def getNewVtkDataArray( scalar_dtype ):
if scalar_dtype == np.ushort:
return vtk.vtkUnsignedShortArray()
if scalar_dtype == np.ubyte:
return vtk.vtkUnsignedCharArray()
if scalar_dtype == np.float:
return vtk.vtkFloatArray()
return None
def getNewVtkDataArray(scalar_dtype):
if scalar_dtype == np.ushort:
return vtk.vtkUnsignedShortArray()
if scalar_dtype == np.ubyte:
return vtk.vtkUnsignedCharArray()
if scalar_dtype == np.float32:
return vtk.vtkFloatArray()
if scalar_dtype == np.float64:
return vtk.vtkDoubleArray()
return None
def get_new_vtk_data_array(self, scalar_dtype):
if scalar_dtype == np.int32:
return vtk.vtkIntArray()
if scalar_dtype == np.ushort:
return vtk.vtkUnsignedShortArray()
if scalar_dtype == np.ubyte:
return vtk.vtkUnsignedCharArray()
if scalar_dtype == np.float32:
return vtk.vtkFloatArray()
print >> sys.stderr, '[ERROR] ' + str(scalar_dtype) + ' is not supported '
return None
def get_new_vtk_data_array(self, scalar_dtype):
if scalar_dtype == np.int32:
return vtk.vtkIntArray()
if scalar_dtype == np.ushort:
return vtk.vtkUnsignedShortArray()
if scalar_dtype == np.ubyte:
return vtk.vtkUnsignedCharArray()
if scalar_dtype == np.float32:
return vtk.vtkFloatArray()
print >> sys.stderr, '[ERROR] ' + str(
scalar_dtype) + ' is not supported '
return None
def createUnsignedShortArray(name,
n_components=1,
n_tuples=0,
init_to_zero=0,
verbose=0):
usarray = vtk.vtkUnsignedShortArray()
usarray.SetName(name)
usarray.SetNumberOfComponents(n_components)
usarray.SetNumberOfTuples(n_tuples)
if (init_to_zero):
for k_tuple in xrange(n_tuples):
iarray.SetTuple(k_tuple, [0] * n_components)
return usarray
def createUnsignedShortArray(
name,
n_components=1,
n_tuples=0,
init_to_zero=0,
verbose=1):
usarray = vtk.vtkUnsignedShortArray()
usarray.SetName(name)
usarray.SetNumberOfComponents(n_components)
usarray.SetNumberOfTuples(n_tuples)
if (init_to_zero):
for k_tuple in xrange(n_tuples):
iarray.SetTuple(k_tuple, [0]*n_components)
return usarray
def set_scaled_scalars(self):
debug ("In StructuredPointsProbe::set_scaled_scalars ()")
out = self.fil.GetOutput()
pd = out.GetPointData()
sc = pd.GetScalars()
if not sc: # no input scalars
return
if self.conv_scalar_var.get() == 0:
orig_sc = self.prev_fil.GetOutput().GetPointData().GetScalars()
if sc.IsA('vtkUnsignedShortArray') and \
sc.GetName() == 'sp_probe_us_data':
pd.SetActiveScalars(orig_sc.GetName())
return
calc = vtk.vtkArrayCalculator()
calc.SetAttributeModeToUsePointData()
s_min, s_max = sc.GetRange()
