def __init__(self, *args):
"""
Double structuring 3D element constructor. A double structuring
element is defined by the first (background points) and second
(foreground points) structuring elements 3D.
You can define it in two ways:
* doubleStructuringElement3D(se0, se1): where 'se0' and 'se1' are
instances of the class structuringElement3D found in erodil3D
module. These structuring elements must be defined on the same grid.
* doubleStructuringElement3D(dse0, dse1, grid): where 'dse0' and
'dse1' are direction lists and 'grid' defines the grid on which the
two structuring elements are defined.
If the constructor is called with inapropriate arguments, it raises a
ValueError exception.
"""
if len(args) == 2:
if args[0].getGrid() != args[1].getGrid():
raise ValueError("Grid value mismatch")
self.se0 = args[0]
self.se1 = args[1]
self.grid = self.se0.getGrid()
elif len(args) == 3:
self.se0 = m3D.structuringElement3D(args[0], args[2])
self.se1 = m3D.structuringElement3D(args[1], args[2])
self.grid = args[2]
else:
raise ValueError("Incorrect constructor call")
def __init__(self, *args):
"""
Double structuring 3D element constructor. A double structuring
element is defined by the first (background points) and second
(foreground points) structuring elements 3D.
You can define it in two ways:
* doubleStructuringElement3D(se0, se1): where 'se0' and 'se1' are
instances of the class structuringElement3D found in erodil3D
module. These structuring elements must be defined on the same grid.
* doubleStructuringElement3D(dse0, dse1, grid): where 'dse0' and
'dse1' are direction lists and 'grid' defines the grid on which the
two structuring elements are defined.
If the constructor is called with inapropriate arguments, it raises a
ValueError exception.
"""
if len(args)==2:
if args[0].getGrid()!=args[1].getGrid():
raise ValueError("Grid value mismatch")
self.se0 = args[0]
self.se1 = args[1]
self.grid = self.se0.getGrid()
elif len(args)==3:
self.se0 = m3D.structuringElement3D(args[0], args[2])
self.se1 = m3D.structuringElement3D(args[1], args[2])
self.grid = args[2]
else:
raise ValueError("Incorrect constructor call")
def mosaicGradient3D(imIn, imOut, grid=m3D.DEFAULT_GRID3D):
"""
Builds the mosaic-gradient 3D image of 'imIn' and puts the result in 'imOut'.
The mosaic-gradient image is built by computing the differences of two
mosaic images generated from 'imIn', the first one having its watershed
lines valued by the suprema of the adjacent catchment basins values, the
second one been valued by the infima.
"""
imWrk1 = m3D.image3DMb(imIn)
imWrk2 = m3D.image3DMb(imIn)
imWrk3 = m3D.image3DMb(imIn)
imWrk4 = m3D.image3DMb(imIn)
imWrk5 = m3D.image3DMb(imIn)
mosaic3D(imIn, imWrk2, imWrk3, grid=grid)
m3D.sub3D(imWrk2, imWrk3, imWrk1)
m3D.logic3D(imWrk2, imWrk3, imWrk2, "sup")
m3D.negate3D(imWrk2, imWrk2)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
while m3D.computeVolume3D(imWrk3) != 0:
m3D.dilate3D(imWrk1, imWrk4, 2, se=se)
m3D.dilate3D(imWrk2, imWrk5, 2, se=se)
m3D.logic3D(imWrk4, imWrk3, imWrk4, "inf")
m3D.logic3D(imWrk5, imWrk3, imWrk5, "inf")
m3D.logic3D(imWrk1, imWrk4, imWrk1, "sup")
m3D.logic3D(imWrk2, imWrk5, imWrk2, "sup")
m3D.erode3D(imWrk3, imWrk3, 2, se=se)
m3D.negate3D(imWrk2, imWrk2)
m3D.sub3D(imWrk1, imWrk2, imOut)
def mosaic3D(imIn, imOut, imWts, grid=m3D.DEFAULT_GRID3D):
"""
Builds the mosaic 3D image of 'imIn' and puts the results into 'imOut'.
The watershed line (pixel values set to 255) is stored in the
greytone 3D image 'imWts'. A mosaic image is a simple image made of various
tiles of uniform grey values. It is built using the watershed of 'imIn'
gradient and original markers made of gradient minima which are labelled by
the maximum value of 'imIn' pixels inside them.
