def __init__(self, sliceLogic):
super().__init__(sliceLogic)
self.paintThreshold = 0
self.paintThresholdMin = 1
self.paintThresholdMax = 1
self.paintOver = 1
self.extractImage = None
self.painter = slicer.vtkImageSlicePaint()
def __init__(self,sliceLogic): super(LabelEffectLogic,self).__init__(sliceLogic) self.paintThreshold = 0 self.paintThresholdMin = 1 self.paintThresholdMax = 1 self.paintOver = 1 self.extractImage = None self.painter = slicer.vtkImageSlicePaint()
def __init__(self,sliceLogic):
self.sliceLogic = sliceLogic
self.editUtil = EditUtil.EditUtil()
# optionally set by users of the class
self.undoRedo = None
self.scope = 'All'
#
# instance variables used internally
# - buffer for result of scoped editing
self.scopedImageBuffer = vtk.vtkImageData()
# - slice paint is used to extract/replace scoped regions
self.scopedSlicePaint = slicer.vtkImageSlicePaint()
def __init__(self, sliceLogic):
self.sliceLogic = sliceLogic
self.editUtil = EditUtil() # Kept for backward compatibility
# optionally set by users of the class
self.undoRedo = None
self.scope = 'All'
#
# instance variables used internally
# - buffer for result of scoped editing
self.scopedImageBuffer = vtk.vtkImageData()
# - slice paint is used to extract/replace scoped regions
self.scopedSlicePaint = slicer.vtkImageSlicePaint()
def paintBrush(self, x, y):
"""
paint with a brush that is circular (or optionally spherical) in XY space
(could be stretched or rotate when transformed to IJK)
- make sure to hit every pixel in IJK space
- apply the threshold if selected
"""
sliceLogic = self.sliceWidget.sliceLogic()
sliceNode = sliceLogic.GetSliceNode()
labelLogic = sliceLogic.GetLabelLayer()
labelNode = labelLogic.GetVolumeNode()
labelImage = labelNode.GetImageData()
backgroundLogic = sliceLogic.GetBackgroundLayer()
backgroundNode = backgroundLogic.GetVolumeNode()
backgroundImage = backgroundNode.GetImageData()
if not labelNode:
# if there's no label, we can't paint
return
#
# get the brush bounding box in ijk coordinates
# - get the xy bounds
# - transform to ijk
# - clamp the bounds to the dimensions of the label image
#
bounds = self.brush.GetPoints().GetBounds()
left = x + bounds[0]
right = x + bounds[1]
bottom = y + bounds[2]
top = y + bounds[3]
xyToIJK = labelLogic.GetXYToIJKTransform()
tlIJK = xyToIJK.TransformDoublePoint((left, top, 0))
trIJK = xyToIJK.TransformDoublePoint((right, top, 0))
blIJK = xyToIJK.TransformDoublePoint((left, bottom, 0))
brIJK = xyToIJK.TransformDoublePoint((right, bottom, 0))
dims = labelImage.GetDimensions()
# clamp the top, bottom, left, right to the
# valid dimensions of the label image
tl = [0, 0, 0]
tr = [0, 0, 0]
bl = [0, 0, 0]
br = [0, 0, 0]
for i in xrange(3):
tl[i] = int(round(tlIJK[i]))
if tl[i] < 0:
tl[i] = 0
if tl[i] >= dims[i]:
tl[i] = dims[i] - 1
tr[i] = int(round(trIJK[i]))
if tr[i] < 0:
tr[i] = 0
if tr[i] >= dims[i]:
tr[i] = dims[i] - 1
bl[i] = int(round(blIJK[i]))
if bl[i] < 0:
bl[i] = 0
if bl[i] >= dims[i]:
bl[i] = dims[i] - 1
br[i] = int(round(brIJK[i]))
if br[i] < 0:
br[i] = 0
if br[i] >= dims[i]:
br[i] = dims[i] - 1
# If the region is smaller than a pixel then paint it using paintPixel mode,
# to make sure at least one pixel is filled on each click
maxRowDelta = 0
maxColumnDelta = 0
for i in xrange(3):
d = abs(tr[i] - tl[i])
if d > maxColumnDelta:
maxColumnDelta = d
d = abs(br[i] - bl[i])
if d > maxColumnDelta:
maxColumnDelta = d
d = abs(bl[i] - tl[i])
if d > maxRowDelta:
maxRowDelta = d
d = abs(br[i] - tr[i])
if d > maxRowDelta:
maxRowDelta = d
if maxRowDelta <= 1 or maxColumnDelta <= 1:
self.paintPixel(x, y)
return
#
# get the layers and nodes
# and ijk to ras matrices including transforms
#
backgroundIJKToRAS = self.logic.getIJKToRASMatrix(backgroundNode)
labelIJKToRAS = self.logic.getIJKToRASMatrix(labelNode)
xyToRAS = sliceNode.GetXYToRAS()
brushCenter = xyToRAS.MultiplyPoint((x, y, 0, 1))[:3]
brushRadius = self.radius
bSphere = self.sphere
parameterNode = EditUtil.getParameterNode()
paintLabel = int(parameterNode.GetParameter("label"))
paintOver = int(parameterNode.GetParameter("LabelEffect,paintOver"))
paintThreshold = int(
parameterNode.GetParameter("LabelEffect,paintThreshold"))
paintThresholdMin = float(
parameterNode.GetParameter("LabelEffect,paintThresholdMin"))
paintThresholdMax = float(
parameterNode.GetParameter("LabelEffect,paintThresholdMax"))
