def initArea(self):
'''
Sets up the VTK simulation area
:return:None
'''
self.actors_dict = {}
self.actorCollection=vtk.vtkActorCollection()
self.borderActor = vtk.vtkActor()
self.borderActorHex = vtk.vtkActor()
self.clusterBorderActor = vtk.vtkActor()
self.clusterBorderActorHex = vtk.vtkActor()
self.cellGlyphsActor = vtk.vtkActor()
self.FPPLinksActor = vtk.vtkActor() # used for both white and colored links
self.outlineActor = vtk.vtkActor()
# self.axesActor = vtk.vtkCubeAxesActor2D()
self.axesActor = vtk.vtkCubeAxesActor()
self.outlineDim=[0,0,0]
self.cellsActor = vtk.vtkActor()
self.cellsActor.GetProperty().SetInterpolationToFlat() # ensures that pixels are drawn exactly not with interpolations/antialiasing
self.hexCellsActor = vtk.vtkActor()
self.hexCellsActor.GetProperty().SetInterpolationToFlat() # ensures that pixels are drawn exactly not with interpolations/antialiasing
self.conActor = vtk.vtkActor()
self.conActor.GetProperty().SetInterpolationToFlat()
self.hexConActor = vtk.vtkActor()
self.hexConActor.GetProperty().SetInterpolationToFlat()
self.contourActor = vtk.vtkActor()
self.glyphsActor=vtk.vtkActor()
#self.linksActor=vtk.vtkActor()
# # Concentration lookup table
self.clut = vtk.vtkLookupTable()
self.clut.SetHueRange(0.67, 0.0)
self.clut.SetSaturationRange(1.0,1.0)
self.clut.SetValueRange(1.0,1.0)
self.clut.SetAlphaRange(1.0,1.0)
self.clut.SetNumberOfColors(1024)
self.clut.Build()
# Contour lookup table
# Do I need lookup table? May be just one color?
self.ctlut = vtk.vtkLookupTable()
self.ctlut.SetHueRange(0.6, 0.6)
self.ctlut.SetSaturationRange(0,1.0)
self.ctlut.SetValueRange(1.0,1.0)
self.ctlut.SetAlphaRange(1.0,1.0)
self.ctlut.SetNumberOfColors(1024)
self.ctlut.Build()
def MakeLUT(tableSize):
'''
Make a lookup table from a set of named colors.
:param: tableSize - The table size
:return: The lookup table.
'''
nc = vtk.vtkNamedColors()
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(tableSize)
lut.Build()
# Fill in a few known colors, the rest will be generated if needed
lut.SetTableValue(0,nc.GetColor4d("Black"))
lut.SetTableValue(1,nc.GetColor4d("Banana"))
lut.SetTableValue(2,nc.GetColor4d("Tomato"))
lut.SetTableValue(3,nc.GetColor4d("Wheat"))
lut.SetTableValue(4,nc.GetColor4d("Lavender"))
lut.SetTableValue(5,nc.GetColor4d("Flesh"))
lut.SetTableValue(6,nc.GetColor4d("Raspberry"))
lut.SetTableValue(7,nc.GetColor4d("Salmon"))
lut.SetTableValue(8,nc.GetColor4d("Mint"))
lut.SetTableValue(9,nc.GetColor4d("Peacock"))
return lut
def get_lookup_table(self, display_mode):
"""
Sets up and returns the lookup table depending upon the display mode
"""
lut = vtkLookupTable()
ref_lut = vtkLookupTable()
num_colours = 256
lut.SetNumberOfColors(num_colours)
ref_lut.SetNumberOfColors(num_colours)
if (display_mode == 'load'):
lut.SetTableRange(0.0, 1.75)
ref_lut.SetTableRange(0.0, 1.75)
else:
lut.SetTableRange(0.0, 1.0)
ref_lut.SetTableRange(0.0, 1.0)
lut.Build()
ref_lut.Build()
# invert the colours: we want red to be at the high end
for j in range(num_colours):
lut.SetTableValue(j, ref_lut.GetTableValue(num_colours-1-j))
return lut
def __init__(self):
self.interactor = None
self.image_original = None
self.image_threshold = None
self.render = None
self.lut = vtk.vtkLookupTable()
self.lut_original = vtk.vtkLookupTable()
self.image_color = vtk.vtkImageMapToColors()
self.blend = blend = vtk.vtkImageBlend()
self.map = map = vtk.vtkImageMapper()
self.actor = actor = vtk.vtkImageActor()
self.actor2 = actor2 = vtk.vtkImageActor()
self.actor3 = actor3 = vtk.vtkImageActor()
self.image_color_o = vtk.vtkImageMapToColors()
self.operation_type = 0
self.w = None
self.slice = 0
self.clicked = 0
self.orientation = AXIAL
self.w = (200, 1200)
def addArrayFromIdList(self, connectedIdList, inputModelNode, arrayName):
if not inputModelNode:
return
inputModelNodePolydata = inputModelNode.GetPolyData()
pointData = inputModelNodePolydata.GetPointData()
numberofIds = connectedIdList.GetNumberOfIds()
hasArrayInt = pointData.HasArray(arrayName)
if hasArrayInt == 1: # ROI Array found
pointData.RemoveArray(arrayName)
arrayToAdd = vtk.vtkDoubleArray()
arrayToAdd.SetName(arrayName)
for i in range(0, inputModelNodePolydata.GetNumberOfPoints()):
arrayToAdd.InsertNextValue(0.0)
for i in range(0, numberofIds):
arrayToAdd.SetValue(connectedIdList.GetId(i), 1.0)
lut = vtk.vtkLookupTable()
tableSize = 2
lut.SetNumberOfTableValues(tableSize)
lut.Build()
ID = inputModelNode.GetDisplayNodeID()
slicer.app.mrmlScene().GetNodeByID(ID)
displayNode = slicer.app.mrmlScene().GetNodeByID(ID)
rgb = displayNode.GetColor()
lut.SetTableValue(0, rgb[0], rgb[1], rgb[2], 1)
lut.SetTableValue(1, 1.0, 0.0, 0.0, 1)
arrayToAdd.SetLookupTable(lut)
pointData.AddArray(arrayToAdd)
inputModelNodePolydata.Modified()
return True
def setParams(self):
# You can use either Build() method (256 color by default) or
# SetNumberOfTableValues() to allocate much more colors!
self.lut = vtk.vtkLookupTable()
# You need to explicitly call Build() when constructing the LUT by hand
self.lut.Build()
self.populateLookupTable()
def do_colour_mask(self, imagedata):
scalar_range = int(imagedata.GetScalarRange()[1])
r, g, b = self.current_mask.colour
# map scalar values into colors
lut_mask = vtk.vtkLookupTable()
lut_mask.SetNumberOfColors(256)
lut_mask.SetHueRange(const.THRESHOLD_HUE_RANGE)
lut_mask.SetSaturationRange(1, 1)
lut_mask.SetValueRange(0, 255)
lut_mask.SetRange(0, 255)
lut_mask.SetNumberOfTableValues(256)
lut_mask.SetTableValue(0, 0, 0, 0, 0.0)
lut_mask.SetTableValue(1, 0, 0, 0, 0.0)
lut_mask.SetTableValue(254, r, g, b, 1.0)
lut_mask.SetTableValue(255, r, g, b, 1.0)
lut_mask.SetRampToLinear()
lut_mask.Build()
# self.lut_mask = lut_mask
# map the input image through a lookup table
img_colours_mask = vtk.vtkImageMapToColors()
img_colours_mask.SetLookupTable(lut_mask)
img_colours_mask.SetOutputFormatToRGBA()
img_colours_mask.SetInput(imagedata)
img_colours_mask.Update()
# self.img_colours_mask = img_colours_mask
return img_colours_mask.GetOutput()
def _set_colour(self, imagedata, colour):
scalar_range = int(imagedata.GetScalarRange()[1])
r, g, b = colour
# map scalar values into colors
lut_mask = vtk.vtkLookupTable()
lut_mask.SetNumberOfColors(256)
lut_mask.SetHueRange(const.THRESHOLD_HUE_RANGE)
lut_mask.SetSaturationRange(1, 1)
lut_mask.SetValueRange(0, 255)
lut_mask.SetRange(0, 255)
lut_mask.SetNumberOfTableValues(256)
lut_mask.SetTableValue(0, 0, 0, 0, 0.0)
lut_mask.SetTableValue(1, 1-r, 1-g, 1-b, 0.50)
lut_mask.SetRampToLinear()
lut_mask.Build()
# map the input image through a lookup table
img_colours_mask = vtk.vtkImageMapToColors()
img_colours_mask.SetLookupTable(lut_mask)
img_colours_mask.SetOutputFormatToRGBA()
img_colours_mask.SetInput(imagedata)
img_colours_mask.Update()
return img_colours_mask.GetOutput()
def polyShowColorScalars(ren, obj):
#@c Show scalar values on poly in renderer in color
#@a ren: renderer
#@a obj: object name
if isinstance(obj,list):
tag = "%s_%s" % (ren[0],obj[0])
elif isinstance(obj,str):
tag = "%s_%s" % (ren[0],obj)
else:
raise ValueError("Argument type unsupported.")
lookupColor = [None]*2
lookupColor[0] = "p_blueToRedLUT_"+tag
lookupColor[1] = vtk.vtkLookupTable()
lookupColor[1].SetHueRange(0.6667 ,0.0)
lookupColor[1].SetSaturationRange(1.,1.)
lookupColor[1].SetValueRange(1.,1.)
lookupColor[1].SetAlphaRange(1.,1.)
lookupColor[1].SetNumberOfColors(16384)
lookupColor[1].Build()
act = polyGetActor(ren,obj)
act[1].GetMapper().SetLookupTable(lookupColor[1])
act[1].GetMapper().ScalarVisibilityOn()
Range = act[1].GetMapper().GetInput().GetPointData().GetScalars().GetRange()
act[1].GetMapper().SetScalarRange(Range[0],Range[1])
vis.render(ren)
setattr(vis,act[0],act)
setattr(vis,lookupColor[0],lookupColor)
return
def __init__(self,data_reader):
self.lut=vtk.vtkLookupTable()
self.lut.SetNumberOfColors(256)
self.lut.SetTableRange(data_reader.get_scalar_range())
self.lut.SetHueRange(0,1)
self.lut.SetRange(data_reader.get_scalar_range())
self.lut.SetRange(data_reader.get_scalar_range())
self.lut.Build()
self.arrow=vtk.vtkArrowSource()
self.arrow.SetTipResolution(6)
self.arrow.SetTipRadius(0.1)
self.arrow.SetTipLength(0.35)
self.arrow.SetShaftResolution(6)
self.arrow.SetShaftRadius(0.03)
self.glyph=vtk.vtkGlyph3D()
self.glyph.SetInput(data_reader.get_data_set())
self.glyph.SetSource(self.arrow.GetOutput())
self.glyph.SetVectorModeToUseVector()
self.glyph.SetColorModeToColorByScalar()
self.glyph.SetScaleModeToScaleByVector()
self.glyph.OrientOn()
self.glyph.SetScaleFactor(0.002)
mapper=vtk.vtkPolyDataMapper()
mapper.SetInput(self.glyph.GetOutput())
mapper.SetLookupTable(self.lut)
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(data_reader.get_scalar_range())
self.actor=vtk.vtkActor()
self.actor.SetMapper(mapper)
def writeAllImageSlices(imgfn,pathfn,ext,output_dir):
reader = vtk.vtkMetaImageReader()
reader.SetFileName(imgfn)
reader.Update()
img = reader.GetOutput()
parsed_path = parsePathFile(pathfn)
slices = getAllImageSlices(img,parsed_path,ext)
writer = vtk.vtkJPEGWriter()
table = vtk.vtkLookupTable()
scalar_range = img.GetScalarRange()
table.SetRange(scalar_range[0], scalar_range[1]) # image intensity range
table.SetValueRange(0.0, 1.0) # from black to white
table.SetSaturationRange(0.0, 0.0) # no color saturation
table.SetRampToLinear()
table.Build()
# Map the image through the lookup table
color = vtk.vtkImageMapToColors()
color.SetLookupTable(table)
mkdir(output_dir)
for i in range(len(slices)):
color.SetInputData(slices[i])
writer.SetInputConnection(color.GetOutputPort())
writer.SetFileName(output_dir+'{}.jpg'.format(i))
writer.Update()
writer.Write()
def setParams(self):
# # You can use either Build() method (256 color by default) or
# # SetNumberOfTableValues() to allocate much more colors!
# self.celltypeLUT = vtk.vtkLookupTable()
# # You need to explicitly call Build() when constructing the LUT by hand
# self.celltypeLUT.Build()
#
# self.populate_cell_type_lookup_table()
# self.populateLookupTable()
# self.dim = [100, 100, 1] # Default values
# for FPP links (and offset also for cell glyphs)
self.eps = 1.e-4 # not sure how small this should be (checking to see if cell volume -> 0)
self.stubSize = 3.0 # dangling line stub size for lines that wraparound periodic BCs
# self.offset = 1.0 # account for fact that COM of cell is offset from visualized lattice
# self.offset = 0.0 # account for fact that COM of cell is offset from visualized lattice
# scaling factors to map square lattice to hex lattice (rf. CC3D Manual)
self.xScaleHex = 1.0
self.yScaleHex = 0.866
self.zScaleHex = 0.816
self.lutBlueRed = vtk.vtkLookupTable()
self.lutBlueRed.SetHueRange(0.667, 0.0)
self.lutBlueRed.Build()
def write(self, file_name):
writer = vtk.vtkPLYWriter()
writer.SetFileName(file_name)
writer.SetInputData(self.vtk_poly_data)
if self.is_color_mode_height:
# set lookup tbale for depth values to colors
lut = vtk.vtkLookupTable()
lut.SetTableRange(self.height_min, self.height_max)
lut.Build()
# in order to be convertable to pcd, use lut to generate colors.
# THIS IS A DIRTY HACK BUT NEEDED SINCE PCL IS STUPID
# writer.SetLookupTable(lut) only works for meshlab
cur_color_data = vtk.vtkUnsignedCharArray()
cur_color_data.SetNumberOfComponents(3)
for id in self.color_ids:
val = self.color_data.GetValue(id)
col = [0., 0., 0.]
lut.GetColor(val, col)
col = [int(c * 255) for c in col]
cur_color_data.InsertNextTuple3(col[0], col[1], col[2])
self.color_data = cur_color_data
self.color_data.SetName("Colors")
self.vtk_poly_data.GetPointData().SetActiveScalars('Colors')
self.vtk_poly_data.GetPointData().SetScalars(self.color_data)
writer.SetArrayName("Colors")
writer.Write()
def __init__(self, filename, max_num_of_vertices=-1, edge_color_filename=None):
super(VTKVisualizer, self).__init__()
self.vertex_id_idx_map = {}
self.next_vertex_id = 0
self.edge_counter = 0
self.lookup_table = vtk.vtkLookupTable()
self.lookup_table.SetNumberOfColors(int(1e8))
self.edge_color_tuples = {}
self.edge_color_filename = edge_color_filename
self.label_vertex_id_map = {}
self.starting_vertex = None
self.starting_vertex_index = -1
self.filename = filename
self.max_num_of_vertices = max_num_of_vertices
self.g = vtk.vtkMutableDirectedGraph()
self.vertex_ids = vtk.vtkIntArray()
self.vertex_ids.SetNumberOfComponents(1)
self.vertex_ids.SetName(VERTEX_ID)
self.labels = vtk.vtkStringArray()
self.labels.SetNumberOfComponents(1)
self.labels.SetName(LABELS)
self.glyph_scales = vtk.vtkFloatArray()
self.glyph_scales.SetNumberOfComponents(1)
self.glyph_scales.SetName(SCALES)
self.edge_weights = vtk.vtkDoubleArray()
self.edge_weights.SetNumberOfComponents(1)
self.edge_weights.SetName(WEIGHTS)
self.edge_colors = vtk.vtkIntArray()
self.edge_colors.SetNumberOfComponents(1)
self.edge_colors.SetName(EDGE_COLORS)
def initArea(self):
# Zoom items
self.zitems = []
self.cellTypeActors={}
self.outlineActor = vtk.vtkActor()
self.outlineDim=[0,0,0]
self.invisibleCellTypes={}
self.typesInvisibleStr=""
self.set3DInvisibleTypes()
axesActor = vtk.vtkActor()
axisTextActor = vtk.vtkFollower()
self.clut = vtk.vtkLookupTable()
self.clut.SetHueRange(0.67, 0.0)
self.clut.SetSaturationRange(1.0,1.0)
self.clut.SetValueRange(1.0,1.0)
self.clut.SetAlphaRange(1.0,1.0)
self.clut.SetNumberOfColors(1024)
self.clut.Build()
## Set up the mapper and actor (3D) for concentration field.
# self.conMapper = vtk.vtkPolyDataMapper()
self.conActor = vtk.vtkActor()
self.glyphsActor=vtk.vtkActor()
# self.glyphsMapper=vtk.vtkPolyDataMapper()
self.cellGlyphsActor = vtk.vtkActor()
self.FPPLinksActor = vtk.vtkActor()
# Weird attributes
self.typeActors = {} # vtkActor
def __MakeLUT(self):
'''
Make a lookup table using vtkColorSeries.
:return: An indexed lookup table.
'''
# Make the lookup table.
pal = "../util/color_circle_Ajj.pal"
tableSize = 255
colorFunc = vtk.vtkColorTransferFunction()
scalars = self.histo()[1]
with open(pal) as f:
lines = f.readlines()
# lines.reverse()
for i, line in enumerate(lines):
l = line.strip()
r, g, b = self.__hex2rgb(l[1:])
# print scalars[i], r, g, b
colorFunc.AddRGBPoint(scalars[i], r, g, b)
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(tableSize)
lut.Build()
for i in range(0, tableSize):
rgb = list(colorFunc.GetColor(float(i)/tableSize))+[1]
lut.SetTableValue(i, rgb)
return lut
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._volume_input = None
self._opacity_tf = vtk.vtkPiecewiseFunction()
self._colour_tf = vtk.vtkColorTransferFunction()
self._lut = vtk.vtkLookupTable()
# list of tuples, where each tuple (scalar_value, (r,g,b,a))
self._config.transfer_function = [
(0, (0,0,0), 0),
(255, (255,255,255), 1)
]
self._view_frame = None
self._create_view_frame()
self._bind_events()
self.view()
# all modules should toggle this once they have shown their
# stuff.
self.view_initialised = True
self.config_to_logic()
self.logic_to_config()
self.config_to_view()
def _makeLut(self):
"""
Creates vtkLookupTable for mapping the volumes
"""
random.seed(0)
lut = vtk.vtkLookupTable()
cm = self._gidToColorMap # Just simple alias
# Number of colors in LUT is equal to the largest GID +1
lut.SetNumberOfColors(max(cm.keys())+1)
# Then, allocate the table with the colors. Iterate over all color
# slots and assign proper color
for i in range(lut.GetNumberOfColors()):
# If given index is defined in indexer:
# assign its color to the lookup table
# otherwise set it to black
if i in cm:
if cm[i][0] == cm[i][1] == cm[i][2] == 119:
c = map(lambda x: float(random.randint(0, 255))/255., [0,0,0])
lut.SetTableValue(i, c[0], c[1], c[2], 1)
else:
c = cm[i]
c = map(lambda x: float(x)/255., c)
lut.SetTableValue(i, c[0], c[1], c[2], 1)
else:
lut.SetTableValue(i, 0., 0., 0., 0.)
