CopickAlignmentFile

Bases: BaseModel

An alignment of a tilt series: per-section rigid projection parameters and where they apply.

Stored as {run}/Alignments/{name}.json, CETS-shaped (see copick.util.cets).

Attributes:

• name (str) –

  Name of the alignment, unique within its run.

• run_name (Optional[str]) –

  Name of the run.

• tilt_series (Optional[str]) –

  Type of the tilt series the alignment aligns.

• tilt_series_portal_id (Optional[int]) –

  CryoET Data Portal identifier of that tilt series, if it is one.

• linked_tomograms (List[str]) –

  Read-only tomograms reconstructed with this alignment that do not record it themselves, as "{tomo_type}@{voxel_size:.3f}".

• alignment_type (Literal['GLOBAL', 'LOCAL']) –

  GLOBAL or LOCAL. Of a local alignment only the rigid (global) part is stored.

• method (Optional[str]) –

  Method that computed the alignment (e.g. patch_tracking).

• source_format (Optional[str]) –

  Format the alignment was imported from (e.g. ARETOMO3).

• native_frame (Dict[str, str]) –

  Centre conventions of the source (image_center, volume_center: half or floor).

• status (Literal['author', 'portal_default', 'no_per_section', 'inconsistent']) –

  author for an alignment from its author; portal_default for a CryoET Data Portal placeholder alignment, no_per_section for another alignment without per-section parameters, inconsistent for one that does not fit its tilt series.

• is_portal_standard (Optional[bool]) –

  Whether the CryoET Data Portal marks the alignment as its standard.

• preferred (bool) –

  Whether the alignment is preferred over others of its tilt series.

• rigid_part_of_local (bool) –

  Whether this is the rigid part of a local alignment.

• reference_volume (Optional[CopickReferenceVolume]) –

  The volume the positions refer to.

• sections (List[CopickSectionAlignment]) –

  Per-section parameters, ordered by section.

• excluded_sections (List[CopickExcludedSection]) –

  Sections not aligned.

• tilt_offset (Optional[float]) –

  Tilt-angle offset reported by the source in degrees; included in tilt_angle.

• x_rotation_offset (Optional[float]) –

  Offset of the rotation about x reported by the source in degrees.

• warnings (List[str]) –

  Losses or assumptions of the import.

• provenance (Dict[str, Any]) –

  Where the alignment came from (program, files, portal identifiers).

name: str

run_name: Optional[str] = None

tilt_series: Optional[str] = None

tilt_series_portal_id: Optional[int] = None

linked_tomograms: List[str] = Field(default_factory=list)

alignment_type: Literal['GLOBAL', 'LOCAL'] = 'GLOBAL'

method: Optional[str] = None

source_format: Optional[str] = None

native_frame: Dict[str, str] = Field(default_factory=lambda: {'image_center': 'floor', 'volume_center': 'floor'})

status: Literal['author', 'portal_default', 'no_per_section', 'inconsistent'] = 'author'

is_portal_standard: Optional[bool] = None

preferred: bool = False

rigid_part_of_local: bool = False

reference_volume: Optional[CopickReferenceVolume] = None

sections: List[CopickSectionAlignment] = Field(default_factory=list)

excluded_sections: List[CopickExcludedSection] = Field(default_factory=list)

tilt_offset: Optional[float] = None

x_rotation_offset: Optional[float] = None

warnings: List[str] = Field(default_factory=list)

provenance: Dict[str, Any] = Field(default_factory=dict)

is_valid: bool

portal_alignment_id: Optional[int]