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CopickTomogram

copick.models.CopickTomogram

Encapsulates all data pertaining to a specific tomogram. This includes the features for this tomogram and the associated Zarr-store.

Attributes:

  • voxel_spacing (CopickVoxelSpacing) –

    Reference to the voxel spacing this tomogram belongs to.

  • meta (CopickTomogramMeta) –

    Metadata for this tomogram.

  • features (List[CopickFeatures]) –

    Features for this tomogram. Either populated from config or lazily loaded when CopickTomogram.features is accessed for the first time.

  • tomo_type (str) –

    Type of the tomogram.

link_id: str

Identifier of this tomogram within its run, as alignments name the tomograms they apply to.

shape 

shape: Optional[Tuple[int, int, int]]

Shape (z, y, x) of the full-size tomogram, or None if it holds no data.

alignment_link: Optional[CopickTomogramLink]

What this tomogram was reconstructed from, or None if unknown.

Resolved from, in order: an alignment of the run naming this (read-only) tomogram, the link recorded with the tomogram, and the link its source records (e.g. the CryoET Data Portal).

alignment 

alignment: Optional[CopickAlignment]

The alignment this tomogram was reconstructed with, or None if unknown.

tilt_series 

tilt_series: Optional[CopickTiltSeries]

The tilt series this tomogram was reconstructed from, or None if unknown.

get_features 

get_features(feature_type: str) -> Union[CopickFeatures, None]

Get feature maps by type.

Parameters:

  • feature_type (str) –

    Type of the feature map to retrieve.

Returns:

  • CopickFeatures ( Union[CopickFeatures, None] ) –

    The feature map with the given type, or None if not found.

new_features 

new_features(feature_type: str, exist_ok: bool = False, **kwargs) -> CopickFeatures

Create a new feature map object. Also creates the Zarr-store for the map in the storage backend.

Parameters:

  • feature_type (str) –

    Type of the feature map to create.

  • exist_ok (bool, default: False ) –

    Whether to raise an error if the feature map already exists.

  • **kwargs –

    Additional keyword arguments for the feature map metadata.

Returns:

  • CopickFeatures ( CopickFeatures ) –

    The newly created feature map object.

Raises:

  • ValueError –

    If a feature map with the given type already exists for this tomogram.

query_features 

query_features() -> List[CopickFeatures]

Override this method to query for features.

refresh_features 

refresh_features() -> None

Refresh CopickTomogram.features from storage.

refresh 

refresh() -> None

Refresh CopickTomogram.features from storage.

delete 

delete() -> None

Delete the tomogram record.

delete_features 

delete_features() -> None

Delete all features for this tomogram.

zarr 

zarr() -> MutableMapping

Override to return the Zarr store for this tomogram. Also needs to handle creating the store if it doesn't exist.

set_alignment 

set_alignment(alignment: Union[CopickAlignment, str, None], reference_offset: Optional[Tuple[float, float, float]] = None, strict: bool = False) -> None

Record the alignment this tomogram was reconstructed with, or remove the record.

A writable tomogram records the link itself. A read-only tomogram is named by the (writable) alignment instead; removing such a link restores the link the tomogram or its source record, if any.

Parameters:

  • alignment (Union[CopickAlignment, str, None]) –

    The alignment or its name; None removes the link.

  • reference_offset (Optional[Tuple[float, float, float]], default: None ) –

    Offset in Angstrom from this tomogram's CETS frame to the alignment's reference volume frame, if they do not share the alignment's rotation centre.

  • strict (bool, default: False ) –

    Whether a tomogram whose extent differs from the alignment's reference volume by more than a voxel is an error rather than a warning.

Raises:

  • ValueError –

    If the alignment is not in this tomogram's run.

  • PermissionError –

    If neither the tomogram nor the alignment can record the link.

numpy 

numpy(zarr_group: str = '0', x: slice = slice(None, None), y: slice = slice(None, None), z: slice = slice(None, None)) -> np.ndarray

Returns the content of the Zarr-File for this tomogram as a numpy array. Multiscale group and slices are supported.

Parameters:

  • zarr_group (str, default: '0' ) –

    Zarr group to access.

  • x (slice, default: slice(None, None) ) –

    Slice for the x-axis.

  • y (slice, default: slice(None, None) ) –

    Slice for the y-axis.

  • z (slice, default: slice(None, None) ) –

    Slice for the z-axis.

Returns:

  • ndarray –

    np.ndarray: The tomogram as a numpy array.

from_numpy 

from_numpy(data: ndarray, levels: int = 3, dtype: Optional[dtype] = np.float32) -> None

Set the tomogram from a numpy array and compute multiscale pyramid. By default, three levels of the pyramid are computed.

Parameters:

  • data (ndarray) –

    The segmentation as a numpy array.

  • levels (int, default: 3 ) –

    Number of levels in the multiscale pyramid.

  • dtype (Optional[dtype], default: float32 ) –

    Data type of the segmentation. Default is np.float32.

set_region 

set_region(data: ndarray, zarr_group: str = '0', x: slice = slice(None, None), y: slice = slice(None, None), z: slice = slice(None, None)) -> None

Set a region of the tomogram from a numpy array.

Parameters:

  • data (ndarray) –

    The tomogram's subregion as a numpy array.

  • zarr_group (str, default: '0' ) –

    Zarr group to access.

  • x (slice, default: slice(None, None) ) –

    Slice for the x-axis.

  • y (slice, default: slice(None, None) ) –

    Slice for the y-axis.

  • z (slice, default: slice(None, None) ) –

    Slice for the z-axis.