[Paraview] Programmable filter VTK/numpy

[Cory Quammen]

Hi Edo,

Documentation for the VTK/Numpy adapter can be found here:

https://www.paraview.org/ParaView/Doc/Nightly/www/py-doc/paraview.vtk.numpy_interface.html?highlight=numpy_interface#numpy-interface-package

You will likely be interested in the dataset_adapter module that provides a
convenient way to wrap VTK data objects in a Python class that provides
easy read/write access to VTK data arrays as Numpy arrays.

You could simplify your code quite a bit using this adapter as in the
following:

import numpy

from vtk.util import numpy_support, vtkImageImportFromArray

import vtk.numpy_interface.dataset_adapter as dsa


inData = dsa.WrapDataObject(inputs[0])

B = inData.PointData['array_name'] # best practice is to name the array


#B = numpy_support.vtk_to_numpy(

#                inputs[0].GetPointData().GetScalars())


ifLarger = lambda x,M: x if x<=M else 0

fgt = numpy.frompyfunc(ifLarger,2,1)

#A = fgt(B,int(2**16*0.8))


ifSmaller = lambda x,M: x if x>M else 0

flt = numpy.frompyfunc(ifSmaller,2,1)

#A = flt(B,int(2**16*0.3))


ifBetween = lambda x,m,M: ifSmaller(x,m) if x<=M else 0

fbetw = numpy.frompyfunc(ifBetween,3,1)


A = fbetw(B,int(2**16*0.3), int(2**16*0.95))


outData = dsa.WrapDataObject(output)

outData.PointData.append(A,'new_array_name')


#A = numpy.asarray(A,dtype=uint16)

#dims = inputs[0].GetDimensions()

#A = numpy.reshape(A, (dims[2],dims[1],dims[0]), order='C')

#A = numpy.ascontiguousarray(A)

#importer = vtkImageImportFromArray.vtkImageImportFromArray()

#importer.SetArray(A)

#importer.SetDataSpacing(inputs[0].GetSpacing())

#importer.SetDataOrigin(inputs[0].GetOrigin())

#importer.Update()


#output.DeepCopy(importer.GetOutput())


Hope that helps,

Cory

On Tue, Oct 17, 2017 at 10:38 AM, Edoardo Pasca <edo.paskino at gmail.com>
wrote:

> Hi there,
>
> In my programmable filter I want to use numpy to perform some operations
> on the pixels (in this case a simple thresholding). I've come up with this
> solution which works. I'm wondering if there are other ways to do the
> conversion from numpy array to vtkImageData.
>
> in the following code I get a numpy array out of the input vtkImageData as
> B. Then I do something on the content an store the result in a numpy array,
> A.
>
> Then I convert the numpy array to a vtkImageData with
> vtkImageImportFromArray importer class.
> Finally I copy the importer output to the output of the programmable
> filter.
>
> Thanks for any suggestions
>
> Edo
>
> import numpy
>
> from vtk.util import numpy_support, vtkImageImportFromArray
>
> import vtk.numpy_interface.dataset_adapter as dsa
>
>
> B = numpy_support.vtk_to_numpy(
>
>                 inputs[0].GetPointData().GetScalars())
>
>
> ifLarger = lambda x,M: x if x<=M else 0
>
> fgt = numpy.frompyfunc(ifLarger,2,1)
>
> #A = fgt(B,int(2**16*0.8))
>
>
> ifSmaller = lambda x,M: x if x>M else 0
>
> flt = numpy.frompyfunc(ifSmaller,2,1)
>
> #A = flt(B,int(2**16*0.3))
>
>
> ifBetween = lambda x,m,M: ifSmaller(x,m) if x<=M else 0
>
> fbetw = numpy.frompyfunc(ifBetween,3,1)
>
>
> A = fbetw(B,int(2**16*0.3), int(2**16*0.95))
>
>
>
> A = numpy.asarray(A,dtype=uint16)
>
> dims = inputs[0].GetDimensions()
>
> A = numpy.reshape(A, (dims[2],dims[1],dims[0]), order='C')
>
> A = numpy.ascontiguousarray(A)
>
> importer = vtkImageImportFromArray.vtkImageImportFromArray()
>
> importer.SetArray(A)
>
> importer.SetDataSpacing(inputs[0].GetSpacing())
>
> importer.SetDataOrigin(inputs[0].GetOrigin())
>
> importer.Update()
>
>
> output.DeepCopy(importer.GetOutput())
>
>
>
> --
> Edo
> I know you think you understand what you thought I said, but I'm not sure
> you realize that what you heard is not what I meant (prob. Alan Greenspan)
> :wq
>
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-- 
Cory Quammen
Staff R&D Engineer
Kitware, Inc.
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