class SurfParams(Viewer):
"""
CLASS: SurfParams
DESCR:
Public attrs:
color # a normed rgb
intensity # intensity to segment on
label # name of segment
useConnect # boolean, whether to use ConnectFilter
useDecimate # boolean, whether to use DecimateFilter
connect # a ConnectFilter or None
deci # a DecimateFilter or None
imageData # default None
"""
label, color = colorSeq[0]
intensity = 3000
useConnect = True
useDecimate = False
def __init__(self, renderer, interactor):
self.connect = ConnectFilter()
self.deci = DecimateFilter()
self.marchingCubes = vtk.vtkMarchingCubes()
self.prog = ProgressBarDialog(
title='Rendering surface %s' % self.label,
parent=None,
msg='Marching cubes ....',
size=(300,40),
)
def start(o, event):
self.prog.show()
while gtk.events_pending(): gtk.main_iteration()
def progress(o, event):
val = o.GetProgress()
self.prog.bar.set_fraction(val)
while gtk.events_pending(): gtk.main_iteration()
def end(o, event):
self.prog.hide()
while gtk.events_pending(): gtk.main_iteration()
self.marchingCubes.AddObserver('StartEvent', start)
self.marchingCubes.AddObserver('ProgressEvent', progress)
self.marchingCubes.AddObserver('EndEvent', end)
self.renderer = renderer
self.interactor = interactor
self.isoActor = None
self.update_pipeline()
def update_pipeline(self):
if self.isoActor is not None:
self.renderer.RemoveActor(self.isoActor)
pipe = self.marchingCubes
if self.useConnect:
self.connect.SetInput( pipe.GetOutput())
pipe = self.connect
if self.useDecimate:
self.deci.SetInput( pipe.GetOutput())
pipe = self.deci
if 0:
plane = vtk.vtkPlane()
clipper = vtk.vtkClipPolyData()
polyData = pipe.GetOutput()
clipper.SetInput(polyData)
clipper.SetClipFunction(plane)
clipper.InsideOutOff()
pipe = clipper
def callback(pw, event):
pw.GetPlane(plane)
self.interactor.Render()
self.planeWidget = vtk.vtkImplicitPlaneWidget()
self.planeWidget.SetInteractor(self.interactor)
self.planeWidget.On()
self.planeWidget.SetPlaceFactor(1.0)
self.planeWidget.SetInput(polyData)
self.planeWidget.PlaceWidget()
self.planeWidget.AddObserver("InteractionEvent", callback)
self.isoMapper = vtk.vtkPolyDataMapper()
self.isoMapper.SetInput(pipe.GetOutput())
self.isoMapper.ScalarVisibilityOff()
self.isoActor = vtk.vtkActor()
self.isoActor.SetMapper(self.isoMapper)
self.renderer.AddActor(self.isoActor)
self.update_properties()
def set_image_data(self, imageData):
if debug:
print "SurfParams.set_image_data(", imageData,")"
self.marchingCubes.SetInput(imageData)
x1,x2,y1,y2,z1,z2 = imageData.GetExtent()
sx, sy, sz = imageData.GetSpacing()
if 0:
self.planeWidget.PlaceWidget((x1*sx, x2*sx, y1*sy, y2*sy, z1*sz, z2*sz))
def update_properties(self):
self.marchingCubes.SetValue(0, self.intensity)
self.isoActor.GetProperty().SetColor(self.color)
if self.useConnect: self.connect.update()
if self.useDecimate: self.deci.update()
def update_viewer(self, event, *args):
if event=='set image data':
imageData = args[0]
self.set_image_data(imageData)
def __del__(self):
if self.isoActor is not None:
self.renderer.RemoveActor(self.isoActor)
class SurfParams(object):
label = "Surface"
colorName, color_ = colorSeq[0]
intensity = 80.
