mmt_dipole_cuboid_inversion.tools.cuboid_decompose

Cuboid decomposition of microCT particle voxel data @author: Karl Fabian, NTNU Licensed under MIT License, 2021

Module Contents

Functions

LEQ(a, b)	Given two lists a and b, returns True only if all elements of a are less
TupleMaxima(lst)	Sorts a list of sequences to find locations to generate largest cuboid
tolen(lst)	Converts a list lst of 0,1 values to the lengths of cosecutive 1's
get_voxel_file(fn)	Reads voxel file and returns system properties to start decomposition
findmax(layer, ldim, a, b)	Find maximum
findmax3(arr, adim, maxdir, a, b, c)
max_cuboid(zarr)
cuboid_decomposition_method(mn, zarr)
CuboidDecomposition(fn, fnout[, format_output])	Perform cuboid aggregation decomposition of pixel data from a text file

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.LEQ(a, b)

Given two lists a and b, returns True only if all elements of a are less or equal than the elements of b. Return False when at least one element of a is >= than an element of b

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.TupleMaxima(lst)

Sorts a list of sequences to find locations to generate largest cuboid

Given a list of sequences (or 2-sequences) perform:

• Sort them by their minimum value and invert sorting

• Choose the one with the largest minimum (first element in sorted list)

  and append it to a list, say MAX

• Iterate through the other sequences

  • If one of the iterated seq is not LEQ with the first element in MAX

    (largest minimum) then append it to the MAX list. The next iteration

    will have to compare if the seq is not LEQ with the two (or more)

    elements in MAX (and so on, MAX can grow during iteration)

Parameters:

lst

Sequence of lists

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.tolen(lst)

Converts a list lst of 0,1 values to the lengths of cosecutive 1’s to the right up to an element containing a 0 tolen( [0,0,1,1,1,0,0,1,1,0,1]) -> [0,0,3,2,1,0,0,2,1,0,1]

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.get_voxel_file(fn)

Reads voxel file and returns system properties to start decomposition

Parameters:

fn

Text file with 4 columns: index, x, y, z. First row is skipped. The data is in integer format, which represent the grain-index and pixel coordinates. Column headers can have any name but should be in order.

Returns:

A 4-elements tuple: (min, max, count, zeros_array) where

min -> minimum of x y z positions ..

max -> maximum of x y z positions ..

count -> number of voxels ..

zeros_array -> a 3D matrix with zeros and ones, with the dimensions ..

according to the grain size, e.g. max_x - min_x ..

Values 1 are placed where x y z positions are located ..

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.findmax(layer, ldim, a, b)

Find maximum

For a layer (2D array) with dimensions (ldim[0], ldim[1]) layer is a 2D array with the number of consecutive 1s to the right at positions row=a, col=b

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.findmax3(arr, adim, maxdir, a, b, c)

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.max_cuboid(zarr)

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.cuboid_decomposition_method(mn, zarr)

mmt_dipole_cuboid_inversion.tools.cuboid_decompose.CuboidDecomposition(fn, fnout, format_output=False)

Perform cuboid aggregation decomposition of pixel data from a text file

Parameters:

fn

Text file with 4 columns: index, x, y, z. First row is skipped. The data is in integer format, which represent the index and pixel coordinates. Column headers can have any name but should be in order.

fnout

File name for output CSV text file with cuboid decomposition.

format_output

If False, the output file contains the lower and upper corners defining the cuboids in pixel coordinates (pixel centers). If True, the output contains the center coordinates of every cuboid, half the cuboid lenghts in every spatial dimension and the indexes as x, y, z, dx, dy, dz, index