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import core.modules
import core.modules.module_registry
from core.modules.vistrails_module import Module, ModuleError
from scipy import sparse
import vtk
from Array import *
from Matrix import *
class ArrayUtilModule(object):
my_namespace = 'numpy|array|utilities'
class ArrayToVTKVectors(ArrayUtilModule, Module):
def compute(self):
v0 = self.forceGetInputFromPort("Array0")
v1 = self.forceGetInputFromPort("Array1")
v2 = self.forceGetInputFromPort("Array2")
ds = self.getInputFromPort("VTK Data")
v_name = self.forceGetInputFromPort("Vector Name")
if v_name == None:
v_name = 'vectors'
vsize = 0
if v0:
vsize += 1
v0 = v0.get_array().flatten()
if v1:
vsize += 1
v1 = v1.get_array().flatten()
if v2:
vsize += 1
v2 = v2.get_array().flatten()
np = ds.vtkInstance.GetNumberOfPoints()
pd = ds.vtkInstance.GetPointData()
vtk_ar = vtk.vtkDoubleArray()
# vtk_ar.SetNumberOfValues(np)
vtk_ar.SetNumberOfComponents(3)
for i in range(np):
if vsize == 2:
vtk_ar.InsertNextTuple3(v0[i], v1[i], 0.)
elif vsize == 3:
vtk_ar.InsertNextTuple3(v0[i], v1[i], v2[i])
vtk_ar.SetName(v_name)
ds.vtkInstance.GetPointData().AddArray(vtk_ar)
ds.vtkInstance.GetPointData().SetVectors(vtk_ar)
# ds.vtkInstance.GetPointData().SetActiveVectors(v_name)
self.setResult("Output", ds)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
@classmethod
def register_ports(cls, reg, basic):
reg.add_input_port(cls, "Array0", (NDArray, 'Scalar Array'))
reg.add_input_port(cls, "Array1", (NDArray, 'Scalar Array'))
reg.add_input_port(cls, "Array2", (NDArray, 'Scalar Array'))
reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
reg.add_input_port(cls, "Vector Name", (basic.String, 'Scalar Name'), True)
reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
class ArrayToTimeVaryingVTKVectors(ArrayUtilModule, Module):
def update_progress(self, cur, total):
t = float(cur) / float(total)
self.logging.update_progress(self, t)
def compute(self):
v0 = self.forceGetInputFromPort("Array0")
v1 = self.forceGetInputFromPort("Array1")
v2 = self.forceGetInputFromPort("Array2")
ds = self.getInputFromPort("VTK Data")
v_name = self.forceGetInputFromPort("Vector Name")
if v_name == None:
v_name = 'vectors'
vsize = 0
if v0:
vsize += 1
if v1:
vsize += 1
if v2:
vsize += 1
num_times = ds.vtkInstance.GetNumberOfTimeSteps()
for i in range(num_times):
self.update_progress(i, num_times)
np = ds.vtkInstance.GetTimeStep(i).GetNumberOfPoints()
pd = ds.vtkInstance.GetTimeStep(i).GetPointData()
vtk_ar = vtk.vtkDoubleArray()
# vtk_ar.SetNumberOfValues(np)
vtk_ar.SetNumberOfComponents(3)
arx = v0.get_array().squeeze()
arx = arx[i,::].squeeze().flatten()
ary = v1.get_array().squeeze()
ary = ary[i,::].squeeze().flatten()
if vsize == 3:
arz = v2.get_array().squeeze()
arz = arz[i,::].squeeze().flatten()
for j in range(np):
if vsize == 2:
vtk_ar.InsertNextTuple3(arx[j], ary[j], 0.)