_opacity = 1.0
useConnect = True
useDecimate = False
def __init__(self, imageData, intensity, color=None):
self._uuid = uuid.uuid1()
if intensity!=None:
self.intensity = intensity
if color==None:
color=self.color_
self.set_color(color)
self.connect = ConnectFilter()
self.deci = DecimateFilter()
self.marchingCubes = vtk.vtkMarchingCubes()
self.marchingCubes.SetInput(imageData)
self.output = vtk.vtkPassThrough()
self.prog = ProgressBarDialog(
title='Rendering surface %s' % self.label,
parent=None,
msg='Marching cubes ....',
size=(300,40),
)
self.prog.set_modal(True)
def start(o, event):
self.prog.show()
while gtk.events_pending(): gtk.main_iteration()
def progress(o, event):
val = o.GetProgress()
self.prog.bar.set_fraction(val)
while gtk.events_pending(): gtk.main_iteration()
def end(o, event):
self.prog.hide()
while gtk.events_pending(): gtk.main_iteration()
self.marchingCubes.AddObserver('StartEvent', start)
self.marchingCubes.AddObserver('ProgressEvent', progress)
self.marchingCubes.AddObserver('EndEvent', end)
self.update_pipeline()
self.notify_add_surface(self.output)
def update_pipeline(self):
pipe = self.marchingCubes
if self.useConnect:
self.connect.SetInputConnection( pipe.GetOutputPort())
pipe = self.connect
if self.useDecimate:
self.deci.SetInputConnection( pipe.GetOutputPort())
pipe = self.deci
self.output.SetInputConnection( pipe.GetOutputPort() )
self.update_properties()
def notify_add_surface(self, pipe):
EventHandler().notify("add surface", self._uuid, pipe, self._color)
def notify_remove_surface(self):
EventHandler().notify("remove surface", self._uuid)
def notify_color_surface(self, color):
EventHandler().notify("color surface", self._uuid, color)
def notify_change_surface_opacity(self, opacity):
EventHandler().notify("change surface opacity", self._uuid, opacity)
def update_properties(self):
self.marchingCubes.SetValue(0, self.intensity)
self.notify_color_surface(self.color)
if self.useConnect: self.connect.update()
if self.useDecimate: self.deci.update()
def update_viewer(self, event, *args):
if event=='set image data':
imageData = args[0]
self.set_image_data(imageData)
def __del__(self):
self.notify_remove_surface()
def set_color(self,color, color_name=""):
#print color, type(color)
self.colorName = color_name
if type(color)==gtk.gdk.Color:
self._color = gdkColor2tuple(color)
else:
self._color = color
self.notify_color_surface(self._color)
def get_color(self):
return self._color
def set_opacity(self,opacity):
self._opacity = opacity
self.notify_change_surface_opacity(self._opacity)
def get_opacity(self):
return self._opacity
def get_uuid(self):
return self._uuid
color = property(get_color,set_color)
opacity = property(get_opacity,set_opacity)
uuid = property(get_uuid)
def destroy(self):
self.notify_remove_surface()
class SurfParams(Viewer):
"""
CLASS: SurfParams
DESCR:
Public attrs:
color # a normed rgb
intensity # intensity to segment on
label # name of segment
useConnect # boolean, whether to use ConnectFilter
useDecimate # boolean, whether to use DecimateFilter
connect # a ConnectFilter or None
deci # a DecimateFilter or None
imageData # default None
"""
label, color = colorSeq[0]
intensity = 3000
useConnect = True
useDecimate = False
def __init__(self, renderer, interactor):
self.connect = ConnectFilter()
self.deci = DecimateFilter()
self.marchingCubes = vtk.vtkMarchingCubes()
self.prog = ProgressBarDialog(
title='Rendering surface %s' % self.label,
parent=None,
msg='Marching cubes ....',
size=(300, 40),
)
def start(o, event):
self.prog.show()
while gtk.events_pending():
gtk.main_iteration()
def progress(o, event):
val = o.GetProgress()
self.prog.bar.set_fraction(val)
while gtk.events_pending():
gtk.main_iteration()
def end(o, event):
self.prog.hide()
while gtk.events_pending():
