porespy.tools

This module contains a variety of functions for manipulating images in ways that do NOT return a modified version of the original image.

Classes

Results	A minimal class for use when returning multiple values from a function
Settings	A dataclass for use at the module level to store settings. This class

Functions

align_image_with_openpnm(im)	Rotates an image to agree with the coordinates used in OpenPNM.
all_to_uniform(im[, scale])	Take an image with some distribution of greyscale values and convert it to
area_of_triangle(p0, p1, p2)	As per Herons formula
ball(r)
bbox_to_slices(bbox)	Given a tuple containing bounding box coordinates, return a tuple of slice
block_size_to_divs(shape, block_size)	Finds the number of blocks in each direction given the size of the blocks
calculate_area_and_volume(img, vertex_index_array[, ...])
center_of_mass(im)
create_mc_template_list([spacing])	Return area and volume lists for the marching cubes templates. Reads the
cube(w)
disk(r)
extend_slice(slices, shape[, pad])	Adjust slice indices to include additional voxles around the slice.
extract_cylinder(im[, r, axis])	Returns a cylindrical section of the image of specified radius.
extract_regions(regions, labels[, trim])	Combine given regions into a single boolean mask
extract_subsection(im, shape)	Extracts the middle section of a image
face_orientation(v0, v1, v2)	Return outward perpendicular vector distance of face along the z axis
find_bbox(im[, order_by])	Finds the lower and upper corner surrounding the foreground in the image
find_outer_region(im[, r])	Find regions of the image that are outside of the solid matrix.
get_block_sizes(im[, block_size_range])	Finds all viable block sizes between lower and upper limits
get_edt()
get_fixtures_path()	Get the path to the test fixtures directory.
get_planes(im[, squeeze])	Extracts three planar images from the volumetric image, one for each
get_skel()
get_slices_grid(im[, divs, block_size, overlap, mode])	Returns slices into an image describing the specified number of sub-arrays.
get_slices_multigrid(im, block_size_range[, overlap, mode])	Creates a set of grids spanning the request block size range
get_slices_random(im[, n, lims, aspect])	Generates a list of slice objects which can be used to obtain cubic subdomains
get_slices_slabs(im[, axis, span, step, mode])	Generates a list of slice objects which can be used to obtain slabs of an image
get_strel()
get_tqdm()	Fetches a version of tqdm function that depends on the environment.
in_hull(points, hull)	Test if a list of coordinates are inside a given convex hull
insert_cylinder(im, xyz0, xyz1, r)	Inserts a cylinder of given radius onto an image
insert_sphere(im, c, r[, v, overwrite])	Inserts a sphere of a specified radius into a given image
isolate_object(region, i[, s])	Given an image containing labels, removes all labels except the specified
jit_extend_slice(slices, shape[, pad])
jit_marching_cubes_area_and_volume(img[, ...])
jit_marching_squares_perimeter_and_area(img[, ...])
make_contiguous(im[, mode])	Take an image with arbitrary greyscale values and adjust them to ensure
marching_cubes_area_and_volume(img[, target_label, ...])
marching_map(path, start)	Use the fast marching method to find distance of each voxel from a starting
mc_templates_generator([override])	Generates a marching cubes template list file, if one is not available
mesh_region(region[, strel, voxel_size])	Creates a tri-mesh of the provided region using the marching cubes
overlay(im1, im2, c)	Overlays im2 onto im1, given voxel coords of center of im2
pad(img)	Assumes pad width=1 and mode is constant = 0
parse_shape(im_or_shape)	Given a list of dimensions or an image finds shape in a clean format
parse_steps(steps, vals[, mask, descending])	Converts given steps into a list of sizes
points_to_spheres(im)	Inserts disks/spheres into an image at locations indicated by non-zero values
ps_ball(r[, smooth])	Creates spherical ball structuring element for morphological operations
ps_disk(r[, smooth])	Creates circular disk structuring element for morphological operations
ps_rect(w, ndim)	Creates rectilinear structuring element with the given size and
ps_round(r, ndim[, smooth])	Creates round structuring element with the given radius and dimensionality
randomize_colors(im[, keep_vals])	Takes a greyscale image and randomly shuffles the greyscale values.
recombine(ims, slices, overlap)	Recombines image blocks back into full image
results_to_df(obj)	A helper function to convert Results objects to pandas DataFrames.
sanitize_filename(filename, ext[, exclude_ext])	Returns a sanitized string in the form of name.extension
show_docstring(func)	Fetches the docstring for a function and returns it in markdown format.
square(w)
tic()	Homemade version of matlab tic and toc function, tic starts or resets
toc([quiet])	Homemade version of matlab tic and toc function, tic starts or resets
unpad(im, pad_width)	Remove padding from a previously padded image given original pad widths

Package Contents

settings