def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
InputArrayChoiceMixin.__init__(self)
self._config.scaleFactor = 1
configList = [
('Scale factor:', 'scaleFactor', 'base:float', 'text',
'The warping will be scaled by this factor'),
('Vectors selection:', 'vectorsSelection', 'base:str', 'choice',
'The attribute that will be used as vectors for the warping.',
(self._defaultVectorsSelectionString, self._userDefinedString))]
self._warpVector = vtk.vtkWarpVector()
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkWarpVector' : self._warpVector})
module_utils.setup_vtk_object_progress(self, self._warpVector,
'Warping points.')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._imageDilate = vtk.vtkImageContinuousDilate3D()
self._imageErode = vtk.vtkImageContinuousErode3D()
self._imageErode.SetInput(self._imageDilate.GetOutput())
module_utils.setup_vtk_object_progress(self, self._imageDilate,
'Performing greyscale 3D dilation')
module_utils.setup_vtk_object_progress(self, self._imageErode,
'Performing greyscale 3D erosion')
self._config.kernelSize = (3, 3, 3)
configList = [
('Kernel size:', 'kernelSize', 'tuple:int,3', 'text',
'Size of the kernel in x,y,z dimensions.')]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkImageContinuousDilate3D' : self._imageDilate,
'vtkImageContinuousErode3D' : self._imageErode})
self.sync_module_logic_with_config()
def __init__(self, module_manager, contourFilterText):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._contourFilterText = contourFilterText
if contourFilterText == 'marchingCubes':
self._contourFilter = vtk.vtkMarchingCubes()
else: # contourFilter == 'contourFilter'
self._contourFilter = vtk.vtkContourFilter()
module_utils.setup_vtk_object_progress(self, self._contourFilter,
'Extracting iso-surface')
# now setup some defaults before our sync
self._config.isoValue = 128;
self._viewFrame = None
self._createViewFrame()
# transfer these defaults to the logic
self.config_to_logic()
# then make sure they come all the way back up via self._config
self.logic_to_config()
self.config_to_view()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
# the decimator only works on triangle data, so we make sure
# that it only gets triangle data
self._triFilter = vtk.vtkTriangleFilter()
self._decimate = vtk.vtkDecimatePro()
self._decimate.PreserveTopologyOn()
self._decimate.SetInput(self._triFilter.GetOutput())
module_utils.setup_vtk_object_progress(self, self._triFilter,
'Converting to triangles')
module_utils.setup_vtk_object_progress(self, self._decimate,
'Decimating mesh')
# now setup some defaults before our sync
self._config.target_reduction = self._decimate.GetTargetReduction() \
* 100.0
config_list = [
('Target reduction (%):', 'target_reduction', 'base:float', 'text',
'Decimate algorithm will attempt to reduce by this much.')]
ScriptedConfigModuleMixin.__init__(
self, config_list,
{'Module (self)' : self,
'vtkDecimatePro' : self._decimate,
'vtkTriangleFilter' : self._triFilter})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._writer = vtk.vtkStructuredPointsWriter()
module_utils.setup_vtk_object_progress(
self, self._writer,
'Writing vtk structured points data')
# we do this to save space - if you're going to be transporting files
# to other architectures, change this to ASCII
# we've set this back to ASCII. Seems the binary mode is screwed
# for some files and manages to produce corrupt files that segfault
# VTK on Windows.
self._writer.SetFileTypeToASCII()
# ctor for this specific mixin
FilenameViewModuleMixin.__init__(
self,
'Select a filename',
'VTK data (*.vtk)|*.vtk|All files (*)|*',
{'vtkStructuredPointsWriter': self._writer},
fileOpen=False)
# set up some defaults
self._config.filename = ''
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._implicitModeller = vtk.vtkImplicitModeller()
module_utils.setup_vtk_object_progress(
self, self._implicitModeller,
'Converting surface to distance field')
self._config.bounds = (-1, 1, -1, 1, -1, 1)
self._config.dimensions = (64, 64, 64)
self._config.maxDistance = 0.1
configList = [
('Bounds:', 'bounds', 'tuple:float,6', 'text',
'The physical location of the sampled volume in space '
'(x0, x1, y0, y1, z0, z1)'),
('Dimensions:', 'dimensions', 'tuple:int,3', 'text',
'The number of points that should be sampled in each dimension.'),
('Maximum distance:', 'maxDistance', 'base:float', 'text',
'The distance will only be calculated up to this maximum.')]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkImplicitModeller' : self._implicitModeller})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._writer = vtk.vtkPolyDataWriter()
# sorry about this, but the files get REALLY big if we write them
# in ASCII - I'll make this a gui option later.
self._writer.SetFileTypeToBinary()
module_utils.setup_vtk_object_progress(
self, self._writer,
'Writing VTK Polygonal data')
# ctor for this specific mixin
FilenameViewModuleMixin.__init__(
self,
'Select a filename',
'VTK data (*.vtk)|*.vtk|All files (*)|*',
{'vtkPolyDataWriter': self._writer},
fileOpen=False)
# set up some defaults
self._config.filename = ''
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._writer = vtk.vtkIVWriter()
