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 lowerGeodesicErode3D(imIn, imMask, imOut, n=1, se=m3D.CUBOCTAHEDRON1):
"""
Performs a lower geodesic erosion of 3D image 'imIn' under 'imMask'.
The result is put inside 'imOut', 'n' controls the size of the erosion.
'se' specifies the type of structuring element used to perform the
computation (CUBOCTAHEDRON by default).
The binary lower geodesic erosion is realised using the fact that the
dilation is the dual operation of the erosion.
Warning! 'imMask' and 'imOut' must be different.
"""
if imIn.getDepth() == 1:
m3D.diff3D(imMask, imIn, imOut)
lowerGeodesicDilate3D(imOut, imMask, imOut, n, se=se)
m3D.diff3D(imMask, imOut, imOut)
else:
imWrk1 = m3D.image3DMb(imIn)
imWrk2 = m3D.image3DMb(imIn, 1)
m3D.logic3D(imIn, imMask, imOut, "inf")
for i in range(n):
m3D.generateSupMask3D(imOut, imMask, imWrk2, False)
m3D.convertByMask3D(imWrk2, imWrk1, 0,
m3D.computeMaxRange3D(imWrk1)[1])
m3D.logic3D(imOut, imWrk1, imOut, "sup")
m3D.erode3D(imOut, imOut, se=se)
m3D.logic3D(imOut, imMask, imOut, "inf")
def lowerGeodesicErode3D(imIn, imMask, imOut, n=1, se=m3D.CUBOCTAHEDRON1):
"""
Performs a lower geodesic erosion of 3D image 'imIn' under 'imMask'.
The result is put inside 'imOut', 'n' controls the size of the erosion.
'se' specifies the type of structuring element used to perform the
computation (CUBOCTAHEDRON by default).
The binary lower geodesic erosion is realised using the fact that the
dilation is the dual operation of the erosion.
Warning! 'imMask' and 'imOut' must be different.
"""
if imIn.getDepth() == 1:
m3D.diff3D(imMask, imIn, imOut)
lowerGeodesicDilate3D(imOut, imMask, imOut, n, se=se)
m3D.diff3D(imMask, imOut, imOut)
else:
imWrk1 = m3D.image3DMb(imIn)
imWrk2 = m3D.image3DMb(imIn, 1)
m3D.logic3D(imIn, imMask, imOut, "inf")
for i in range(n):
m3D.generateSupMask3D(imOut, imMask, imWrk2, False)
m3D.convertByMask3D(imWrk2, imWrk1, 0, m3D.computeMaxRange3D(imWrk1)[1])
m3D.logic3D(imOut, imWrk1, imOut, "sup")
m3D.erode3D(imOut, imOut, se=se)
m3D.logic3D(imOut, imMask, imOut, "inf")
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 buildOpen3D(imIn, imOut, n=1, se=m3D.CUBOCTAHEDRON1):
"""
Performs an opening by reconstruction operation on 3D image 'imIn' and
puts the result in 'imOut'. 'n' controls the size of the opening.
"""
imWrk = m3D.image3DMb(imIn)
m3D.copy3D(imIn, imWrk)
m3D.erode3D(imIn, imOut, n, se=se)
m3D.build3D(imWrk, imOut, grid=se.getGrid())
def buildOpen3D(imIn, imOut, n=1, se=m3D.CUBOCTAHEDRON1):
"""
Performs an opening by reconstruction operation on 3D image 'imIn' and
puts the result in 'imOut'. 'n' controls the size of the opening.
"""
imWrk = m3D.image3DMb(imIn)
m3D.copy3D(imIn, imWrk)
m3D.erode3D(imIn, imOut, n, se=se)
m3D.build3D(imWrk, imOut, grid=se.getGrid())
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 gradient3D(imIn, imOut, n=1, se=m3D.CUBOCTAHEDRON1):
"""
Computes the morphological gradient of 3D image 'imIn' and puts the
result in 'imOut'. The thickness can be controlled using parameter 'n'
(1 by default). The structuring element used by the erosion and dilation
is defined by 'se' (CUBOCTAHEDRON1 by default).
"""
imWrk = m3D.image3DMb(imIn)
m3D.erode3D(imIn, imWrk, n, se=se)
m3D.dilate3D(imIn, imOut, n, se=se)
m3D.sub3D(imOut, imWrk, imOut)
def opening3D(imIn, imOut, n=1, se=m3D.CUBOCTAHEDRON1, edge=mamba.FILLED):
"""
Performs an opening operation on 3D image 'imIn' and puts the result
in 'imOut'. 'n' controls the size of the opening and 'se' the
structuring element used.
