Create a TomoStack instance, used to represent tomographic tilt series data.

All arguments are passed to the Signal2D constructor and should be used as documented for that method.

Constructors¶

TomoStack(data: ndarray | Signal2D, ...)[source]

Create a TomoStack signal instance.

Methods¶

shift_and_tilt_setter(mode, ...) → TomoShifts | TomoTilts[source]

Set either self._tilts or self._shifts to an array.

deepcopy()[source]

Return a “deep copy” of this Stack.

copy()[source]

Return a “shallow copy” of this Stack.

plot_sinos(*args: tuple, **kwargs: dict)[source]

Plot the TomoStack in sinogram orientation.

remove_projections(projections: list | None = None) → TomoStack[source]

Return a copy of the TomoStack with certain projections removed from the series.

save(filename=None, overwrite=None, extension=None, ...)[source]

Save the signal in the specified format.

test_correlation(...) → Figure[source]

Test output of cross-correlation prior to alignment.

align_other(other: TomoStack) → TomoStack[source]

Apply the alignment calculated for one dataset to another.

filter(...) → TomoStack[source]

Apply one of several image filters to an entire TomoStack.

stack_register(...) → TomoStack[source]

Register stack spatially.

tilt_align(method: 'CoM' | 'MaxImage', ...)[source]

Align the tilt axis of a TomoStack.

reconstruct(...) → RecStack[source]

Reconstruct a TomoStack series using one of the available methods.

test_align(tilt_shift: float = 0.0, ...) → Figure[source]

Perform a reconstruction with limited slices for visual inspection.

set_tilts(start: float, increment: float)[source]

Calibrate the tilt axis of the image stack.

manual_align(nslice: int, xshift: int = 0, ...) → TomoStack[source]

Manually shift part of a stack with respect to another and return it as a copy.

recon_error(...) → tuple[Signal2D, Signal1D][source]

Determine the optimum number of iterations for reconstruction.

extract_sinogram(column: int | float) → Signal2D[source]

Extract a sinogram from a single column of the TomoStack.

plot(navigator: str = 'slider', *args, **kwargs)[source]

Override of plot function to set default HyperSpy navigator to ‘slider’.

change_data_type(dtype: str | dtype)[source]

Change the data type of a stack.

invert() → Self[source]

Create a copy of a Stack with inverted contrast levels.

normalize(width: int = 3) → Self[source]

Create a copy of a stack with normalized contrast levels.

save_movie(start: int, stop: int, ...)[source]

Save the Stack as an AVI movie file.

save_raw(filename: str | Path | None = None) → Path[source]

Save Stack data as a .raw/.rpl file pair.

stats()[source]

Print some basic statistics about Stack data.

trans_stack(xshift: float = 0.0, yshift: float = 0.0, ...) → Self[source]

Create a copy of a Stack, transformed using the skimage Affine transform.

Properties¶

property shifts : TomoShifts

The stack’s image shift values (in pixels).

property tilts : TomoTilts

The stack’s tilt values (in degrees).