#
# set up the painter class and let 'r rip!
#
if not hasattr(self, "painter"):
self.painter = slicer.vtkImageSlicePaint()
self.painter.SetBackgroundImage(backgroundImage)
self.painter.SetBackgroundIJKToWorld(backgroundIJKToRAS)
self.painter.SetWorkingImage(labelImage)
self.painter.SetWorkingIJKToWorld(labelIJKToRAS)
self.painter.SetTopLeft(tl[0], tl[1], tl[2])
self.painter.SetTopRight(tr[0], tr[1], tr[2])
self.painter.SetBottomLeft(bl[0], bl[1], bl[2])
self.painter.SetBottomRight(br[0], br[1], br[2])
self.painter.SetBrushCenter(brushCenter[0], brushCenter[1],
brushCenter[2])
self.painter.SetBrushRadius(brushRadius)
self.painter.SetPaintLabel(paintLabel)
self.painter.SetPaintOver(paintOver)
self.painter.SetThresholdPaint(paintThreshold)
self.painter.SetThresholdPaintRange(paintThresholdMin,
paintThresholdMax)
if bSphere: # fill volume of a sphere rather than a circle on the currently displayed image slice
# Algorithm:
###########################
# Assume brushRadius is in mm
# Estimate zVoxelSize
# Compute number of slices spanned by sphere, that are still within the volume
# For each spanned slice
# reposition the brushCenter using xy(z)ToRAS transform: i.e. canvas to patient world coordinates
# resize the radius: brushRadiusOffset=sqrt(brushRadius*brushRadius - zOffset_mm*zOffset_mm)
# invoke Paint()
# Finally paint on the center slice, leaving the gui on the center slice being most visibly edited
#------------------
# Estimate zVoxelSize_mm
brushCenter1 = xyToRAS.MultiplyPoint((x, y, 0, 1))[:3]
brushCenter2 = xyToRAS.MultiplyPoint((x, y, 100, 1))[:3]
dx1 = brushCenter1[0] - brushCenter2[0]
dx2 = brushCenter1[1] - brushCenter2[1]
dx3 = brushCenter1[2] - brushCenter2[2]
distanceSpannedBy100Slices = sqrt(dx1 * dx1 + dx2 * dx2 +
dx3 * dx3) # compute L2 norm
if distanceSpannedBy100Slices == 0:
zVoxelSize_mm = 1
else:
zVoxelSize_mm = distanceSpannedBy100Slices / 100
# --
# Compute number of slices spanned by sphere
nNumSlicesInEachDirection = brushRadius / zVoxelSize_mm
nNumSlicesInEachDirection = nNumSlicesInEachDirection - 1
sliceOffsetArray = numpy.concatenate((-1 * numpy.arange(
1,
nNumSlicesInEachDirection + 1,
), numpy.arange(1, nNumSlicesInEachDirection + 1)))
for iSliceOffset in sliceOffsetArray:
# x,y uses slice (canvas) coordinate system and actually has a 3rd z component (index into the slice you're looking at)
# hence xyToRAS is really performing xyzToRAS. RAS is patient world coordinate system. Note the 1 is because the trasform uses homogeneous coordinates
iBrushCenter = xyToRAS.MultiplyPoint(
(x, y, iSliceOffset, 1))[:3]
self.painter.SetBrushCenter(iBrushCenter[0], iBrushCenter[1],
iBrushCenter[2])
# [ ] Need to just continue (pass this loop iteration if the brush center is not within the volume
zOffset_mm = zVoxelSize_mm * iSliceOffset
brushRadiusOffset = sqrt(brushRadius * brushRadius -
zOffset_mm * zOffset_mm)
self.painter.SetBrushRadius(brushRadiusOffset)
# --
tlIJKtemp = xyToIJK.TransformDoublePoint(
(left, top, iSliceOffset))