The default edge is set to 'FILLED'. Note that the edge setting
operates in the erosion only.
"""
m3D.erode3D(imIn, imOut, n, se=se, edge=edge)
m3D.dilate3D(imOut, imOut, n, se=se.transpose())
def opening3D(imIn, imOut, n=1, se=m3D.CUBOCTAHEDRON1, edge=mamba.FILLED):
"""
Performs an opening operation on 3D image 'imIn' and puts the result
in 'imOut'. 'n' controls the size of the opening and 'se' the
structuring element used.
The default edge is set to 'FILLED'. Note that the edge setting
operates in the erosion only.
"""
m3D.erode3D(imIn, imOut, n, se=se, edge=edge)
m3D.dilate3D(imOut, imOut, n, se=se.transpose())
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 upperGeodesicErode3D(imIn, imMask, imOut, n=1, se=m3D.CUBOCTAHEDRON1):
"""
Performs a upper geodesic erosion of 3D image 'imIn' above 'imMask'.
The result is put inside 'imOut', 'n' controls the size of the erosion.
'se' specifies the type of structuring element used to perform the
computation (CUBOCTAHEDRON by default).
Warning! 'imMask' and 'imOut' must be different.
"""
m3D.logic3D(imIn, imMask, imOut, "sup")
for i in range(n):
m3D.erode3D(imOut, imOut, se=se)
m3D.logic3D(imOut, imMask, imOut, "sup")
def upperGeodesicErode3D(imIn, imMask, imOut, n=1, se=m3D.CUBOCTAHEDRON1):
"""
Performs a upper geodesic erosion of 3D image 'imIn' above 'imMask'.
The result is put inside 'imOut', 'n' controls the size of the erosion.
'se' specifies the type of structuring element used to perform the
computation (CUBOCTAHEDRON by default).
Warning! 'imMask' and 'imOut' must be different.
"""
m3D.logic3D(imIn, imMask, imOut, "sup")
for i in range(n):
m3D.erode3D(imOut, imOut, se=se)
m3D.logic3D(imOut, imMask, imOut, "sup")
def closing3D(imIn, imOut, n=1, se=m3D.CUBOCTAHEDRON1, edge=mamba.FILLED):
"""
Performs a closing operation on 3D image 'imIn' and puts the result
in 'imOut'. 'n' controls the size of the closing and 'se' the
structuring element used.
The default edge is set to 'FILLED'. If 'edge' is set to 'EMPTY', the
operation is slightly modified to avoid errors (non extensivity).
"""
imWrk = m3D.image3DMb(imIn)
if edge == mamba.EMPTY:
m3D.copy3D(imIn, imWrk)
m3D.dilate3D(imIn, imOut, n, se=se)
m3D.erode3D(imOut, imOut, n, se=se.transpose(), edge=edge)
if edge == mamba.EMPTY:
m3D.logic3D(imOut, imWrk, imOut, "sup")
def closing3D(imIn, imOut, n=1, se=m3D.CUBOCTAHEDRON1, edge=mamba.FILLED):
"""
Performs a closing operation on 3D image 'imIn' and puts the result
in 'imOut'. 'n' controls the size of the closing and 'se' the
structuring element used.
The default edge is set to 'FILLED'. If 'edge' is set to 'EMPTY', the
operation is slightly modified to avoid errors (non extensivity).
"""
imWrk = m3D.image3DMb(imIn)
if edge == mamba.EMPTY:
m3D.copy3D(imIn, imWrk)
m3D.dilate3D(imIn, imOut, n, se=se)
m3D.erode3D(imOut, imOut, n, se=se.transpose(), edge=edge)
if edge == mamba.EMPTY:
m3D.logic3D(imOut, imWrk, imOut, "sup")
def halfGradient3D(imIn, imOut, type="intern", n=1, se=m3D.CUBOCTAHEDRON1):
"""
Computes the half morphological gradient of 3D image 'imIn' ond puts
the result in 'imOut'.
'type' indicates if the half gradient should be internal or external.
Possible values are :
"extern" : dilation(imIn) - imIn
"intern" : imIn - erosion(imIn)
The thickness can be controlled using parameter 'n' (1 by default). The
structuring element used by the erosion or the dilation is defined by 'se'.
"""
imWrk = m3D.image3DMb(imIn)
if type=="extern":
m3D.dilate3D(imIn, imWrk, n, se=se)
m3D.sub3D(imWrk, imIn, imOut)
else:
m3D.erode3D(imIn, imWrk, n, se=se)
m3D.sub3D(imIn, imWrk, imOut)
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)