# sorry about this, but the files get REALLY big if we write them
# in ASCII - I'll make this a gui option later.
#self._writer.SetFileTypeToBinary()
# following is the standard way of connecting up the devide progress
# callback to a VTK object; you should do this for all objects in
module_utils.setup_vtk_object_progress(
self, self._writer, 'Writing polydata to Inventor Viewer format')
# ctor for this specific mixin
FilenameViewModuleMixin.__init__(
self,
'Select a filename',
'InventorViewer data (*.iv)|*.iv|All files (*)|*',
{'vtkIVWriter': self._writer},
fileOpen=False)
# set up some defaults
self._config.filename = ''
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._reader = vtkgdcm.vtkGDCMImageReader()
# NB NB NB: for now we're SWITCHING off the VTK-compatible
# Y-flip, until the X-mirror issues can be solved.
self._reader.SetFileLowerLeft(1)
self._ici = vtk.vtkImageChangeInformation()
self._ici.SetInputConnection(0, self._reader.GetOutputPort(0))
# create output MedicalMetaData and populate it with the
# necessary bindings.
mmd = MedicalMetaData()
mmd.medical_image_properties = \
self._reader.GetMedicalImageProperties()
mmd.direction_cosines = \
self._reader.GetDirectionCosines()
self._output_mmd = mmd
module_utils.setup_vtk_object_progress(self, self._reader,
'Reading DICOM data')
self._view_frame = None
self._file_dialog = None
self._config.dicom_filenames = []
# if this is true, module will still try to load set even if
# IPP sorting fails by sorting images alphabetically
self._config.robust_spacing = False
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._imageInput = None
self._meshInput = None
self._flipper = vtk.vtkImageFlip()
self._flipper.SetFilteredAxis(1)
module_utils.setup_vtk_object_progress(
self, self._flipper, 'Flipping Y axis.')
self._config.cpt_driver_path = \
'd:\\misc\\stuff\\driver.bat'
#'/home/cpbotha/build/cpt/3d/driver/driver.exe'
self._config.max_distance = 5
config_list = [
('CPT driver path', 'cpt_driver_path',
'base:str', 'filebrowser',
'Path to CPT driver executable',
{'fileMode' : module_mixins.wx.OPEN,
'fileMask' : 'All files (*.*)|*.*'}),
('Maximum distance', 'max_distance',
'base:float', 'text',
'The maximum (absolute) distance up to which the field is computed.')]
ScriptedConfigModuleMixin.__init__(
self, config_list,
{'Module (self)' : self})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._reslicer = vtk.vtkImageReslice()
self._probefilter = vtk.vtkProbeFilter()
self._config.paddingValue = 0.0
#This is retarded - we (sometimes, see below) need the padder
#to get the image extent big enough to satisfy the probe filter.
#No apparent logical reason, but it throws an exception if we don't.
self._padder = vtk.vtkImageConstantPad()
configList = [(
'Padding value:', 'paddingValue', 'base:float', 'text',
'The value used to pad regions that are outside the supplied volume.'
)]
# initialise any mixins we might have
ScriptedConfigModuleMixin.__init__(
self, configList, {
'Module (self)': self,
'vtkImageReslice': self._reslicer,
'vtkProbeFilter': self._probefilter,
'vtkImageConstantPad': self._padder
})
module_utils.setup_vtk_object_progress(
self, self._reslicer, 'Transforming image (Image Reslice)')
module_utils.setup_vtk_object_progress(
self, self._probefilter, 'Performing remapping (Probe Filter)')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# what a lame-assed filter, we have to make dummy inputs!
# if we don't have a dummy input (but instead a None input) it
# bitterly complains when we do a GetOutput() (it needs the input
# to know the type of the output) - and GetPolyDataOutput() also
# doesn't work.
# NB: this does mean that our probeFilter NEEDS a PolyData as
# probe geometry!
ss = vtk.vtkSphereSource()
ss.SetRadius(0)
self._dummyInput = ss.GetOutput()
#This is also retarded - we (sometimes, see below) need the "padder"
#to get the image extent big enough to satisfy the probe filter.
#No apparent logical reason, but it throws an exception if we don't.
self._padder = vtk.vtkImageConstantPad()
self._source = None
self._input = None
self._probeFilter = vtk.vtkProbeFilter()
self._probeFilter.SetInput(self._dummyInput)
NoConfigModuleMixin.__init__(
self,
{'Module (self)' : self,
'vtkProbeFilter' : self._probeFilter})
module_utils.setup_vtk_object_progress(self, self._probeFilter,
'Mapping source on input')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._reslicer = vtk.vtkImageReslice()
self._probefilter = vtk.vtkProbeFilter()
self._config.paddingValue = 0.0
#This is retarded - we (sometimes, see below) need the padder
#to get the image extent big enough to satisfy the probe filter.
#No apparent logical reason, but it throws an exception if we don't.
self._padder = vtk.vtkImageConstantPad()
configList = [
('Padding value:', 'paddingValue', 'base:float', 'text',
'The value used to pad regions that are outside the supplied volume.')]
