Source code for ClearMap.ImageProcessing.Filter.StructureElement

# -*- coding: utf-8 -*-
"""
StrutureElement
===============

Routines to generate structure elements for filters.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Public License v3 (see LICENSE.txt)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__ = 'https://idisco.info'
__download__ = 'https://www.github.com/ChristophKirst/ClearMap2'


import numpy as np




def disk(shape=(3, 3)):
    """Disk structuring element."""
    return sphere(shape=shape) > 0





def sphere(shape=(3, 3)):
    """Disk structuring element."""
    offsets = structure_element_offsets(shape)
    mesh = [range(-o[0], o[1]) for o in offsets]
    mesh = np.array(np.meshgrid(*mesh, indexing='ij'), dtype=float)

    add = ((np.array(shape) + 1) % 2) / 2.0
    nrm = np.max(offsets, axis=1)
    for d in range(len(add)):
        mesh[d] = (mesh[d] + add[d]) / nrm[d]

    r = 1 - np.sum(mesh * mesh, axis=0)
    r[r < 0] = 0
    r /= r.sum()
    return r





def cube(shape=(3, 3)):
    """Cube structuring element."""
    return np.ones(shape, dtype=bool)





def structure_element(shape=(3, 3), form='Disk', ndim=None):
    """Creates specific 2d and 3d structuring elements
      
    Arguments
    ---------
    shape : array or tuple
      shape of the structure element
    form : str
      structure element type      
    ndim: int or None
      dimension of the structuring element
    
    Returns
    -------
        array
            structure element
    """
    if isinstance(shape, int) and ndim is not None:
        shape = (shape,) * ndim

    form = form.lower()

    if isinstance(shape, (list, tuple)):  # FIXME: iterable
        shape = np.array([shape]).flatten()

        if ndim is None:
            ndim = len(shape)  # FIXME: this makes no sense
        else:
            shape = np.pad(shape[:ndim], (0, max(0, ndim - len(shape))), 'wrap')

        if form in ['disk', 'd']:
            return disk(shape=shape)
        elif form in ['sphere', 's']:
            return sphere(shape=shape)
        elif form in ['cube', 'c', 'rectangle', 'r']:
            return cube(shape=shape)
        else:
            ValueError(f'Form {form} for structuring element not valid!')
    else:
        return shape





def structure_element_offsets(shape):
    """Calculates offsets to center for a structural element given its shape.
    
    Arguments
    ---------
    shape : array or tuple
      Shape of the structure element
    
    Returns
    -------
    offsets : array
      Offsets to center taking care of even/odd number of elements.
    """
    off = np.array([shape], dtype=int).flatten() // 2
    off = np.array([off, shape - off]).T
    return off



########################################################################################################################
# Tests
########################################################################################################################

def _test():
    import ClearMap.ImageProcessing.Filter.StructureElement as se
  
    from importlib import reload
    reload(se)

    element = se.sphere((150, 50, 10))

    import ClearMap.Visualization.Plot3d as p3d
    p3d.plot(element)