[ITK-users] simpleitk + python + vector type in sitk.mirrorpad args?

Mon Nov 28 09:18:01 EST 2016

Further question ... 

>Here is an example for manual padding for FFTs:
>https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/FFTConvolution.py

# pad the image 
img = sitk.MirrorPad( img, [128] *2, [128]*2 )
size = img.GetSize();

I don't understand what this line does. I expect it would increase the size of the array by adding 128 on the top and bottom. This does not guarantee that the final size is within the restriction of powers of 2,3, and 5 required by the fft module, does it? Or do I not follow what MirrorPad is doing with the input vectors?

Or can I get rid of this restriction some other way... 

  --- Is it possible to configure sitk to  use fftw (or pyfftw)  instead?

Thanks! 
Robert

-----Original Message-----
From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp at mail.nih.gov] 
Sent: Monday, November 28, 2016 2:08 PM
To: Atwood, Robert (DLSLtd,RAL,SCI)
Cc: insight-users at itk.org
Subject: Re: [ITK-users] simpleitk + python + vector type in sitk.mirrorpad args?

Hello,

It looks like there is rightfully so no implicit conversion from numpy.int32 to “unsigned int” for value in tuples.

The following worked for me:

 padim=sitk.MirrorPad(medim,padextra.astype(int),padtop.astype(int))

and so does the following:

padim=sitk.MirrorPad(medim,padextra.astype(np.int),padtop.astype(np.int))

Here is an example for manual padding for FFTs:
https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/FFTConvolution.py

HTH,
Brad

> On Nov 28, 2016, at 8:46 AM, Robert.Atwood at diamond.ac.uk wrote:
> 
> Hi,
> I just can't get this to work, I've tried any permutation I can think of. 
> I want to pad an array up to a calculated value on all dimensions. The calculation is easy to do in vectors with numpy , but whatever I try to do the mirrorpad function will not accept the data type. 
> 
> 
> Fsize is the array size and padsize is the  desired size in all 
> dimensions. The calculation produces initially a floating point number The line in comment # works, but I can't find a simple way to get the calculated output into a type that the function accepts.
> So my question :
> 
>  1. is there a more integrated  way to make the image fit the requirements of the FFT filter, because that's what all this is in aid of.
>  2. if this is the best way to do it, how do I make the function accept the dimension vector??
> 
> 
> Thanks! 
> 
> The error is as follows: 
> 
> _____________________________
> 
> Traceback (most recent call last):
>  File "/home/kny48981/progs/segment_sitk/trysitkmask.py", line 92, in <module>
>    padim=sitk.MirrorPad(medim,padextratup,padtoptup)
>  File "/home/kny48981/.local/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 35916, in MirrorPad
>    return _SimpleITK.MirrorPad(*args, **kwargs)
> TypeError: in method 'MirrorPad', argument 2 of type 'std::vector< unsigned int,std::allocator< unsigned int > > const &'
> 
> _____________________
> 
> 
> Complete reproducer with dummy image: (full output below)
> 
> 
> reproducer.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
> import SimpleITK as sitk
> import numpy as np
> 
> 
> 
> medim=sitk.Image(120,122,135,sitk.sitkFloat32)
> 
> fsize=np.array(medim.GetSize())
> fctr=fsize/2.0
> 
> padsize=(256,256,256)
> 
> padextra=(((padsize-fsize)/2.0)).astype(np.int32)
> 
> print "fsize=",fsize
> print "padsize=",padsize
> print"padextra=", padextra
> print type(padextra)
> padfix = padsize - fsize - padextra - padextra print "padfix",padfix 
> padtop=(padextra + padfix).astype(np.int32)
> 
> 
> padextratup=tuple(padextra)
> padtoptup=tuple(padtop)
> 
> #padextratup=(125,125,100)
> 
> print type(padtoptup)
> print padtoptup
> print type(padtoptup[0])
> print type(padtoptup[1])
> print type(padtoptup[2])
> 
> print type(padextratup)
> print padextratup
> print type(padextratup[0])
> print type(padextratup[1])
> print type(padextratup[2])
> 
> 
> padim=sitk.MirrorPad(medim,padextratup,padtoptup)
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> Output: 
> 
> python ./reproducer.py
> fsize= [120 122 135]
> padsize= (256, 256, 256)
> padextra= [68 67 60]
> <type 'numpy.ndarray'>
> padfix [0 0 1]
> <type 'tuple'>
> (68, 67, 61)
> <type 'numpy.int32'>
> <type 'numpy.int32'>
> <type 'numpy.int32'>
> <type 'tuple'>
> (68, 67, 60)
> <type 'numpy.int32'>
> <type 'numpy.int32'>
> <type 'numpy.int32'>
> Traceback (most recent call last):
>  File "./reproducer.py", line 42, in <module>
>    padim=sitk.MirrorPad(medim,padextratup,padtoptup)
>  File "/home/kny48981/.local/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 35916, in MirrorPad
>    return _SimpleITK.MirrorPad(*args, **kwargs)
> TypeError: in method 'MirrorPad', argument 2 of type 'std::vector< unsigned int,std::allocator< unsigned int > > const &'
> [kny48981 at i12-ws011 testseg_sitk]$
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