# initialise any mixins we might have
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)': self,
'vtkImageReslice': self._reslicer,
'vtkProbeFilter': self._probefilter,
'vtkImageConstantPad': self._padder})
module_utils.setup_vtk_object_progress(self, self._reslicer,
'Transforming image (Image Reslice)')
module_utils.setup_vtk_object_progress(self, self._probefilter,
'Performing remapping (Probe Filter)')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._writer = vtk.vtkXMLPolyDataWriter()
module_utils.setup_vtk_object_progress(
self, self._writer,
'Writing VTK PolyData')
self._writer.SetDataModeToBinary()
# ctor for this specific mixin
FilenameViewModuleMixin.__init__(
self,
'Select a filename',
'VTK PolyData (*.vtp)|*.vtp|All files (*)|*',
{'vtkXMLPolyDataWriter': self._writer},
fileOpen=False)
# set up some defaults
self._config.filename = ''
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._writer = vtk.vtkXMLImageDataWriter()
# ctor for this specific mixin
FilenameViewModuleMixin.__init__(
self,
'Select a filename',
'VTK Image Data (*.vti)|*.vti|All files (*)|*',
{'vtkXMLImageDataWriter': self._writer},
fileOpen=False)
module_utils.setup_vtk_object_progress(
self, self._writer,
'Writing VTK ImageData')
self._writer.SetDataModeToBinary()
# set up some defaults
self._config.filename = ''
self._module_manager.sync_module_logic_with_config(self)
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._writer = vtk.vtkStructuredPointsWriter()
module_utils.setup_vtk_object_progress(
self, self._writer, 'Writing vtk structured points data')
# we do this to save space - if you're going to be transporting files
# to other architectures, change this to ASCII
# we've set this back to ASCII. Seems the binary mode is screwed
# for some files and manages to produce corrupt files that segfault
# VTK on Windows.
self._writer.SetFileTypeToASCII()
# ctor for this specific mixin
FilenameViewModuleMixin.__init__(
self,
'Select a filename',
'VTK data (*.vtk)|*.vtk|All files (*)|*',
{'vtkStructuredPointsWriter': self._writer},
fileOpen=False)
# set up some defaults
self._config.filename = ''
self.sync_module_logic_with_config()
def _create_pipeline(self):
# setup our pipeline
self._otf = vtk.vtkPiecewiseFunction()
self._ctf = vtk.vtkColorTransferFunction()
self._volume_property = vtk.vtkVolumeProperty()
self._volume_property.SetScalarOpacity(self._otf)
self._volume_property.SetColor(self._ctf)
self._volume_property.ShadeOn()
self._volume_property.SetAmbient(0.1)
self._volume_property.SetDiffuse(0.7)
self._volume_property.SetSpecular(0.2)
self._volume_property.SetSpecularPower(10)
self._volume_raycast_function = vtk.vtkVolumeRayCastMIPFunction()
self._volume_mapper = vtk.vtkVolumeRayCastMapper()
# can also used FixedPoint, but then we have to use:
# SetBlendModeToMaximumIntensity() and not SetVolumeRayCastFunction
#self._volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
self._volume_mapper.SetVolumeRayCastFunction(
self._volume_raycast_function)
module_utils.setup_vtk_object_progress(self, self._volume_mapper,
'Preparing render.')
self._volume = vtk.vtkVolume()
self._volume.SetProperty(self._volume_property)
self._volume.SetMapper(self._volume_mapper)
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._tubeFilter = vtk.vtkTubeFilter()
module_utils.setup_vtk_object_progress(self, self._tubeFilter,
'Generating tubes.')
self._config.NumberOfSides = 3
self._config.Radius = 0.01
configList = [('Number of sides:', 'NumberOfSides', 'base:int', 'text',
'Number of sides that the tube should have.'),
('Tube radius:', 'Radius', 'base:float', 'text',
'Radius of the generated tube.')]
ScriptedConfigModuleMixin.__init__(self, configList)
self._viewFrame = self._createWindow({
'Module (self)': self,
'vtkTubeFilter': self._tubeFilter
})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.syncViewWithLogic()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self)
self._imageReslice = vtk.vtkImageReslice()
self._imageReslice.SetInterpolationModeToCubic()
self._matrixToHT = vtk.vtkMatrixToHomogeneousTransform()
self._matrixToHT.Inverse()
module_utils.setup_vtk_object_progress(self, self._imageReslice,
'Resampling volume')
self._viewFrame = self._createViewFrame({
'Module (self)':
self,
'vtkImageReslice':
self._imageReslice
})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.syncViewWithLogic()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._imageMath = vtk.vtkImageMathematics()
self._imageMath.SetInput1(None)
self._imageMath.SetInput2(None)
module_utils.setup_vtk_object_progress(self, self._imageMath,
'Performing image math')
self._config.operation = 'subtract'
self._config.constantC = 0.0
self._config.constantK = 1.0
configList = [('Operation:', 'operation', 'base:str', 'choice',
'The operation that should be performed.',
tuple(OPS_DICT.keys())),
('Constant C:', 'constantC', 'base:float', 'text',
'The constant C used in some operations.'),
('Constant K:', 'constantK', 'base:float', 'text',
'The constant C used in some operations.')]
