[Paraview] What is the "numpy way"?

[Adam Lyon]

Thanks Cory! That was very helpful. One subtlety - my np.genfromtxt has the
names argument set, so that returns a structured numpy array. So I had to
do,

bfieldVtkArray = ns.numpy_to_vtk( d[ ["Bx", "By", "Bz"] ].view(
(np.float,3) ), 1, vtk.VTK_FLOAT )
bfieldVtkArray.SetName("BField")

That seems to work.

The one-column arrays are a little easier. E.g.,
timeVtkArray  = ns.numpy_to_vtk( d["time"].ravel(), 1, vtk.VTK_FLOAT)
timeVtkArray.SetName("time")

I have to do the .ravel() or else I get the "non-contiguous" error.

Avoiding that old-fashioned loops seems to make it quite a bit faster too.

Thanks again for the help! -- Adam





*------*

*Adam L. Lyon*
*Scientist; Associate Division Head for Systems for Scientific Applications*

Scientific Computing Division & Muon g-2 Experiment
Fermi National Accelerator Laboratory
630 840 5522 office
www.fnal.gov
lyon at fnal.gov

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On Fri, Jun 19, 2015 at 12:36 PM, Cory Quammen <cory.quammen at kitware.com>
wrote:

> Hi Adam,
>
> There are some utilities in VTK for converting back and forth from VTK
> arrays to numpy arrays. Here is an example of usage from within
> pvpython that should work:
>
> >>> import numpy as np
> >>> d = np.genfromtxt('/home/cory/sample.csv', skip_header=1,
> delimiter=',')
> >>> d
> array([[ 1.,  2.,  3.],
>        [ 4.,  5.,  6.],
>        [ 7.,  8.,  9.]])
> >>> import vtk
> >>> import vtk.util.numpy_support as ns
> >>> vtk_array = ns.numpy_to_vtk(d, 1, vtk.VTK_FLOAT)
> >>> vtk_array
> (vtkFloatArray)0x7f76a9b92410
> >>> vtk_array.GetNumberOfComponents()
> 3
> >>> vtk_array.GetNumberOfTuples()
> 3L
> >>> vtk_array.GetTuple(0)
> (1.0, 2.0, 3.0)
>
> vtk_array is a vtkDoubleArray holding the values in the numpy array d.
> The 1 in the second argument means that the data should be deep copied
> into the VTK array - this is usually what you want unless you hold a
> reference to the numpy array d somewhere else in your code.
>
> I hope that helps.
>
> Best regards,
> Cory
>
> On Fri, Jun 19, 2015 at 12:26 PM, Adam Lyon <lyon at fnal.gov> wrote:
> > Hi all, I've been debugging a simulation of particle physics experiment
> -- I
> > usually have the program make a csv file of some data to visualize (for
> > example, x,y,z,time,Bx,By,Bz) where, e.g., Bx is a component of a
> magnetic
> > field. I can read that file straight into ParaView with its text file
> > reader, but I find it more convenient to run the csv file through a
> python
> > script that makes a vtp file and I load that into ParaView. These files
> tend
> > to be big, and having a compressed binary vtp file means that ParaView
> can
> > read it very quickly (e.g. I parse csv file once with my script instead
> of
> > loading it into ParaView to parse each time I open it).
> >
> > The examples in the documentation show how to use the vtk-numpy
> interface to
> > make a vector of points and "dump" them into a vtkPoints object. For
> > example,
> >
> > d = np.genfromtxt(fname, ...)  # more arguments not shown for brevity
> >
> > coord = algs.make_vector(d["x"], d["y"], d["z"])
> > pts = vtk.vtkPoints()
> > pts.SetData(dsa.numpyTovtkDataArray(coord, "Points"))
> >
> > That looks very nice and must be very efficient.
> >
> > I don't see an obvious way to do the same thing with point or cell data.
> So,
> > for example, I have...
> >
> > numPts = pts.GetNumberOfPoints()
> > bfield = vtk.vtkFloatArray()
> > bfield.SetNumberOfComponents(3)
> > bfield.SetNumberOfTuples(numPts)
> > bfield.SetName("BField")
> >
> > for a in xrange(numPts):
> >    bfield.InsertTuple(a, [ d["Bx"][a], d["By"][a], d["Bz"][a] ])
> >
> > polyData.GetPointData().AddArray(bfield)  # polyData is a vtkPolyData
> object
> >
> > That loop and explicitly decomposing the "d" array to get at the magnetic
> > field components looks "old fashioned" to me.
> >
> > What would be the "numpy way" to make that work? Thanks! -- Adam
> >
> > ------
> >
> > Adam L. Lyon
> > Scientist; Associate Division Head for Systems for Scientific
> Applications
> >
> > Scientific Computing Division & Muon g-2 Experiment
> > Fermi National Accelerator Laboratory
> > 630 840 5522 office
> > www.fnal.gov
> > lyon at fnal.gov
> >
> > Connect with us!
> > Newsletter  |  Facebook  |  Twitter
> >
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>
>
> --
> Cory Quammen
> R&D Engineer
> Kitware, Inc.
>
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