topostats.array_manipulation#

Functions for manipulating numpy arrays.

Attributes#

LOGGER

Functions#

re_crop_grain_image_and_mask_to_set_size_nm(...)

Re-crop a grain image and mask to be a target size in nanometres.

pad_bounding_box_dynamically_at_limits(→ tuple[int, ...)

Pad a bounding box within limits. If the padding would exceed the limits bounds, pad in the other direction.

Module Contents#

topostats.array_manipulation.LOGGER#
topostats.array_manipulation.re_crop_grain_image_and_mask_to_set_size_nm(filename: str, grain_number: int, grain_bbox: tuple[int, int, int, int], pixel_to_nm_scaling: float, full_image: numpy.typing.NDArray[numpy.float32], full_mask_tensor: numpy.typing.NDArray[numpy.bool_], target_size_nm: float) → tuple[numpy.typing.NDArray[numpy.float32], numpy.typing.NDArray[numpy.bool_]][source]#

Re-crop a grain image and mask to be a target size in nanometres.

Parameters:

  • filename (str) – The name of the file being processed, used for logging.

  • grain_number (int) – The number of the grain being processed, used for logging.

  • grain_bbox (tuple[int, int, int, int]) – The bounding box of the grain in the form (min_row, min_col, max_row (exclusive), max_col (exclusive)).

  • pixel_to_nm_scaling (float) – Pixel to nanometre scaling factor.

  • full_image (npt.NDArray[np.float32]) – The full image from which to crop the grain image.

  • full_mask_tensor (npt.NDArray[np.bool_]) – The full mask tensor from which to crop the mask.

  • target_size_nm (float) – The target size in nanometres to crop the grain image and mask to.

Returns:

The cropped grain image and mask, both as numpy arrays.

Return type:

tuple[npt.NDArray[np.float32], npt.NDArray[np.bool_]]

Raises:

ValueError – If the target size in nanometres is larger than the full image or mask dimensions.

topostats.array_manipulation.pad_bounding_box_dynamically_at_limits(bbox: tuple[int, int, int, int], limits: tuple[int, int, int, int], padding: int) → tuple[int, int, int, int][source]#

Pad a bounding box within limits. If the padding would exceed the limits bounds, pad in the other direction.

Parameters:

  • bbox (tuple[int, int, int, int]) – The bounding box to pad.

  • limits (tuple[int, int, int, int]) – The region to limit the bounding box to in the form (min_row, min_col, max_row, max_col).

  • padding (int) – The padding to apply to the bounding box.

Returns:

The new bounding box indices.

Return type:

tuple[int, int, int, int]