ScriptedConfigModuleMixin.__init__(
self, configList, {
'Module (self)': self,
'vtkImageMathematics': self._imageMath
})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._imageMath = vtk.vtkImageMathematics()
self._imageMath.SetInput1(None)
self._imageMath.SetInput2(None)
module_utils.setup_vtk_object_progress(self, self._imageMath,
'Performing image math')
self._config.operation = 'subtract'
self._config.constantC = 0.0
self._config.constantK = 1.0
configList = [
('Operation:', 'operation', 'base:str', 'choice',
'The operation that should be performed.',
tuple(OPS_DICT.keys())),
('Constant C:', 'constantC', 'base:float', 'text',
'The constant C used in some operations.'),
('Constant K:', 'constantK', 'base:float', 'text',
'The constant C used in some operations.')]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkImageMathematics' : self._imageMath})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._reader = vtk.vtkMetaImageReader()
module_utils.setup_vtk_object_progress(self, self._reader,
'Reading MetaImage data.')
self._config.filename = ''
configList = [
('File name:', 'filename', 'base:str', 'filebrowser',
'The name of the MetaImage file you want to load.',
{'fileMode' : wx.OPEN,
'fileMask' :
'MetaImage single file (*.mha)|*.mha|MetaImage separate header '
'(*.mhd)|*.mhd|All files (*.*)|*.*'})]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkMetaImageReader' : self._reader})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._imageDilate = vtk.vtkImageContinuousDilate3D()
module_utils.setup_vtk_object_progress(self, self._imageDilate,
'Performing greyscale 3D dilation')
self._config.kernelSize = (3, 3, 3)
configList = [
('Kernel size:', 'kernelSize', 'tuple:int,3', 'text',
'Size of the kernel in x,y,z dimensions.')]
ScriptedConfigModuleMixin.__init__(self, configList)
self._viewFrame = self._createWindow(
{'Module (self)' : self,
'vtkImageContinuousDilate3D' : self._imageDilate})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.logic_to_config()
self.config_to_view()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
InputArrayChoiceMixin.__init__(self)
self._config.scaleFactor = 1
configList = [
('Scale factor:', 'scaleFactor', 'base:float', 'text',
'The warping will be scaled by this factor'),
('Vectors selection:', 'vectorsSelection', 'base:str', 'choice',
'The attribute that will be used as vectors for the warping.',
(self._defaultVectorsSelectionString, self._userDefinedString))
]
self._warpVector = vtk.vtkWarpVector()
ScriptedConfigModuleMixin.__init__(self, configList, {
'Module (self)': self,
'vtkWarpVector': self._warpVector
})
module_utils.setup_vtk_object_progress(self, self._warpVector,
'Warping points.')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
"""Constructor (initialiser) for the PD reader.
This is almost standard code for most of the modules making use of
the FilenameViewModuleMixin mixin.
"""
# call the constructor in the "base"
ModuleBase.__init__(self, module_manager)
# setup necessary VTK objects
self._reader = vtk.vtkOBJReader()
# ctor for this specific mixin
FilenameViewModuleMixin.__init__(
self,
'Select a filename',
'Wavefront OBJ data (*.obj)|*.obj|All files (*)|*',
{'vtkOBJReader': self._reader})
module_utils.setup_vtk_object_progress(self, self._reader,
'Reading Wavefront OBJ data')
# set up some defaults
self._config.filename = ''
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# we'll be playing around with some vtk objects, this could
# be anything
self._triangleFilter = vtk.vtkTriangleFilter()
self._curvatures = vtk.vtkCurvatures()
self._curvatures.SetCurvatureTypeToMaximum()
self._curvatures.SetInput(self._triangleFilter.GetOutput())
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self,
{'Module (self)' : self,
'vtkTriangleFilter' : self._triangleFilter,
'vtkCurvatures' : self._curvatures})
module_utils.setup_vtk_object_progress(self, self._triangleFilter,
'Triangle filtering...')
module_utils.setup_vtk_object_progress(self, self._curvatures,
'Calculating curvatures...')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._shepardFilter = vtk.vtkShepardMethod()
module_utils.setup_vtk_object_progress(self, self._shepardFilter,
'Applying Shepard Method.')
self._config.maximum_distance = 1.0
configList = [
('Kernel size:', 'kernelSize', 'tuple:int,3', 'text',
'Size of the kernel in x,y,z dimensions.')]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkImageContinuousDilate3D' : self._imageDilate})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
InputArrayChoiceMixin.__init__(self)
# 0 = RK2
# 1 = RK4
# 2 = RK45
self._config.integrator = INTEG_TYPE.index('RK2')
self._config.max_prop = 5.0
self._config.integration_direction = INTEG_DIR.index('FORWARD')
configList = [
('Vectors selection:', 'vectorsSelection', 'base:str', 'choice',
'The attribute that will be used as vectors for the warping.',
(input_array_choice_mixin.DEFAULT_SELECTION_STRING, )),
('Max propagation:', 'max_prop', 'base:float', 'text',
'The streamline will propagate up to this lenth.'),
('Integration direction:', 'integration_direction', 'base:int',
'choice', 'Select an integration direction.', INTEG_DIR_TEXTS),
('Integrator type:', 'integrator', 'base:int', 'choice',
'Select an integrator for the streamlines.', INTEG_TYPE_TEXTS)
]
self._streamTracer = vtk.vtkStreamTracer()
ScriptedConfigModuleMixin.__init__(
self, configList, {
'Module (self)': self,
'vtkStreamTracer': self._streamTracer
})
module_utils.setup_vtk_object_progress(self, self._streamTracer,
'Tracing stream lines.')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._reader = vtk.vtkMetaImageReader()
module_utils.setup_vtk_object_progress(self, self._reader,
'Reading MetaImage data.')
