[Paraview] Programmable filter VTK/numpy

Fri Oct 20 10:48:50 EDT 2017

On Thu, Oct 19, 2017 at 11:02 AM, Edoardo Pasca <edo.paskino at gmail.com>
wrote:

> Hi Cory,
>
> thanks for your reply. I'd love to simplify the code like that but there
> are 2 issues with that programmable filter
>
> 1) I miss information on the input and output variables. Where are defined?
>

It's a bit complicated to select them in the user interface, but it is
possible. There was a related discussion on the mailing list recently on
how to do this: http://paraview.markmail.org/thread/j4ynkclxcucpqoa5

In the worst case, you can hard-code the array names if they don't change.
Relying on the active scalar attribute is old-style VTK and may go away
someday in the not-too-near future. Or you could just keep your original
code for defining array B.

> 2) Paraview crashes. Paraview for windows 5.4.1 and 5.3.0 (official
> kitware build)
>
> It seems a memory access problem.
>

To debug, I suggest writing your Programmable Filter script a few lines at
a time to determine which line causes the crash.

HTH,
Cory

> Edo
>
> On Thu, Oct 19, 2017 at 2:52 PM, Cory Quammen <cory.quammen at kitware.com>
> wrote:
>
>> 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.
>>
>
>
>
> --
> 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
>

-- 
Cory Quammen
Staff R&D Engineer
Kitware, Inc.
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