__all__ = ['morphology']
from .iMath import iMath
[docs]def morphology(image, operation, radius, mtype='binary', value=1,
shape='ball', radius_is_parametric=False, thickness=1,
lines=3, include_center=False):
"""
Apply morphological operations to an image
ANTsR function: `morphology`
Arguments
---------
input : ANTsImage
input image
operation : string
operation to apply
"close" Morpholgical closing
"dilate" Morpholgical dilation
"erode" Morpholgical erosion
"open" Morpholgical opening
radius : scalar
radius of structuring element
mtype : string
type of morphology
"binary" Binary operation on a single value
"grayscale" Grayscale operations
value : scalar
value to operation on (type='binary' only)
shape : string
shape of the structuring element ( type='binary' only )
"ball" spherical structuring element
"box" box shaped structuring element
"cross" cross shaped structuring element
"annulus" annulus shaped structuring element
"polygon" polygon structuring element
radius_is_parametric : boolean
used parametric radius boolean (shape='ball' and shape='annulus' only)
thickness : scalar
thickness (shape='annulus' only)
lines : integer
number of lines in polygon (shape='polygon' only)
include_center : boolean
include center of annulus boolean (shape='annulus' only)
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> fi = ants.image_read( ants.get_ants_data('r16') , 2 )
>>> mask = ants.get_mask( fi )
>>> dilated_ball = ants.morphology( mask, operation='dilate', radius=3, mtype='binary', shape='ball')
>>> eroded_box = ants.morphology( mask, operation='erode', radius=3, mtype='binary', shape='box')
>>> opened_annulus = ants.morphology( mask, operation='open', radius=5, mtype='binary', shape='annulus', thickness=2)
"""
if image.components > 1:
raise ValueError('multichannel images not yet supported')
_sflag_dict = {'ball': 1, 'box': 2, 'cross': 3, 'annulus': 4, 'polygon': 5}
sFlag = _sflag_dict.get(shape, 0)
if sFlag == 0:
raise ValueError('invalid element shape')
radius_is_parametric = radius_is_parametric * 1
include_center = include_center * 1
if (mtype == 'binary'):
if (operation == 'dilate'):
if (sFlag == 5):
ret = iMath(image, 'MD', radius, value, sFlag, lines)
else:
ret = iMath(image, 'MD', radius, value, sFlag, radius_is_parametric, thickness, include_center)
elif (operation == 'erode'):
if (sFlag == 5):
ret = iMath(image, 'ME', radius, value, sFlag, lines)
else:
ret = iMath(image, 'ME', radius, value, sFlag, radius_is_parametric, thickness, include_center)
elif (operation == 'open'):
if (sFlag == 5):
ret = iMath(image, 'MO', radius, value, sFlag, lines)
else:
ret = iMath(image, 'MO', radius, value, sFlag, radius_is_parametric, thickness, include_center)
elif (operation == 'close'):
if (sFlag == 5):
ret = iMath(image, 'MC', radius, value, sFlag, lines)
else:
ret = iMath(image, 'MC', radius, value, sFlag, radius_is_parametric, thickness, include_center)
else:
raise ValueError('Invalid morphology operation')
elif (mtype == 'grayscale'):
if (operation == 'dilate'):
ret = iMath(image, 'GD', radius)
elif (operation == 'erode'):
ret = iMath(image, 'GE', radius)
elif (operation == 'open'):
ret = iMath(image, 'GO', radius)
elif (operation == 'close'):
ret = iMath(image, 'GC', radius)
else:
raise ValueError('Invalid morphology operation')
else:
raise ValueError('Invalid morphology type')
return ret