# Build the LUT and return it
lut.SetRange(0, max(cm.keys()))
lut.Build()
return lut
def jet(self, m=256):
# blue, cyan, green, yellow, red, black
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(m)
lut.SetHueRange(0.667,0.0)
lut.Build()
return lut
def __init__( self, interactor, **args ):
ListWidget.__init__( self, interactor, **args )
self.lut = vtk.vtkLookupTable()
self.image_data = {}
self.colorMapManager = ColorMapManager( self.lut )
self.textMapper = None
self.build()
def __init__(self):
self.lookupTable = vtk.vtkLookupTable()
self.lookupTable.SetRampToLinear()
self.lookupTable.SetNumberOfTableValues(2)
self.lookupTable.SetTableRange(0, 1)
self.lookupTable.SetTableValue(0, 0, 0, 0, 0)
self.colorMapper = vtk.vtkImageMapToRGBA()
self.colorMapper.SetOutputFormatToRGBA()
self.colorMapper.SetLookupTable(self.lookupTable)
self.thresholdFilter = vtk.vtkImageThreshold()
self.thresholdFilter.SetInValue(1)
self.thresholdFilter.SetOutValue(0)
self.thresholdFilter.SetOutputScalarTypeToUnsignedChar()
# Feedback actor
self.mapper = vtk.vtkImageMapper()
self.dummyImage = vtk.vtkImageData()
self.dummyImage.AllocateScalars(vtk.VTK_UNSIGNED_INT, 1)
self.mapper.SetInputData(self.dummyImage)
self.actor = vtk.vtkActor2D()
self.actor.VisibilityOff()
self.actor.SetMapper(self.mapper)
self.mapper.SetColorWindow(255)
self.mapper.SetColorLevel(128)
# Setup pipeline
self.colorMapper.SetInputConnection(self.thresholdFilter.GetOutputPort())
self.mapper.SetInputConnection(self.colorMapper.GetOutputPort())
def putMaskOnVTKGrid(data,grid,actorColor=None,deep=True):
#Ok now looking
msk = data.mask
imsk = VN.numpy_to_vtk(msk.astype(numpy.int).flat,deep=deep)
mapper = None
if msk is not numpy.ma.nomask:
msk = VN.numpy_to_vtk(numpy.logical_not(msk).astype(numpy.uint8).flat,deep=deep)
if actorColor is not None:
grid2 = vtk.vtkStructuredGrid()
grid2.CopyStructure(grid)
geoFilter = vtk.vtkDataSetSurfaceFilter()
if grid.IsA("vtkStructuredGrid"):
grid2.GetPointData().SetScalars(imsk)
#grid2.SetCellVisibilityArray(imsk)
p2c = vtk.vtkPointDataToCellData()
p2c.SetInputData(grid2)
geoFilter.SetInputConnection(p2c.GetOutputPort())
else:
grid2.GetCellData().SetScalars(imsk)
geoFilter.SetInputData(grid)
geoFilter.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(geoFilter.GetOutput())
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(1)
r,g,b = actorColor
lut.SetNumberOfTableValues(2)
lut.SetTableValue(0,r/100.,g/100.,b/100.)
lut.SetTableValue(1,r/100.,g/100.,b/100.)
mapper.SetLookupTable(lut)
mapper.SetScalarRange(1,1)
if grid.IsA("vtkStructuredGrid"):
grid.SetPointVisibilityArray(msk)
#grid.SetCellVisibilityArray(msk)
return mapper
def SetLookupTable(self, lut):
if not lut:
return
vtkViewImage.SetLookupTable(self, lut)
v_min = self.Level - 0.5*self.Window
v_max = self.Level + 0.5+self.Window
#==========================================================================
# In the case of a shift/scale, one must set the lut range to values
# without this shift/scale, because the object can be shared by different
# views.
#==========================================================================
lut.SetRange( (v_min-0.5*self.Shift)/self.Scale,
(v_max-1.5*self.Shift)/self.Scale)
#==========================================================================
# Due to the same problem as above (shift/scale), one must copy the lut
# so that it does not change values of the shared object.
#==========================================================================
realLut = vtk.vtkLookupTable.SafeDownCast(lut)
if not realLut:
raise RuntimeError, "Error: Cannot cast vtkScalarsToColors to vtkLookupTable."
newLut = vtk.vtkLookupTable()
newLut.DeepCopy(realLut)
newLut.SetRange(v_min, v_max)
self.WindowLevel.SetLookupTable(newLut)
del newLut
def setupLuts(self):
self.luts = []
# HSV (Blue to REd) Default
lut = vtk.vtkLookupTable()
lut.SetHueRange(0.667, 0.0)
lut.SetNumberOfColors(256)
lut.Build()
self.luts.append(lut)
# Diverging (Cool to Warm) color scheme
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToDiverging()
ctf.AddRGBPoint(0.0, 0.230, 0.299, 0.754)
ctf.AddRGBPoint(1.0, 0.706, 0.016, 0.150)
cc = list()
for i in xrange(256):
cc.append(ctf.GetColor(float(i) / 255.0))
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(256)
for i, item in enumerate(cc):
lut.SetTableValue(i, item[0], item[1], item[2], 1.0)
lut.Build()
self.luts.append(lut)
# Shock
ctf = vtk.vtkColorTransferFunction()
min = 93698.4
max = 230532
ctf.AddRGBPoint(self._normalize(min, max, 93698.4), 0.0, 0.0, 1.0)
ctf.AddRGBPoint(self._normalize(min, max, 115592.0), 0.0, 0.905882, 1.0)
ctf.AddRGBPoint(self._normalize(min, max, 138853.0), 0.0941176, 0.733333, 0.027451)
ctf.AddRGBPoint(self._normalize(min, max, 159378.0), 1.0, 0.913725, 0.00784314)
ctf.AddRGBPoint(self._normalize(min, max, 181272.0), 1.0, 0.180392, 0.239216)
ctf.AddRGBPoint(self._normalize(min, max, 203165.0), 1.0, 0.701961, 0.960784)
ctf.AddRGBPoint(self._normalize(min, max, 230532.0), 1.0, 1.0, 1.0)
cc = list()
for i in xrange(256):
cc.append(ctf.GetColor(float(i) / 255.0))
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(256)
for i, item in enumerate(cc):
lut.SetTableValue(i, item[0], item[1], item[2], 1.0)
lut.Build()
self.luts.append(lut)
self.current_lut = self.luts[0]
def draw(self, gfxwindow, device):
device.comment("Material Color")
if config.dimension() == 2:
themesh = self.who().resolve(gfxwindow)
polygons = self.polygons(gfxwindow, themesh)
# colorcache is a dictionary of colors keyed by Material. It
# prevents us from having to call material.fetchProperty for
# each element.
colorcache = {}
for polygon, material in zip(polygons,
self.materials(gfxwindow, themesh)):
if material is not None:
try:
# If material has been seen already, retrieve its color.
color = colorcache[material]
except KeyError:
# This material hasn't been seen yet.
try:
colorprop = material.fetchProperty('Color')
color = colorprop.color()
except ooferror.ErrNoSuchProperty:
color = None
colorcache[material] = color
if color is not None:
device.set_fillColor(color)
device.fill_polygon(primitives.Polygon(polygon))
elif config.dimension() == 3:
# TODO 3D: clean up this code in general, perhaps the look
# up table should be a member of the microstructure...
themesh = self.who().resolve(gfxwindow).getObject()
grid = themesh.skelgrid
numCells = grid.GetNumberOfCells()
# TODO 3D: will need to handle the creation and deletion of this array within canvas...
materialdata = vtk.vtkIntArray()
materialdata.SetNumberOfValues(numCells)
grid.GetCellData().SetScalars(materialdata)
lut = vtk.vtkLookupTable()
colordict = {}
for i in xrange(numCells):
cat = themesh.elements[i].dominantPixel(themesh.MS)
materialdata.SetValue(i,cat)
mat = themesh.elements[i].material(themesh)
if mat is not None:
try:
color = colordict[cat]
except KeyError:
colorprop = mat.fetchProperty('Color')
color = colorprop.color()
colordict[cat] = color
lut.SetNumberOfColors(max(colordict.keys())+1)
lut.SetTableRange(min(colordict.keys()), max(colordict.keys()))
for i in colordict:
color = colordict[i]
if color is not None:
lut.SetTableValue(i,color.getRed(),color.getGreen(),color.getBlue(),1)
else:
lut.SetTableValue(i,0,0,0,0)
device.draw_unstructuredgrid_with_lookuptable(grid, lut, mode="cell", scalarbar=False)
def __init__(self):
'''
Constructor
'''
self.__OrientationMatrix = vtk.vtkMatrix4x4()
self.__CornerAnnotation = vtk.vtkCornerAnnotation()
self.__TextProperty = vtk.vtkTextProperty()
self.__LookupTable = vtk.vtkLookupTable()
self.__ScalarBarActor = vtk.vtkScalarBarActor()
self.__Prop3DCollection = vtk.vtkProp3DCollection()
self.__DataSetCollection = vtk.vtkDataSetCollection()
self.__OrientationTransform = vtk.vtkMatrixToLinearTransform()
self.__OrientationMatrix.Identity()
self.__CornerAnnotation.SetNonlinearFontScaleFactor(0.30)
self.__CornerAnnotation.SetText(0, "Jolly - (c) summit 2009 ref vtkINRIA3D")
self.__CornerAnnotation.SetMaximumFontSize(46)
self.__ScalarBarActor.SetLabelTextProperty(self.__TextProperty)
self.__ScalarBarActor.GetLabelTextProperty().BoldOff()
self.__ScalarBarActor.GetLabelTextProperty().ItalicOff()
self.__ScalarBarActor.SetNumberOfLabels(3)
self.__ScalarBarActor.SetWidth(0.1)
self.__ScalarBarActor.SetHeight(0.5)
self.__ScalarBarActor.SetPosition(0.9, 0.3)
self.__LookupTable.SetTableRange(0, 1)
self.__LookupTable.SetSaturationRange(0, 0)
self.__LookupTable.SetHueRange(0, 0)
self.__LookupTable.SetValueRange(0, 1)
self.__LookupTable.Build()
self.__ShowAnnotations = True
self.__ShowScalarBar = True
self.__OrientationTransform.SetInput(self.__OrientationMatrix)
self.__WindowLevel = self.GetWindowLevel()
self.__WindowLevel.SetLookupTable( self.__LookupTable )
self.__ScalarBarActor.SetLookupTable(self.__LookupTable)
self.__Renderer = self.GetRenderer()
self.__Renderer.AddViewProp(self.__CornerAnnotation)
self.__Renderer.AddViewProp(self.__ScalarBarActor)
self.__ImageActor = self.GetImageActor()
self.__RenderWindow = self.GetRenderWindow ()
self.__InteractorStyle = self.GetInteractorStyle()
self.__Interactor = None
self.__CornerAnnotation.SetWindowLevel(self.__WindowLevel)
self.__CornerAnnotation.SetImageActor(self.__ImageActor)
self.__CornerAnnotation.ShowSliceAndImageOn()
# Sometime we would want to set the default window/level value instead
# of the ImageData's ScalarRange
self.__RefWindow = None
self.__RefLevel = None
def __init__(self, parent = None):
super(VTKFrame, self).__init__(parent)
self.vtkWidget = QVTKRenderWindowInteractor(self)
vl = QtGui.QVBoxLayout(self)
vl.addWidget(self.vtkWidget)
vl.setContentsMargins(0, 0, 0, 0)
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.1, 0.2, 0.4)
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
# Provide some geometry
resolution = 8
aPlane = vtk.vtkPlaneSource()
aPlane.SetXResolution(resolution)
aPlane.SetYResolution(resolution)
# Create cell data
cellData = vtk.vtkFloatArray()
for i in range(resolution * resolution):
cellData.InsertNextValue(i+1)
# Create a lookup table to map cell data to colors
lut = vtk.vtkLookupTable()
tableSize = max(resolution*resolution+1, 10)
lut.SetNumberOfTableValues(tableSize)
lut.Build()
# Fill in a few known colors, the rest will be generated if needed
lut.SetTableValue(0 , 0 , 0 , 0, 1)# Black
lut.SetTableValue(1, 0.8900, 0.8100, 0.3400, 1)# Banana
lut.SetTableValue(2, 1.0000, 0.3882, 0.2784, 1)# Tomato
lut.SetTableValue(3, 0.9608, 0.8706, 0.7020, 1)# Wheat
lut.SetTableValue(4, 0.9020, 0.9020, 0.9804, 1)# Lavender
lut.SetTableValue(5, 1.0000, 0.4900, 0.2500, 1)# Flesh
lut.SetTableValue(6, 0.5300, 0.1500, 0.3400, 1)# Raspberry
lut.SetTableValue(7, 0.9804, 0.5020, 0.4471, 1)# Salmon
lut.SetTableValue(8, 0.7400, 0.9900, 0.7900, 1)# Mint
lut.SetTableValue(9, 0.2000, 0.6300, 0.7900, 1)# Peacock
aPlane.Update() #Force an update so we can set cell data
aPlane.GetOutput().GetCellData().SetScalars(cellData)
# Create a mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(aPlane.GetOutputPort())
mapper.SetScalarRange(0, tableSize - 1)
mapper.SetLookupTable(lut)
# Create an actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
self.ren.AddActor(actor)
self.ren.ResetCamera()
self._initialized = False
def init_lut (self):
"Set up the default LookupTable. Defaults to a blue to red table."
debug ("In LutHandler::init_lut ()")
self.lut = vtk.vtkLookupTable ()
self.lut.SetHueRange (0.667, 0.0)
self.lut.SetNumberOfTableValues (self.n_color_var.get ())
self.lut.SetRampToSQRT()
self.lut.Build ()
def SetCliplingLookuptable(self, tipo):
if tipo == 'Green':
lut = vtk.vtkLookupTable()
lut.SetHueRange(0.0, 0.66667)
lut.SetAlphaRange(0.0,0.8)
self.PickPlaneZ.SetLookupTable(lut)
self.PickPlaneY.SetLookupTable(lut)
self.PickPlaneX.SetLookupTable(lut)
def autumn(self, m=256):
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(m)
lut.SetHueRange(0.0, 0.15)
lut.SetSaturationRange(1.0, 1.0)
lut.SetValueRange(1.0, 1.0)
lut.Build()
return lut
Stream0.SetTerminalSpeed(1e-12)
#del mbds
aa = vtk.vtkAssignAttribute()
aa.SetInputConnection(Stream0.GetOutputPort())
aa.Assign("Normals", "NORMALS", "POINT_DATA")
Ribbon0 = vtk.vtkRibbonFilter()
Ribbon0.SetInputConnection(aa.GetOutputPort())
Ribbon0.SetWidth(0.1)
Ribbon0.SetAngle(0)
Ribbon0.SetDefaultNormal(0, 0, 1)
Ribbon0.SetVaryWidth(0)
LookupTable1 = vtk.vtkLookupTable()
LookupTable1.SetNumberOfTableValues(256)
LookupTable1.SetHueRange(0, 0.66667)
LookupTable1.SetSaturationRange(1, 1)
LookupTable1.SetValueRange(1, 1)
LookupTable1.SetTableRange(0.197813, 0.710419)
LookupTable1.SetVectorComponent(0)
LookupTable1.Build()
Mapper10 = vtk.vtkPolyDataMapper()
Mapper10.SetInputConnection(Ribbon0.GetOutputPort())
Mapper10.SetImmediateModeRendering(1)
Mapper10.UseLookupTableScalarRangeOn()
Mapper10.SetScalarVisibility(1)
Mapper10.SetScalarModeToUsePointFieldData()
Mapper10.SelectColorArray("Density")
def _plotInternal(self):
tmpLevels = []
tmpColors = []
indices = self._gm.fillareaindices
if indices is None:
indices = [1,]
while len(indices) < len(self._contourColors):
indices.append(indices[-1])
if len(self._contourLevels) > len(self._contourColors):
raise RuntimeError(
"You asked for %i levels but provided only %i colors\n"
"Graphic Method: %s of type %s\nLevels: %s"
% (len(self._contourLevels), len(self._contourColors),
self._gm.name, self._gm.g_name), repr(self._contourLevels))
elif len(self._contourLevels) < len(self._contourColors) - 1:
warnings.warn(
"You asked for %i lgridevels but provided %i colors, extra "
"ones will be ignored\nGraphic Method: %s of type %s"
% (len(self._contourLevels), len(self._contourColors),
self._gm.name, self._gm.g_name))
for i, l in enumerate(self._contourLevels):
if i == 0:
C = [self._contourColors[i],]
if numpy.allclose(self._contourLevels[0][0], -1.e20):
## ok it's an extension arrow
L = [self._scalarRange[0] - 1., self._contourLevels[0][1]]
else:
L = list(self._contourLevels[i])
I = [indices[i],]
else:
if l[0] == L[-1] and I[-1] == indices[i]:
# Ok same type lets keep going
if numpy.allclose(l[1], 1.e20):
L.append(self._scalarRange[1] + 1.)
else:
L.append(l[1])
C.append(self._contourColors[i])
else: # ok we need new contouring
tmpLevels.append(L)
tmpColors.append(C)
C = [self._contourColors[i],]
L = self._contourLevels[i]
I = [indices[i],]
tmpLevels.append(L)
tmpColors.append(C)
mappers = []
luts = []
cots = []
geos = []
for i,l in enumerate(tmpLevels):
# Ok here we are trying to group together levels can be, a join will
# happen if: next set of levels contnues where one left off AND
# pattern is identical
wholeDataMin, wholeDataMax = vcs.minmax(self._originalData1)
# TODO this should really just be a single polydata that is
# colored by scalars:
for j,color in enumerate(tmpColors[i]):
mapper = vtk.vtkPolyDataMapper()
lut = vtk.vtkLookupTable()
th = vtk.vtkThreshold()
th.ThresholdBetween(l[j], l[j+1])
th.SetInputConnection(self._vtkPolyDataFilter.GetOutputPort())
geoFilter2 = vtk.vtkDataSetSurfaceFilter()
geoFilter2.SetInputConnection(th.GetOutputPort())
geos.append(geoFilter2)
mapper.SetInputConnection(geoFilter2.GetOutputPort())
lut.SetNumberOfTableValues(1)
r, g, b = self._colorMap.index[color]
lut.SetTableValue(0, r/100., g/100., b/100.)
mapper.SetLookupTable(lut)
mapper.SetScalarRange(l[j], l[j+1])
luts.append([lut, [l[j], l[j+1], True]])
## Store the mapper only if it's worth it?
## Need to do it with the whole slab min/max for animation
## purposes
if not (l[j+1] < wholeDataMin or l[j] > wholeDataMax):
mappers.append(mapper)
self._resultDict["vtk_backend_luts"]=luts
if len(cots) > 0:
self._resultDict["vtk_backend_contours"] = cots
if len(geos) > 0:
self._resultDict["vtk_backend_geofilters"] = geos
numLevels = len(self._contourLevels)
if mappers == []: # ok didn't need to have special banded contours
mapper = vtk.vtkPolyDataMapper()
mappers = [mapper,]
## Colortable bit
# make sure length match
while len(self._contourColors) < numLevels:
self._contourColors.append(self._contourColors[-1])
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(numLevels)
for i in range(numLevels):
r, g, b = self._colorMap.index[self._contourColors[i]]
lut.SetTableValue(i, r / 100., g / 100., b / 100.)
mapper.SetLookupTable(lut)
if numpy.allclose(self._contourLevels[0], -1.e20):
lmn = mn - 1.
else:
lmn = self._contourLevels[0]
if numpy.allclose(self._contourLevels[-1], 1.e20):
lmx = mx + 1.
else:
lmx = self._contourLevels[-1]
mapper.SetScalarRange(lmn, lmx)
self._resultDict["vtk_backend_luts"] = [[lut, [lmn, lmx, True]],]
if self._maskedDataMapper is not None:
# Note that this is different for meshfill -- others prepend.
mappers.append(self._maskedDataMapper)
# This is also different for meshfill, others use
# vcs.utils.getworldcoordinates
x1, x2, y1, y2 = vcs2vtk.getRange(self._gm,
self._vtkDataSetBounds[0],
self._vtkDataSetBounds[1],
self._vtkDataSetBounds[2],
self._vtkDataSetBounds[3])
# Add a second mapper for wireframe meshfill:
if self._gm.mesh:
lineMappers = []
wireLUT = vtk.vtkLookupTable()
wireLUT.SetNumberOfTableValues(1)
wireLUT.SetTableValue(0, 0, 0, 0)
for polyMapper in mappers:
lineMapper = vtk.vtkPolyDataMapper()
lineMapper.SetInputConnection(polyMapper.GetInputConnection(0, 0))
lineMapper._useWireFrame = True
# Setup depth resolution so lines stay above points:
polyMapper.SetResolveCoincidentTopologyPolygonOffsetParameters(0, 1)
polyMapper.SetResolveCoincidentTopologyToPolygonOffset()
lineMapper.SetResolveCoincidentTopologyPolygonOffsetParameters(1, 1)
lineMapper.SetResolveCoincidentTopologyToPolygonOffset()
lineMapper.SetLookupTable(wireLUT)
lineMappers.append(lineMapper)
mappers.extend(lineMappers)
# And now we need actors to actually render this thing
actors = []
for mapper in mappers:
act = vtk.vtkActor()
act.SetMapper(mapper)
if hasattr(mapper, "_useWireFrame"):
prop = act.GetProperty()
prop.SetRepresentationToWireframe()
if self._vtkGeoTransform is None:
# If using geofilter on wireframed does not get wrppaed not sure
# why so sticking to many mappers
act = vcs2vtk.doWrap(act, [x1,x2,y1,y2], self._dataWrapModulo)
# TODO See comment in boxfill.
if mapper is self._maskedDataMapper:
actors.append([act, self._maskedDataMapper, [x1,x2,y1,y2]])
else:
actors.append([act, [x1,x2,y1,y2]])
# create a new renderer for this mapper
# (we need one for each mapper because of cmaera flips)
ren = self._context.fitToViewport(
act, [self._template.data.x1,
self._template.data.x2,
self._template.data.y1,
self._template.data.y2],
wc=[x1, x2, y1, y2], geo=self._vtkGeoTransform,
priority=self._template.data.priority)
self._resultDict["vtk_backend_actors"] = actors
self._template.plot(self._context.canvas, self._data1, self._gm,
bg=self._context.bg,
X=numpy.arange(self._vtkDataSetBounds[0],
self._vtkDataSetBounds[1] * 1.1,
(self._vtkDataSetBounds[1] -
self._vtkDataSetBounds[0]) / 10.),
Y=numpy.arange(self._vtkDataSetBounds[2],
self._vtkDataSetBounds[3] * 1.1,
(self._vtkDataSetBounds[3] -
self._vtkDataSetBounds[2]) / 10.))
