Skip to content

File System

The filesystem implementation is a concrete implementation of the abstract copick API that reads and writes data to/from any storage supported by fsspec. The filesystem implementation is defined in the copick.impl.filesystem module.

Metadata Models

copick.impl.filesystem.CopickConfigFSSpec

Bases: CopickConfig

Copick configuration for fsspec-based storage.

Attributes:

  • overlay_root (str) –

    The root URL for the overlay storage.

  • static_root (Optional[str]) –

    The root URL for the static storage.

  • overlay_fs_args (Optional[Dict[str, Any]]) –

    Additional arguments for the overlay filesystem.

  • static_fs_args (Optional[Dict[str, Any]]) –

    Additional arguments for the static filesystem.

Data Entities

copick.impl.filesystem.CopickRootFSSpec

Bases: CopickRoot

CopickRoot class backed by fspec storage.

Attributes:

  • fs_overlay (AbstractFileSystem) –

    The filesystem for the overlay storage.

  • fs_static (Optional[AbstractFileSystem]) –

    The filesystem for the static storage.

  • root_overlay (str) –

    The root path for the overlay storage.

  • root_static (Optional[str]) –

    The root path for the static storage.

__init__ 

__init__(config: CopickConfigFSSpec)

Parameters:

from_file 

from_file(path: str) -> CopickRootFSSpec

Initialize a CopickRootFSSpec from a configuration file on disk.

Parameters:

  • path (str) –

    Path to the configuration file on disk.

Returns:

  • CopickRootFSSpec ( CopickRootFSSpec ) –

    The initialized CopickRootFSSpec object.

copick.impl.filesystem.CopickObjectFSSpec

Bases: CopickObjectOverlay

CopickObject class backed by fsspec storage.

Attributes:

  • static_path (str) –

    The path to the object on the static source.

  • overlay_path (str) –

    The path to the object on the overlay source.

  • fs_static (AbstractFileSystem) –

    The filesystem for the static source.

  • fs_overlay (AbstractFileSystem) –

    The filesystem for the overlay source.

zarr 

zarr() -> Union[None, zarr.storage.FSStore]

Get the zarr store for the object.

Returns:

  • Union[None, FSStore] –

    Union[None, zarr.storage.FSStore]: The zarr store for the object, or None if the object is not a particle.

copick.impl.filesystem.CopickRunFSSpec

Bases: CopickRunOverlay

CopickRun class backed by fsspec storage.

Attributes:

  • static_path (str) –

    The path to the run on the static source.

  • overlay_path (str) –

    The path to the run on the overlay source.

  • fs_static (AbstractFileSystem) –

    The filesystem containing the run on the static source.

  • fs_overlay (AbstractFileSystem) –

    The filesystem containing the run on the overlay source.

  • static_is_overlay (bool) –

    Whether the static and overlay sources are the same.

ensure 

ensure(create: bool = False) -> bool

Checks if the run record exists in the static or overlay directory, optionally creating it in the overlay filesystem if it does not.

Parameters:

  • create (bool, default: False ) –

    Whether to create the run record if it does not exist.

Returns:

  • bool ( bool ) –

    True if the run record exists, False otherwise.

copick.impl.filesystem.CopickPicksFSSpec

Bases: CopickPicksOverlay

CopickPicks class backed by fsspec storage.

Attributes:

  • path (str) –

    The path to the picks file.

  • directory (str) –

    The directory containing the picks file.

  • fs (AbstractFileSystem) –

    The filesystem containing the picks file.

copick.impl.filesystem.CopickMeshFSSpec

Bases: CopickMeshOverlay

CopickMesh class backed by fspec storage.

Attributes:

  • path (str) –

    The path to the mesh file.

  • directory (str) –

    The directory containing the mesh file.

  • fs (AbstractFileSystem) –

    The filesystem containing the mesh file.

copick.impl.filesystem.CopickSegmentationFSSpec

Bases: CopickSegmentationOverlay

CopickSegmentation class backed by fsspec storage.

Attributes:

  • filename (str) –

    The filename of the segmentation file.

  • path (str) –

    The path to the segmentation file.

  • fs (AbstractFileSystem) –

    The filesystem containing the segmentation file.

zarr 

zarr() -> zarr.storage.FSStore

Get the zarr store for the segmentation object.

Returns:

  • FSStore –

    zarr.storage.FSStore: The zarr store for the segmentation object.

copick.impl.filesystem.CopickVoxelSpacingFSSpec

Bases: CopickVoxelSpacingOverlay

CopickVoxelSpacing class backed by fsspec storage.

Attributes:

  • static_path (str) –

    The path to the voxel spacing on the static source.

  • overlay_path (str) –

    The path to the voxel spacing on the overlay source.

  • fs_static (AbstractFileSystem) –

    The filesystem containing the voxel spacing on the static source.

  • fs_overlay (AbstractFileSystem) –

    The filesystem containing the voxel spacing on the overlay source.

  • static_is_overlay (bool) –

    Whether the static and overlay sources are the same.

ensure 

ensure(create: bool = False) -> bool

Checks if the voxel spacing record exists in the static or overlay directory, optionally creating it in the overlay filesystem if it does not.

Parameters:

  • create (bool, default: False ) –

    Whether to create the voxel spacing record if it does not exist.

Returns:

  • bool ( bool ) –

    True if the voxel spacing record exists, False otherwise.

copick.impl.filesystem.CopickTomogramFSSpec

Bases: CopickTomogramOverlay

CopickTomogram class backed by fsspec storage.

Attributes:

  • static_path (str) –

    The path to the tomogram on the static source.

  • overlay_path (str) –

    The path to the tomogram on the overlay source.

  • static_stem (str) –

    The stem of the tomogram on the static source.

  • overlay_stem (str) –

    The stem of the tomogram on the overlay source.

  • fs_static (AbstractFileSystem) –

    The filesystem containing the tomogram on the static source.

  • fs_overlay (AbstractFileSystem) –

    The filesystem containing the tomogram on the overlay source.

  • static_is_overlay (bool) –

    Whether the static and overlay sources are the same.

zarr 

zarr() -> zarr.storage.FSStore

Get the zarr store for the tomogram object.

Returns:

  • FSStore –

    zarr.storage.FSStore: The zarr store for the tomogram object.

copick.impl.filesystem.CopickFeaturesFSSpec

Bases: CopickFeaturesOverlay

CopickFeatures class backed by fsspec storage.

Attributes:

  • path (str) –

    The path to the features file.

  • fs (AbstractFileSystem) –

    The filesystem containing the features file.

zarr 

zarr() -> zarr.storage.FSStore

Get the zarr store for the features object.

Returns:

  • FSStore –

    zarr.storage.FSStore: The zarr store for the features object.