# checking to see if input array is constant.
avg = (s_max + s_min)*0.5
diff = 1
if (s_max > avg) and (avg > s_min):
diff = s_max - s_min
base = sc.CreateDataArray(sc.GetDataType())
base.SetNumberOfTuples(sc.GetNumberOfTuples())
base.SetNumberOfComponents(1)
base.SetName('sp_probe_us_base')
base.FillComponent(0, s_min)
pd.AddArray(base)
calc.SetInput(out)
calc.AddScalarVariable("s", sc.GetName(), 0)
calc.AddScalarVariable("sb", base.GetName(), 0)
calc.SetFunction("(s - sb)*%f"%(65535.0/diff))
calc.SetResultArrayName('sp_probe_us_data')
calc.Update()
sc = calc.GetOutput().GetPointData().GetScalars()
uca = vtk.vtkUnsignedShortArray()
uca.SetName(sc.GetName())
uca.DeepCopy(sc)
pd.AddArray(uca)
pd.SetActiveScalars('sp_probe_us_data')
def new_array_set_scalars(self, scalar_dtype, image_data, num_components):
if scalar_dtype == np.ushort:
image_data.AllocateScalars(vtk.VTK_UNSIGNED_SHORT, num_components)
return vtk.vtkUnsignedShortArray()
if scalar_dtype == np.int32:
image_data.AllocateScalars(vtk.VTK_INT, num_components)
return vtk.vtkIntArray()
if scalar_dtype == np.ubyte:
image_data.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, num_components)
return vtk.vtkUnsignedCharArray()
if scalar_dtype == np.float32:
image_data.AllocateScalars(vtk.VTK_FLOAT, num_components)
return vtk.vtkFloatArray()
if scalar_dtype == np.float64:
# // @todo: check if this type is supported
image_data.AllocateScalars(vtk.VTK_TYPE_FLOAT64, num_components)
return vtk.vtkDoubleArray()
print >> sys.stderr, '[ERROR] ' + str(scalar_dtype) + ' is not supported '
return None
def GetShortImageData(self, varName, iTimeIndex, fieldData):
vtkdata = vtk.vtkUnsignedShortArray()
SCALARMAX = vtkdata.GetDataTypeMax(vtkdata.GetDataType())
img = vtk.vtkImageData()
img.SetScalarTypeToUnsignedShort()
img.GetPointData().SetScalars(vtkdata)
dataArray = self.GetDataArray(varName, iTimeIndex)
dmin = dataArray.min()
dmax = dataArray.max()
scaledData = SCALARMAX * (dataArray - dmin) / (dmax - dmin)
usData = scaledData.astype(N.UInt16)
vtkdata.SetNumberOfTuples(N.size(data))
vtkdata.SetVoidArray(data, N.size(data), 1)
vtkdata.Modified()
self.enc_mdata = encodeToString({'bounds': self.GetDataBounds()})
fieldData.AddArray(getStringDataArray('metadata', [self.enc_mdata]))
fieldData.AddArray(getFloatDataArray('valueRange', self.dataRange))
return img
def GetShortImageData( self, varName, iTimeIndex, fieldData ):
vtkdata = vtk.vtkUnsignedShortArray()
SCALARMAX = vtkdata.GetDataTypeMax( vtkdata.GetDataType() )
img = vtk.vtkImageData()
img.SetScalarTypeToUnsignedShort()
img.GetPointData().SetScalars(vtkdata)
dataArray = self.GetDataArray( varName, iTimeIndex )
dmin = dataArray.min()
dmax = dataArray.max()
scaledData = SCALARMAX * ( dataArray - dmin ) / ( dmax - dmin )
usData = scaledData.astype(N.UInt16)
vtkdata.SetNumberOfTuples(N.size(data))
vtkdata.SetVoidArray( data, N.size(data), 1)
vtkdata.Modified()
self.enc_mdata = encodeToString( { 'bounds' : self.GetDataBounds() } )
fieldData.AddArray( getStringDataArray( 'metadata', [ self.enc_mdata ] ) )
fieldData.AddArray( getFloatDataArray( 'valueRange', self.dataRange ) )
return img
from pytestvtk.assert_vtk import assert_vtk
@pytest.fixture(params=[
vtk.vtkDoubleArray(),
vtk.vtkFloatArray(),
vtk.vtkIntArray(),
vtk.vtkIdTypeArray(),
vtk.vtkLongArray(),
vtk.vtkShortArray(),
vtk.vtkUnsignedCharArray(),
vtk.vtkUnsignedIntArray(),
vtk.vtkUnsignedLongArray(),
vtk.vtkUnsignedLongLongArray(),
vtk.vtkUnsignedShortArray(),
vtk.vtkCharArray(),
])
def vtk_array(request):
array = request.param
array.SetName('testing_array')
array.SetNumberOfTuples(3)
array.SetNumberOfComponents(3)
array.InsertTuple3(0, 1, 2, 3)
array.InsertTuple3(1, 4, 5, 6)
array.InsertTuple3(2, 7, 8, 9)