legend = getattr(self._gm, "legend", None)
if self._gm.ext_1:
if isinstance(self._contourLevels[0], list):
if numpy.less(abs(self._contourLevels[0][0]), 1.e20):
## Ok we need to add the ext levels
self._contourLevels.insert(0, [-1.e20, levs[0][0]])
else:
if numpy.less(abs(self._contourLevels[0]), 1.e20):
## need to add an ext
self._contourLevels.insert(0, -1.e20)
if self._gm.ext_2:
if isinstance(self._contourLevels[-1],list):
if numpy.less(abs(self._contourLevels[-1][1]), 1.e20):
## need ext
self._contourLevels.append([self._contourLevels[-1][1],
1.e20])
else:
if numpy.less(abs(self._contourLevels[-1]), 1.e20):
## need exts
self._contourLevels.append(1.e20)
self._resultDict.update(
self._context.renderColorBar(self._template, self._contourLevels,
self._contourColors, legend,
self._colorMap))
if self._context.canvas._continents is None:
self._useContinents = False
if self._useContinents:
projection = vcs.elements["projection"][self._gm.projection]
self._context.plotContinents(x1, x2, y1, y2, projection,
self._dataWrapModulo, self._template)
def prepareDelaunayData3d(dimension, agg_globalnodeidx, global_nodecoords, aggpolygons, aggid, aggid2nodes, aggid2procs):
local_nodeidx2global_nodeidx = {}
no_of_aggnodes = len(agg_globalnodeidx)
no_aggs = len(aggid2nodes)
Points = vtk.vtkPoints()
Vertices = vtk.vtkCellArray()
for i in range(0,len(agg_globalnodeidx)):
id = -1
local_nodeidx2global_nodeidx[i] = agg_globalnodeidx[i]
nodecoords = global_nodecoords[int(agg_globalnodeidx[i])]
id = Points.InsertNextPoint(nodecoords[0]+ 0.0001 * random.random(),nodecoords[1]+ 0.0001 * random.random(),nodecoords[2]+ 0.0001 * random.random())
Vertices.InsertNextCell(1)
Vertices.InsertCellPoint(id)
polydata2 = vtk.vtkPolyData()
polydata2.SetPoints(Points)
polydata2.Modified()
polydata2.Update()
delaunay = vtk.vtkDelaunay3D()
delaunay.SetInput(polydata2)
delaunay.Update()
# create surfaceFilter
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
surfaceFilter.Update()
pt_polydata = surfaceFilter.GetOutput()
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(no_aggs)
lookupTable.Build()
Ids = vtk.vtkUnsignedIntArray()
Ids.SetNumberOfComponents(1)
Ids.SetName("Ids")
for i in range(0,Points.GetNumberOfPoints()):
Ids.InsertNextTuple1(int(aggid))
Ids.SetLookupTable(lookupTable)
Procs = vtk.vtkUnsignedCharArray()
Procs.SetNumberOfComponents(1)
Procs.SetName("proc")
for i in range(0,Points.GetNumberOfPoints()):
Procs.InsertNextTuple1(aggid2procs[aggid])
polydata3 = vtk.vtkPolyData()
polydata3 = surfaceFilter.GetOutput()
polydata3.GetPointData().SetScalars(Ids)
polydata3.GetPointData().AddArray(Procs)
polydata4 = vtk.vtkPolyData()
polydata4.SetPoints(Points)
polydata4.SetVerts(Vertices)
polydata4.GetPointData().SetScalars(Ids)
polydata4.GetPointData().AddArray(Procs)
#datamapper = vtk.vtkDataSetMapper()
#datamapper.SetInputConnection(delaunay.GetOutputPort())
#datamapper.SetInput(polydata3)
#actor = vtk.vtkActor()
#actor.SetMapper(datamapper)
#renderer = vtk.vtkRenderer()
#renderWindow = vtk.vtkRenderWindow()
#renderWindow.AddRenderer(renderer)
#renderWindowInteractor = vtk.vtkRenderWindowInteractor()
#renderWindowInteractor.SetRenderWindow(renderWindow)
#renderer.AddActor(actor)
#renderWindow.Render()
#renderWindowInteractor.Start()
#print polydata.GetVertices()
aggpolygons.AddInput(polydata3)
aggpolygons.AddInput(polydata4)
b = float(j) / N
v = 0.5 + 0.5 * cos(13 * a) * cos(8 * b + 3 * a * a)
v = v**2
method(i, j, 0, 0, v)
geometry_filter = vtk.vtkImageDataGeometryFilter()
geometry_filter.SetInput(image_data)
warp = vtk.vtkWarpScalar()
warp.SetInput(geometry_filter.GetOutput())
warp.SetScaleFactor(8.1)
normal_filter = vtk.vtkPolyDataNormals()
normal_filter.SetInput(warp.GetOutput())
data_mapper = vtk.vtkDataSetMapper()
data_mapper.SetInput(normal_filter.GetOutput())
data_actor = vtk.vtkActor()
data_actor.SetMapper(data_mapper)
renderer.AddActor(data_actor)
table = vtk.vtkLookupTable()
data_mapper.SetLookupTable(table)
# the actual gradient editor code.
def on_color_table_changed():
render_window.Render()
# Gradient editor only works with tvtk objects, so convert the lut
# to a tvtk version.
tvtk_table = tvtk.to_tvtk(table)
editor = GradientEditor(root, tvtk_table, on_color_table_changed)
root.mainloop()
def testPlatonicSolids(self):
# Create five instances of vtkPlatonicSolidSource
# corresponding to each of the five Platonic solids.
#
tet = vtk.vtkPlatonicSolidSource()
tet.SetSolidTypeToTetrahedron()
tetMapper = vtk.vtkPolyDataMapper()
tetMapper.SetInputConnection(tet.GetOutputPort())
tetActor = vtk.vtkActor()
tetActor.SetMapper(tetMapper)
cube = vtk.vtkPlatonicSolidSource()
cube.SetSolidTypeToCube()
cubeMapper = vtk.vtkPolyDataMapper()
cubeMapper.SetInputConnection(cube.GetOutputPort())
cubeActor = vtk.vtkActor()
cubeActor.SetMapper(cubeMapper)
cubeActor.AddPosition(2.0, 0, 0)
oct = vtk.vtkPlatonicSolidSource()
oct.SetSolidTypeToOctahedron()
octMapper = vtk.vtkPolyDataMapper()
octMapper.SetInputConnection(oct.GetOutputPort())
octActor = vtk.vtkActor()
octActor.SetMapper(octMapper)
octActor.AddPosition(4.0, 0, 0)
icosa = vtk.vtkPlatonicSolidSource()
icosa.SetSolidTypeToIcosahedron()
icosaMapper = vtk.vtkPolyDataMapper()
icosaMapper.SetInputConnection(icosa.GetOutputPort())
icosaActor = vtk.vtkActor()
icosaActor.SetMapper(icosaMapper)
icosaActor.AddPosition(6.0, 0, 0)
dode = vtk.vtkPlatonicSolidSource()
dode.SetSolidTypeToDodecahedron()
dodeMapper = vtk.vtkPolyDataMapper()
dodeMapper.SetInputConnection(dode.GetOutputPort())
dodeActor = vtk.vtkActor()
dodeActor.SetMapper(dodeMapper)
dodeActor.AddPosition(8.0, 0, 0)
# Create rendering stuff
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
# Add the actors to the renderer, set the background and size
#
ren.AddActor(tetActor)
ren.AddActor(cubeActor)
ren.AddActor(octActor)
ren.AddActor(icosaActor)
ren.AddActor(dodeActor)
colors = self.Colors()
# Create a lookup table with colors for each face
#
math = vtk.vtkMath()
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(20)
lut.Build()
lut.SetTableValue(0, colors.GetRGBAColor("red"))
lut.SetTableValue(1, colors.GetRGBAColor("lime"))
lut.SetTableValue(2, colors.GetRGBAColor("yellow"))
lut.SetTableValue(3, colors.GetRGBAColor("blue"))
lut.SetTableValue(4, colors.GetRGBAColor("magenta"))
lut.SetTableValue(5, colors.GetRGBAColor("cyan"))
lut.SetTableValue(6, colors.GetRGBAColor("spring_green"))
lut.SetTableValue(7, colors.GetRGBAColor("lavender"))
lut.SetTableValue(8, colors.GetRGBAColor("mint_cream"))
lut.SetTableValue(9, colors.GetRGBAColor("violet"))
lut.SetTableValue(10, colors.GetRGBAColor("ivory_black"))
lut.SetTableValue(11, colors.GetRGBAColor("coral"))
lut.SetTableValue(12, colors.GetRGBAColor("pink"))
lut.SetTableValue(13, colors.GetRGBAColor("salmon"))
lut.SetTableValue(14, colors.GetRGBAColor("sepia"))
lut.SetTableValue(15, colors.GetRGBAColor("carrot"))
lut.SetTableValue(16, colors.GetRGBAColor("gold"))
lut.SetTableValue(17, colors.GetRGBAColor("forest_green"))
lut.SetTableValue(18, colors.GetRGBAColor("turquoise"))
lut.SetTableValue(19, colors.GetRGBAColor("plum"))
lut.SetTableRange(0, 19)
tetMapper.SetLookupTable(lut)
tetMapper.SetScalarRange(0, 19)
cubeMapper.SetLookupTable(lut)
cubeMapper.SetScalarRange(0, 19)
octMapper.SetLookupTable(lut)
octMapper.SetScalarRange(0, 19)
icosaMapper.SetLookupTable(lut)
icosaMapper.SetScalarRange(0, 19)
dodeMapper.SetLookupTable(lut)
dodeMapper.SetScalarRange(0, 19)
cam = ren.GetActiveCamera()
cam.SetPosition(3.89696, 7.20771, 1.44123)
cam.SetFocalPoint(3.96132, 0, 0)
cam.SetViewUp(-0.0079335, 0.196002, -0.980571)
cam.SetClippingRange(5.42814, 9.78848)
ren.SetBackground(colors.GetRGBColor("black"))
renWin.SetSize(400, 150)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin)
renWin.Render()
img_file = "TestPlatonicSolids.png"
vtk.test.Testing.compareImage(
iRen.GetRenderWindow(),
vtk.test.Testing.getAbsImagePath(img_file),
threshold=25)
vtk.test.Testing.interact()
def _plotInternal(self):
prepedContours = self._prepContours()
tmpLevels = prepedContours["tmpLevels"]
tmpIndices = prepedContours["tmpIndices"]
tmpColors = prepedContours["tmpColors"]
tmpOpacities = prepedContours["tmpOpacities"]
style = self._gm.fillareastyle
fareapixelspacing, fareapixelscale = self._patternSpacingAndScale()
mappers = []
luts = []
geos = []
wholeDataMin, wholeDataMax = vcs.minmax(self._originalData1)
plotting_dataset_bounds = self.getPlottingBounds()
x1, x2, y1, y2 = plotting_dataset_bounds
_colorMap = self.getColorMap()
for i, l in enumerate(tmpLevels):
# Ok here we are trying to group together levels can be, a join
# will happen if: next set of levels contnues where one left off
# AND pattern is identical
# TODO this should really just be a single polydata that is
# colored by scalars:
for j, color in enumerate(tmpColors[i]):
mapper = vtk.vtkPolyDataMapper()
lut = vtk.vtkLookupTable()
th = vtk.vtkThreshold()
th.ThresholdBetween(l[j], l[j + 1])
th.SetInputConnection(self._vtkPolyDataFilter.GetOutputPort())
geoFilter2 = vtk.vtkDataSetSurfaceFilter()
geoFilter2.SetInputConnection(th.GetOutputPort())
# Make the polydata output available here for patterning later
geoFilter2.Update()
geos.append(geoFilter2)
mapper.SetInputConnection(geoFilter2.GetOutputPort())
lut.SetNumberOfTableValues(1)
r, g, b, a = self.getColorIndexOrRGBA(_colorMap, color)
if style == 'solid':
tmpOpacity = tmpOpacities[j]
if tmpOpacity is None:
tmpOpacity = a / 100.
else:
tmpOpacity = tmpOpacities[j] / 100.
lut.SetTableValue(0, r / 100., g / 100., b / 100.,
tmpOpacity)
else:
lut.SetTableValue(0, 1., 1., 1., 0.)
mapper.SetLookupTable(lut)
mapper.SetScalarRange(l[j], l[j + 1])
luts.append([lut, [l[j], l[j + 1], True]])
# Store the mapper only if it's worth it?
# Need to do it with the whole slab min/max for animation
# purposes
if not (l[j + 1] < wholeDataMin or l[j] > wholeDataMax):
mappers.append(mapper)
self._resultDict["vtk_backend_luts"] = luts
if len(geos) > 0:
self._resultDict["vtk_backend_geofilters"] = geos
"""
numLevels = len(self._contourLevels)
if mappers == []: # ok didn't need to have special banded contours
mapper = vtk.vtkPolyDataMapper()
mappers = [mapper]
# Colortable bit
# make sure length match
while len(self._contourColors) < numLevels:
self._contourColors.append(self._contourColors[-1])
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(numLevels)
for i in range(numLevels):
r, g, b, a = self._colorMap.index[self._contourColors[i]]
lut.SetTableValue(i, r / 100., g / 100., b / 100., a / 100.)
mapper.SetLookupTable(lut)
if numpy.allclose(self._contourLevels[0], -1.e20):
lmn = self._min - 1.
else:
lmn = self._contourLevels[0]
if numpy.allclose(self._contourLevels[-1], 1.e20):
lmx = self._max + 1.
else:
lmx = self._contourLevels[-1]
mapper.SetScalarRange(lmn, lmx)
self._resultDict["vtk_backend_luts"] = [[lut, [lmn, lmx, True]]]
"""
if self._maskedDataMapper is not None:
# Note that this is different for meshfill -- others prepend.
mappers.append(self._maskedDataMapper)
# Add a second mapper for wireframe meshfill:
if self._gm.mesh:
lineMappers = []
wireLUT = vtk.vtkLookupTable()
wireLUT.SetNumberOfTableValues(1)
wireLUT.SetTableValue(0, 0, 0, 0)
for polyMapper in mappers:
lineMapper = vtk.vtkPolyDataMapper()
lineMapper.SetInputConnection(
polyMapper.GetInputConnection(0, 0))
lineMapper._useWireFrame = True
# 'noqa' comments disable pep8 checking for these lines. There
# is not a readable way to shorten them due to the unwieldly
# method name.
#
# Setup depth resolution so lines stay above points:
polyMapper.SetResolveCoincidentTopologyPolygonOffsetParameters(
0, 1) # noqa
polyMapper.SetResolveCoincidentTopologyToPolygonOffset()
lineMapper.SetResolveCoincidentTopologyPolygonOffsetParameters(
1, 1) # noqa
lineMapper.SetResolveCoincidentTopologyToPolygonOffset()
lineMapper.SetLookupTable(wireLUT)
lineMappers.append(lineMapper)
mappers.extend(lineMappers)
# And now we need actors to actually render this thing
actors = []
vp = self._resultDict.get('ratio_autot_viewport', [
self._template.data.x1, self._template.data.x2,
self._template.data.y1, self._template.data.y2
])
dataset_renderer = None
xScale, yScale = (1, 1)
cti = 0
ctj = 0
for mapper in mappers:
act = vtk.vtkActor()
act.SetMapper(mapper)
wireframe = False
if hasattr(mapper, "_useWireFrame"):
prop = act.GetProperty()
prop.SetRepresentationToWireframe()
wireframe = True
# create a new renderer for this mapper
# (we need one for each mapper because of cmaera flips)
dataset_renderer, xScale, yScale = self._context().fitToViewport(
act,
vp,
wc=plotting_dataset_bounds,
geoBounds=self._vtkDataSetBoundsNoMask,
geo=self._vtkGeoTransform,
priority=self._template.data.priority,
create_renderer=(dataset_renderer is None),
add_actor=(wireframe or (style == "solid")))
# TODO See comment in boxfill.
if mapper is self._maskedDataMapper:
actors.append(
[act, self._maskedDataMapper, plotting_dataset_bounds])
else:
actors.append([act, plotting_dataset_bounds])
if not wireframe:
# Since pattern creation requires a single color, assuming the
# first
if ctj >= len(tmpColors[cti]):
ctj = 0
cti += 1
c = self.getColorIndexOrRGBA(_colorMap,
tmpColors[cti][ctj])
# Get the transformed contour data
transform = act.GetUserTransform()
transformFilter = vtk.vtkTransformFilter()
transformFilter.SetInputData(mapper.GetInput())
transformFilter.SetTransform(transform)
transformFilter.Update()
patact = fillareautils.make_patterned_polydata(
transformFilter.GetOutput(),
fillareastyle=style,
fillareaindex=tmpIndices[cti],
fillareacolors=c,
fillareaopacity=tmpOpacities[cti],
fillareapixelspacing=fareapixelspacing,
fillareapixelscale=fareapixelscale,
size=self._context().renWin.GetSize(),
renderer=dataset_renderer)
ctj += 1
if patact is not None:
actors.append([patact, plotting_dataset_bounds])
dataset_renderer.AddActor(patact)
t = self._originalData1.getTime()
if self._originalData1.ndim > 2:
z = self._originalData1.getAxis(-3)
else:
z = None
self._resultDict["vtk_backend_actors"] = actors
kwargs = {
"vtk_backend_grid": self._vtkDataSet,
"dataset_bounds": self._vtkDataSetBounds,
"plotting_dataset_bounds": plotting_dataset_bounds,
"vtk_dataset_bounds_no_mask": self._vtkDataSetBoundsNoMask,
"vtk_backend_geo": self._vtkGeoTransform
}
if ("ratio_autot_viewport" in self._resultDict):
kwargs["ratio_autot_viewport"] = vp
self._resultDict.update(self._context().renderTemplate(
self._template,
self._data1,
self._gm,
t,
z,
X=numpy.arange(min(x1, x2),
max(x1, x2) * 1.1,
abs(x2 - x1) / 10.),
Y=numpy.arange(min(y1, y2),
max(y1, y2) * 1.1,
abs(y2 - y1) / 10.),
**kwargs))
legend = getattr(self._gm, "legend", None)
if self._gm.ext_1:
if isinstance(self._contourLevels[0], list):
if numpy.less(abs(self._contourLevels[0][0]), 1.e20):
# Ok we need to add the ext levels
self._contourLevels.insert(
0, [-1.e20, self._contourLevels[0][0]])
else:
if numpy.less(abs(self._contourLevels[0]), 1.e20):
# need to add an ext
self._contourLevels.insert(0, -1.e20)
if self._gm.ext_2:
if isinstance(self._contourLevels[-1], list):
if numpy.less(abs(self._contourLevels[-1][1]), 1.e20):
# need ext
self._contourLevels.append(
[self._contourLevels[-1][1], 1.e20])
else:
if numpy.less(abs(self._contourLevels[-1]), 1.e20):
# need exts
self._contourLevels.append(1.e20)
patternArgs = {}
patternArgs['style'] = self._gm.fillareastyle
patternArgs['index'] = self._gm.fillareaindices
if patternArgs['index'] is None:
patternArgs['index'] = [
1,
]
# Compensate for the different viewport size of the colorbar
patternArgs['opacity'] = self._gm.fillareaopacity
patternArgs['pixelspacing'] = [
int(fareapixelspacing[0] / (vp[1] - vp[0])),
int(fareapixelspacing[1] / (vp[3] - vp[2]))
]
patternArgs['pixelscale'] = fareapixelscale / (vp[1] - vp[0])
self._resultDict.update(self._context().renderColorBar(
self._template, self._contourLevels, self._contourColors, legend,
self.getColorMap(), **patternArgs))
if self._context().canvas._continents is None:
self._useContinents = False
if self._useContinents:
projection = vcs.elements["projection"][self._gm.projection]
continents_renderer, xScale, yScale = self._context(
).plotContinents(plotting_dataset_bounds, projection,
self._dataWrapModulo, vp,
self._template.data.priority, **kwargs)
def main():
# setup the dataset filepath
all_filename = ['pv_insitu_300x300x300_29072.vti','pv_insitu_300x300x300_29263.vti',
'pv_insitu_300x300x300_29449.vti','pv_insitu_300x300x300_29638.vti',
'pv_insitu_300x300x300_29827.vti','pv_insitu_300x300x300_30015.vti',
'pv_insitu_300x300x300_30205.vti','pv_insitu_300x300x300_30395.vti',
'pv_insitu_300x300x300_30587.vti','pv_insitu_300x300x300_30778.vti',
'pv_insitu_300x300x300_30966.vti']
# iso_value_1 = average mean + 3*std
# ios_value_2 = average median + 3*std
# we calculate it in other file "finalproject_T2"
iso_value_1 = 0.3544;
iso_value_2 = 0.3246;
#for i in range(0, 2):
for i in range(0, len(all_filename)):
filename = "yC31/"+all_filename[i];
print(filename);
#filename = "yC31/pv_insitu_300x300x300_29072.vti"
# the name of data array which is used in this example
daryName = "tev";
#'v03' 'prs' 'tev'
# for accessomg build-in color access
colors = vtk.vtkNamedColors();