elif vsize == 3:
vtk_ar.InsertNextTuple3(arz[j], ary[j], arz[j])
vtk_ar.SetName(v_name)
ds.vtkInstance.GetTimeStep(i).GetPointData().AddArray(vtk_ar)
ds.vtkInstance.GetTimeStep(i).GetPointData().SetVectors(vtk_ar)
# ds.vtkInstance.GetPointData().SetActiveVectors(v_name)
self.setResult("Output", ds)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
@classmethod
def register_ports(cls, reg, basic):
reg.add_input_port(cls, "Array0", (NDArray, 'Scalar Array'))
reg.add_input_port(cls, "Array1", (NDArray, 'Scalar Array'))
reg.add_input_port(cls, "Array2", (NDArray, 'Scalar Array'))
reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
reg.add_input_port(cls, "Vector Name", (basic.String, 'Scalar Name'), True)
reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
class ArrayToTimeVaryingVTKScalars(ArrayUtilModule, Module):
def update_progress(self, cur, total):
t = float(cur) / float(total)
self.logging.update_progress(self, t)
def compute(self):
ds = self.getInputFromPort("VTK Data")
ar = self.getInputFromPort("Scalars")
v_name = self.forceGetInputFromPort("Array Name")
if v_name == None:
v_name = 'scalars'
num_times = ds.vtkInstance.GetNumberOfTimeSteps()
ar_ = ar.get_array()
if ar_.shape[0] != num_times:
raise ModuleError("Cannot process array with num timesteps = " +
str(ar_.shape[0]) +
" and vtkdata with " +
str(num_times) + " timesteps")
for i in range(num_times):
self.update_progress(i, num_times)
s_ar = ar_[i,::].squeeze().flatten()
vtk_ar = vtk.vtkDoubleArray()
vtk_ar.SetNumberOfValues(s_ar.size)
vtk_ar.SetName(v_name)
for j in range(s_ar.size):
vtk_ar.InsertNextValue(s_ar[j])
ds.vtkInstance.GetTimeStep(i).GetPointData().AddArray(vtk_ar)
ds.vtkInstance.GetTimeStep(i).GetPointData().SetScalars(vtk_ar)
self.setResult("Output", ds)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
@classmethod
def register_ports(cls, reg, basic):
reg.add_input_port(cls, "Scalars", (NDArray, 'Scalar Array'))
reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
reg.add_input_port(cls, "Array Name", (basic.String, 'Scalar Name'), True)
reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
class ArrayToVTKScalars(ArrayUtilModule, Module):
""" Take a scalar array and consider it as an array of scalars
to assign to a VTK dataset. The number of elements in the
scalar array must be equivalent to the number of points in
the VTK dataset. Please note that this module adds a scalar
array to the input dataset and can be considered a mutating filter
because of this."""
def compute(self):
a = self.getInputFromPort("Array")
ds = self.getInputFromPort("VTK Data")
scalar_name = ''
if self.hasInputFromPort("Scalar Name"):
scalar_name = self.getInputFromPort("Scalar Name")
else:
scalar_name = 'scalars'
s_ar = a.get_array().flatten()
np = ds.vtkInstance.GetNumberOfPoints()
# if s_ar.size != np:
# raise ModuleError("Could not assign scalars to VTK dataset with different number of elements")
pd = ds.vtkInstance.GetPointData()
vtk_ar = vtk.vtkDoubleArray()
vtk_ar.SetNumberOfValues(np)
for i in xrange(np):
vtk_ar.SetValue(i, s_ar[i])
vtk_ar.SetName(scalar_name)
ds.vtkInstance.GetPointData().AddArray(vtk_ar)
# ds.vtkinstance.GetPointData().SetActiveScalars(scalar_name)
ds.vtkInstance.GetPointData().SetScalars(vtk_ar)
self.setResult("Output", ds)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
@classmethod
def register_ports(cls, reg, basic):
reg.add_input_port(cls, "Array", (NDArray, 'Scalar Array'))
reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
reg.add_input_port(cls, "Scalar Name", (basic.String, 'Scalar Name'), True)
reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
class VTKDataSetToPointArray(ArrayUtilModule, Module):
"""
Extract points and scalar values from a vtkDataSet. The
output will be of the form [[x,y,z,v]] with the v component
optionally added if the IncludeScalars flag is set.
"""
def compute(self):
data = self.getInputFromPort("vtkDataSet").vtkInstance
flag = self.forceGetInputFromPort("IncludeScalars")
np = data.GetNumberOfPoints()
ndim = 3
if flag:
ndim = 4
out_ar = numpy.ones((np, ndim))
for i in xrange(np):
(out_ar[i,0], out_ar[i,1], out_ar[i,2]) = data.GetPoint(i)
if flag:
out_ar[i,3] = data.GetPointData().GetArray(0).GetTuple1(i)
out = NDArray()
out.set_array(out_ar)
self.setResult("Output", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
@classmethod
def register_ports(cls, reg, basic):
reg.add_input_port(cls, "vtkDataSet", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
reg.add_input_port(cls, "IncludeScalars", (basic.Boolean, 'Include Scalars in Output'), True)
reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
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