return array
@pytest.fixture(params=[
vtk.vtkDoubleArray(),
### End File input ### #Image Data definition. Variable declarations are not necessary in python. #set imData to an instance of vtkImageData imData = vtk.vtkImageData(); #The dimensions imData.SetDimensions(xDim,yDim,zDim); #We set the scalar type to unsigned short, scalar components to 1 and allocate it imData.SetScalarTypeToUnsignedShort(); imData.SetNumberOfScalarComponents(1); imData.AllocateScalars(); #Scalars array definition and memory allocation scalars = vtk.vtkUnsignedShortArray(); scalars.SetNumberOfValues(xDim*yDim*zDim); #The three 'for' loops to enter the scalar values into the image data for i in range(0, zDim): z = i; iOffset = (i*xDim*yDim); for j in range(0,yDim): y = j; jOffset = (j*xDim); for k in range(0,xDim): x = k; offset = (k+iOffset+jOffset); for m in range(0, len(layerLocs)-1):
def generate(self, name, imDim1, imDim2, imDim3, rotation_azimuth, rotation_elevation):
#THIS METHOD NEEDS SERIOUS REFACTORING
FILE = open("/home/jchiang/dev/django/vizlit/generator/vtk_scripts/problem1.txt","r");
#Define readlist to store non-empty lines from the input.txt file
readlist = [];
#Read from the file one line at a time and store it in readlist
for line in FILE:
readlist.append(line);line
#for now we will use
#imDimensions = readlist[2].split(' ');
layerLocs = readlist[4].split(' ');
layerColors = readlist[6].split(' ');
originSlice = readlist[8].split(' ');
point1Slice = readlist[10].split(' ');
point2Slice = readlist[12].split(' ');
rotationDiagram = readlist[14].split(' ');
fileOutput = '/home/jchiang/dev/django/vizlit/generator/images/' + name;
print originSlice;
xDim = imDim1 #int(imDimensions[0]);
yDim = imDim2 #int(imDimensions[1]);
zDim = imDim3 #int(imDimensions[2]);
### End File input ###
#Image Data definition. Variable declarations are not necessary in python.
#set imData to an instance of vtkImageData
imData = vtk.vtkImageData();
#The dimensions
imData.SetDimensions(xDim,yDim,zDim);
#We set the scalar type to unsigned short, scalar components to 1 and allocate it
imData.SetScalarTypeToUnsignedShort();
imData.SetNumberOfScalarComponents(1);
imData.AllocateScalars();
#Scalars array definition and memory allocation
scalars = vtk.vtkUnsignedShortArray();
scalars.SetNumberOfValues(xDim*yDim*zDim);
#The three 'for' loops to enter the scalar values into the image data
for i in range(0, zDim):
z = i;
iOffset = (i*xDim*yDim);
for j in range(0,yDim):
y = j;
jOffset = (j*xDim);
for k in range(0,xDim):
x = k;
offset = (k+iOffset+jOffset);
for m in range(0, len(layerLocs)-1):
if y>=int(layerLocs[m]) and y<int(layerLocs[m+1]):
scalars.InsertTuple1(offset, m+1);
(imData.GetPointData()).SetScalars(scalars);
colorTransferFunction = vtk.vtkColorTransferFunction();
colorTransferFunction.AddRGBPoint(0,1,1,1);
for i in range(1, len(layerColors)):
tempColor = layerColors[i-1].split(',');
colorTransferFunction.AddRGBPoint(float(i),float(tempColor[0]), float(tempColor[1]), float(tempColor[2]));
opacityTransferFunction = vtk.vtkPiecewiseFunction();
opacityTransferFunction.AddPoint(0,0);
opacityTransferFunction.AddPoint(1,1);
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction();
volMapper = vtk.vtkVolumeRayCastMapper();
volMapper.SetInput(imData);
volMapper.SetVolumeRayCastFunction(compositeFunction);
volumeProperty = vtk.vtkVolumeProperty();
volumeProperty.SetColor(colorTransferFunction);
volumeProperty.SetScalarOpacity(opacityTransferFunction);
volumeProperty.ShadeOn();
volumeProperty.SetDiffuse(0.7);
volumeProperty.SetAmbient(0.8);
volumeProperty.SetSpecular(0.5);
volumeProperty.SetSpecularPower(70.0);
volVolume = vtk.vtkVolume();
volVolume.SetMapper(volMapper);