# Create the renderer, the render window, and the interactor.
# The renderer draws into the render window.
# The interactor enables mouse and keyboard-based interaction
# with the data within the render windows.
aRenderer = vtk.vtkRenderer();
renWin = vtk.vtkRenderWindow();
renWin.AddRenderer(aRenderer);
iren = vtk.vtkRenderWindowInteractor();
iren.SetRenderWindow(renWin);
# Set a background color for the renderer
# and set the size of the render window.
aRenderer.SetBackground(colors.GetColor3d("Silver"));
renWin.SetSize(600, 600);
# data reader
reader = vtk.vtkXMLImageDataReader();
reader.SetFileName(filename);
reader.Update();
# specify the data array in the file to process
reader.GetOutput().GetPointData().SetActiveAttribute(daryName, 0);
# convert the data array to numpy array and get the min and maximum value
dary = VN.vtk_to_numpy(reader.GetOutput().GetPointData().GetScalars(daryName));
dary = dary[dary!= 0]
dMax = np.amax(dary);
dMin = np.amin(dary);
dRange = dMax - dMin;
dMean = np.mean(dary);
dMedian = np.median(dary);
dstd = np.std(dary);
print("Data array max: ", dMax);
print("Data array min: ", dMin);
print("Data array range: ", dRange);
print("Data array mean: ", dMean);
print("Data array median: ", dMedian);
print("Data array std: ", dstd);
############ setup color map #########
# Now create a loopup table that consists of the full hue circle
# (from HSV).
hueLut = vtk.vtkLookupTable();
hueLut.SetTableRange(dMin, dMax);
hueLut.Build();
# An outline provides context around the data.
outlineData = vtk.vtkOutlineFilter();
outlineData.SetInputConnection(reader.GetOutputPort());
outlineData.Update()
mapOutline = vtk.vtkPolyDataMapper();
mapOutline.SetInputConnection(outlineData.GetOutputPort());
outline = vtk.vtkActor();
outline.SetMapper(mapOutline);
outline.GetProperty().SetColor(colors.GetColor3d("Black"));
#################### create isosurface tev = mean + 3*std ######################################
# isosurface
iso = vtk.vtkContourFilter();
iso.SetInputConnection(reader.GetOutputPort());
iso.Update();
#iso.SetValue(0, iso_value_1);
iso.SetValue(0, iso_value_2);
normals = vtk.vtkPolyDataNormals();
normals.SetInputConnection(iso.GetOutputPort());
normals.SetFeatureAngle(45);
isoMapper = vtk.vtkPolyDataMapper();
isoMapper.SetInputConnection(normals.GetOutputPort());
isoMapper.ScalarVisibilityOff();
isoActor = vtk.vtkActor();
isoActor.SetMapper(isoMapper);
isoActor.GetProperty().SetColor(colors.GetColor3d("bisque"));
isoActor.GetProperty().SetOpacity(0.3);
#################################################################################################
aCamera = vtk.vtkCamera();
aCamera.SetViewUp(0, 0, 1);
aCamera.SetPosition(1, 1, 2);
aCamera.SetFocalPoint(0, 0, 0);
aCamera.ComputeViewPlaneNormal();
aCamera.Azimuth(45.0);
aCamera.Elevation(45.0);
######################## create a text #####################
# create a text actor
txt = vtk.vtkTextActor()
txt_str = "isosurface value (median+3*std)(bisque) = "+ str(iso_value_2)[:5]
#txt_str = "isosurface value (mean+3*std)(bisque) = "+ str(iso_value_1)[:5]
txt.SetInput(txt_str)
txtprop=txt.GetTextProperty()
txtprop.SetFontFamilyToArial()
txtprop.SetFontSize(24)
txtprop.SetColor(colors.GetColor3d("bisque"))
txt.SetDisplayPosition(50,550)
##########################################################
txt3 = vtk.vtkTextActor()
txt_str3 = "timestep = "+filename[27:32]
txt3.SetInput(txt_str3)
txtprop3=txt3.GetTextProperty()
txtprop3.SetFontFamilyToArial()
txtprop3.SetFontSize(24)
txtprop3.SetColor(0,0,0)
txt3.SetDisplayPosition(50,500)
# Actors are added to the renderer.
aRenderer.AddActor(outline);
aRenderer.AddActor(isoActor);
aRenderer.AddActor(txt);
aRenderer.AddActor(txt3);
# An initial camera view is created. The Dolly() method moves
# the camera towards the FocalPoint, thereby enlarging the image.
aRenderer.SetActiveCamera(aCamera);
# Calling Render() directly on a vtkRenderer is strictly forbidden.
# Only calling Render() on the vtkRenderWindow is a valid call.
renWin.Render();
aRenderer.ResetCamera();
aCamera.Dolly(-2.0);
####################################################################
# screenshot code:
w2if = vtk.vtkWindowToImageFilter()
w2if.SetInput(renWin)
w2if.Update()
writer = vtk.vtkPNGWriter()
saveName = "plots/ios/tev/median/"+daryName+"_t_"+filename[27:32]+".png";
#saveName = "plots/ios/tev/mean/"+daryName+"_t_"+filename[27:32]+".png";
writer.SetFileName(saveName)
writer.SetInputData(w2if.GetOutput())
writer.Write()
#####################################################################
# Note that when camera movement occurs (as it does in the Dolly() method),
# the clipping planes often need adjusting.
# Clipping planes consist of two planes:
# near and far along the view direction.
# The near plane clips out objects in front of the plane;
# the far plane clips out objects behind the plane.
# This way only what is drawn between the planes is actually rendered.
aRenderer.ResetCameraClippingRange();
# Interact with the data.
renWin.Render();
def main():
colors = vtk.vtkNamedColors()
# Create the RenderWindow, Renderer and interactive renderer.
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Generate the tensors.
ptLoad = vtk.vtkPointLoad()
ptLoad.SetLoadValue(100.0)
ptLoad.SetSampleDimensions(6, 6, 6)
ptLoad.ComputeEffectiveStressOn()
ptLoad.SetModelBounds(-10, 10, -10, 10, -10, 10)
# Extract a plane of data.
plane = vtk.vtkImageDataGeometryFilter()
plane.SetInputConnection(ptLoad.GetOutputPort())
plane.SetExtent(2, 2, 0, 99, 0, 99)
# Generate the ellipsoids.
sphere = vtk.vtkSphereSource()
sphere.SetThetaResolution(8)
sphere.SetPhiResolution(8)
tensorEllipsoids = vtk.vtkTensorGlyph()
tensorEllipsoids.SetInputConnection(ptLoad.GetOutputPort())
tensorEllipsoids.SetSourceConnection(sphere.GetOutputPort())
tensorEllipsoids.SetScaleFactor(10)
tensorEllipsoids.ClampScalingOn()
ellipNormals = vtk.vtkPolyDataNormals()
ellipNormals.SetInputConnection(tensorEllipsoids.GetOutputPort())
# Map contour
lut = vtk.vtkLookupTable()
MakeLogLUT(lut)
# lut.SetHueRange(.6667, 0.0)
tensorEllipsoidsMapper = vtk.vtkPolyDataMapper()
tensorEllipsoidsMapper.SetInputConnection(ellipNormals.GetOutputPort())
tensorEllipsoidsMapper.SetLookupTable(lut)
plane.Update() # force update for scalar range
tensorEllipsoidsMapper.SetScalarRange(plane.GetOutput().GetScalarRange())
tensorActor = vtk.vtkActor()
tensorActor.SetMapper(tensorEllipsoidsMapper)
# Create an outline around the data.
#
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(ptLoad.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(colors.GetColor3d('Black'))
# Create a cone whose apex indicates the application of load.
#
coneSrc = vtk.vtkConeSource()
coneSrc.SetRadius(.5)
coneSrc.SetHeight(2)
coneMap = vtk.vtkPolyDataMapper()
coneMap.SetInputConnection(coneSrc.GetOutputPort())
coneActor = vtk.vtkActor()
coneActor.SetMapper(coneMap)
coneActor.SetPosition(0, 0, 11)
coneActor.RotateY(90)
coneActor.GetProperty().SetColor(colors.GetColor3d('Red'))
camera = vtk.vtkCamera()
camera.SetFocalPoint(0.113766, -1.13665, -1.01919)
camera.SetPosition(-29.4886, -63.1488, 26.5807)
camera.SetViewAngle(24.4617)
camera.SetViewUp(0.17138, 0.331163, 0.927879)
camera.SetClippingRange(1, 100)
ren.AddActor(tensorActor)
ren.AddActor(outlineActor)
ren.AddActor(coneActor)
ren.SetBackground(colors.GetColor3d('WhiteSmoke'))
ren.SetActiveCamera(camera)
renWin.SetSize(512, 512)
renWin.SetWindowName('TensorEllipsoids')
iren.Initialize()
renWin.Render()
iren.Start()
def main():
colors = vtk.vtkNamedColors()
# We are going to handle two different sources.
# The first source is a superquadric source.
torus = vtk.vtkSuperquadricSource()
torus.SetCenter(0.0, 0.0, 0.0)
torus.SetScale(1.0, 1.0, 1.0)
torus.SetPhiResolution(64)
torus.SetThetaResolution(64)
torus.SetThetaRoundness(1)
torus.SetThickness(0.5)
torus.SetSize(0.5)
torus.SetToroidal(1)
# Rotate the torus towards the observer (around the x-axis)
torusT = vtk.vtkTransform()
torusT.RotateX(55)
torusTF = vtk.vtkTransformFilter()
torusTF.SetInputConnection(torus.GetOutputPort())
torusTF.SetTransform(torusT)
# The quadric is made of strips, so pass it through a triangle filter as
# the curvature filter only operates on polys
tri = vtk.vtkTriangleFilter()
tri.SetInputConnection(torusTF.GetOutputPort())
# The quadric has nasty discontinuities from the way the edges are generated
# so let's pass it though a CleanPolyDataFilter and merge any points which
# are coincident, or very close
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(tri.GetOutputPort())
cleaner.SetTolerance(0.005)
# The next source will be a parametric function
rh = vtk.vtkParametricRandomHills()
rhFnSrc = vtk.vtkParametricFunctionSource()
rhFnSrc.SetParametricFunction(rh)
# Now we have the sources, lets put them into a list.
sources = list()
sources.append(cleaner)
sources.append(cleaner)
sources.append(rhFnSrc)
sources.append(rhFnSrc)
# Colour transfer function.
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToDiverging()
p1 = [0.0] + list(colors.GetColor3d('MidnightBlue'))
p2 = [1.0] + list(colors.GetColor3d('DarkOrange'))
ctf.AddRGBPoint(*p1)
ctf.AddRGBPoint(*p2)
cc = list()
for i in range(256):
cc.append(ctf.GetColor(float(i) / 255.0))
# Lookup table.
lut = list()
for idx in range(len(sources)):
lut.append(vtk.vtkLookupTable())
lut[idx].SetNumberOfColors(256)
for i, item in enumerate(cc):
lut[idx].SetTableValue(i, item[0], item[1], item[2], 1.0)
if idx == 0:
lut[idx].SetRange(-10, 10)
if idx == 1:
lut[idx].SetRange(0, 4)
if idx == 2:
lut[idx].SetRange(-1, 1)
if idx == 3:
lut[idx].SetRange(-1, 1)
lut[idx].Build()
curvatures = list()
for idx in range(len(sources)):
curvatures.append(vtk.vtkCurvatures())
if idx % 2 == 0:
curvatures[idx].SetCurvatureTypeToGaussian()
else:
curvatures[idx].SetCurvatureTypeToMean()
renderers = list()
mappers = list()
actors = list()
textmappers = list()
textactors = list()
# Create a common text property.
textProperty = vtk.vtkTextProperty()
textProperty.SetFontSize(24)
textProperty.SetJustificationToCentered()
names = [
'Torus - Gaussian Curvature', 'Torus - Mean Curvature',
'Random Hills - Gaussian Curvature', 'Random Hills - Mean Curvature'
]
# Link the pipeline together.
for idx, item in enumerate(sources):
sources[idx].Update()
curvatures[idx].SetInputConnection(sources[idx].GetOutputPort())
mappers.append(vtk.vtkPolyDataMapper())
mappers[idx].SetInputConnection(curvatures[idx].GetOutputPort())
mappers[idx].SetLookupTable(lut[idx])
mappers[idx].SetUseLookupTableScalarRange(1)
actors.append(vtk.vtkActor())
actors[idx].SetMapper(mappers[idx])
textmappers.append(vtk.vtkTextMapper())
textmappers[idx].SetInput(names[idx])
textmappers[idx].SetTextProperty(textProperty)
textactors.append(vtk.vtkActor2D())
textactors[idx].SetMapper(textmappers[idx])
textactors[idx].SetPosition(250, 16)
renderers.append(vtk.vtkRenderer())
gridDimensions = 2
rendererSize = 512
for idx in range(len(sources)):
if idx < gridDimensions * gridDimensions:
renderers.append(vtk.vtkRenderer)
# Create the RenderWindow
#
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(rendererSize * gridDimensions,
rendererSize * gridDimensions)
renderWindow.SetWindowName('CurvaturesDemo')
# Add and position the renders to the render window.
viewport = list()
for row in range(gridDimensions):
for col in range(gridDimensions):
idx = row * gridDimensions + col
viewport[:] = []
viewport.append(float(col) / gridDimensions)
viewport.append(float(gridDimensions - (row + 1)) / gridDimensions)
viewport.append(float(col + 1) / gridDimensions)
viewport.append(float(gridDimensions - row) / gridDimensions)
if idx > (len(sources) - 1):
continue
renderers[idx].SetViewport(viewport)
renderWindow.AddRenderer(renderers[idx])
renderers[idx].AddActor(actors[idx])
renderers[idx].AddActor(textactors[idx])
renderers[idx].SetBackground(colors.GetColor3d('CornflowerBlue'))
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
renderWindow.Render()
interactor.Start()
def main():
# setup the dataset filepath
#all_filename = np.genfromtxt('stats/yA31/filenames.csv', dtype=None)
path = "D:/data/"
files = os.listdir(path)
time_index = []
for i in range(180, len(files)):
if (i % 5 == 0):
time_index.append(i)
#print(files);
daryName = "v02"
#'v03' 'prs' 'tev'
#for i in range(236, 237):
#for i in range(0, 1):
for i in range(0, len(time_index)):
filename = path + files[time_index[i]]
#filename = path+ files[i];
print(filename)
# for accessomg build-in color access
colors = vtk.vtkNamedColors()
# Create the renderer, the render window, and the interactor.
# The renderer draws into the render window.
# The interactor enables mouse and keyboard-based interaction
# with the data within the render windows.
aRenderer = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(aRenderer)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Set a background color for the renderer
# and set the size of the render window.
aRenderer.SetBackground(colors.GetColor3d("Silver"))
renWin.SetSize(600, 600)
# data reader
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(filename)
reader.Update()
# specify the data array in the file to process
reader.GetOutput().GetPointData().SetActiveAttribute(daryName, 0)
# convert the data array to numpy array and get the min and maximum value
dary = VN.vtk_to_numpy(
reader.GetOutput().GetPointData().GetScalars(daryName))
dary = dary[dary != 0]
dMax = np.amax(dary)
#dary = dary[dary>dMax/2]
dMin = np.amin(dary)
dRange = dMax - dMin
dMean = np.mean(dary)
dMedian = np.median(dary)
#dary = dary[dary>dMax/2]
print("Data array max: ", dMax)
print("Data array min: ", dMin)
print("Data array range: ", dRange)
print("Data array mean: ", dMean)
print("Data array median: ", dMedian)
############ setup color map #########
hueLut = vtk.vtkLookupTable()
# This creates a red ,white, blue lut.
hueLut.SetHueRange(0.67, 0.0)
hueLut.Build()
# An outline provides context around the data.
outlineData = vtk.vtkOutlineFilter()
outlineData.SetInputConnection(reader.GetOutputPort())
outlineData.Update()
mapOutline = vtk.vtkPolyDataMapper()
mapOutline.SetInputConnection(outlineData.GetOutputPort())
outline = vtk.vtkActor()
outline.SetMapper(mapOutline)
outline.GetProperty().SetColor(colors.GetColor3d("Black"))
################## create volume rendering ################################
# Create transfer mapping scalar value to opacity
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(0.0, 0.0001)
opacityTransferFunction.AddPoint(0.5, 0.0001)
opacityTransferFunction.AddPoint(1.0, 0.005)
# int AddRGBPoint (double x, double r, double g, double b)
# int AddHSVPoint (double x, double h, double s, double v)
# Create transfer mapping scalar value to color.
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(dMin, 0.0, 0.0, 1.0)
colorTransferFunction.AddRGBPoint(0.5, 0.0, 1.0, 0.0)
colorTransferFunction.AddRGBPoint(dMax, 1.0, 0.0, 0.0)
# The property describes how the data will look.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorTransferFunction)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
volumeProperty.SetScalarOpacityUnitDistance(100)
volumeProperty.SetInterpolationTypeToLinear()
# The mapper / ray cast function know how to render the data.
volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
volumeMapper.SetInputConnection(reader.GetOutputPort())
# The volume holds the mapper and the property and
# can be used to position/orient the volume.
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
######################## create a text #####################
# create a text actor
txt = vtk.vtkTextActor()
txt.SetInput("Color map")
txtprop = txt.GetTextProperty()
txtprop.SetFontFamilyToArial()
txtprop.SetFontSize(24)
txtprop.SetColor(0.0, 0.0, 0.0)
txt.SetDisplayPosition(450, 550)
############################################################
txt2 = vtk.vtkTextActor()
txt_str2 = "timestep = " + filename[30:35] + ", Scalar Value (v02)"
txt2.SetInput(txt_str2)
txtprop2 = txt2.GetTextProperty()
txtprop2.SetFontFamilyToArial()
txtprop2.SetFontSize(24)
txtprop2.SetColor(0, 0, 0)
txt2.SetDisplayPosition(20, 550)
############################ create a color bar ###########################
# create the scalar_bar
scalar_bar = vtk.vtkScalarBarActor()
scalar_bar.SetOrientationToHorizontal()
scalar_bar.SetLookupTable(hueLut)
# create the scalar_bar_widget
scalar_bar_widget = vtk.vtkScalarBarWidget()
scalar_bar_widget.SetInteractor(iren)
scalar_bar_widget.SetScalarBarActor(scalar_bar)
scalar_bar_widget.On()
aCamera = vtk.vtkCamera()
aCamera.SetViewUp(0, 1, 0)
aCamera.SetPosition(-0.2, 0.2, 0.5)
aCamera.SetFocalPoint(0, 0, 0)
aCamera.ComputeViewPlaneNormal()
#aCamera.Azimuth(45.0);
#aCamera.Elevation(45.0);
#aCamera.Zoom(0.01);
#aCamera.Dolly(10.0);
# Actors are added to the renderer.
aRenderer.AddActor(outline)
aRenderer.AddVolume(volume)
aRenderer.AddActor(txt)
aRenderer.AddActor(txt2)
# An initial camera view is created. The Dolly() method moves
# the camera towards the FocalPoint, thereby enlarging the image.
aRenderer.SetActiveCamera(aCamera)
# Calling Render() directly on a vtkRenderer is strictly forbidden.
# Only calling Render() on the vtkRenderWindow is a valid call.
renWin.Render()
aRenderer.ResetCamera()
#aCamera.Dolly(-2.0);
####################################################################
# screenshot code:
w2if = vtk.vtkWindowToImageFilter()
w2if.SetInput(renWin)
w2if.Update()
writer = vtk.vtkPNGWriter()
saveName = "plots/yA31/v_r/v02/" + daryName + "_t_" + filename[
30:35] + ".png"
writer.SetFileName(saveName)
writer.SetInputData(w2if.GetOutput())
writer.Write()
#####################################################################
# Note that when camera movement occurs (as it does in the Dolly() method),
# the clipping planes often need adjusting.
# Clipping planes consist of two planes:
# near and far along the view direction.
# The near plane clips out objects in front of the plane;
# the far plane clips out objects behind the plane.
# This way only what is drawn between the planes is actually rendered.
aRenderer.ResetCameraClippingRange()
# Interact with the data.
renWin.Render()
def _plotInternal(self):
"""Overrides baseclass implementation."""
numLevels = len(self._contourLevels)
cot = vtk.vtkContourFilter()
if self._useCellScalars:
cot.SetInputConnection(self._vtkPolyDataFilter.GetOutputPort())
else:
cot.SetInputData(self._vtkDataSet)
cot.SetNumberOfContours(numLevels)
if self._contourLevels[0] == 1.e20:
self._contourLevels[0] = -1.e20
for i in range(numLevels):
cot.SetValue(i, self._contourLevels[i])
cot.SetValue(numLevels, self._contourLevels[-1])
# TODO remove update
cot.Update()
mappers = []
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(len(self._contourColors))
cmap = self._context().canvas.getcolormapname()
cmap = vcs.elements["colormap"][cmap]
for i, col in enumerate(self._contourColors):
r, g, b = cmap.index[col]
lut.SetTableValue(i, r / 100., g / 100., b / 100.)
