mantidimaging.core.data.imagestack module

class mantidimaging.core.data.imagestack.ImageStack(data: ndarray | SharedArray, filenames: list[Path] | None = None, indices: list[int] | Indices | None = None, metadata: dict[str, Any] | None = None, sinograms: bool = False, name: str | None = None)

Bases: object

cleanup() → None

copy(flip_axes: bool = False) → ImageStack

copy_roi(roi: SensibleROI) → ImageStack

count() → int

counts() → Counts | None

static create_empty_image_stack(shape: tuple[int, ...], dtype: npt.DTypeLike, metadata: dict[str, Any]) → ImageStack

create_geometry(angles: ProjectionAngles, geom_type: GeometryType = GeometryType.PARALLEL3D) → None

Creates a Geometry of given type belonging to the ImageStack Angles should be given in radians

create_geometry_from_cil_acq(acquisition_geometry: AcquisitionGeometry) → None

Creates a Geometry belong to the ImageStack from a CIL AcquisitionGeometry object.

property data: ndarray

Get a reference to the internal numpy array holding the image data

Note

Do not hold on to this reference longer than the lifetime of the ImageStack. ImageStack use the operating system’s shared memory, which will be freed when the ImageStack has no remaining references. A reference to this array will not keep that shared memory alive.

property dtype: dtype

property filenames: list[Path] | None

find_image_from_angle(target_angle: float, tol: float | None = None) → int

property full_stack_shape: tuple[int, ...] | None

The original shape of the stack irrespective of preview subsetting. For preview subsets: Returns the full shape instead of the sliced shape.

Property should be set when preview is updated, allowing operations to validate against the stacks full shape instead of the preview subset shape.

Returns:

The full shape of the stack as a tuple of ints (z, y, x) or None if not set.

geometry: Geometry | None = None

property h_middle: float

Returns the horizontal middle (middle column) of the projections

has_proj180deg() → bool

property height: int

property id: UUID

property is_processed: bool

Returns:

True if any of the data has been processed, False otherwise.

property is_sinograms: bool

is_temporary: bool = False

load_metadata(f: TextIO) → None

Load metadata json without overwriting existing values

property log_file: InstrumentLog | None

make_name_unique(existing_names: list[str]) → None

name: str

property ndim: int

property num_images: int

property num_projections: int

property num_sinograms: int

property pixel_size: float

property proj180deg: ImageStack | None

proj_180_degree_shape_matches_images() → bool

projection(projection_idx: int) → ndarray

projection_angles() → ProjectionAngles | None

Return projection angles from actual data sources (log files or manually loaded files).

This method returns angles that were either:

• Explicitly set via projection_angles setter

• Read from a log file during data loading

Returns:

Real projection angles if they were found, None otherwise.

property projections: ndarray

record_operation(func_name: str, display_name: str, *args, **kwargs) → None

reorder_images_by_index(index: ndarray) → None

save_metadata(f: TextIO, rescale_params: dict[str, str | float] | None = None) → None

set_geometry_panels() → None

Updates the geometry’s panel data based on its parent ImageStack’s array data if both geometry and array data are present.

Set the number of pixels and the pixel size for the geometry panel based on the current width and height of the image stack.

Side effects:

Modifies self.geometry by updating its panel configuration.

set_projection_angles(angles: ProjectionAngles) → None

Assigns a set of projection angles to the image stack and updates the associated geometry.

This method validates that the number of provided angles matches the number of images in the stack. If the geometry object is present, it updates its angles accordingly.

Parameters:

angles – An object containing the projection angles to assign, in radians.

Raises:

RuntimeError – If the number of angles does not match the number of images in the stack.

Side effects:

Updates the internal projection angles and, if available, updates the geometry’s angles.

property shape: tuple[int, ...]

property shared_array: SharedArray

property shutter_count_file: ShutterCount | None

sino(slice_idx: int) → ndarray

sino_as_image_stack(index: int) → ImageStack

A single sinogram slice as an ImageStack in projection ordering

property sinograms: ndarray

property size: int

slice_as_array(index: int) → ndarray

slice_as_image_stack(index: int) → ImageStack

A slice, either projection or sinogram depending on current ordering

property uses_shared_memory: bool

property width: int

exception mantidimaging.core.data.imagestack.StackNotFoundError(message: str, log_level: int = 40)

Bases: RuntimeError