trIJKtemp = xyToIJK.TransformDoublePoint(
(right, top, iSliceOffset))
blIJKtemp = xyToIJK.TransformDoublePoint(
(left, bottom, iSliceOffset))
brIJKtemp = xyToIJK.TransformDoublePoint(
(right, bottom, iSliceOffset))
# clamp the top, bottom, left, right to the
# valid dimensions of the label image
tltemp = [0, 0, 0]
trtemp = [0, 0, 0]
bltemp = [0, 0, 0]
brtemp = [0, 0, 0]
for i in xrange(3):
tltemp[i] = int(round(tlIJKtemp[i]))
if tltemp[i] < 0:
tltemp[i] = 0
if tltemp[i] >= dims[i]:
tltemp[i] = dims[i] - 1
trtemp[i] = int(round(trIJKtemp[i]))
if trtemp[i] < 0:
trtemp[i] = 0
if trtemp[i] > dims[i]:
trtemp[i] = dims[i] - 1
bltemp[i] = int(round(blIJKtemp[i]))
if bltemp[i] < 0:
bltemp[i] = 0
if bltemp[i] > dims[i]:
bltemp[i] = dims[i] - 1
brtemp[i] = int(round(brIJKtemp[i]))
if brtemp[i] < 0:
brtemp[i] = 0
if brtemp[i] > dims[i]:
brtemp[i] = dims[i] - 1
self.painter.SetTopLeft(tltemp[0], tltemp[1], tltemp[2])
self.painter.SetTopRight(trtemp[0], trtemp[1], trtemp[2])
self.painter.SetBottomLeft(bltemp[0], bltemp[1], bltemp[2])
self.painter.SetBottomRight(brtemp[0], brtemp[1], brtemp[2])
self.painter.Paint()
# paint the slice: same for circular and spherical brush modes
self.painter.SetTopLeft(tl[0], tl[1], tl[2])
self.painter.SetTopRight(tr[0], tr[1], tr[2])
self.painter.SetBottomLeft(bl[0], bl[1], bl[2])
self.painter.SetBottomRight(br[0], br[1], br[2])
self.painter.SetBrushCenter(brushCenter[0], brushCenter[1],
brushCenter[2])
self.painter.SetBrushRadius(brushRadius)
self.painter.Paint()
def paintBrush(self, x, y):
"""
paint with a brush that is circular (or optionally spherical) in XY space
(could be stretched or rotate when transformed to IJK)
- make sure to hit every pixel in IJK space
- apply the threshold if selected
"""
sliceLogic = self.sliceWidget.sliceLogic()
sliceNode = sliceLogic.GetSliceNode()
labelLogic = sliceLogic.GetLabelLayer()
labelNode = labelLogic.GetVolumeNode()
labelImage = labelNode.GetImageData()
backgroundLogic = sliceLogic.GetBackgroundLayer()
backgroundNode = backgroundLogic.GetVolumeNode()
backgroundImage = backgroundNode.GetImageData()
if not labelNode:
# if there's no label, we can't paint
return
#
# get the brush bounding box in ijk coordinates
# - get the xy bounds
# - transform to ijk
# - clamp the bounds to the dimensions of the label image
#
bounds = self.brush.GetPoints().GetBounds()
left = x + bounds[0]
right = x + bounds[1]
bottom = y + bounds[2]
top = y + bounds[3]
xyToIJK = labelLogic.GetXYToIJKTransform()
tlIJK = xyToIJK.TransformDoublePoint( (left, top, 0) )
trIJK = xyToIJK.TransformDoublePoint( (right, top, 0) )
blIJK = xyToIJK.TransformDoublePoint( (left, bottom, 0) )
brIJK = xyToIJK.TransformDoublePoint( (right, bottom, 0) )
dims = labelImage.GetDimensions()
# clamp the top, bottom, left, right to the
# valid dimensions of the label image
tl = [0,0,0]
tr = [0,0,0]
bl = [0,0,0]
br = [0,0,0]
for i in range(3):
tl[i] = int(round(tlIJK[i]))
if tl[i] < 0:
tl[i] = 0
if tl[i] >= dims[i]:
tl[i] = dims[i] - 1
tr[i] = int(round(trIJK[i]))