self._config.filename = ''
configList = [(
'File name:', 'filename', 'base:str', 'filebrowser',
'The name of the MetaImage file you want to load.', {
'fileMode':
wx.OPEN,
'fileMask':
'MetaImage single file (*.mha)|*.mha|MetaImage separate header '
'(*.mhd)|*.mhd|All files (*.*)|*.*'
})]
ScriptedConfigModuleMixin.__init__(self, configList, {
'Module (self)': self,
'vtkMetaImageReader': self._reader
})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# we'll be playing around with some vtk objects, this could
# be anything
self._triangleFilter = vtk.vtkTriangleFilter()
self._curvatures = vtk.vtkCurvatures()
self._curvatures.SetCurvatureTypeToMaximum()
self._curvatures.SetInput(self._triangleFilter.GetOutput())
# initialise any mixins we might have
NoConfigModuleMixin.__init__(
self, {
'Module (self)': self,
'vtkTriangleFilter': self._triangleFilter,
'vtkCurvatures': self._curvatures
})
module_utils.setup_vtk_object_progress(self, self._triangleFilter,
'Triangle filtering...')
module_utils.setup_vtk_object_progress(self, self._curvatures,
'Calculating curvatures...')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._imageInput = None
self._meshInput = None
self._flipper = vtk.vtkImageFlip()
self._flipper.SetFilteredAxis(1)
module_utils.setup_vtk_object_progress(self, self._flipper,
'Flipping Y axis.')
self._config.cpt_driver_path = \
'd:\\misc\\stuff\\driver.bat'
#'/home/cpbotha/build/cpt/3d/driver/driver.exe'
self._config.max_distance = 5
config_list = [
('CPT driver path', 'cpt_driver_path', 'base:str', 'filebrowser',
'Path to CPT driver executable', {
'fileMode': module_mixins.wx.OPEN,
'fileMask': 'All files (*.*)|*.*'
}),
('Maximum distance', 'max_distance', 'base:float', 'text',
'The maximum (absolute) distance up to which the field is computed.'
)
]
ScriptedConfigModuleMixin.__init__(self, config_list,
{'Module (self)': self})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self)
self._imageReslice = vtk.vtkImageReslice()
self._imageReslice.SetInterpolationModeToCubic()
self._matrixToHT = vtk.vtkMatrixToHomogeneousTransform()
self._matrixToHT.Inverse()
module_utils.setup_vtk_object_progress(self, self._imageReslice,
'Resampling volume')
self._viewFrame = self._createViewFrame(
{'Module (self)' : self,
'vtkImageReslice' : self._imageReslice})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.syncViewWithLogic()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._glyph3d = vtktud.vtkMyGlyph3D()
module_utils.setup_vtk_object_progress(self, self._glyph3d,
'Making 3D glyphs')
self._config.scaling = 1.0
self._config.scalemode = 1.0
configList = [
('Scaling:', 'scaling', 'base:float', 'text',
'Glyphs will be scaled by this factor.'),
('Scalemode:', 'scalemode', 'base:int', 'text',
'Scaling will occur by scalar, vector direction or magnitude.')]
ScriptedConfigModuleMixin.__init__(self, configList)
self._viewFrame = self._createWindow(
{'Module (self)' : self,
'vtkMyGlyph3D' : self._glyph3d})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.logic_to_config()
self.config_to_view()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._tubeFilter = vtk.vtkTubeFilter()
module_utils.setup_vtk_object_progress(self, self._tubeFilter,
'Generating tubes.')
self._config.NumberOfSides = 3
self._config.Radius = 0.01
configList = [
('Number of sides:', 'NumberOfSides', 'base:int', 'text',
'Number of sides that the tube should have.'),
('Tube radius:', 'Radius', 'base:float', 'text',
'Radius of the generated tube.')]
ScriptedConfigModuleMixin.__init__(self, configList)
self._viewFrame = self._createWindow(
{'Module (self)' : self,
'vtkTubeFilter' : self._tubeFilter})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.syncViewWithLogic()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._extract = vtk.vtkImageExtractComponents()
module_utils.setup_vtk_object_progress(self, self._extract,
'Extracting components.')
self._config.component1 = 0
self._config.component2 = 1
self._config.component3 = 2
self._config.numberOfComponents = 1
self._config.fileLowerLeft = False
configList = [
('Component 1:', 'component1', 'base:int', 'text',
'Zero-based index of first component to extract.'),
('Component 2:', 'component2', 'base:int', 'text',
'Zero-based index of second component to extract.'),
('Component 3:', 'component3', 'base:int', 'text',
'Zero-based index of third component to extract.'),
('Number of components:', 'numberOfComponents', 'base:int',
'choice',
'Number of components to extract. Only this number of the '
'above-specified component indices will be used.',
('1', '2', '3'))]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkImageExtractComponents' : self._extract})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._histogram = vtkdevide.vtkImageHistogram2D()
module_utils.setup_vtk_object_progress(self, self._histogram,
'Calculating 2D histogram')
self._config.input1Bins = 256
self._config.input2Bins = 256
self._config.maxSamplesPerBin = 512
configList = [
('Number of bins for input 1', 'input1Bins', 'base:int', 'text',
'The full range of input 1 values will be divided into this many '
'classes.'),
('Number of bins for input 2', 'input2Bins', 'base:int', 'text',
'The full range of input 2 values will be divided into this many '
'classes.'),
('Maximum samples per bin', 'maxSamplesPerBin', 'base:int', 'text',
'The number of samples per 2D bin/class will be truncated to '
'this value.')]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkImageHistogram2D' : self._histogram})
self.sync_module_logic_with_config()
self._input0 = None
self._input1 = None
def __init__(self, module_manager):
"""Constructor (initialiser) for the PD reader.