# Setup isoline labels
if self._gm.label:
# Setup label mapping array:
tpropMap = vtk.vtkDoubleArray()
tpropMap.SetNumberOfComponents(1)
tpropMap.SetNumberOfTuples(numLevels)
for i, val in enumerate(self._contourLevels):
tpropMap.SetTuple(i, [val])
# Prep text properties:
tprops = vtk.vtkTextPropertyCollection()
if self._gm.text or self._gm.textcolors:
# Text objects:
if self._gm.text:
texts = self._gm.text
while len(texts) < numLevels:
texts.append(texts[-1])
else:
texts = [None] * len(self._gm.textcolors)
# Custom colors:
if self._gm.textcolors:
colorOverrides = self._gm.textcolors
while len(colorOverrides) < numLevels:
colorOverrides.append(colorOverrides[-1])
else:
colorOverrides = [None] * len(self._gm.text)
for tc, colorOverride in zip(texts, colorOverrides):
if vcs.queries.istextcombined(tc):
tt, to = tuple(tc.name.split(":::"))
elif tc is None:
tt = "default"
to = "default"
elif vcs.queries.istexttable(tc):
tt = tc.name
to = "default"
elif vcs.queries.istextorientation(tc):
to = tc.name
tt = "default"
if colorOverride is not None:
tt = vcs.createtexttable(None, tt)
tt.color = colorOverride
tt = tt.name
tprop = vtk.vtkTextProperty()
vcs2vtk.prepTextProperty(tprop,
self._context().renWin.GetSize(),
to, tt)
tprops.AddItem(tprop)
if colorOverride is not None:
del (vcs.elements["texttable"][tt])
else: # No text properties specified. Use the default:
tprop = vtk.vtkTextProperty()
vcs2vtk.prepTextProperty(tprop,
self._context().renWin.GetSize())
tprops.AddItem(tprop)
self._resultDict["vtk_backend_contours_labels_text_properties"] = \
tprops
mapper = vtk.vtkLabeledContourMapper()
mapper.SetTextProperties(tprops)
mapper.SetTextPropertyMapping(tpropMap)
mapper.SetLabelVisibility(1)
mapper.SetSkipDistance(self._gm.labelskipdistance)
pdMapper = mapper.GetPolyDataMapper()
self._resultDict["vtk_backend_labeled_luts"] = [[
lut, [self._contourLevels[0], self._contourLevels[-1], False]
]]
else: # No isoline labels:
mapper = vtk.vtkPolyDataMapper()
pdMapper = mapper
self._resultDict["vtk_backend_luts"] = \
[[lut, [self._contourLevels[0],
self._contourLevels[-1], False]]]
pdMapper.SetLookupTable(lut)
pdMapper.SetScalarRange(self._contourLevels[0],
self._contourLevels[-1])
pdMapper.SetScalarModeToUsePointData()
stripper = vtk.vtkStripper()
stripper.SetInputConnection(cot.GetOutputPort())
mapper.SetInputConnection(stripper.GetOutputPort())
# TODO remove update, make pipeline
stripper.Update()
mappers.append(mapper)
self._resultDict["vtk_backend_contours"] = [cot]
if self._maskedDataMapper is not None:
mappers.insert(0, self._maskedDataMapper)
x1, x2, y1, y2 = vcs.utils.getworldcoordinates(self._gm,
self._data1.getAxis(-1),
self._data1.getAxis(-2))
# And now we need actors to actually render this thing
actors = []
for mapper in mappers:
act = vtk.vtkActor()
act.SetMapper(mapper)
if self._vtkGeoTransform is None:
# If using geofilter on wireframed does not get wrppaed not
# sure why so sticking to many mappers
act = vcs2vtk.doWrap(act, [x1, x2, y1, y2],
self._dataWrapModulo)
# TODO See comment in boxfill.
if mapper is self._maskedDataMapper:
actors.append([act, self._maskedDataMapper, [x1, x2, y1, y2]])
else:
actors.append([act, [x1, x2, y1, y2]])
# create a new renderer for this mapper
# (we need one for each mapper because of cmaera flips)
self._context().fitToViewport(
act, [
self._template.data.x1, self._template.data.x2,
self._template.data.y1, self._template.data.y2
],
wc=[x1, x2, y1, y2],
geo=self._vtkGeoTransform,
priority=self._template.data.priority,
create_renderer=True)
self._resultDict["vtk_backend_actors"] = actors
t = self._originalData1.getTime()
if self._originalData1.ndim > 2:
z = self._originalData1.getAxis(-3)
else:
z = None
self._resultDict.update(self._context().renderTemplate(
self._template, self._data1, self._gm, t, z))
if self._context().canvas._continents is None:
self._useContinents = False
if self._useContinents:
projection = vcs.elements["projection"][self._gm.projection]
self._context().plotContinents(x1, x2, y1, y2, projection,
self._dataWrapModulo,
self._template)
def surface(points, triangles, labels, ctab, opacity=1):
""" Create a colored triangular surface.
Parameters
----------
points: array (n_vertices, 3)
the surface vertices.
triangles: array
nfaces x 3 array defining mesh triangles.
labels: array (n_vertices)
Annotation id at each vertex.
If a vertex does not belong to any label its id must be negative.
ctab: ndarray (n_labels, 5)
RGBA + label id color table array.
opacity: float
the actor global opacity.
Returns
-------
actor: vtkActor
one actor handling the surface.
"""
# First setup points, triangles and colors
vtk_points = vtk.vtkPoints()
vtk_triangles = vtk.vtkCellArray()
vtk_colors = vtk.vtkUnsignedCharArray()
vtk_colors.SetNumberOfComponents(1)
labels[numpy.where(labels < 0)] = 0
for index in range(len(points)):
vtk_points.InsertNextPoint(points[index])
vtk_colors.InsertNextTuple1(labels[index])
for cnt, triangle in enumerate(triangles):
vtk_triangle = vtk.vtkTriangle()
vtk_triangle.GetPointIds().SetId(0, triangle[0])
vtk_triangle.GetPointIds().SetId(1, triangle[1])
vtk_triangle.GetPointIds().SetId(2, triangle[2])
vtk_triangles.InsertNextCell(vtk_triangle)
# Make a lookup table using vtkColorSeries
nb_of_labels = len(ctab)
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(nb_of_labels)
lut.Build()
for cnt, lut_element in enumerate(ctab):
lut.SetTableValue(cnt, lut_element[0] / 255., lut_element[1] / 255.,
lut_element[2] / 255., lut_element[3] / 255.)
lut.SetNanColor(1, 0, 0, 1)
# Create (geometry and topology) the associated polydata
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
polydata.GetPointData().SetScalars(vtk_colors)
polydata.SetPolys(vtk_triangles)
# Create the mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(polydata)
mapper.SetLookupTable(lut)
mapper.SetColorModeToMapScalars()
mapper.SetScalarRange(0, nb_of_labels)
mapper.SetScalarModeToUsePointData()
# Create the actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetOpacity(opacity)
return actor
def makeLUT(colorlist,
interpolate=False,
vmin=None,
vmax=None,
belowColor=None,
aboveColor=None,
nanColor=None):
"""
Generate colors in a vtk lookup table.
:param list colorlist: a list in the form ``[(scalar1, [r,g,b]), (scalar2, 'blue'), ...]``.
:param bool interpolate: interpolate or not intermediate scalars
:param float vmin: specify minimum value of scalar range
:param float vmax: specify maximum value of scalar range
:param belowColor: color for scalars below the minimum in range
:param aboveColor: color for scalars above the maximum in range
:return: the lookup table object ``vtkLookupTable``. This can be fed into ``colorMap``.
.. hint:: Example: |mesh_lut.py|_
"""
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(256)
if nanColor is not None:
lut.SetNanColor(list(getColor(nanColor)) + [1])
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToRGB()
ctf.SetScaleToLinear()
if belowColor is not None:
ctf.SetBelowRangeColor(getColor(belowColor))
ctf.SetUseBelowRangeColor(True)
rgba = list(getColor(belowColor)) + [1]
if aboveColor is not None:
ctf.SetAboveRangeColor(getColor(aboveColor))
ctf.SetUseAboveRangeColor(True)
rgba = list(getColor(aboveColor)) + [1]
for sc in colorlist:
if len(sc) == 3:
scalar, col, _ = sc
else:
scalar, col = sc
r, g, b = getColor(col)
ctf.AddRGBPoint(scalar, r, g, b)
x0, x1 = ctf.GetRange()
if vmin is not None:
x0 = vmin
if vmax is not None:
x1 = vmax
ctf.SetRange(x0, x1)
lut.SetRange(x0, x1)
for i in range(256):
p = i / 255
x = (1 - p) * x0 + p * x1
if interpolate:
rgba = list(ctf.GetColor(x)) + [1]
else:
rgba = [0.5, 0.5, 0.5, 1]
for c in colorlist:
if x <= c[0]:
if len(c) == 3:
al = c[2]
else:
al = 1
rgba = list(getColor(c[1])) + [al]
break
lut.SetTableValue(i, rgba)
lut.Build()
return lut
def prepareDelaunayData(dimension, agg_globalnodeidx, global_nodecoords, aggpolygons, aggid, aggid2nodes, aggid2procs):
local_nodeidx2global_nodeidx = {}
no_of_aggnodes = len(agg_globalnodeidx)
dim = len(global_nodecoords[0])
no_aggs = len(aggid2nodes)
Points = vtk.vtkPoints()
Vertices = vtk.vtkCellArray()
for i in range(0,len(agg_globalnodeidx)):
local_nodeidx2global_nodeidx[i] = agg_globalnodeidx[i]
nodecoords = global_nodecoords[int(agg_globalnodeidx[i])]
if dimension==2:
id = Points.InsertNextPoint(nodecoords[0],nodecoords[1],0.0)
elif dimension==3:
id = Points.InsertNextPoint(nodecoords[0]+ 0.001 * random.random(),nodecoords[1]+ 0.001 * random.random(),nodecoords[2]+ 0.001 * random.random())
Vertices.InsertNextCell(1)
Vertices.InsertCellPoint(id)
# create polygon for current aggregate
polydata = vtk.vtkPolyData()
polydata.SetPoints(Points)
polydata.SetVerts(Vertices)
polydata.Modified()
polydata.Update()
polydata2 = vtk.vtkPolyData()
if Points.GetNumberOfPoints()>2: # todo: avoid error messages + add support for lines/surfaces
# create delaunay object
if dimension==2:
delaunay = vtk.vtkDelaunay2D()
elif dimension==3:
delaunay = vtk.vtkDelaunay3D()
#delaunay.SetAlpha(0.1)
delaunay.SetInput(polydata)
delaunay.Update()
# create surfaceFilter
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
surfaceFilter.Update()
polydata2 = surfaceFilter.GetOutput()
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(no_aggs)
lookupTable.Build()
Ids = vtk.vtkUnsignedIntArray()
Ids.SetNumberOfComponents(1)
Ids.SetName("Ids")
for i in range(0,Points.GetNumberOfPoints()):
Ids.InsertNextTuple1(int(aggid))
Ids.SetLookupTable(lookupTable)
Procs = vtk.vtkUnsignedCharArray()
Procs.SetNumberOfComponents(1)
Procs.SetName("proc")
for i in range(0,Points.GetNumberOfPoints()):
Procs.InsertNextTuple1(aggid2procs[aggid])
polydata2.SetPoints(Points)
polydata2.SetVerts(Vertices)
polydata2.GetPointData().SetScalars(Ids)
polydata2.GetPointData().AddArray(Procs)
polydata2.Modified()
polydata2.Update()
aggpolygons.AddInput(polydata2)
def main():
xyzFile, qFile = get_program_parameters()
colors = vtk.vtkNamedColors()
# Create pipeline. Read structured grid data.
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(xyzFile)
pl3d.SetQFileName(qFile)
pl3d.SetScalarFunctionNumber(100)
pl3d.SetVectorFunctionNumber(202)
pl3d.Update()
pl3dOutput = pl3d.GetOutput().GetBlock(0)
# A convenience
extract = vtk.vtkExtractGrid()
extract.SetVOI(1, 55, -1000, 1000, -1000, 1000)
extract.SetInputData(pl3dOutput)
# The plane is used to do the cutting
plane = vtk.vtkPlane()
plane.SetOrigin(0, 4, 2)
plane.SetNormal(0, 1, 0)
# compositing.
cutter = vtk.vtkCutter()
cutter.SetInputConnection(extract.GetOutputPort())
cutter.SetCutFunction(plane)
cutter.GenerateCutScalarsOff()
cutter.SetSortByToSortByCell()
clut = vtk.vtkLookupTable()
clut.SetHueRange(0, 0.67)
clut.Build()
cutterMapper = vtk.vtkPolyDataMapper()
cutterMapper.SetInputConnection(cutter.GetOutputPort())
cutterMapper.SetScalarRange(0.18, 0.7)
cutterMapper.SetLookupTable(clut)
cut = vtk.vtkActor()
cut.SetMapper(cutterMapper)
# Add in some surface geometry for interest.
iso = vtk.vtkContourFilter()
iso.SetInputData(pl3dOutput)
iso.SetValue(0, .22)
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(iso.GetOutputPort())
normals.SetFeatureAngle(60)
isoMapper = vtk.vtkPolyDataMapper()
isoMapper.SetInputConnection(normals.GetOutputPort())
isoMapper.ScalarVisibilityOff()
isoActor = vtk.vtkActor()
isoActor.SetMapper(isoMapper)
isoActor.GetProperty().SetDiffuseColor(colors.GetColor3d("Tomato"))
isoActor.GetProperty().SetSpecularColor(colors.GetColor3d("White"))
isoActor.GetProperty().SetDiffuse(0.8)
isoActor.GetProperty().SetSpecular(0.5)
isoActor.GetProperty().SetSpecularPower(30)
outline = vtk.vtkStructuredGridOutlineFilter()
outline.SetInputData(pl3dOutput)
outlineStrip = vtk.vtkStripper()
outlineStrip.SetInputConnection(outline.GetOutputPort())
outlineTubes = vtk.vtkTubeFilter()
outlineTubes.SetInputConnection(outline.GetOutputPort())
outlineTubes.SetInputConnection(outlineStrip.GetOutputPort())
outlineTubes.SetRadius(0.1)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outlineTubes.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# Create the RenderWindow, Renderer and Interactor.
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Add the actors to the renderer, set the background and size.
ren1.AddActor(outlineActor)
outlineActor.GetProperty().SetColor(colors.GetColor3d("Banana"))
ren1.AddActor(isoActor)
isoActor.VisibilityOn()
ren1.AddActor(cut)
n = 20
opacity = 1.0 / float(n) * 5.0
cut.GetProperty().SetOpacity(1)
ren1.SetBackground(colors.GetColor3d("SlateGray"))
renWin.SetSize(640, 480)
ren1.GetActiveCamera().SetClippingRange(3.95297, 50)
ren1.GetActiveCamera().SetFocalPoint(9.71821, 0.458166, 29.3999)
ren1.GetActiveCamera().SetPosition(2.7439, -37.3196, 38.7167)
ren1.GetActiveCamera().ComputeViewPlaneNormal()
ren1.GetActiveCamera().SetViewUp(-0.16123, 0.264271, 0.950876)
# Cut: generates n cut planes normal to camera's view plane.
plane.SetNormal(ren1.GetActiveCamera().GetViewPlaneNormal())
plane.SetOrigin(ren1.GetActiveCamera().GetFocalPoint())
cutter.GenerateValues(n, -5, 5)
clut.SetAlphaRange(opacity, opacity)
renWin.Render()
iren.Start()
def setEdgesPolydata(self):
for e in self.edges:
self.myscreen.removeActor(e)
self.edges = []
self.edgePoints = vtk.vtkPoints()
self.lineCells = vtk.vtkCellArray()
self.colorLUT = vtk.vtkLookupTable()
idx = 0
last_idx = 0
vd_edges = []
if self.offsetEdges == 0:
vd_edges = self.vd.getVoronoiEdges()
else:
vd_edges = self.vd.getVoronoiEdgesOffset()
for e in vd_edges:
epts = e[0] # points
etype = e[1] # type
first = 1
segs = []
for p in epts:
self.edgePoints.InsertNextPoint(p.x, p.y, 0)
if first == 0:
seg = [last_idx, idx]
segs.append(seg)
first = 0
last_idx = idx
idx = idx + 1
# create line and cells
for seg in segs:
line = vtk.vtkLine()
line.GetPointIds().SetId(0, seg[0])
line.GetPointIds().SetId(1, seg[1])
#print " indexes: ", seg[0]," to ",seg[1]
self.lineCells.InsertNextCell(line)
Colors = vtk.vtkUnsignedCharArray()
self.colorLUT = vtk.vtkUnsignedCharArray()
self.colorLUT.SetNumberOfComponents(3)
self.colorLUT.SetName("Colors")
# go through edges once more and set colors
m = 0
for e in vd_edges:
src_status = e[2] # src status
trg_status = e[3] # trg status
ecolor = self.edgeTypeColor(e[1], e[2], e[3])
for dummy in e[0]: # go through all the points
self.colorLUT.InsertNextTuple3(255 * ecolor[0],
255 * ecolor[1],
255 * ecolor[2])
m = m + 1
linePolyData = vtk.vtkPolyData()
linePolyData.SetPoints(self.edgePoints)
linePolyData.SetLines(self.lineCells)
linePolyData.GetPointData().SetScalars(self.colorLUT)
linePolyData.Modified()
linePolyData.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(linePolyData)
self.edge_actor = vtk.vtkActor()
self.edge_actor.SetMapper(mapper)
self.myscreen.addActor(self.edge_actor)
self.edges.append(self.edge_actor)
def _plotInternalCustomBoxfill(self):
"""Implements the logic to render a custom boxfill."""
self._mappers = []
tmpLevels = []
tmpColors = []
indices = self._gm.fillareaindices
if indices is None:
indices = [
1,
]
while len(indices) < len(self._contourColors):
indices.append(indices[-1])
if len(self._contourLevels) > len(self._contourColors):
raise RuntimeError(
"You asked for %i levels but provided only %i colors\n"
"Graphic Method: %s of type %s\nLevels: %s" %
(len(self._contourLevels), len(
self._contourColors), self._gm.name, self._gm.g_name),
repr(self._contourLevels))
elif len(self._contourLevels) < len(self._contourColors) - 1:
warnings.warn(
"You asked for %i lgridevels but provided %i colors, "
"extra ones will be ignored\nGraphic Method: %s of type %s" %
(len(self._contourLevels), len(
self._contourColors), self._gm.name, self._gm.g_name))
for i, l in enumerate(self._contourLevels):
if i == 0:
C = [
self._contourColors[i],
]
if numpy.allclose(self._contourLevels[0][0], -1.e20):
## ok it's an extension arrow
L = [self._scalarRange[0] - 1., self._contourLevels[0][1]]
else:
L = list(self._contourLevels[i])
I = [
indices[i],
]
else:
if l[0] == L[-1] and I[-1] == indices[i]:
# Ok same type lets keep going
if numpy.allclose(l[1], 1.e20):
L.append(self._scalarRange[1] + 1.)
