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############################################################################
##
## Copyright (C) 2006-2007 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software Foundation
## and appearing in the file LICENSE.GPL included in the packaging of
## this file. Please review the following to ensure GNU General Public
## Licensing requirements will be met:
## http://www.opensource.org/licenses/gpl-license.php
##
## If you are unsure which license is appropriate for your use (for
## instance, you are interested in developing a commercial derivative
## of VisTrails), please contact us at contact@vistrails.org.
##
## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
##
############################################################################
import core.modules
import core.modules.module_registry
from core.modules.vistrails_module import Module, ModuleError
from SciPy import SciPy
from Matrix import Matrix, COOMatrix, SparseMatrix, CSRMatrix
from scipy import sparse
import numpy, scipy
class MatrixConvert(SciPy):
def compute(self):
m = self.getInputFromPort("InputMatrix")
to = self.getInputFromPort("OutputType")
to = to.upper()
if to == 'Dense':
self.matrix = DenseMatrix(m.matrix.todense())
self.setResult("SparseOutput", self.matrix)
else:
self.matrix = SparseMatrix(m.matrix.tocsc())
self.setResult("SparseOutput", self.matrix)
class vtkDataSetToMatrix(SciPy):
''' In some cases, particularly in terms of user-defined VTK Filters, the
output of the filter is a vtk datatype representing '''
def from_unstructured_grid(self, vtkalgout):
import vtk
prod = vtkalgout.vtkInstance.GetProducer()
prod.Update()
grid = prod.GetOutput()
pt_set = grid.GetPoints()
scalars = grid.GetPointData().GetScalars()
''' Points in vtk are always 3D... so we must assume this. '''
self.matrix_ = SparseMatrix()
self.matrix_.matrix = sparse.csc_matrix((grid.GetNumberOfPoints(), 3))
i = 0
while i < grid.GetNumberOfPoints():
(x,y,z) = pt_set.GetPoint(i)
self.matrix_.matrix[i,0] = x
self.matrix_.matrix[i,1] = y
self.matrix_.matrix[i,2] = z
print x, y, z
i += 1
def compute(self):
if self.hasInputFromPort("vtkUnstructuredGrid"):
self.from_unstructured_grid(self.getInputFromPort("vtkUnstructuredGrid"))
else:
pass
self.setResult("Output Matrix", self.matrix_)
class PhaseHistogramToVTKPoints(SciPy):
def form_point_set(self, histo, point_set):
(slices, numbins) = histo.shape
phases = numpy.arange(numbins)
phases = phases * (360. / numbins)
phases += phases[1] / 2.
phi_step = phases[0]
for time in xrange(slices):
z = float(time)
for bin in xrange(numbins):
r = histo[time,bin]
theta = phi_step * (bin+1)
theta *= (scipy.pi / 180.)
x = r*scipy.cos(theta)
y = r*scipy.sin(theta)
point_set.InsertNextPoint(x, y, z)
for bin in xrange(numbins):
curbin = bin
lastbin = bin-1
if lastbin < 0:
lastbin = numbins-1
r = (histo[time,bin] - histo[time,lastbin]) / 2.
theta = curbin * 360. / numbins
x = r*scipy.cos(theta)
y = r*scipy.sin(theta)
point_set.InsertNextPoint(x, y, z)
def compute(self):
import vtk
phasors = self.getInputFromPort("FFT Input")
numbins = self.getInputFromPort("Num Bins")
phasor_matrix = phasors.matrix.toarray()
(timeslices,phases) = phasor_matrix.shape
point_set = vtk.vtkPoints()
histo = numpy.zeros((timeslices, numbins))
for time in xrange(timeslices):
phase_slice = phasor_matrix[time,:]
reals = phase_slice.real
imaginary = phase_slice.imag
phases = scipy.arctan2(imaginary, reals)
phases = phases * (180. / scipy.pi)
bins = phases % numbins
for b in bins:
histo[time,b] += 1
self.form_point_set(histo, point_set)
pointdata = vtk.vtkUnstructuredGrid()
pointdata.SetPoints(point_set)
self.surf_filter = vtk.vtkSurfaceReconstructionFilter()
self.surf_filter.SetInput(0,pointdata)
# self.surf_filter.Update()
reg = core.modules.module_registry
vtk_set = reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput').module()
vtk_set.vtkInstance = self.surf_filter.GetOutputPort()
histo_mat = SparseMatrix()
histo_mat.matrix = sparse.csc_matrix(histo)
self.setResult("Num Slices", timeslices)
self.setResult("Phase Histogram", histo_mat)
self.setResult("Phase Geometry", vtk_set)
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