This is almost standard code for most of the modules making use of
the FilenameViewModuleMixin mixin.
"""
# call the constructor in the "base"
ModuleBase.__init__(self, module_manager)
# setup necessary VTK objects
self._reader = vtk.vtkSTLReader()
# ctor for this specific mixin
FilenameViewModuleMixin.__init__(
self, 'Select a filename',
'STL data (*.stl)|*.stl|All files (*)|*',
{'vtkSTLReader': self._reader})
module_utils.setup_vtk_object_progress(self, self._reader,
'Reading STL data')
# set up some defaults
self._config.filename = ''
self.sync_module_logic_with_config()
def _create_pipeline(self):
# setup our pipeline
self._otf = vtk.vtkPiecewiseFunction()
self._ctf = vtk.vtkColorTransferFunction()
self._volume_property = vtk.vtkVolumeProperty()
self._volume_property.SetScalarOpacity(self._otf)
self._volume_property.SetColor(self._ctf)
self._volume_property.ShadeOn()
self._volume_property.SetAmbient(0.1)
self._volume_property.SetDiffuse(0.7)
self._volume_property.SetSpecular(0.2)
self._volume_property.SetSpecularPower(10)
self._volume_raycast_function = vtk.vtkVolumeRayCastMIPFunction()
self._volume_mapper = vtk.vtkVolumeRayCastMapper()
# can also used FixedPoint, but then we have to use:
# SetBlendModeToMaximumIntensity() and not SetVolumeRayCastFunction
#self._volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
self._volume_mapper.SetVolumeRayCastFunction(
self._volume_raycast_function)
module_utils.setup_vtk_object_progress(self, self._volume_mapper,
'Preparing render.')
self._volume = vtk.vtkVolume()
self._volume.SetProperty(self._volume_property)
self._volume.SetMapper(self._volume_mapper)
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._histogram = vtkdevide.vtkImageHistogram2D()
module_utils.setup_vtk_object_progress(self, self._histogram,
'Calculating 2D histogram')
self._config.input1Bins = 256
self._config.input2Bins = 256
self._config.maxSamplesPerBin = 512
configList = [
('Number of bins for input 1', 'input1Bins', 'base:int', 'text',
'The full range of input 1 values will be divided into this many '
'classes.'),
('Number of bins for input 2', 'input2Bins', 'base:int', 'text',
'The full range of input 2 values will be divided into this many '
'classes.'),
('Maximum samples per bin', 'maxSamplesPerBin', 'base:int', 'text',
'The number of samples per 2D bin/class will be truncated to '
'this value.')
]
ScriptedConfigModuleMixin.__init__(
self, configList, {
'Module (self)': self,
'vtkImageHistogram2D': self._histogram
})
self.sync_module_logic_with_config()
self._input0 = None
self._input1 = None
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._image_logic = vtk.vtkImageLogic()
module_utils.setup_vtk_object_progress(self, self._image_logic,
'Performing image logic')
self._image_cast = vtk.vtkImageCast()
module_utils.setup_vtk_object_progress(
self, self._image_cast, 'Casting scalar type before image logic')
self._config.operation = 0
self._config.output_true_value = 1.0
# 'choice' widget with 'base:int' type will automatically get cast
# to index of selection that user makes.
config_list = [
('Operation:', 'operation', 'base:int',
'choice', 'The operation that should be performed.',
tuple(self._operations)),
('Output true value:', 'output_true_value', 'base:float', 'text',
'Output voxels that are TRUE will get this value.')