if tr[i] < 0:
tr[i] = 0
if tr[i] >= dims[i]:
tr[i] = dims[i] - 1
bl[i] = int(round(blIJK[i]))
if bl[i] < 0:
bl[i] = 0
if bl[i] >= dims[i]:
bl[i] = dims[i] - 1
br[i] = int(round(brIJK[i]))
if br[i] < 0:
br[i] = 0
if br[i] >= dims[i]:
br[i] = dims[i] - 1
# If the region is smaller than a pixel then paint it using paintPixel mode,
# to make sure at least one pixel is filled on each click
maxRowDelta = 0
maxColumnDelta = 0
for i in range(3):
d = abs(tr[i] - tl[i])
if d > maxColumnDelta:
maxColumnDelta = d
d = abs(br[i] - bl[i])
if d > maxColumnDelta:
maxColumnDelta = d
d = abs(bl[i] - tl[i])
if d > maxRowDelta:
maxRowDelta = d
d = abs(br[i] - tr[i])
if d > maxRowDelta:
maxRowDelta = d
if maxRowDelta<=1 or maxColumnDelta<=1 :
self.paintPixel(x,y)
return
#
# get the layers and nodes
# and ijk to ras matrices including transforms
#
backgroundIJKToRAS = self.logic.getIJKToRASMatrix(backgroundNode)
labelIJKToRAS = self.logic.getIJKToRASMatrix(labelNode)
xyToRAS = sliceNode.GetXYToRAS()
brushCenter = xyToRAS.MultiplyPoint( (x, y, 0, 1) )[:3]
brushRadius = self.radius
bSphere = self.sphere
parameterNode = EditUtil.getParameterNode()
paintLabel = int(parameterNode.GetParameter("label"))
paintOver = int(parameterNode.GetParameter("LabelEffect,paintOver"))
paintThreshold = int(parameterNode.GetParameter("LabelEffect,paintThreshold"))
paintThresholdMin = float(
parameterNode.GetParameter("LabelEffect,paintThresholdMin"))
paintThresholdMax = float(
parameterNode.GetParameter("LabelEffect,paintThresholdMax"))
#
# set up the painter class and let 'r rip!
#
if not hasattr(self,"painter"):
self.painter = slicer.vtkImageSlicePaint()
self.painter.SetBackgroundImage(backgroundImage)
self.painter.SetBackgroundIJKToWorld(backgroundIJKToRAS)
self.painter.SetWorkingImage(labelImage)
self.painter.SetWorkingIJKToWorld(labelIJKToRAS)
self.painter.SetTopLeft( tl[0], tl[1], tl[2] )
self.painter.SetTopRight( tr[0], tr[1], tr[2] )
self.painter.SetBottomLeft( bl[0], bl[1], bl[2] )
self.painter.SetBottomRight( br[0], br[1], br[2] )
self.painter.SetBrushCenter( brushCenter[0], brushCenter[1], brushCenter[2] )
self.painter.SetBrushRadius( brushRadius )
self.painter.SetPaintLabel(paintLabel)
self.painter.SetPaintOver(paintOver)
self.painter.SetThresholdPaint(paintThreshold)
self.painter.SetThresholdPaintRange(paintThresholdMin, paintThresholdMax)
if bSphere: # fill volume of a sphere rather than a circle on the currently displayed image slice
# Algorithm:
###########################
# Assume brushRadius is in mm
# Estimate zVoxelSize
# Compute number of slices spanned by sphere, that are still within the volume
# For each spanned slice
# reposition the brushCenter using xy(z)ToRAS transform: i.e. canvas to patient world coordinates
# resize the radius: brushRadiusOffset=sqrt(brushRadius*brushRadius - zOffset_mm*zOffset_mm)
# invoke Paint()
# Finally paint on the center slice, leaving the gui on the center slice being most visibly edited
#------------------
