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 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 markerControlledWatershed3D(imIn, imMarkers, imOut, grid=m3D.DEFAULT_GRID3D):
"""
Marker-controlled watershed transform of greyscale or 32-bit 3D image 'imIn'.
The binary 3D image 'imMarkers' contains the markers which control the
flooding process. 'imOut' contains the valued watershed.
"""
im_mark = m3D.image3DMb(imIn, 32)
imWrk = m3D.image3DMb(imIn)
label3D(imMarkers, im_mark, grid=grid)
watershedSegment3D(imIn, im_mark, grid=grid)
m3D.copyBytePlane3D(im_mark, 3, imWrk)
m3D.logic3D(imWrk, imIn, imOut, 'inf')
def mamba_ws(self, NEED_WL, res_type):
imDist = image3DMb(*self.dist.shape, 32)
fillImageWithArray_3D(self.dist, imDist)
imMarkers = image3DMb(*self.markers.shape, 32)
fillImageWithArray_3D(self.markers.astype(np.uint32), imMarkers)
if NEED_WL:
labels, res = decorator(watershedSegment3D, res_type)(imDist, imMarkers, grid=CUBIC)
else:
labels, res = decorator(basinSegment3D,res_type)(imDist, imMarkers, grid=CUBIC)
tmp = image3DMb(*self.markers.shape, 8)
copyBytePlane3D(tmp, 3, imMarkers)
self.labels = getArrayFromImage_3D(imMarkers, self.size)
return res
def markerControlledWatershed3D(imIn,
imMarkers,
imOut,
grid=m3D.DEFAULT_GRID3D):
"""
Marker-controlled watershed transform of greyscale or 32-bit 3D image 'imIn'.
The binary 3D image 'imMarkers' contains the markers which control the
flooding process. 'imOut' contains the valued watershed.
"""
im_mark = m3D.image3DMb(imIn, 32)
imWrk = m3D.image3DMb(imIn)
label3D(imMarkers, im_mark, grid=grid)
watershedSegment3D(imIn, im_mark, grid=grid)
m3D.copyBytePlane3D(im_mark, 3, imWrk)
m3D.logic3D(imWrk, imIn, imOut, 'inf')
def _convertIntoVTKImage(self):
# Converts the associated sequence into a VTK image
# structure to be able to display it using the rendering
# mechanisms of VTK
W, H, L = self.im_ref().getSize()
depth = self.im_ref().getDepth()
if depth==8:
# 8-bit 3D image
self.planeLabel.config(text="")
raw_data = self.im_ref().extractRaw()
elif depth==32:
# 32-bit 3D image
im3D_8 = m3D.image3DMb(self.im_ref(), 8)
if self.master.bplane==4:
self.planeLabel.config(text="Plane : all")
m3D.convert3D(self.im_ref(), im3D_8)
else:
self.planeLabel.config(text="Plane : %d" % (self.master.bplane))
m3D.copyBytePlane3D(self.im_ref(), self.master.bplane, im3D_8)
raw_data = im3D_8.extractRaw()
else:
# binary 3D image
self.planeLabel.config(text="")
im8 = mamba.imageMb(W, H, 8)
raw_data = b""
for im2D in self.im_ref():
mamba.convert(im2D, im8)
raw_data += im8.extractRaw()
volume = m3D.computeVolume3D(self.im_ref())
self.vtk_im.CopyImportVoidPointer(raw_data, len(raw_data))
self.vtk_im.SetNumberOfScalarComponents(1)
extent = self.vtk_im.GetDataExtent()
self.vtk_im.SetDataExtent(extent[0], extent[0] + W - 1,
extent[2], extent[2] + H - 1,
extent[4], extent[4] + L - 1)
self.vtk_im.SetWholeExtent(extent[0], extent[0] + W - 1,
extent[2], extent[2] + H - 1,
extent[4], extent[4] + L - 1)
self.volLabel.config(text="Volume = %d" % (volume))