]
ScriptedConfigModuleMixin.__init__(self, config_list, {
'Module (self)': self,
'vtkImageLogic': self._image_logic
})
self.sync_module_logic_with_config()
def __init__(self, module_manager, contourFilterText):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._contourFilterText = contourFilterText
if contourFilterText == 'marchingCubes':
self._contourFilter = vtk.vtkMarchingCubes()
else: # contourFilter == 'contourFilter'
self._contourFilter = vtk.vtkContourFilter()
module_utils.setup_vtk_object_progress(self, self._contourFilter,
'Extracting iso-surface')
# now setup some defaults before our sync
self._config.isoValue = 128
self._viewFrame = None
self._createViewFrame()
# transfer these defaults to the logic
self.config_to_logic()
# then make sure they come all the way back up via self._config
self.logic_to_config()
self.config_to_view()
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._writer = vtk.vtkMetaImageWriter()
module_utils.setup_vtk_object_progress(
self, self._writer,
'Writing VTK ImageData')
# set up some defaults
self._config.filename = ''
self._config.compression = True
config_list = [
('Filename:', 'filename', 'base:str', 'filebrowser',
'Output filename for MetaImage file.',
{'fileMode' : wx.SAVE,
'fileMask' : 'MetaImage single file (*.mha)|*.mha|MetaImage separate header/(z)raw files (*.mhd)|*.mhd|All files (*)|*',
'defaultExt' : '.mha'}
),
('Compression:', 'compression', 'base:bool', 'checkbox',
'Compress the image / volume data')
]
ScriptedConfigModuleMixin.__init__(self, config_list,
{'Module (self)' : self})
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
# setup config
self._config.toroidal = True
self._config.thickness = 0.3333
self._config.phiRoundness = 0.2
self._config.thetaRoundness = 0.8
self._config.size = 0.5
self._config.center = (0, 0, 0)
self._config.scale = (1, 1, 1)
self._config.thetaResolution = 64
self._config.phiResolution = 64
# and then our scripted config
configList = [
('Toroidal: ', 'toroidal', 'base:bool', 'checkbox',
'Should the quadric be toroidal.'),
('Thickness: ', 'thickness', 'base:float', 'text',
'Thickness of the toroid, scaled between 0 and 1'),
('Phi Roundness: ', 'phiRoundness', 'base:float', 'text',
'Controls shape of superquadric'),
('Theta Roundness: ', 'thetaRoundness', 'base:float', 'text',
'Controls shape of superquadric'),
('Size: ', 'size', 'base:float', 'text',
'The size of the superquadric.'),
('Centre: ', 'center', 'tuple:float,3', 'text',
'The translation transform of the resultant superquadric.'),
('Scale: ', 'scale', 'tuple:float,3', 'text',
'The scale transformof the resultant superquadric.'),
('Theta resolution: ', 'thetaResolution', 'base:int', 'text',
'The resolution of the output polydata'),
('Phi resolution: ', 'phiResolution', 'base:int', 'text',
'The resolution of the output polydata')
]
# now create the necessary VTK modules
self._superquadric = vtk.vtkSuperquadric()
self._superquadricSource = vtk.vtkSuperquadricSource()
# we need these temporary outputs
self._outputs = [self._superquadric, vtk.vtkPolyData()]
# setup progress for the processObject
module_utils.setup_vtk_object_progress(self, self._superquadricSource,
"Synthesizing polydata.")
# mixin ctor
ScriptedConfigModuleMixin.__init__(
self, configList, {
'Module (self)': self,
'vtkSuperquadric': self._superquadric,
'vtkSuperquadricSource': self._superquadricSource
})
self.sync_module_logic_with_config()
def _setup_for_shell_splatting(self):
self._volume_mapper = vtkdevide.vtkOpenGLVolumeShellSplatMapper()
self._volume_mapper.SetOmegaL(0.9)
self._volume_mapper.SetOmegaH(0.9)
# high-quality rendermode
self._volume_mapper.SetRenderMode(0)
module_utils.setup_vtk_object_progress(self, self._volume_mapper,
'Preparing render.')
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# main morph gradient
self._imageDilate = vtk.vtkImageContinuousDilate3D()
self._imageErode = vtk.vtkImageContinuousErode3D()
self._imageMath = vtk.vtkImageMathematics()
self._imageMath.SetOperationToSubtract()
self._imageMath.SetInput1(self._imageDilate.GetOutput())
self._imageMath.SetInput2(self._imageErode.GetOutput())
# inner gradient
self._innerImageMath = vtk.vtkImageMathematics()
self._innerImageMath.SetOperationToSubtract()
self._innerImageMath.SetInput1(None) # has to take image
self._innerImageMath.SetInput2(self._imageErode.GetOutput())
# outer gradient
self._outerImageMath = vtk.vtkImageMathematics()
self._outerImageMath.SetOperationToSubtract()
self._outerImageMath.SetInput1(self._imageDilate.GetOutput())
self._outerImageMath.SetInput2(None) # has to take image
module_utils.setup_vtk_object_progress(
self, self._imageDilate, 'Performing greyscale 3D dilation')
module_utils.setup_vtk_object_progress(
self, self._imageErode, 'Performing greyscale 3D erosion')
module_utils.setup_vtk_object_progress(
self, self._imageMath, 'Subtracting erosion from '
'dilation')
module_utils.setup_vtk_object_progress(
self, self._innerImageMath, 'Subtracting erosion from '
'image (inner)')
module_utils.setup_vtk_object_progress(
self, self._outerImageMath, 'Subtracting image from '
'dilation (outer)')
self._config.kernelSize = (3, 3, 3)
configList = [('Kernel size:', 'kernelSize', 'tuple:int,3', 'text',
'Size of the kernel in x,y,z dimensions.')]
