[Paraview] Programmable filter VTK/numpy

Wed Oct 25 07:46:46 EDT 2017

Hallo Cory and all,

I've spent a few minutes trying to find out where my script crashes:

1) I load a MetaImage and the scalars are named 'MetaImage'

2) Paraview crashes if I use inData = dsa.WrapDataObject(inputs[0])

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

3) If I use the outData = dsa.WrapDataObject(output)

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

the output contains nothing. It says type Uniform Rectilinear Grid but
there is no point inside.

Thanks

Edo

On Fri, Oct 20, 2017 at 3:48 PM, Cory Quammen <cory.quammen at kitware.com>
wrote:

> 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/par
>>> aview.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.
>

-- 
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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