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

clear_proj180deg() → 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

property data: ndarray

property dtype: dtype

property filenames: list[Path] | None

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

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 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(max_angle: float = 360.0) → ProjectionAngles

Return projection angles, in priority order: - From a log - From the manually loaded file with a list of angles - Automatically generated with equidistant step

Parameters:

max_angle – The maximum angle up to which the angles will be generated. Only used when the angles are generated, if they are provided via a log or a file the argument will be ignored.

property projections: ndarray

real_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.

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

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

set_geometry() → None

Creates an AcquisitionGeometry belonging to the ImageStack.

set_geometry_angles() → None

Updates the geometry’s angle data based on its parent ImageStack’s projection angles if both geometry and projection angles are present.

Side effects:

Modifies self.geometry by updating its angle configuration.

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 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

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