ScriptedConfigModuleMixin.__init__(
self, configList, {
'Module (self)': self,
'vtkImageContinuousDilate3D': self._imageDilate,
'vtkImageContinuousErode3D': self._imageErode,
'vtkImageMathematics': self._imageMath
})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
# setup config
self._config.toroidal = True
self._config.thickness = 0.3333
self._config.phiRoundness = 0.2
self._config.thetaRoundness = 0.8
self._config.size = 0.5
self._config.center = (0,0,0)
self._config.scale = (1,1,1)
self._config.thetaResolution = 64
self._config.phiResolution = 64
# and then our scripted config
configList = [
('Toroidal: ', 'toroidal', 'base:bool', 'checkbox',
'Should the quadric be toroidal.'),
('Thickness: ', 'thickness', 'base:float', 'text',
'Thickness of the toroid, scaled between 0 and 1'),
('Phi Roundness: ', 'phiRoundness', 'base:float', 'text',
'Controls shape of superquadric'),
('Theta Roundness: ', 'thetaRoundness', 'base:float', 'text',
'Controls shape of superquadric'),
('Size: ', 'size', 'base:float', 'text',
'The size of the superquadric.'),
('Centre: ', 'center', 'tuple:float,3', 'text',
'The translation transform of the resultant superquadric.'),
('Scale: ', 'scale', 'tuple:float,3', 'text',
'The scale transformof the resultant superquadric.'),
('Theta resolution: ', 'thetaResolution', 'base:int', 'text',
'The resolution of the output polydata'),
('Phi resolution: ', 'phiResolution', 'base:int', 'text',
'The resolution of the output polydata')]
# now create the necessary VTK modules
self._superquadric = vtk.vtkSuperquadric()
self._superquadricSource = vtk.vtkSuperquadricSource()
# we need these temporary outputs
self._outputs = [self._superquadric, vtk.vtkPolyData()]
# setup progress for the processObject
module_utils.setup_vtk_object_progress(self, self._superquadricSource,
"Synthesizing polydata.")
# mixin ctor
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkSuperquadric' : self._superquadric,
'vtkSuperquadricSource' : self._superquadricSource})
self.sync_module_logic_with_config()
def _setup_for_raycast(self):
self._volume_raycast_function = \
vtk.vtkVolumeRayCastCompositeFunction()
self._volume_mapper = vtk.vtkVolumeRayCastMapper()
self._volume_mapper.SetVolumeRayCastFunction(
self._volume_raycast_function)
module_utils.setup_vtk_object_progress(self, self._volume_mapper,
'Preparing render.')
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
InputArrayChoiceMixin.__init__(self)
self._config.scaling = True
self._config.scaleFactor = 1
self._config.scaleMode = glyphScaleMode.index('SCALE_BY_VECTOR')
self._config.colourMode = glyphColourMode.index('COLOUR_BY_VECTOR')
self._config.vectorMode = glyphVectorMode.index('USE_VECTOR')
self._config.mask_on_ratio = 5
self._config.mask_random = True
configList = [
('Scale glyphs:', 'scaling', 'base:bool', 'checkbox',
'Should the size of the glyphs be scaled?'),
('Scale factor:', 'scaleFactor', 'base:float', 'text',
'By how much should the glyph size be scaled if scaling is '
'active?'),
('Scale mode:', 'scaleMode', 'base:int', 'choice',
'Should scaling be performed by vector, scalar or only factor?',
glyphScaleModeTexts),
('Colour mode:', 'colourMode', 'base:int', 'choice',
'Colour is determined based on scalar or vector magnitude.',
glyphColourModeTexts),
('Vector mode:', 'vectorMode', 'base:int', 'choice',
'Should vectors or normals be used for scaling and orientation?',
glyphVectorModeTexts),
('Vectors selection:', 'vectorsSelection', 'base:str', 'choice',
'The attribute that will be used as vectors for the warping.',
(input_array_choice_mixin.DEFAULT_SELECTION_STRING,)),
('Mask on ratio:', 'mask_on_ratio', 'base:int', 'text',
'Every Nth point will be glyphed.'),
('Random masking:', 'mask_random', 'base:bool', 'checkbox',
'Pick random distribution of Nth points.')]
self._mask_points = vtk.vtkMaskPoints()
module_utils.setup_vtk_object_progress(self,
self._mask_points, 'Masking points.')
self._glyphFilter = vtk.vtkGlyph3D()
asrc = vtk.vtkArrowSource()
self._glyphFilter.SetSource(0, asrc.GetOutput())
self._glyphFilter.SetInput(self._mask_points.GetOutput())
module_utils.setup_vtk_object_progress(self, self._glyphFilter,
'Creating glyphs.')
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkGlyph3D' : self._glyphFilter})
self.sync_module_logic_with_config()
def _setup_for_fixed_point(self):
"""This doesn't seem to work. After processing is complete,
it stalls on actually rendering the volume. No idea.
"""
import vtktudoss
self._volume_mapper = vtktudoss.vtkCVFixedPointVolumeRayCastMapper()
self._volume_mapper.SetBlendModeToComposite()
#self._volume_mapper.SetBlendModeToMaximumIntensity()
module_utils.setup_vtk_object_progress(self, self._volume_mapper,
'Preparing render.')
def _setup_for_gpu_raycasting(self):
"""This doesn't seem to work. After processing is complete,
it stalls on actually rendering the volume. No idea.
"""
self._volume_mapper = vtk.vtkGPUVolumeRayCastMapper()
self._volume_mapper.SetBlendModeToComposite()
#self._volume_mapper.SetBlendModeToMaximumIntensity()
module_utils.setup_vtk_object_progress(self, self._volume_mapper,
'Preparing render.')