volVolume.SetProperty(volumeProperty);
light = vtk.vtkLight();
light.SetColor(1,1,1);
light.SetPosition(30,500,150);
light.SetFocalPoint(50,50,50);
light.SetIntensity(0.9);
volMapper2 = vtk.vtkVolumeRayCastMapper();
volMapper2.SetInput(imData);
volMapper2.SetVolumeRayCastFunction(compositeFunction);
plane1 = vtk.vtkPlaneSource();
plane1.SetOrigin(float(originSlice[0]),float(originSlice[1]),float(originSlice[2]));
plane1.SetPoint1(float(point1Slice[0]),float(point1Slice[1]),float(point1Slice[2]));
plane1.SetPoint2(float(point2Slice[0]),float(point2Slice[1]),float(point2Slice[2]));
planeProperty = vtk.vtkProperty();
#planeProperty.SetColor(1,1,1);
planeMapper = vtk.vtkPolyDataMapper();
planeMapper.SetInputConnection(plane1.GetOutputPort());
planeProperty = vtk.vtkProperty();
#planeProperty.SetOpacity(1);
planeProperty.SetLineWidth(5);
planeActor = vtk.vtkActor();
planeActor.SetMapper(planeMapper);
planeActor.SetProperty(planeProperty);
(planeActor.GetProperty()).SetColor(0,0,0);
planeNormal = plane1.GetNormal();
planeCenter = plane1.GetCenter();
testNormal = [0,0,0];
testNormal[0] = planeNormal[0]*-1;
testNormal[1] = planeNormal[1]*-1;
testNormal[2] = planeNormal[2]*-1;
clipPlane1 = vtk.vtkPlane();
clipPlane1.SetOrigin(float(originSlice[0]),float(originSlice[1]),float(originSlice[2]));
clipPlane1.SetNormal(plane1.GetNormal());
volMapper2.AddClippingPlane(clipPlane1);
print testNormal;
originSlice2 = [0,0,0];
originSlice2[0] = float(originSlice[0]) - float(testNormal[0])*3;
originSlice2[1] = float(originSlice[1]) - float(testNormal[1])*3;
originSlice2[2] = float(originSlice[2]) - float(testNormal[2])*3;
print originSlice2;
clipPlane2 = vtk.vtkPlane();
clipPlane2.SetOrigin(float(originSlice2[0]),float(originSlice2[1]),float(originSlice2[2]));
clipPlane2.SetNormal(testNormal);
volMapper2.AddClippingPlane(clipPlane2);
volVolume2 = vtk.vtkVolume();
volVolume2.SetMapper(volMapper2);
volVolume2.SetProperty(volumeProperty);
ren = vtk.vtkRenderer();
ren2 = vtk.vtkRenderer();
ren2.AddProp(volVolume2);
renWin = vtk.vtkRenderWindow();
renWin.SetSize(800,800);
renWin2 = vtk.vtkRenderWindow();
renWin2.SetSize(800,800);
ren.SetViewport(0,0,1,1);
ren2.SetViewport(0,0,1,1);
renWin.AddRenderer(ren);
renWin2.AddRenderer(ren2);
iren = vtk.vtkRenderWindowInteractor();
iren.SetRenderWindow(renWin);
iren = vtk.vtkRenderWindowInteractor();
iren.SetRenderWindow(renWin2);
(ren.GetActiveCamera()).Azimuth(float(rotation_azimuth));
(ren.GetActiveCamera()).Elevation(float(rotation_elevation));
(ren.GetActiveCamera()).SetParallelProjection(0);
ren.SetBackground(1,1,1);
ren2.SetBackground(1,1,1);
ren.AddLight(light);
ren.AddProp(volVolume);
ren.AddActor(planeActor);
ren.ResetCamera();
(ren2.GetActiveCamera()).SetFocalPoint(planeCenter);
upDirection = [float(point1Slice[0])-float(originSlice[0]),float(point1Slice[1])-float(originSlice[1]), float(point1Slice[2])-float(originSlice[2])];
(ren2.GetActiveCamera()).SetViewUp(upDirection);
camPosition = [planeCenter[0]-planeNormal[0]*300, planeCenter[1]-planeNormal[1]*300, planeCenter[2]-planeNormal[2]*300];
(ren2.GetActiveCamera()).SetPosition(camPosition);
win2imageFilter = vtk.vtkWindowToImageFilter();
win2imageFilter.SetInput(renWin);
writerJPEG = vtk.vtkJPEGWriter();
writerJPEG.SetQuality(100);
writerJPEG.SetInput(win2imageFilter.GetOutput());
writerJPEG.SetFileName(fileOutput+".jpg");
writerJPEG.Write();
for i in range(0,370,20):
time.sleep(.03);
(ren.GetActiveCamera()).Azimuth(-20);
renWin.AddRenderer(ren);
win2imageFilter = vtk.vtkWindowToImageFilter();
win2imageFilter.SetInput(renWin);
writerJPEG = vtk.vtkJPEGWriter();
writerJPEG.SetInput(win2imageFilter.GetOutput());
writerJPEG.SetFileName(fileOutput+"_rotate_"+str(i)+".jpg");
writerJPEG.Write();