else:
L.append(l[1])
C.append(self._contourColors[i])
else: # ok we need new contouring
tmpLevels.append(L)
tmpColors.append(C)
C = [
self._contourColors[i],
]
L = self._contourLevels[i]
I = [
indices[i],
]
tmpLevels.append(L)
tmpColors.append(C)
luts = []
cots = []
geos = []
wholeDataMin, wholeDataMax = vcs.minmax(self._originalData1)
for i, l in enumerate(tmpLevels):
# Ok here we are trying to group together levels can be, a join will
# happen if: next set of levels contnues where one left off AND
# pattern is identical
# TODO this should really just be a single polydata/mapper/actor:
for j, color in enumerate(tmpColors[i]):
mapper = vtk.vtkPolyDataMapper()
lut = vtk.vtkLookupTable()
th = vtk.vtkThreshold()
th.ThresholdBetween(l[j], l[j + 1])
th.SetInputConnection(self._vtkPolyDataFilter.GetOutputPort())
geoFilter2 = vtk.vtkDataSetSurfaceFilter()
geoFilter2.SetInputConnection(th.GetOutputPort())
geos.append(geoFilter2)
mapper.SetInputConnection(geoFilter2.GetOutputPort())
lut.SetNumberOfTableValues(1)
r, g, b = self._colorMap.index[color]
lut.SetTableValue(0, r / 100., g / 100., b / 100.)
mapper.SetLookupTable(lut)
mapper.SetScalarRange(l[j], l[j + 1])
luts.append([lut, [l[j], l[j + 1], False]])
## Store the mapper only if it's worth it?
## Need to do it with the whole slab min/max for animation
# purposes
if not (l[j + 1] < wholeDataMin or l[j] > wholeDataMax):
self._mappers.append(mapper)
self._resultDict["vtk_backend_luts"] = luts
if len(cots) > 0:
self._resultDict["vtk_backend_contours"] = cots
if len(geos) > 0:
self._resultDict["vtk_backend_geofilters"] = geos
def create(self, filename, orie='coronal', maxint=1000, op=0.99):
# set up the source
source = vtk.vtkNIFTIImageReader()
source.SetFileName(filename)
self.source = source
# Calculate the center of the volume
source.Update()
(xMin, xMax, yMin, yMax, zMin,
zMax) = source.GetExecutive().GetWholeExtent(
source.GetOutputInformation(0))
(xSpacing, ySpacing, zSpacing) = source.GetOutput().GetSpacing()
(x0, y0, z0) = source.GetOutput().GetOrigin()
self.center = [
x0 + xSpacing * 0.5 * (xMin + xMax),
y0 + ySpacing * 0.5 * (yMin + yMax),
z0 + zSpacing * 0.5 * (zMin + zMax)
]
# Matrices for axial, coronal, sagittal, oblique view orientations
orie_mat = _get_orie_mat(self, orie=orie)
# Extract a slice in the desired orientation
self.reslice = vtk.vtkImageReslice()
self.reslice.SetInputConnection(source.GetOutputPort())
self.reslice.SetOutputDimensionality(2)
self.reslice.SetResliceAxes(orie_mat)
self.reslice.SetInterpolationModeToLinear()
# Create a greyscale lookup table
if filename == 'T1w_acpc_dc_restore_brain.nii.gz':
table = vtk.vtkLookupTable()
table.SetRange(0, maxint) # image intensity range
table.SetValueRange(0.0, 1.0) # from black to white
table.SetSaturationRange(0.0, 0.0) # no color saturation
table.SetRampToLinear()
table.Build()
# Map the image through the lookup table
color = vtk.vtkImageMapToColors()
color.SetLookupTable(table)
color.SetInputConnection(self.reslice.GetOutputPort())
# Display the image
actor = vtk.vtkImageActor()
actor.GetMapper().SetInputConnection(color.GetOutputPort())
actor.GetProperty().SetOpacity(op)
else:
table = vtk.vtkLookupTable()
table.SetNumberOfTableValues(2)
table.Build()
nc = vtk.vtkNamedColors()
table.SetTableValue(0, nc.GetColor4d("Black"))
table.SetTableValue(1, nc.GetColor4d(self.colour))
color = vtk.vtkImageMapToColors()
color.SetLookupTable(table)
color.SetInputConnection(self.reslice.GetOutputPort())
actor = vtk.vtkImageActor()
actor.GetMapper().SetInputConnection(color.GetOutputPort())
actor.GetProperty().SetOpacity(op)
return actor, self.center, self.reslice
def tensor(coeff,
order,
position=(0, 0, 0),
radius=0.5,
thetares=20,
phires=20,
opacity=1,
tessel=0):
""" Generate a generic tensor actor.
"""
# Create a sphere that we will deform
sphere = vtk.vtkSphereSource()
sphere.SetRadius(radius)
sphere.SetLatLongTessellation(tessel)
sphere.SetThetaResolution(thetares)
sphere.SetPhiResolution(phires)
# Get the polydata
poly = sphere.GetOutput()
poly.Update()
# Get the mesh
numPts = poly.GetNumberOfPoints()
mesh = numpy.zeros((numPts, 3), dtype=numpy.single)
for i in range(numPts):
mesh[i, :] = (poly.GetPoint(i)[0], poly.GetPoint(i)[1],
poly.GetPoint(i)[2])
# Deform mesh
design_matrix = construct_matrix_of_monomials(mesh, order)
signal = numpy.dot(design_matrix, coeff)
#signal = np.maximum(signal, 0.0)
signal /= signal.max()
signal *= 0.5
scalars = vtk.vtkFloatArray()
pts = vtk.vtkPoints()
pts.SetNumberOfPoints(numPts)
for i in range(numPts):
pts.SetPoint(i, signal[i] * mesh[i, 0], signal[i] * mesh[i, 1],
signal[i] * mesh[i, 2])
scalars.InsertTuple1(i, signal[i])
poly.SetPoints(pts)
poly.GetPointData().SetScalars(scalars)
poly.Update()
lut = vtk.vtkLookupTable()
lut.SetHueRange(0.667, 0.0)
lut.Build()
spherem = vtk.vtkPolyDataMapper()
spherem.SetInput(poly)
spherem.SetLookupTable(lut)
spherem.ScalarVisibilityOn()
spherem.SetColorModeToMapScalars()
spherem.SetScalarRange(0.0, 0.5)
actor = vtk.vtkActor()
actor.SetMapper(spherem)
actor.SetPosition(position)
actor.GetProperty().SetOpacity(opacity)
return actor
def displaySurfaces(self, progress_callback):
"""
Create the VTK data structures and display a 3D surface based on the input image.
:param (function) progress_callback:
Function to emit progress signals
"""
# Points coordinates structure
triangle_vertices = vtk.vtkPoints()
# associate the points to triangles
triangle = vtk.vtkTriangle()
trianglePointIds = triangle.GetPointIds()
# put all triangles in an array
triangles = vtk.vtkCellArray()
surface_data = vtk.vtkIntArray()
surface_data.SetNumberOfComponents(1)
surface_data.SetName("SurfaceId")
isTriangle = 0
nTriangle = 0
surface = 0
# associate each coordinate with a point: 3 coordinates are needed for a point
# in 3D. Additionally we perform a shift from image coordinates (pixel) which
# is the default of the Contour Tree Algorithm to the World Coordinates.
origin = self.origin
spacing = self.spacing
# augmented matrix for affine transformations
mScaling = numpy.asarray([
spacing[0], 0, 0, 0, 0, spacing[1], 0, 0, 0, 0, spacing[2], 0, 0,
0, 0, 1
]).reshape((4, 4))
mShift = numpy.asarray([
1, 0, 0, origin[0], 0, 1, 0, origin[1], 0, 0, 1, origin[2], 0, 0,
0, 1
]).reshape((4, 4))
mTransform = numpy.dot(mScaling, mShift)
point_count = 0
surf_list = self.segmentor.getSurfaces()
# Calculate the increment for each of the surfaces
increment = 60.0 / len(surf_list)
for n, surf in enumerate(surf_list, 1):
print("Image-to-world coordinate trasformation ... %d" % surface)
for point in surf:
world_coord = numpy.dot(mTransform, point)
triangle_vertices.InsertNextPoint(world_coord[0],
world_coord[1],
world_coord[2])
# The id of the vertex of the triangle (0,1,2) is linked to
# the id of the points in the list, so in facts we just link id-to-id
trianglePointIds.SetId(isTriangle, point_count)
isTriangle += 1
point_count += 1
if (isTriangle == 3):
isTriangle = 0
# insert the current triangle in the triangles array
triangles.InsertNextCell(triangle)
surface_data.InsertNextValue(surface)
progress_callback.emit(int(n * increment + 30))
surface += 1
# polydata object
trianglePolyData = vtk.vtkPolyData()
trianglePolyData.SetPoints(triangle_vertices)
trianglePolyData.SetPolys(triangles)
trianglePolyData.GetCellData().AddArray(surface_data)
self.viewer3DWidget.viewer.displayPolyData(trianglePolyData)
actors = self.viewer3DWidget.viewer.actors
if self.surfaceColourCheck.isChecked():
# Change the colour of the polydata actors
named_colours = vtk.vtkNamedColors()
all_colours = named_colours.GetColorNames().split('\n')
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(surface)
lut.Build()
for i in range(surface):
R, G, B = named_colours.GetColor3d(all_colours[i])
lut.SetTableValue(i, R, G, B)
actors[1][0].GetMapper().SetLookupTable(lut)
actors[1][0].GetMapper().SetScalarRange(0, surface)
actors[1][0].GetMapper().SetScalarModeToUseCellFieldData()
actors[1][0].GetMapper().SelectColorArray('SurfaceId')
actors[1][0].GetMapper().Update()
self.viewer3DWidget.viewer.renWin.Render()
def testVolumePicker(self):
# volume render a medical data set
# renderer and interactor
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin)
# read the volume
v16 = vtk.vtkVolume16Reader()
v16.SetDataDimensions(64, 64)
v16.SetImageRange(1, 93)
v16.SetDataByteOrderToLittleEndian()
v16.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
v16.SetDataSpacing(3.2, 3.2, 1.5)
#---------------------------------------------------------
# set up the volume rendering
rayCastFunction = vtk.vtkVolumeRayCastCompositeFunction()
volumeMapper = vtk.vtkVolumeRayCastMapper()
volumeMapper.SetInputConnection(v16.GetOutputPort())
volumeMapper.SetVolumeRayCastFunction(rayCastFunction)
volumeColor = vtk.vtkColorTransferFunction()
volumeColor.AddRGBPoint(0, 0.0, 0.0, 0.0)
volumeColor.AddRGBPoint(180, 0.3, 0.1, 0.2)
volumeColor.AddRGBPoint(1000, 1.0, 0.7, 0.6)
volumeColor.AddRGBPoint(2000, 1.0, 1.0, 0.9)
volumeScalarOpacity = vtk.vtkPiecewiseFunction()
volumeScalarOpacity.AddPoint(0, 0.0)
volumeScalarOpacity.AddPoint(180, 0.0)
volumeScalarOpacity.AddPoint(1000, 0.2)
volumeScalarOpacity.AddPoint(2000, 0.8)
volumeGradientOpacity = vtk.vtkPiecewiseFunction()
volumeGradientOpacity.AddPoint(0, 0.0)
volumeGradientOpacity.AddPoint(90, 0.5)
volumeGradientOpacity.AddPoint(100, 1.0)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(volumeColor)
volumeProperty.SetScalarOpacity(volumeScalarOpacity)
volumeProperty.SetGradientOpacity(volumeGradientOpacity)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOn()
volumeProperty.SetAmbient(0.6)
volumeProperty.SetDiffuse(0.6)
volumeProperty.SetSpecular(0.1)
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
#---------------------------------------------------------
# Do the surface rendering
boneExtractor = vtk.vtkMarchingCubes()
boneExtractor.SetInputConnection(v16.GetOutputPort())
boneExtractor.SetValue(0, 1150)
boneNormals = vtk.vtkPolyDataNormals()
boneNormals.SetInputConnection(boneExtractor.GetOutputPort())
boneNormals.SetFeatureAngle(60.0)
boneStripper = vtk.vtkStripper()
boneStripper.SetInputConnection(boneNormals.GetOutputPort())
boneMapper = vtk.vtkPolyDataMapper()
boneMapper.SetInputConnection(boneStripper.GetOutputPort())
boneMapper.ScalarVisibilityOff()
boneProperty = vtk.vtkProperty()
boneProperty.SetColor(1.0, 1.0, 0.9)
bone = vtk.vtkActor()
bone.SetMapper(boneMapper)
bone.SetProperty(boneProperty)
#---------------------------------------------------------
# Create an image actor
table = vtk.vtkLookupTable()
table.SetRange(0, 2000)
table.SetRampToLinear()
table.SetValueRange(0, 1)
table.SetHueRange(0, 0)
table.SetSaturationRange(0, 0)
mapToColors = vtk.vtkImageMapToColors()
mapToColors.SetInputConnection(v16.GetOutputPort())
mapToColors.SetLookupTable(table)
imageActor = vtk.vtkImageActor()
imageActor.GetMapper().SetInputConnection(mapToColors.GetOutputPort())
imageActor.SetDisplayExtent(32, 32, 0, 63, 0, 92)
#---------------------------------------------------------
# make a transform and some clipping planes
transform = vtk.vtkTransform()
transform.RotateWXYZ(-20, 0.0, -0.7, 0.7)
volume.SetUserTransform(transform)
bone.SetUserTransform(transform)
imageActor.SetUserTransform(transform)
c = volume.GetCenter()
volumeClip = vtk.vtkPlane()
volumeClip.SetNormal(0, 1, 0)
volumeClip.SetOrigin(c)
boneClip = vtk.vtkPlane()
boneClip.SetNormal(0, 0, 1)
boneClip.SetOrigin(c)
volumeMapper.AddClippingPlane(volumeClip)
boneMapper.AddClippingPlane(boneClip)
#---------------------------------------------------------
ren.AddViewProp(volume)
ren.AddViewProp(bone)
ren.AddViewProp(imageActor)
camera = ren.GetActiveCamera()
camera.SetFocalPoint(c)
camera.SetPosition(c[0] + 500, c[1] - 100, c[2] - 100)
camera.SetViewUp(0, 0, -1)
ren.ResetCameraClippingRange()
renWin.Render()
#---------------------------------------------------------
# the cone should point along the Z axis
coneSource = vtk.vtkConeSource()
coneSource.CappingOn()
coneSource.SetHeight(12)
coneSource.SetRadius(5)
coneSource.SetResolution(31)
coneSource.SetCenter(6, 0, 0)
coneSource.SetDirection(-1, 0, 0)
#---------------------------------------------------------
picker = vtk.vtkVolumePicker()
picker.SetTolerance(1.0e-6)
picker.SetVolumeOpacityIsovalue(0.01)
# This should usually be left alone, but is used here to increase coverage
picker.UseVolumeGradientOpacityOn()
# A function to point an actor along a vector
def PointCone(actor, n):
if n[0] < 0.0:
actor.RotateWXYZ(180, 0, 1, 0)
actor.RotateWXYZ(180, (n[0] - 1.0) * 0.5, n[1] * 0.5,
n[2] * 0.5)
else:
actor.RotateWXYZ(180, (n[0] + 1.0) * 0.5, n[1] * 0.5,
n[2] * 0.5)
# Pick the actor
picker.Pick(192, 103, 0, ren)
#print picker
p = picker.GetPickPosition()
n = picker.GetPickNormal()
coneActor1 = vtk.vtkActor()
coneActor1.PickableOff()
coneMapper1 = vtk.vtkDataSetMapper()
coneMapper1.SetInputConnection(coneSource.GetOutputPort())
coneActor1.SetMapper(coneMapper1)
coneActor1.GetProperty().SetColor(1, 0, 0)
coneActor1.SetPosition(p)
PointCone(coneActor1, n)
ren.AddViewProp(coneActor1)
# Pick the volume
picker.Pick(90, 180, 0, ren)
p = picker.GetPickPosition()
n = picker.GetPickNormal()
coneActor2 = vtk.vtkActor()
coneActor2.PickableOff()
coneMapper2 = vtk.vtkDataSetMapper()
coneMapper2.SetInputConnection(coneSource.GetOutputPort())
coneActor2.SetMapper(coneMapper2)
coneActor2.GetProperty().SetColor(1, 0, 0)
coneActor2.SetPosition(p)
PointCone(coneActor2, n)
ren.AddViewProp(coneActor2)
# Pick the image
picker.Pick(200, 200, 0, ren)
p = picker.GetPickPosition()
n = picker.GetPickNormal()
coneActor3 = vtk.vtkActor()
coneActor3.PickableOff()
coneMapper3 = vtk.vtkDataSetMapper()
coneMapper3.SetInputConnection(coneSource.GetOutputPort())
coneActor3.SetMapper(coneMapper3)
coneActor3.GetProperty().SetColor(1, 0, 0)
coneActor3.SetPosition(p)
PointCone(coneActor3, n)
ren.AddViewProp(coneActor3)
# Pick a clipping plane
picker.PickClippingPlanesOn()
picker.Pick(145, 160, 0, ren)
p = picker.GetPickPosition()
n = picker.GetPickNormal()
coneActor4 = vtk.vtkActor()
coneActor4.PickableOff()
coneMapper4 = vtk.vtkDataSetMapper()
coneMapper4.SetInputConnection(coneSource.GetOutputPort())
coneActor4.SetMapper(coneMapper4)
coneActor4.GetProperty().SetColor(1, 0, 0)
coneActor4.SetPosition(p)
PointCone(coneActor4, n)
ren.AddViewProp(coneActor4)
ren.ResetCameraClippingRange()
# render and interact with data
renWin.Render()
img_file = "VolumePicker.png"
vtk.test.Testing.compareImage(
iRen.GetRenderWindow(),
vtk.test.Testing.getAbsImagePath(img_file),
threshold=25)
vtk.test.Testing.interact()
def line(lines, scalar, lut=None, opacity=1, linewidth=1):
""" Create a line actor for one or more lines.
Parameters
----------
lines : list
a list of array representing a line as 3d points (N, 3)
scalar : a float
0 <= scalar <= 1 to associate a color to the bloc of lines.
opacity : float (default = 1)
the transparency of the bloc of lines: 0 <= transparency <= 1.
linewidth : float (default = 1)
the line thickness.
Returns
----------
actor: vtkActor
the bloc of lines actor.