# Estimate zVoxelSize_mm
brushCenter1 = xyToRAS.MultiplyPoint( (x, y, 0, 1) )[:3]
brushCenter2 = xyToRAS.MultiplyPoint( (x, y, 100, 1) )[:3]
dx1=brushCenter1[0]-brushCenter2[0]
dx2=brushCenter1[1]-brushCenter2[1]
dx3=brushCenter1[2]-brushCenter2[2]
distanceSpannedBy100Slices = sqrt(dx1*dx1+dx2*dx2+dx3*dx3) # compute L2 norm
if distanceSpannedBy100Slices==0:
zVoxelSize_mm=1
else:
zVoxelSize_mm = int(distanceSpannedBy100Slices / 100)
# --
# Compute number of slices spanned by sphere
nNumSlicesInEachDirection=int(brushRadius / zVoxelSize_mm);
nNumSlicesInEachDirection=nNumSlicesInEachDirection-1
sliceOffsetArray=numpy.concatenate((-1*numpy.arange(1,nNumSlicesInEachDirection+1,), numpy.arange(1,nNumSlicesInEachDirection+1)))
for iSliceOffset in sliceOffsetArray:
# x,y uses slice (canvas) coordinate system and actually has a 3rd z component (index into the slice you're looking at)
# hence xyToRAS is really performing xyzToRAS. RAS is patient world coordinate system. Note the 1 is because the trasform uses homogeneous coordinates
iBrushCenter = xyToRAS.MultiplyPoint( (x, y, iSliceOffset, 1) )[:3]
self.painter.SetBrushCenter( iBrushCenter[0], iBrushCenter[1], iBrushCenter[2] )
# [ ] Need to just continue (pass this loop iteration if the brush center is not within the volume
zOffset_mm=zVoxelSize_mm*iSliceOffset;
brushRadiusOffset=sqrt(brushRadius*brushRadius - zOffset_mm*zOffset_mm)
self.painter.SetBrushRadius( brushRadiusOffset )
# --
tlIJKtemp = xyToIJK.TransformDoublePoint( (left, top, iSliceOffset) )
trIJKtemp = xyToIJK.TransformDoublePoint( (right, top, iSliceOffset) )
blIJKtemp = xyToIJK.TransformDoublePoint( (left, bottom, iSliceOffset) )
brIJKtemp = xyToIJK.TransformDoublePoint( (right, bottom, iSliceOffset) )
# clamp the top, bottom, left, right to the
# valid dimensions of the label image
tltemp = [0,0,0]
trtemp = [0,0,0]
bltemp = [0,0,0]
brtemp = [0,0,0]
for i in range(3):
tltemp[i] = int(round(tlIJKtemp[i]))
if tltemp[i] < 0:
tltemp[i] = 0
if tltemp[i] >= dims[i]:
tltemp[i] = dims[i] - 1
trtemp[i] = int(round(trIJKtemp[i]))
if trtemp[i] < 0:
trtemp[i] = 0
if trtemp[i] > dims[i]:
trtemp[i] = dims[i] - 1
bltemp[i] = int(round(blIJKtemp[i]))
if bltemp[i] < 0:
bltemp[i] = 0
if bltemp[i] > dims[i]:
bltemp[i] = dims[i] - 1
brtemp[i] = int(round(brIJKtemp[i]))
if brtemp[i] < 0:
brtemp[i] = 0
if brtemp[i] > dims[i]:
brtemp[i] = dims[i] - 1
self.painter.SetTopLeft( tltemp[0], tltemp[1], tltemp[2] )
self.painter.SetTopRight( trtemp[0], trtemp[1], trtemp[2] )
self.painter.SetBottomLeft( bltemp[0], bltemp[1], bltemp[2] )
self.painter.SetBottomRight( brtemp[0], brtemp[1], brtemp[2] )
self.painter.Paint()
# paint the slice: same for circular and spherical brush modes
self.painter.SetTopLeft( tl[0], tl[1], tl[2] )
self.painter.SetTopRight( tr[0], tr[1], tr[2] )
self.painter.SetBottomLeft( bl[0], bl[1], bl[2] )
self.painter.SetBottomRight( br[0], br[1], br[2] )
self.painter.SetBrushCenter( brushCenter[0], brushCenter[1], brushCenter[2] )
self.painter.SetBrushRadius( brushRadius )
self.painter.Paint()