gtk.main_iteration()
self.marchingCubes.AddObserver('StartEvent', start)
self.marchingCubes.AddObserver('ProgressEvent', progress)
self.marchingCubes.AddObserver('EndEvent', end)
self.renderer = renderer
self.interactor = interactor
self.isoActor = None
self.update_pipeline()
def update_pipeline(self):
if self.isoActor is not None:
self.renderer.RemoveActor(self.isoActor)
pipe = self.marchingCubes
if self.useConnect:
self.connect.SetInput(pipe.GetOutput())
pipe = self.connect
if self.useDecimate:
self.deci.SetInput(pipe.GetOutput())
pipe = self.deci
if 0:
plane = vtk.vtkPlane()
clipper = vtk.vtkClipPolyData()
polyData = pipe.GetOutput()
clipper.SetInput(polyData)
clipper.SetClipFunction(plane)
clipper.InsideOutOff()
pipe = clipper
def callback(pw, event):
pw.GetPlane(plane)
self.interactor.Render()
self.planeWidget = vtk.vtkImplicitPlaneWidget()
self.planeWidget.SetInteractor(self.interactor)
self.planeWidget.On()
self.planeWidget.SetPlaceFactor(1.0)
self.planeWidget.SetInput(polyData)
self.planeWidget.PlaceWidget()
self.planeWidget.AddObserver("InteractionEvent", callback)
self.isoMapper = vtk.vtkPolyDataMapper()
self.isoMapper.SetInput(pipe.GetOutput())
self.isoMapper.ScalarVisibilityOff()
self.isoActor = vtk.vtkActor()
self.isoActor.SetMapper(self.isoMapper)
self.renderer.AddActor(self.isoActor)
self.update_properties()
def set_image_data(self, imageData):
if debug:
print "SurfParams.set_image_data(", imageData, ")"
self.marchingCubes.SetInput(imageData)
x1, x2, y1, y2, z1, z2 = imageData.GetExtent()
sx, sy, sz = imageData.GetSpacing()
if 0:
self.planeWidget.PlaceWidget(
(x1 * sx, x2 * sx, y1 * sy, y2 * sy, z1 * sz, z2 * sz))
def update_properties(self):
self.marchingCubes.SetValue(0, self.intensity)
self.isoActor.GetProperty().SetColor(self.color)
if self.useConnect: self.connect.update()
if self.useDecimate: self.deci.update()
def update_viewer(self, event, *args):
if event == 'set image data':
imageData = args[0]
self.set_image_data(imageData)
def __del__(self):
if self.isoActor is not None:
self.renderer.RemoveActor(self.isoActor)
def get_reader(o):
if o.readerClass=='vtkBMPReader':
ReaderClass = vtk.vtkBMPReader
elif o.readerClass=='vtkImageReader2':
ReaderClass = vtk.vtkImageReader2
elif o.readerClass=='vtkDICOMImageReader':
ReaderClass = vtk.vtkDICOMImageReader
elif o.readerClass=='vtkNiftiImageReader':
ReaderClass = vtkNiftiImageReader
reader = ReaderClass()
if ReaderClass==vtk.vtkImageReader2:
reader.SetDataScalarTypeToUnsignedShort()
if o.order=='big endian':
reader.SetDataByteOrderToBigEndian()
else:
reader.SetDataByteOrderToLittleEndian()
rows, cols = o.dimensions
reader.SetFileNameSliceOffset(o.first)
reader.SetDataExtent(0, rows-1, 0, cols-1, 0, o.last-o.first)
reader.FileLowerLeftOn()
if o.mask is not None:
reader.SetDataMask(o.mask)
if o.header!=0:
reader.SetHeaderSize(o.header)
elif ReaderClass==vtk.vtkBMPReader:
reader.SetDataExtent(0, o.dimensions[0]-1,
0, o.dimensions[1]-1,
o.first, o.last)
elif ReaderClass==vtk.vtkDICOMImageReader:
reader.SetDirectoryName(o.dir)
reader.Update()
#Update Param file from the reader
o.dimensions = [reader.GetWidth() , reader.GetHeight()]
if reader.GetDataByteOrder()==1:
o.order=='big endian'
else:
o.order=='little endian'
o.spacing = spc[2]
o.dfov = o.dimensions[0] * spc[0]
elif ReaderClass==vtkNiftiImageReader:
reader.SetDirectoryName(o.dir)
pattern = o.pattern
if len(o.extension) > 0:
pattern += '.' + o.extension
reader.SetFilePattern(pattern)
reader.Update()
o.dimensions = [reader.GetWidth() , reader.GetHeight()]
spc = reader.GetDataSpacing()
o.spacing = spc[2]
o.dfov = o.dimensions[0] * spc[0]
else:
raise NotImplementedError, "Can't handle reader %s" % o.readerClass
if ReaderClass!=vtkNiftiImageReader:
progressDlg = ProgressBarDialog(title='Loading files',
parent=widgets['dlgReader'],
msg='Almost there....',
size=(300,40)
)
progressDlg.show()
def progress(r, event):
#print 'abort progress', r.GetAbortExecute()
val = r.GetProgress()
progressDlg.bar.set_fraction(val)
if val==1: progressDlg.destroy()
while gtk.events_pending(): gtk.main_iteration()
reader.AddObserver('ProgressEvent', progress)
if os.path.isdir(o.dir): dir = o.dir
else:
infopath = widgets['entryInfoFile'].get_text()
dir, fname = os.path.split(infopath)
if ReaderClass!=vtkNiftiImageReader:
reader.SetFilePrefix(dir)
pattern = os.path.join( '%s', o.prefix + o.pattern )
if len(o.extension) > 0:
pattern += '.' + o.extension
reader.SetFilePattern(pattern)
print "reader.SetDataSpacing(", o.dfov/o.dimensions[0], o.dfov/o.dimensions[1], o.spacing , "). dfov=", o.dfov, "dimensions=", o.dimensions, "spacing=", o.spacing
reader.SetDataSpacing(float(o.dfov)/float(o.dimensions[0]),
float(o.dfov)/float(o.dimensions[1]),
float(o.spacing) )
reader.Update()
return reader
def get_reader(o):
if o.readerClass == 'vtkBMPReader':
ReaderClass = vtk.vtkBMPReader
elif o.readerClass == 'vtkImageReader2':
ReaderClass = vtk.vtkImageReader2
elif o.readerClass == 'vtkDICOMImageReader':
ReaderClass = vtk.vtkDICOMImageReader
elif o.readerClass == 'vtkNiftiImageReader':
ReaderClass = vtkNiftiImageReader
reader = ReaderClass()
if ReaderClass == vtk.vtkImageReader2:
reader.SetDataScalarTypeToUnsignedShort()
if o.order == 'big endian':
reader.SetDataByteOrderToBigEndian()
else:
reader.SetDataByteOrderToLittleEndian()
rows, cols = o.dimensions
reader.SetFileNameSliceOffset(o.first)
reader.SetDataExtent(0, rows - 1, 0, cols - 1, 0, o.last - o.first)
reader.FileLowerLeftOn()
if o.mask is not None:
reader.SetDataMask(o.mask)
if o.header != 0:
reader.SetHeaderSize(o.header)
elif ReaderClass == vtk.vtkBMPReader:
reader.SetDataExtent(0, o.dimensions[0] - 1, 0, o.dimensions[1] - 1,
o.first, o.last)
elif ReaderClass == vtk.vtkDICOMImageReader:
reader.SetDirectoryName(o.dir)
reader.Update()
#Update Param file from the reader
o.dimensions = [reader.GetWidth(), reader.GetHeight()]
if reader.GetDataByteOrder() == 1:
o.order == 'big endian'
else:
o.order == 'little endian'
o.spacing = spc[2]
o.dfov = o.dimensions[0] * spc[0]
elif ReaderClass == vtkNiftiImageReader:
reader.SetDirectoryName(o.dir)
pattern = o.pattern
if len(o.extension) > 0:
pattern += '.' + o.extension
reader.SetFilePattern(pattern)
reader.Update()
o.dimensions = [reader.GetWidth(), reader.GetHeight()]
spc = reader.GetDataSpacing()
o.spacing = spc[2]
o.dfov = o.dimensions[0] * spc[0]
else:
raise NotImplementedError, "Can't handle reader %s" % o.readerClass
if ReaderClass != vtkNiftiImageReader:
progressDlg = ProgressBarDialog(title='Loading files',
parent=widgets['dlgReader'],
msg='Almost there....',
size=(300, 40))
progressDlg.show()
def progress(r, event):
#print 'abort progress', r.GetAbortExecute()
val = r.GetProgress()
progressDlg.bar.set_fraction(val)
if val == 1: progressDlg.destroy()
while gtk.events_pending():
gtk.main_iteration()
reader.AddObserver('ProgressEvent', progress)
if os.path.isdir(o.dir): dir = o.dir
else:
infopath = widgets['entryInfoFile'].get_text()
dir, fname = os.path.split(infopath)
if ReaderClass != vtkNiftiImageReader:
reader.SetFilePrefix(dir)
pattern = os.path.join('%s', o.prefix + o.pattern)
if len(o.extension) > 0:
pattern += '.' + o.extension
reader.SetFilePattern(pattern)
if debug:
print "reader.SetDataSpacing(", o.dfov / o.dimensions[0], o.dfov / o.dimensions[
1], o.spacing, "). dfov=", o.dfov, "dimensions=", o.dimensions, "spacing=", o.spacing
reader.SetDataSpacing(
float(o.dfov) / float(o.dimensions[0]),
float(o.dfov) / float(o.dimensions[1]), float(o.spacing))
reader.Update()
return reader