"""
# Consteruct le lookup table if necessary
if lut is None:
lut = vtk.vtkLookupTable()
lut.SetHueRange(0.667, 0.0)
lut.Build()
# If one line is passed as a numpy array, create virtually a list around
# this structure
if not isinstance(lines, types.ListType):
lines = [lines]
# Create vtk structures
vtk_points = vtk.vtkPoints()
vtk_line = vtk.vtkCellArray()
vtk_scalars = vtk.vtkFloatArray()
# Go through all lines for the rendering
point_id = 0
for line in lines:
# Get the line size
nb_of_points, line_dim = line.shape
# Associate one scalar to each point of the line for color rendering
scalars = [scalar] * nb_of_points
# Fill the vtk structure for the curretn line
for point_position in range(nb_of_points - 1):
# Get the segment [p0, p1]
p0 = line[point_position]
p1 = line[point_position + 1]
# Set line points
vtk_points.InsertNextPoint(p0)
vtk_points.InsertNextPoint(p1)
# Set color property
vtk_scalars.SetNumberOfComponents(1)
vtk_scalars.InsertNextTuple1(scalars[point_position])
vtk_scalars.InsertNextTuple1(scalars[point_position])
# Set line segment
vtk_line.InsertNextCell(2)
vtk_line.InsertCellPoint(point_id)
vtk_line.InsertCellPoint(point_id + 1)
point_id += 2
# Create the line polydata
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
polydata.SetLines(vtk_line)
polydata.GetPointData().SetScalars(vtk_scalars)
# Create the line mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(polydata)
mapper.SetLookupTable(lut)
mapper.SetColorModeToMapScalars()
mapper.SetScalarRange(0.0, 1.0)
mapper.SetScalarModeToUsePointData()
# Create the line actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetOpacity(opacity)
actor.GetProperty().SetLineWidth(linewidth)
return actor
def draw_scene(int_filename, color_mode=0, screen_name=None):
###############################################################################
# read polydata file
#
offscreen = False
draw_axes = False
segs = []
segs_mapper = []
segs_actor = []
transforms = []
transforms_filter = []
seg_fileformat = '/mnt/data1/bah2015/seg2/seg%05d.vtk'
# seg_fileformat = '/media/nebula/data/bah/vtk/seg%05d.vtk'
# int_filename = '../matching_area/result.txt'
int_data = read_intensity_data(int_filename)
int_sum = sum(int_data.values())
int_average = int_sum / 39
int_data_sorted = {}
transform = vtk.vtkTransform()
transform.RotateWXYZ(90, 0, 1, 0)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetTransform(transform)
for i in range(1, 39):
segs.append(vtk.vtkPolyDataReader())
segs[-1].SetFileName(seg_fileformat % i)
transforms.append(vtk.vtkTransform())
# transforms[-1].RotateWXYZ(90., 0, 1, 0)
transforms_filter.append(vtk.vtkTransformPolyDataFilter())
transforms_filter[-1].SetTransform(transforms[-1])
transforms_filter[-1].SetInputConnection(segs[-1].GetOutputPort())
transforms_filter[-1].Update()
segs_mapper.append(vtk.vtkPolyDataMapper())
# segs_mapper[-1].SetInputConnection(segs[-1].GetOutputPort())
segs_mapper[-1].SetInputConnection(transforms_filter[-1].GetOutputPort())
segs_actor.append(vtk.vtkActor())
segs_actor[-1].SetMapper(segs_mapper[-1])
segs_actor[-1].GetProperty().SetOpacity(0.1)
# segs_actor[-1].GetProperty().SetColor(color[0], color[1], color[2])
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(64)
lut.SetHueRange(0.66667, 0.0)
lut.SetSaturationRange(1, 1)
lut.SetValueRange(1, 1)
lut.Build()
scalar_bar = vtk.vtkScalarBarActor()
scalar_bar.SetLookupTable(lut)
scalar_bar.SetNumberOfLabels(4)
i = 0
for k, v in sorted(int_data.items(), key=lambda x: x[1], reverse=True):
if i < 6:
segs_actor[k - 1].GetProperty().SetOpacity(0.7)
rgb = [0.0, 0.0, 0.0]
val = float(v - int_average) / (max(int_data.values()) - int_average)
lut.GetColor(val, rgb)
segs_actor[k - 1].GetProperty().SetColor(rgb)
print(' Rank %d : %s (%d) = %d (%f)' % (i + 1, LABEL_NAMES[k - 1], k, v, val))
# print color
i += 1
# int_data_sorted[k] = v
# print 'Lank %5d : %d (%d)' % (i, k, v)
###############################################################################
# draw axis
#
if draw_axes:
axesActor = vtk.vtkAxesActor()
###############################################################################
# prepare rendering
#
ren = vtk.vtkRenderer()
ren.SetBackground(0.0, 0.0, 0.0)
if draw_axes:
ren.AddActor(axesActor)
for seg in segs_actor:
ren.AddActor(seg)
ren.AddActor(scalar_bar)
renWin = vtk.vtkRenderWindow()
if offscreen:
renWin.SetOffScreenRendering(True)
renWin.AddRenderer(ren)
renWin.SetWindowName('Mouse Brain Viewer 2 + (%s)' % screen_name)
renWin.SetSize(1600, 1600)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.Initialize()
renWin.Render()
get_screenshot(renWin, screen_name + '_1.png')
for trans in transforms:
trans.RotateWXYZ(90., 0, 1, 0)
for trans_filter in transforms_filter:
trans_filter.Update()
renWin.Render()
get_screenshot(renWin, screen_name + '_2.png')
for trans in transforms:
trans.RotateWXYZ(90., 0, 1, 0)
for trans_filter in transforms_filter:
trans_filter.Update()
renWin.Render()
get_screenshot(renWin, screen_name + '_3.png')
def AddASDNeigh_actors(self, ren, renWin, mode, viz_type, iren):
# Reading the data for the nieghbours
ASD_data = ASDVTKReading.ASDReading()
ASD_data.ReadingWrapper(mode, viz_type)
# Set the maximum number of entried in the slider to be equal to the number of atoms
########################################################################
# Data structures for the atoms in the neighbour map
########################################################################
AtomGrid = vtk.vtkPolyData()
AtomGrid.SetPoints(ASD_data.coord)
ASDNeighActors.SLMax = AtomGrid.GetNumberOfPoints()
# Atom sphere
Atom = vtk.vtkSphereSource()
Atom.SetRadius(0.50)
Atom.SetThetaResolution(10)
Atom.SetPhiResolution(10)
# Atom glyph
Atoms = vtk.vtkGlyph3DMapper()
Atoms.SetInputData(AtomGrid)
Atoms.SetSourceConnection(Atom.GetOutputPort())
Atoms.SetScaleFactor(0.5)
Atoms.ClampingOn()
Atoms.SetScaleModeToNoDataScaling()
Atoms.SetColorModeToMapScalars()
Atoms.Update()
# Atoms actors
ASDNeighActors.AtomsActor = vtk.vtkLODActor()
ASDNeighActors.AtomsActor.SetMapper(Atoms)
ASDNeighActors.AtomsActor.GetProperty().SetOpacity(0.9)
ASDNeighActors.AtomsActor.GetProperty().SetColor(0.5, 0.5, 0.5)
########################################################################
# Data structures for the neighbours in the neighbour mapper
########################################################################
#Grid for neighbours
ASDNeighActors.NeighGrid = vtk.vtkPolyData()
ASDNeighActors.NeighGrid.SetPoints(ASD_data.neighs)
ASDNeighActors.NeighGrid.GetPointData().SetScalars(ASD_data.nTypes)
ASDNeighActors.NumNeigh = ASDNeighActors.NeighGrid.GetNumberOfPoints()
#Neighbour glyphs
ASDNeighActors.Neigh = vtk.vtkSphereSource()
ASDNeighActors.Neigh.SetRadius(0.50)
ASDNeighActors.Neigh.SetThetaResolution(20)
ASDNeighActors.Neigh.SetPhiResolution(20)
# Set up Neighbour glyphs
ASDNeighActors.Neighs = vtk.vtkGlyph3DMapper()
ASDNeighActors.Neighs.SetInputData(ASDNeighActors.NeighGrid)
ASDNeighActors.Neighs.SetSourceConnection(
ASDNeighActors.Neigh.GetOutputPort())
ASDNeighActors.Neighs.SetScaleFactor(1.25)
ASDNeighActors.Neighs.SetColorModeToMapScalars()
ASDNeighActors.Neighs.SetScaleModeToNoDataScaling()
ASDNeighActors.Neighs.SetScalarRange(
ASDNeighActors.NeighGrid.GetPointData().GetScalars().GetRange())
# Color lookup table for neighbours
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(2)
lut.SetTableValue(0, 0.0, 1.0, 0.0, 0.5)
lut.SetTableValue(1, 0.0, 0.0, 1.0, 0.5)
lut.SetTableRange(ASD_data.nTypes.GetRange())
lut.Build()
# Fill up Lookup Table with appropiate colors
ASDNeighActors.Neighs.SetLookupTable(lut)
ASDNeighActors.Neighs.Update()
# Neighbour actors
ASDNeighActors.NeighActor = vtk.vtkLODActor()
ASDNeighActors.NeighActor.SetMapper(ASDNeighActors.Neighs)
ASDNeighActors.NeighActor.GetProperty().SetSpecularColor(0.4, 0.8, 0.4)
ASDNeighActors.NeighActor.GetProperty().SetSpecular(0.3)
ASDNeighActors.NeighActor.GetProperty().SetSpecularPower(60)
ASDNeighActors.NeighActor.GetProperty().SetAmbient(0.2)
ASDNeighActors.NeighActor.GetProperty().SetDiffuse(0.8)
# Setting up information needed for the camera
self.xmin, self.xmax = self.AtomsActor.GetXRange()
self.ymin, self.ymax = self.AtomsActor.GetYRange()
self.zmin, self.zmax = self.AtomsActor.GetZRange()
self.xmid = (self.xmin + self.xmax) / 2
self.ymid = (self.ymin + self.ymax) / 2
self.zmid = (self.zmin + self.zmax) / 2
self.height = max(self.xmax, self.ymax, self.zmax) * 1.75
# Defining the camera directions
ren.GetActiveCamera().Azimuth(0)
ren.GetActiveCamera().Elevation(0)
ren.GetActiveCamera().SetFocalPoint(self.xmid, self.ymid, self.zmid)
ren.GetActiveCamera().SetPosition(self.xmid, self.ymid, self.height)
# Adding the actors for the neighbour mapping
ren.AddActor(ASDNeighActors.NeighActor)
ren.AddActor(ASDNeighActors.AtomsActor)
iren.Start()
renWin.Render()
def __init__(self, reader, orientation, min_value=0, max_value=2000):
#xmin xmax ymin ymax zmin zmax
self.bounds = reader.GetExecutive().GetWholeExtent(
reader.GetOutputInformation(0))
#x y z
self.spacing = (xSpacing, ySpacing,
zSpacing) = reader.GetOutput().GetSpacing()
self.origin = reader.GetOutput().GetOrigin()
xMin, xMax, yMin, yMax, zMin, zMax = self.bounds
xspacing, ySpacing, zSpacing = self.spacing
x0, y0, z0 = self.origin
self.center = [
x0 + xSpacing * 0.5 * (xMin + xMax),
y0 + ySpacing * 0.5 * (yMin + yMax),
z0 + zSpacing * 0.5 * (zMin + zMax)
]
# Matrices for axial, coronal, sagittal, oblique view orientations
self.axial = vtk.vtkMatrix4x4()
self.axial.DeepCopy((1, 0, 0, self.center[0], 0, 1, 0, self.center[1],
0, 0, 1, self.center[2], 0, 0, 0, 1))
self.coronal = vtk.vtkMatrix4x4()
self.coronal.DeepCopy(
(1, 0, 0, self.center[0], 0, 0, 1, self.center[1], 0, -1, 0,
self.center[2], 0, 0, 0, 1))
self.sagittal = vtk.vtkMatrix4x4()
self.sagittal.DeepCopy(
(0, 0, -1, self.center[0], 1, 0, 0, self.center[1], 0, -1, 0,
self.center[2], 0, 0, 0, 1))
# Extract a slice in the desired orientation
self.reslice = vtk.vtkImageReslice()
self.reslice.SetInputConnection(reader.GetOutputPort())
self.reslice.SetOutputDimensionality(2)
if orientation == 'sagittal':
self.reslice.SetResliceAxes(self.sagittal)
elif orientation == 'coronal':
self.reslice.SetResliceAxes(self.coronal)
else:
self.reslice.SetResliceAxes(self.axial)
self.reslice.SetInterpolationModeToLinear()
# Create a greyscale lookup table
self.table = vtk.vtkLookupTable()
self.table.SetRange(min_value, max_value) # image intensity range
self.table.SetValueRange(0.0, 1.0) # from black to white
self.table.SetSaturationRange(0.0, 0.0) # no color saturation
self.table.SetRampToLinear()
self.table.Build()
# Map the image through the lookup self.table
self.color = vtk.vtkImageMapToColors()
self.color.SetLookupTable(self.table)
self.color.SetInputConnection(self.reslice.GetOutputPort())
# Display the image
self.actor = vtk.vtkImageActor()
self.actor.GetMapper().SetInputConnection(self.color.GetOutputPort())
self.slicing = False
geometry.SetInputData(reflection)
print('With Geometry Filter (HTG to NS)')
# Shrink Filter
if True:
print('With Shrink Filter (NS)')
# En 3D, le shrink ne doit pas se faire sur la geometrie car elle ne represente que la peau
shrink = vtk.vtkShrinkFilter()
shrink.SetInputConnection(geometry.GetOutputPort())
shrink.SetShrinkFactor(.8)
else:
print('No Shrink Filter (NS)')
shrink = geometry
# LookupTable
lut = vtk.vtkLookupTable()
lut.SetHueRange(0.66, 0)
lut.UsingLogScale()
lut.Build()
# Mappers
mapper = vtk.vtkDataSetMapper()
mapper.SetInputConnection(geometry.GetOutputPort())
mapper.SetLookupTable(lut)
mapper.SetColorModeToMapScalars()
mapper.SetScalarModeToUseCellFieldData()
mapper.SelectColorArray('scalar')
dataRange = [1, 53] # Forced for compare with 3DMask
mapper.SetScalarRange(dataRange[0], dataRange[1])
def main(args):
# Demonstrate generation of extruded objects from a segmentation map, where
# the extrusion is trimmed by a terrain surface.
parser = argparse.ArgumentParser(
description=
'Generate extruded buildings given a segmentation map, DSM and DTM')
parser.add_argument("segmentation", help="Image with labeled buildings")
parser.add_argument("dsm", help="Digital surface model (DSM)")
parser.add_argument("dtm", help="Digital terain model (DTM)")
parser.add_argument("destination",
help="Extruded buildings polygonal file (.vtp)")
parser.add_argument(
'-l',
"--label",
type=int,
nargs="*",
help="Label value(s) used for buildings outlines."
"If not specified, [6, 17] (buildings, roads) are used.")
parser.add_argument("--no_decimation",
action="store_true",
help="Do not decimate the contours")
parser.add_argument("--no_render",
action="store_true",
help="Do not render")
parser.add_argument("--debug",
action="store_true",
help="Save intermediate results")
args = parser.parse_args(args)
# Read the terrain data
print("Reading and warping the DTM ...")
dtmReader = vtk.vtkGDALRasterReader()
dtmReader.SetFileName(args.dtm)
dtmC2p = vtk.vtkCellDataToPointData()
dtmC2p.SetInputConnection(dtmReader.GetOutputPort())
dtmC2p.Update()
# Range of terrain data
lo = dtmC2p.GetOutput().GetScalarRange()[0]
hi = dtmC2p.GetOutput().GetScalarRange()[1]
# Convert the terrain into a polydata.
surface = vtk.vtkImageDataGeometryFilter()
surface.SetInputConnection(dtmC2p.GetOutputPort())
# Make sure the polygons are planar, so need to use triangles.
tris = vtk.vtkTriangleFilter()
tris.SetInputConnection(surface.GetOutputPort())
# Warp the surface by scalar values
warp = vtk.vtkWarpScalar()
warp.SetInputConnection(tris.GetOutputPort())
warp.SetScaleFactor(1)
warp.UseNormalOn()
warp.SetNormal(0, 0, 1)
warp.Update()
# Read the segmentation of buildings. Original data in GDAL is cell data.
# Point data is interpolated.
print("Reading the segmentation ...")
segmentationReader = vtk.vtkGDALRasterReader()
segmentationReader.SetFileName(args.segmentation)
segmentationC2p = vtk.vtkCellDataToPointData()
segmentationC2p.SetInputConnection(segmentationReader.GetOutputPort())
segmentationC2p.PassCellDataOn()
segmentationC2p.Update()
segmentation = segmentationC2p.GetOutput()
if (args.debug):
segmentationWriter = vtk.vtkXMLImageDataWriter()
segmentationWriter.SetFileName("segmentation.vti")
segmentationWriter.SetInputConnection(segmentationC2p.GetOutputPort())
segmentationWriter.Update()
segmentation = segmentationC2p.GetOutput()
sb = segmentation.GetBounds()
print("segmentation bounds: \t{}".format(sb))
# Extract polygons
# as an alternative, could use vtk.vtkMarchingSquares()
contours = vtk.vtkDiscreteFlyingEdges2D()
contours.SetInputConnection(segmentationC2p.GetOutputPort())
# default labels
# 2 -- no building
# 6 -- building
# 17 -- road or highway
# 65 -- don't score
labels = [6, 17]
if (args.label):
labels = args.label
if (args.debug):
scalarName = segmentation.GetCellData().GetScalars().GetName()
segmentationNp = dsa.WrapDataObject(segmentation)
scalars = segmentationNp.CellData[scalarName]
allLabels = numpy.unique(scalars)
print("Contouring on labels: {} of {}".format(labels, allLabels))
else:
print("Contouring on labels: {}".format(labels))
contours.SetNumberOfContours(len(labels))
for i in range(len(labels)):
contours.SetValue(i, labels[i])
if (args.debug):
contoursWriter = vtk.vtkXMLPolyDataWriter()
contoursWriter.SetFileName("contours.vtp")
contoursWriter.SetInputConnection(contours.GetOutputPort())
contoursWriter.Update()
contoursData = contours.GetOutput()
cb = contoursData.GetBounds()
print("contours bounds: \t{}".format(cb))
if (not args.no_decimation):
print("Decimating the contours ...")
# combine lines into a polyline
stripperContours = vtk.vtkStripper()
stripperContours.SetInputConnection(contours.GetOutputPort())
stripperContours.SetMaximumLength(3000)
if (args.debug):
stripperWriter = vtk.vtkXMLPolyDataWriter()
stripperWriter.SetFileName("stripper.vtp")
stripperWriter.SetInputConnection(stripperContours.GetOutputPort())
stripperWriter.Update()
# decimate polylines
decimateContours = vtk.vtkDecimatePolylineFilter()
decimateContours.SetMaximumError(0.01)
decimateContours.SetInputConnection(stripperContours.GetOutputPort())
if (args.debug):
decimateWriter = vtk.vtkXMLPolyDataWriter()
decimateWriter.SetFileName("decimate.vtp")
decimateWriter.SetInputConnection(decimateContours.GetOutputPort())
decimateWriter.Update()
contours = decimateContours
# Create loops
print("Creating the loops ...")
loops = vtk.vtkContourLoopExtraction()
loops.SetInputConnection(contours.GetOutputPort())
if (args.debug):
loopsWriter = vtk.vtkXMLPolyDataWriter()
loopsWriter.SetFileName("loops.vtp")
loopsWriter.SetInputConnection(loops.GetOutputPort())
loopsWriter.Update()
# Read the DSM
print("Reading the DSM ...")
dsmReader = vtk.vtkGDALRasterReader()
dsmReader.SetFileName(args.dsm)
dsmC2p = vtk.vtkCellDataToPointData()
dsmC2p.SetInputConnection(dsmReader.GetOutputPort())
dsmC2p.Update()
print("Extruding the buildings ...")
fit = vtk.vtkFitToHeightMapFilter()
fit.SetInputConnection(loops.GetOutputPort())
fit.SetHeightMapConnection(dsmC2p.GetOutputPort())
fit.UseHeightMapOffsetOn()
fit.SetFittingStrategyToPointMaximumHeight()
if (args.debug):
fitWriter = vtk.vtkXMLPolyDataWriter()
fitWriter.SetFileName("fit.vtp")
fitWriter.SetInputConnection(fit.GetOutputPort())
fitWriter.Update()
# Extrude polygon down to surface
extrude = vtk.vtkTrimmedExtrusionFilter()
extrude.SetInputConnection(fit.GetOutputPort())
extrude.SetTrimSurfaceConnection(warp.GetOutputPort())
extrude.SetExtrusionDirection(0, 0, 1)
extrude.CappingOn()
extrudeWriter = vtk.vtkXMLPolyDataWriter()
extrudeWriter.SetFileName(args.destination)
extrudeWriter.SetInputConnection(extrude.GetOutputPort())
extrudeWriter.Update()
if (not args.no_render):
# Create the RenderWindow, Renderer
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Create pipeline. Load terrain data.
lut = vtk.vtkLookupTable()
lut.SetHueRange(0.6, 0)
lut.SetSaturationRange(1.0, 0)
lut.SetValueRange(0.5, 1.0)
# Show the terrain
dtmMapper = vtk.vtkPolyDataMapper()
dtmMapper.SetInputConnection(warp.GetOutputPort())
dtmMapper.SetScalarRange(lo, hi)
dtmMapper.SetLookupTable(lut)
dtmActor = vtk.vtkActor()
dtmActor.SetMapper(dtmMapper)
# show the buildings
trisExtrude = vtk.vtkTriangleFilter()
trisExtrude.SetInputConnection(extrude.GetOutputPort())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(trisExtrude.GetOutputPort())
mapper.ScalarVisibilityOff()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# Render it
ren.AddActor(dtmActor)
ren.AddActor(actor)
ren.GetActiveCamera().Elevation(-60)
ren.ResetCamera()
renWin.Render()
iren.Start()
def createPipeline(srcLats, srcLons, dstLats, dstLons, nitersData, radius=1.0):
# create the src grid pipeline
srcN0, srcN1 = srcLats.shape
srcNumPts = srcN0 * srcN1
srcSg = vtk.vtkStructuredGrid()
srcPt = vtk.vtkPoints()
srcPt.SetNumberOfPoints(srcNumPts)
k = 0
for i1 in range(srcN1):
for i0 in range(srcN0):
r = radius * 1.05
x = r * math.cos(srcLats[i0, i1] * math.pi / 180.) * math.cos(
srcLons[i0, i1] * math.pi / 180.)
y = r * math.cos(srcLats[i0, i1] * math.pi / 180.) * math.sin(
srcLons[i0, i1] * math.pi / 180.)
z = r * math.sin(srcLats[i0, i1] * math.pi / 180.)
srcPt.SetPoint(k, x, y, z)
k += 1
srcSg.SetDimensions(1, srcN0, srcN1)
srcSg.SetPoints(srcPt)
srcEd = vtk.vtkExtractEdges()
srcEt = vtk.vtkTubeFilter()
srcEm = vtk.vtkPolyDataMapper()
srcEa = vtk.vtkActor()
srcEt.SetRadius(0.005)
srcEd.SetInputData(srcSg)
srcEt.SetInputConnection(srcEd.GetOutputPort())
srcEm.SetInputConnection(srcEt.GetOutputPort())
srcEa.SetMapper(srcEm)
srcEa.GetProperty().SetColor(0., 1., 0.)