"""
imWrk1 = m3D.image3DMb(imIn, 1)
imWrk2 = m3D.image3DMb(imIn)
m3D.copy3D(imIn, imWrk2)
im_mark = m3D.image3DMb(imIn, 32)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
m3D.gradient3D(imIn, imOut, se=se)
m3D.minima3D(imOut, imWrk1, grid=grid)
m3D.add3D(im_mark, imWrk1, im_mark)
imWrk1.convert(8)
m3D.build3D(imWrk1, imWrk2, grid=grid)
m3D.add3D(im_mark, imWrk2, im_mark)
m3D.watershedSegment3D(imOut, im_mark, grid=grid)
m3D.copyBytePlane3D(im_mark, 3, imWts)
m3D.subConst3D(im_mark, 1, im_mark)
m3D.copyBytePlane3D(im_mark, 0, imOut)
def mosaicGradient3D(imIn, imOut, grid=m3D.DEFAULT_GRID3D):
"""
Builds the mosaic-gradient 3D image of 'imIn' and puts the result in 'imOut'.
The mosaic-gradient image is built by computing the differences of two
mosaic images generated from 'imIn', the first one having its watershed
lines valued by the suprema of the adjacent catchment basins values, the
second one been valued by the infima.
"""
imWrk1 = m3D.image3DMb(imIn)
imWrk2 = m3D.image3DMb(imIn)
imWrk3 = m3D.image3DMb(imIn)
imWrk4 = m3D.image3DMb(imIn)
imWrk5 = m3D.image3DMb(imIn)
mosaic3D(imIn, imWrk2, imWrk3, grid=grid)
m3D.sub3D(imWrk2, imWrk3, imWrk1)
m3D.logic3D(imWrk2, imWrk3, imWrk2, "sup")
m3D.negate3D(imWrk2, imWrk2)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
while m3D.computeVolume3D(imWrk3) != 0:
m3D.dilate3D(imWrk1, imWrk4, 2, se=se)
m3D.dilate3D(imWrk2, imWrk5, 2, se=se)
m3D.logic3D(imWrk4, imWrk3, imWrk4, "inf")
m3D.logic3D(imWrk5, imWrk3, imWrk5, "inf")
m3D.logic3D(imWrk1, imWrk4, imWrk1, "sup")
m3D.logic3D(imWrk2, imWrk5, imWrk2, "sup")
m3D.erode3D(imWrk3, imWrk3, 2, se=se)
m3D.negate3D(imWrk2, imWrk2)
m3D.sub3D(imWrk1, imWrk2, imOut)
def mosaic3D(imIn, imOut, imWts, grid=m3D.DEFAULT_GRID3D):
"""
Builds the mosaic 3D image of 'imIn' and puts the results into 'imOut'.
The watershed line (pixel values set to 255) is stored in the
greytone 3D image 'imWts'. A mosaic image is a simple image made of various
tiles of uniform grey values. It is built using the watershed of 'imIn'
gradient and original markers made of gradient minima which are labelled by
the maximum value of 'imIn' pixels inside them.
"""
imWrk1 = m3D.image3DMb(imIn, 1)
imWrk2 = m3D.image3DMb(imIn)
m3D.copy3D(imIn, imWrk2)
im_mark = m3D.image3DMb(imIn, 32)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
m3D.gradient3D(imIn, imOut, se=se)
m3D.minima3D(imOut, imWrk1, grid=grid)
m3D.add3D(im_mark, imWrk1, im_mark)
imWrk1.convert(8)
m3D.build3D(imWrk1, imWrk2, grid=grid)
m3D.add3D(im_mark, imWrk2, im_mark)
m3D.watershedSegment3D(imOut, im_mark, grid=grid)
m3D.copyBytePlane3D(im_mark, 3, imWts)
m3D.subConst3D(im_mark, 1, im_mark)
m3D.copyBytePlane3D(im_mark, 0, imOut)
def drawEdge3D(imOut, thick=1):
"""
Draws a frame around the edge of 'imOut' whose value equals the maximum
range value and whose thickness is given by 'thick' (default 1).
"""
imOut.reset()
se=m3D.structuringElement3D(list(m3D.getDirections3D(m3D.CUBIC)), m3D.CUBIC)
m3D.dilate3D(imOut, imOut, thick, se=se, edge=mamba.FILLED)
def drawEdge3D(imOut, thick=1):
"""
Draws a frame around the edge of 'imOut' whose value equals the maximum
range value and whose thickness is given by 'thick' (default 1).
"""
imOut.reset()
se = m3D.structuringElement3D(list(m3D.getDirections3D(m3D.CUBIC)),
m3D.CUBIC)
m3D.dilate3D(imOut, imOut, thick, se=se, edge=mamba.FILLED)
def linearErode3D( imIn, imOut, d, n=1, grid=m3D.DEFAULT_GRID3D, edge=mamba.FILLED):
"""
Performs an erosion in direction 'd' of 3D image 'imIn' and puts the
result in 'imOut'. The operation is repeated 'n' times (default is 1).
This function will assume a FILLED edge unless specified otherwise using
'edge'.
