.

_query_overlay_filaments

_query_overlay_filaments() -> List[CopickFilamentsOverlay]

Override to query the overlay source for filaments. Sources without filaments return none.

query_filaments

query_filaments() -> List[CopickFilamentsOverlay]

Query all filaments.

Returns:

List[CopickFilamentsOverlay] –

List[CopickFilamentsOverlay]: List of filaments from both sources.

_query_static_tilt_series

_query_static_tilt_series() -> List[CopickTiltSeriesOverlay]

Override to query the static source for tilt series; all returned tilt series must be read-only. Sources without tilt series return none.

_query_overlay_tilt_series

_query_overlay_tilt_series() -> List[CopickTiltSeriesOverlay]

Override to query the overlay source for tilt series. Sources without tilt series return none.

query_tilt_series

query_tilt_series() -> List[CopickTiltSeriesOverlay]

Query all tilt series.

Returns:

List[CopickTiltSeriesOverlay] –

List[CopickTiltSeriesOverlay]: List of tilt series from both sources.

_query_static_alignments

_query_static_alignments() -> List[CopickAlignmentOverlay]

Override to query the static source for alignments; all returned alignments must be read-only. Sources without alignments return none.

_query_overlay_alignments

_query_overlay_alignments() -> List[CopickAlignmentOverlay]

Override to query the overlay source for alignments. Sources without alignments return none.

query_alignments

query_alignments() -> List[CopickAlignmentOverlay]

Query all alignments. An overlay alignment of the same name as a static one is not listed.

Returns:

List[CopickAlignmentOverlay] –

List[CopickAlignmentOverlay]: List of alignments from both sources.

_query_static_meshes

_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

_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

query_meshes() -> List[CopickMeshOverlay]

Query all meshes.

Returns:

List[CopickMeshOverlay] –

List[CopickMeshOverlay]: List of meshes from both sources.

_query_static_segmentations

_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

_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

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.

delete

delete()

Delete the object, making sure the source is writable.

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()

Store the picks, making sure the source is writable.

delete

delete()

Delete the picks, making sure the source is writable.

copick.impl.overlay.CopickFilamentsOverlay

Bases: CopickFilaments

CopickFilaments class that keeps track of whether the filaments are read-only.

Attributes:

read_only (bool) –

Whether the filaments are read-only.

store

store()

Store the filaments, making sure the source is writable.

delete

delete()

Delete the filaments, 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()

Store the mesh, making sure the source is writable.

delete

delete()

Delete 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.

delete

delete()

Delete the segmentation, making sure the source is writable.

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

_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

_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

query_tomograms() -> List[CopickTomogramOverlay]

Query all tomograms.

Returns:

List[CopickTomogramOverlay] –

List[CopickTomogramOverlay]: List of tomograms from both sources.

copick.impl.overlay.CopickAlignmentOverlay

Bases: CopickAlignment

CopickAlignment class that keeps track of whether the alignment is read-only.

Attributes:

read_only (bool) –

Whether the alignment is read-only.

store

store() -> None

Store the alignment, making sure the source is writable.

delete

delete(unlink: bool = True) -> None

Delete the alignment, making sure the source is writable.

copick.impl.overlay.CopickTiltSeriesOverlay

Bases: CopickTiltSeries

CopickTiltSeries class that keeps track of whether the tilt series is read-only.

Attributes:

read_only (bool) –

Whether the tilt series is read-only.

from_numpy

from_numpy(*args, **kwargs) -> None

Write the images, making sure the source is writable.

set_region

set_region(*args, **kwargs) -> None

Write a region of the images, making sure the source is writable.

store_metadata

store_metadata(*args, **kwargs) -> None

Store the metadata, making sure the source is writable.

delete

delete() -> None

Delete the tilt series, making sure the source is writable.

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

_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

_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

query_features() -> List[CopickFeaturesOverlay]

Query all features.

Returns:

List[CopickFeaturesOverlay] –

List[CopickFeaturesOverlay]: List of features from both sources.

delete

delete() -> None

Delete the tomogram, making sure the source is writable.

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.

delete

delete()

Delete the features, making sure the source is writable.