#srcEa.GetProperty().SetOpacity(0.5)
dstN0, dstN1 = dstLats.shape
numPoints = dstN0 * dstN1
sg = vtk.vtkStructuredGrid()
pt = vtk.vtkPoints()
pt.SetNumberOfPoints(numPoints)
ar = vtk.vtkDoubleArray()
numPts = nitersData.shape[0] * nitersData.shape[1]
ar.SetNumberOfComponents(1)
ar.SetNumberOfTuples(numPts)
#ar.SetVoidArray(nitersData, 1, 1)
k = 0
for i1 in range(dstN1):
for i0 in range(dstN0):
elev = 0.0 #0.10 * math.log10(nitersData[i0, i1])
r = radius * (1. + elev)
x = r * math.cos(dstLats[i0, i1] * math.pi / 180.) * math.cos(
dstLons[i0, i1] * math.pi / 180.)
y = r * math.cos(dstLats[i0, i1] * math.pi / 180.) * math.sin(
dstLons[i0, i1] * math.pi / 180.)
z = r * math.sin(dstLats[i0, i1] * math.pi / 180.)
pt.SetPoint(k, x, y, z)
ar.SetTuple(k, (float(nitersData[i0, i1]), ))
k += 1
sg = vtk.vtkStructuredGrid()
sg.SetDimensions(1, dstN0, dstN1)
sg.SetPoints(pt)
sg.GetPointData().SetScalars(ar)
lu = vtk.vtkLookupTable()
lu.SetScaleToLog10()
#lu.SetTableRange(1, 10)
lu.SetNumberOfColors(256)
lu.SetHueRange(0.666, 0.)
lu.Build()
# add a scalar bar
sb = vtk.vtkScalarBarActor()
sb.SetLookupTable(lu)
sb.SetTitle("Number of iters")
sb.SetNumberOfLabels(4)
# show the dst grid
dstEd = vtk.vtkExtractEdges()
dstEt = vtk.vtkTubeFilter()
dstEm = vtk.vtkPolyDataMapper()
dstEa = vtk.vtkActor()
dstEt.SetRadius(0.005)
dstEd.SetInputData(sg)
dstEt.SetInputConnection(dstEd.GetOutputPort())
dstEm.SetInputConnection(dstEt.GetOutputPort())
dstEa.SetMapper(dstEm)
dstEa.GetProperty().SetColor(1., 0., 0.)
#dstEa.GetProperty().SetOpacity(0.5)
# show number of iterations as a color plot
mp = vtk.vtkDataSetMapper()
mp.SetInputData(sg)
mp.SetLookupTable(lu)
mp.SetScalarRange(1, args.nitermax)
ac = vtk.vtkActor()
ac.SetMapper(mp)
return {
'actors': [
ac,
sb,
],
'stuff': (sg, pt, mp, ar, lu, srcSg, srcPt, srcEd, srcEt, srcEm, dstEd,
dstEt, dstEm)
}
def extract_branches(self):
'''Extract branches from the centerlines based on CenterlinesIds.
'''
print("[centerlines] ========== extract_branches ==========")
data_array = self.geometry.GetPointData().GetArray(self.cids_array_name)
num_centerlines = self.get_centerline_info()
min_id = 0
max_id = num_centerlines-1
cid_list = list(range(min_id,max_id+1))
print("[extract_branches] Centerline IDs: {0:s}".format(str(cid_list)))
self.cid_list = cid_list
# Create a color lookup table for branch geometry.
self.lut = vtk.vtkLookupTable()
self.lut.SetTableRange(min_id, max_id+1)
self.lut.SetHueRange(0, 1)
self.lut.SetSaturationRange(1, 1)
self.lut.SetValueRange(1, 1)
self.lut.Build()
max_radius_data = self.geometry.GetPointData().GetArray(self.max_radius_array_name)
num_lines = self.geometry.GetNumberOfLines()
num_points = self.geometry.GetNumberOfPoints()
points = self.geometry.GetPoints()
print("[centerlines] Number of centerline lines: {0:d}".format(num_lines))
print("[centerlines] Number of centerline points: {0:d}".format(num_points))
# Find the longest branch.
max_num_lines = 0
longest_cid = None
for cid in range(min_id,max_id+1):
branch_geom = self.extract_branch_geom(cid)
if branch_geom.GetNumberOfLines() > max_num_lines:
max_num_lines = branch_geom.GetNumberOfLines()
longest_cid = cid
print("\n[centerlines] Longest branch cid: {0:d} Number of lines: {1:d}".format(longest_cid, max_num_lines))
self.longest_cid = longest_cid
# Create cell_id -> centerline id map.
cell_cids = defaultdict(list)
for cid in cid_list:
#print("\n---------- cid {0:d} ----------".format(cid))
for i in range(num_lines):
cell = self.geometry.GetCell(i)
cell_pids = cell.GetPointIds()
num_ids = cell_pids.GetNumberOfIds()
pid1 = cell_pids.GetId(0)
pid2 = cell_pids.GetId(1)
value1 = int(data_array.GetComponent(pid1, cid))
value2 = int(data_array.GetComponent(pid2, cid))
if (value1 == 1) or (value2 == 1):
cell_cids[i].append(cid)
#_for j in range(num_ids)
#_for i in range(num_lines)
#_for cid in range(min_id,max_id+1)
# Determine branch cells.
branch_cells = defaultdict(list)
for cid in cid_list:
for i in range(num_lines):
cids = cell_cids[i]
if longest_cid in cids:
if i not in branch_cells[longest_cid]:
branch_cells[longest_cid].append(i)
else:
if (len(cids) == 1) and (cids[0] == cid):
branch_cells[cid].append(i)
if cid in cell_cids[i]:
cell_cids[i].remove(cid)
#_for j in range(num_ids)
#_for cid in cid_list
# Create branch geomerty.
self.branches = []
end_point_ids = self.ends_node_ids
for cid in cid_list:
self.branches.append( self.create_branch(cid, branch_cells, end_point_ids) )
def vtk_scalar_actor(filename):
import vtk
colobar_agros2d = [[ 0.125500, 0.162200, 0.960000 ],
[ 0.132175, 0.167787, 0.954839 ],
[ 0.138849, 0.173373, 0.949678 ],
[ 0.145524, 0.178960, 0.944518 ],
[ 0.152198, 0.184547, 0.939357 ],
[ 0.158873, 0.190133, 0.934196 ],
[ 0.165547, 0.195720, 0.929035 ],
[ 0.172222, 0.201307, 0.923875 ],
[ 0.178896, 0.206893, 0.918714 ],
[ 0.185571, 0.212480, 0.913553 ],
[ 0.192245, 0.218067, 0.908392 ],
[ 0.198920, 0.223653, 0.903231 ],
[ 0.205594, 0.229240, 0.898071 ],
[ 0.212269, 0.234827, 0.892910 ],
[ 0.218943, 0.240413, 0.887749 ],
[ 0.225618, 0.246000, 0.882588 ],
[ 0.232292, 0.251587, 0.877427 ],
[ 0.238967, 0.257173, 0.872267 ],
[ 0.245641, 0.262760, 0.867106 ],
[ 0.252316, 0.268347, 0.861945 ],
[ 0.258990, 0.273933, 0.856784 ],
[ 0.265665, 0.279520, 0.851624 ],
[ 0.272339, 0.285107, 0.846463 ],
[ 0.279014, 0.290693, 0.841302 ],
[ 0.285688, 0.296280, 0.836141 ],
[ 0.292363, 0.301867, 0.830980 ],
[ 0.299037, 0.307453, 0.825820 ],
[ 0.305712, 0.313040, 0.820659 ],
[ 0.312386, 0.318627, 0.815498 ],
[ 0.319061, 0.324213, 0.810337 ],
[ 0.325735, 0.329800, 0.805176 ],
[ 0.332410, 0.335387, 0.800016 ],
[ 0.339084, 0.340973, 0.794855 ],
[ 0.345759, 0.346560, 0.789694 ],
[ 0.352433, 0.352147, 0.784533 ],
[ 0.359108, 0.357733, 0.779373 ],
[ 0.365782, 0.363320, 0.774212 ],
[ 0.372457, 0.368907, 0.769051 ],
[ 0.379131, 0.374493, 0.763890 ],
[ 0.385806, 0.380080, 0.758729 ],
[ 0.392480, 0.385667, 0.753569 ],
[ 0.399155, 0.391253, 0.748408 ],
[ 0.405829, 0.396840, 0.743247 ],
[ 0.412504, 0.402427, 0.738086 ],
[ 0.419178, 0.408013, 0.732925 ],
[ 0.425853, 0.413600, 0.727765 ],
[ 0.432527, 0.419187, 0.722604 ],
[ 0.439202, 0.424773, 0.717443 ],
[ 0.445876, 0.430360, 0.712282 ],
[ 0.452551, 0.435947, 0.707122 ],
[ 0.459225, 0.441533, 0.701961 ],
[ 0.465900, 0.447120, 0.696800 ],
[ 0.472575, 0.452707, 0.691639 ],
[ 0.479249, 0.458293, 0.686478 ],
[ 0.485924, 0.463880, 0.681318 ],
[ 0.492598, 0.469467, 0.676157 ],
[ 0.499273, 0.475053, 0.670996 ],
[ 0.505947, 0.480640, 0.665835 ],
[ 0.512622, 0.486227, 0.660675 ],
[ 0.519296, 0.491813, 0.655514 ],
[ 0.525971, 0.497400, 0.650353 ],
[ 0.532645, 0.502987, 0.645192 ],
[ 0.539320, 0.508573, 0.640031 ],
[ 0.545994, 0.514160, 0.634871 ],
[ 0.552669, 0.519747, 0.629710 ],
[ 0.559343, 0.525333, 0.624549 ],
[ 0.566018, 0.530920, 0.619388 ],
[ 0.572692, 0.536507, 0.614227 ],
[ 0.579367, 0.542093, 0.609067 ],
[ 0.586041, 0.547680, 0.603906 ],
[ 0.592716, 0.553267, 0.598745 ],
[ 0.599390, 0.558853, 0.593584 ],
[ 0.606065, 0.564440, 0.588424 ],
[ 0.612739, 0.570027, 0.583263 ],
[ 0.619414, 0.575613, 0.578102 ],
[ 0.626088, 0.581200, 0.572941 ],
[ 0.632763, 0.586787, 0.567780 ],
[ 0.639437, 0.592373, 0.562620 ],
[ 0.646112, 0.597960, 0.557459 ],
[ 0.652786, 0.603547, 0.552298 ],
[ 0.659461, 0.609133, 0.547137 ],
[ 0.666135, 0.614720, 0.541976 ],
[ 0.672810, 0.620307, 0.536816 ],
[ 0.679484, 0.625893, 0.531655 ],
[ 0.686159, 0.631480, 0.526494 ],
[ 0.692833, 0.637067, 0.521333 ],
[ 0.699508, 0.642653, 0.516173 ],
[ 0.706182, 0.648240, 0.511012 ],
[ 0.712857, 0.653827, 0.505851 ],
[ 0.719531, 0.659413, 0.500690 ],
[ 0.726206, 0.665000, 0.495529 ],
[ 0.732880, 0.670587, 0.490369 ],
[ 0.739555, 0.676173, 0.485208 ],
[ 0.746229, 0.681760, 0.480047 ],
[ 0.752904, 0.687347, 0.474886 ],
[ 0.759578, 0.692933, 0.469725 ],
[ 0.766253, 0.698520, 0.464565 ],
[ 0.772927, 0.704107, 0.459404 ],
[ 0.779602, 0.709693, 0.454243 ],
[ 0.786276, 0.715280, 0.449082 ],
[ 0.792951, 0.720867, 0.443922 ],
[ 0.799625, 0.726453, 0.438761 ],
[ 0.806300, 0.732040, 0.433600 ],
[ 0.812975, 0.737627, 0.428439 ],
[ 0.819649, 0.743213, 0.423278 ],
[ 0.826324, 0.748800, 0.418118 ],
[ 0.832998, 0.754387, 0.412957 ],
[ 0.839673, 0.759973, 0.407796 ],
[ 0.846347, 0.765560, 0.402635 ],
[ 0.853022, 0.771147, 0.397475 ],
[ 0.859696, 0.776733, 0.392314 ],
[ 0.866371, 0.782320, 0.387153 ],
[ 0.873045, 0.787907, 0.381992 ],
[ 0.879720, 0.793493, 0.376831 ],
[ 0.886394, 0.799080, 0.371671 ],
[ 0.893069, 0.804667, 0.366510 ],
[ 0.899743, 0.810253, 0.361349 ],
[ 0.906418, 0.815840, 0.356188 ],
[ 0.913092, 0.821427, 0.351027 ],
[ 0.919767, 0.827013, 0.345867 ],
[ 0.926441, 0.832600, 0.340706 ],
[ 0.933116, 0.838187, 0.335545 ],
[ 0.939790, 0.843773, 0.330384 ],
[ 0.946465, 0.849360, 0.325224 ],
[ 0.953139, 0.854947, 0.320063 ],
[ 0.959814, 0.860533, 0.314902 ],
[ 0.966488, 0.866120, 0.309741 ],
[ 0.973163, 0.871707, 0.304580 ],
[ 0.976435, 0.871778, 0.301400 ],
[ 0.976306, 0.866334, 0.300200 ],
[ 0.976176, 0.860890, 0.299000 ],
[ 0.976047, 0.855446, 0.297800 ],
[ 0.975918, 0.850002, 0.296600 ],
[ 0.975788, 0.844558, 0.295400 ],
[ 0.975659, 0.839115, 0.294200 ],
[ 0.975529, 0.833671, 0.293000 ],
[ 0.975400, 0.828227, 0.291800 ],
[ 0.975271, 0.822783, 0.290600 ],
[ 0.975141, 0.817339, 0.289400 ],
[ 0.975012, 0.811895, 0.288200 ],
[ 0.974882, 0.806451, 0.287000 ],
[ 0.974753, 0.801007, 0.285800 ],
[ 0.974624, 0.795563, 0.284600 ],
[ 0.974494, 0.790119, 0.283400 ],
[ 0.974365, 0.784675, 0.282200 ],
[ 0.974235, 0.779231, 0.281000 ],
[ 0.974106, 0.773787, 0.279800 ],
[ 0.973976, 0.768344, 0.278600 ],
[ 0.973847, 0.762900, 0.277400 ],
[ 0.973718, 0.757456, 0.276200 ],
[ 0.973588, 0.752012, 0.275000 ],
[ 0.973459, 0.746568, 0.273800 ],
[ 0.973329, 0.741124, 0.272600 ],
[ 0.973200, 0.735680, 0.271400 ],
[ 0.973071, 0.730236, 0.270200 ],
[ 0.972941, 0.724792, 0.269000 ],
[ 0.972812, 0.719348, 0.267800 ],
[ 0.972682, 0.713904, 0.266600 ],
[ 0.972553, 0.708460, 0.265400 ],
[ 0.972424, 0.703016, 0.264200 ],
[ 0.972294, 0.697573, 0.263000 ],
[ 0.972165, 0.692129, 0.261800 ],
[ 0.972035, 0.686685, 0.260600 ],
[ 0.971906, 0.681241, 0.259400 ],
[ 0.971776, 0.675797, 0.258200 ],
[ 0.971647, 0.670353, 0.257000 ],
[ 0.971518, 0.664909, 0.255800 ],
[ 0.971388, 0.659465, 0.254600 ],
[ 0.971259, 0.654021, 0.253400 ],
[ 0.971129, 0.648577, 0.252200 ],
[ 0.971000, 0.643133, 0.251000 ],
[ 0.970871, 0.637689, 0.249800 ],
[ 0.970741, 0.632245, 0.248600 ],
[ 0.970612, 0.626802, 0.247400 ],
[ 0.970482, 0.621358, 0.246200 ],
[ 0.970353, 0.615914, 0.245000 ],
[ 0.970224, 0.610470, 0.243800 ],
[ 0.970094, 0.605026, 0.242600 ],
[ 0.969965, 0.599582, 0.241400 ],
[ 0.969835, 0.594138, 0.240200 ],
[ 0.969706, 0.588694, 0.239000 ],
[ 0.969576, 0.583250, 0.237800 ],
[ 0.969447, 0.577806, 0.236600 ],
[ 0.969318, 0.572362, 0.235400 ],
[ 0.969188, 0.566918, 0.234200 ],
[ 0.969059, 0.561475, 0.233000 ],
[ 0.968929, 0.556031, 0.231800 ],
[ 0.968800, 0.550587, 0.230600 ],
[ 0.968671, 0.545143, 0.229400 ],
[ 0.968541, 0.539699, 0.228200 ],
[ 0.968412, 0.534255, 0.227000 ],
[ 0.968282, 0.528811, 0.225800 ],
[ 0.968153, 0.523367, 0.224600 ],
[ 0.968024, 0.517923, 0.223400 ],
[ 0.967894, 0.512479, 0.222200 ],
[ 0.967765, 0.507035, 0.221000 ],
[ 0.967635, 0.501591, 0.219800 ],
[ 0.967506, 0.496147, 0.218600 ],
[ 0.967376, 0.490704, 0.217400 ],
[ 0.967247, 0.485260, 0.216200 ],
[ 0.967118, 0.479816, 0.215000 ],
[ 0.966988, 0.474372, 0.213800 ],
[ 0.966859, 0.468928, 0.212600 ],
[ 0.966729, 0.463484, 0.211400 ],
[ 0.966600, 0.458040, 0.210200 ],
[ 0.966471, 0.452596, 0.209000 ],
[ 0.966341, 0.447152, 0.207800 ],
[ 0.966212, 0.441708, 0.206600 ],
[ 0.966082, 0.436264, 0.205400 ],
[ 0.965953, 0.430820, 0.204200 ],
[ 0.965824, 0.425376, 0.203000 ],
[ 0.965694, 0.419933, 0.201800 ],
[ 0.965565, 0.414489, 0.200600 ],
[ 0.965435, 0.409045, 0.199400 ],
[ 0.965306, 0.403601, 0.198200 ],
[ 0.965176, 0.398157, 0.197000 ],
[ 0.965047, 0.392713, 0.195800 ],
[ 0.964918, 0.387269, 0.194600 ],
[ 0.964788, 0.381825, 0.193400 ],
[ 0.964659, 0.376381, 0.192200 ],
[ 0.964529, 0.370937, 0.191000 ],
[ 0.964400, 0.365493, 0.189800 ],
[ 0.964271, 0.360049, 0.188600 ],
[ 0.964141, 0.354605, 0.187400 ],
[ 0.964012, 0.349162, 0.186200 ],
[ 0.963882, 0.343718, 0.185000 ],
[ 0.963753, 0.338274, 0.183800 ],
[ 0.963624, 0.332830, 0.182600 ],
[ 0.963494, 0.327386, 0.181400 ],
[ 0.963365, 0.321942, 0.180200 ],
[ 0.963235, 0.316498, 0.179000 ],
[ 0.963106, 0.311054, 0.177800 ],
[ 0.962976, 0.305610, 0.176600 ],
[ 0.962847, 0.300166, 0.175400 ],
[ 0.962718, 0.294722, 0.174200 ],
[ 0.962588, 0.289278, 0.173000 ],
[ 0.962459, 0.283835, 0.171800 ],
[ 0.962329, 0.278391, 0.170600 ],
[ 0.962200, 0.272947, 0.169400 ],
[ 0.962071, 0.267503, 0.168200 ],
[ 0.961941, 0.262059, 0.167000 ],
[ 0.961812, 0.256615, 0.165800 ],
[ 0.961682, 0.251171, 0.164600 ],
[ 0.961553, 0.245727, 0.163400 ],
[ 0.961424, 0.240283, 0.162200 ],
[ 0.961294, 0.234839, 0.161000 ],
[ 0.961165, 0.229395, 0.159800 ],
[ 0.961035, 0.223951, 0.158600 ],
[ 0.960906, 0.218507, 0.157400 ],
[ 0.960776, 0.213064, 0.156200 ],
[ 0.960647, 0.207620, 0.155000 ],
[ 0.960518, 0.202176, 0.153800 ],
[ 0.960388, 0.196732, 0.152600 ],
[ 0.960259, 0.191288, 0.151400 ],
[ 0.960129, 0.185844, 0.150200 ],
[ 0.960000, 0.180400, 0.149000 ]]
# read the source file.
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
output = reader.GetOutput()
scalar_range = output.GetScalarRange()
# create own palette
lut = vtk.vtkLookupTable()
lut.SetRange(scalar_range)
for i in range(len(colobar_agros2d)):
lut.SetTableValue(i, colobar_agros2d[i][0], colobar_agros2d[i][1], colobar_agros2d[i][2])
lut.Build()
# create the mapper that corresponds the objects of the vtk file into graphics elements
mapper = vtk.vtkDataSetMapper()
mapper.SetInput(output)
mapper.SetScalarRange(scalar_range)
mapper.SetLookupTable(lut)
# actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
return actor