"""
se = m3D.structuringElement3D([0,d], grid)
m3D.copy3D(imIn, imOut)
m3D.erode3D(imOut, imOut, n, se=se, edge=edge)
def linearDilate3D(imIn, imOut, d, n=1, grid=m3D.DEFAULT_GRID3D, edge=mamba.EMPTY):
"""
Dilation by a segment in direction 'd' of 3D image 'imIn', result in 'imOut'.
The operation is repeated 'n' times (default is 1).This function will assume
an EMPTY edge unless specified otherwise using 'edge'. The directions
are defined according to the grid in use.
"""
se = m3D.structuringElement3D([0,d], grid)
m3D.copy3D(imIn, imOut)
m3D.dilate3D(imOut, imOut, n, se=se, edge=edge)
def removeEdgeParticles3D(imIn, imOut, grid=m3D.DEFAULT_GRID3D):
"""
Removes particles (connected components) touching the edge in 3D image
'imIn'. The resulting image is put in image 'imOut'.
Although this operator may be used with greytone images, it should be
considered with caution.
"""
imWrk = m3D.image3DMb(imIn)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
m3D.dilate3D(imWrk, imWrk, se=se, edge=mamba.FILLED)
m3D.logic3D(imIn, imWrk, imWrk, "inf")
build3D(imIn, imWrk, grid=grid)
m3D.diff3D(imIn, imWrk, imOut)
def removeEdgeParticles3D(imIn, imOut, grid=m3D.DEFAULT_GRID3D):
"""
Removes particles (connected components) touching the edge in 3D image
'imIn'. The resulting image is put in image 'imOut'.
Although this operator may be used with greytone images, it should be
considered with caution.
"""
imWrk = m3D.image3DMb(imIn)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
m3D.dilate3D(imWrk, imWrk, se=se, edge=mamba.FILLED)
m3D.logic3D(imIn, imWrk, imWrk, "inf")
build3D(imIn, imWrk, grid=grid)
m3D.diff3D(imIn, imWrk, imOut)
def regularisedGradient3D(imIn, imOut, n, grid=m3D.DEFAULT_GRID3D):
"""
Computes the regularized gradient of 3D image 'imIn' of size 'n'.
The result is put in 'imOut'. A regularized gradient of size 'n' extracts
in the 3D image contours thinner than 'n' while avoiding false detections.
This operation is only valid for omnidirectional structuring elements.
"""
imWrk = m3D.image3DMb(imIn)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
gradient3D(imIn, imWrk, n, se=se)
whiteTopHat3D(imWrk, imWrk, n, se=se)
m3D.erode3D(imWrk, imOut, n-1, se=se)
def strongLevelling3D(imIn, imOut, n, eroFirst, grid=m3D.DEFAULT_GRID3D):
"""
Strong levelling of 'imIn', result in 'imOut'. 'n' defines the size of the
erosion and dilation of 'imIn' in the operation. If 'eroFirst' is true, the
operation starts with an erosion, it starts with a dilation otherwise.
This filter is stronger (more efficient) that simpleLevelling3D. However, the
order of the initial operations (erosion and dilation) matters.
"""
imWrk = m3D.image3DMb(imIn)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
if eroFirst:
m3D.erode3D(imIn, imWrk, n, se=se)
m3D.build3D(imIn, imWrk, grid=grid)
m3D.dilate3D(imIn, imOut, n, se=se)
m3D.dualBuild3D(imWrk, imOut, grid=grid)
else:
m3D.dilate3D(imIn, imWrk, n, se=se)
m3D.dualBuild3D(imIn, imWrk, grid=grid)
m3D.erode3D(imIn, imOut, n, se=se)
m3D.build3D(imWrk, imOut, grid=grid)
def strongLevelling3D(imIn, imOut, n, eroFirst, grid=m3D.DEFAULT_GRID3D):
"""
Strong levelling of 'imIn', result in 'imOut'. 'n' defines the size of the
erosion and dilation of 'imIn' in the operation. If 'eroFirst' is true, the
operation starts with an erosion, it starts with a dilation otherwise.
This filter is stronger (more efficient) that simpleLevelling3D. However, the
order of the initial operations (erosion and dilation) matters.
"""
imWrk = m3D.image3DMb(imIn)
se = m3D.structuringElement3D(m3D.getDirections3D(grid), grid)
if eroFirst:
m3D.erode3D(imIn, imWrk, n, se=se)
m3D.build3D(imIn, imWrk, grid=grid)
m3D.dilate3D(imIn, imOut, n, se=se)
m3D.dualBuild3D(imWrk, imOut, grid=grid)
else:
m3D.dilate3D(imIn, imWrk, n, se=se)
m3D.dualBuild3D(imIn, imWrk, grid=grid)
m3D.erode3D(imIn, imOut, n, se=se)
m3D.build3D(imWrk, imOut, grid=grid)
