[ITK-users] [ITK] ITK PyBuffer get physical point coordinates
D'Isidoro Fabio
fisidoro at ethz.ch
Mon May 8 07:40:14 EDT 2017
Thank you for your reply.
I am now working on a itk project with C++ (no Python binding), but I can’t reproduce what I did in Python with the PhysicalPointImageSource filter:
typedef itk::Image< itk::Vector<Ctype, 3>, Dimension > PhyImageType;
typedef itk:: typedef itk::PhysicalPointImageSource< PhyImageType > PhysicalPointImagefilter; // error ITK has no member PhysicalPointImageSource
It is strange to me, since it is part of manual… Is this filter not for the ITK C++ distribution? If this is the case, how can I get an image of physical coordinates with itk C++?
Thank you again,
Fabio.
From: Francois Budin [mailto:francois.budin at kitware.com]
Sent: Dienstag, 2. Mai 2017 17:49
To: D'Isidoro Fabio <fisidoro at ethz.ch>
Cc: Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov>; insight-users at itk.org
Subject: Re: [ITK-users] [ITK] ITK PyBuffer get physical point coordinates
Hello Fabio,
The main difference between itk.GetArrayFromImage() and itk.PyBuffer[ImageType].GetArrayFromImage() is that itk.GetAraryFromImage() is a wrapping of itk.PyBuffer[ImageType].GetArrayFromImage() in Python that automatically finds the type of the input image (and is a shorted command line). The reason why this worked but not itk.PyBuffer[ImageType.GetArrayFromImage() is because in the wrapping, if a filter is given instead of an image, the output of the filter will be used.
Which means that what really happen is that you gave a filter to a function (itk.PyBuffer[ImageType].GetArrayFromImage()) expecting an image.
If you want to work with the long command, you have to make sure that the input is an image:
image=source.GetOutput()
itk.PyBuffer[ImageType].GetArrayFromImage(image)
And then it should work.
Hope this helps,
Francois
On Tue, May 2, 2017 at 11:20 AM, D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>> wrote:
Hi Francois,
It works with your commands, the difference being the use of:
itk.GetArrayFromImage(source)
in your version, instead of:
itk.PyBuffer[ImageType].GetArrayFromImage(source)
in my version.
May you explain me the difference, and why using PyBuffer does not work for this case?
Also, when using VectorImage I get the error “No module named 'ITKQuadEdgeMeshPython'”. This is the only module that failed in my ITK Python build. Is this a known bug or it was just for my build?
Thank you!
Fabio.
From: Francois Budin [mailto:francois.budin at kitware.com<mailto:francois.budin at kitware.com>]
Sent: Freitag, 28. April 2017 23:12
To: D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>>
Cc: Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>>; insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK-users] [ITK] ITK PyBuffer get physical point coordinates
Hello Fabio,
I was able to use this filter in Python. Here is the commands I typed:
In [14]: ImageType=itk.Image[itk.Vector[itk.F,2],2]
In [15]: source=itk.PhysicalPointImageSource[ImageType].New()
In [16]: source.SetSize([5,5])
In [17]: source.SetOrigin([0,0])
In [18]: source.SetSpacing([.5,.5])
In [19]: source.Update()
In [20]: itk.GetArrayFromImage(source)
Out[20]:
itkndarray([[[ 0. , 0. ],
[ 0.5, 0. ],
[ 1. , 0. ],
[ 1.5, 0. ],
[ 2. , 0. ]],
[[ 0. , 0.5],
[ 0.5, 0.5],
[ 1. , 0.5],
[ 1.5, 0.5],
[ 2. , 0.5]],
[[ 0. , 1. ],
[ 0.5, 1. ],
[ 1. , 1. ],
[ 1.5, 1. ],
[ 2. , 1. ]],
[[ 0. , 1.5],
[ 0.5, 1.5],
[ 1. , 1.5],
[ 1.5, 1.5],
[ 2. , 1.5]],
[[ 0. , 2. ],
[ 0.5, 2. ],
[ 1. , 2. ],
[ 1.5, 2. ],
[ 2. , 2. ]]], dtype=float32)
It also worked with VectorImages:
In [22]: ImageType=itk.VectorImage[itk.F,2]
In [23]: source=itk.PhysicalPointImageSource[ImageType].New()
In [24]: source.SetOrigin([0,0])
In [25]: source.SetSize([5,5])
In [26]: source.SetSpacing([.5,.5])
In [27]: source.Update()
In [28]: itk.GetArrayFromImage(source)
To answer your questions:
1) This filter is only wrapped over image of vectors and vector images. You can have the list of types that are available in Python with itk.PhysicalPointImageSource.GetTypes()
2) You may have a version of ITK Python for which VectorImage is not wrapped for PyBuffer. You can try to update your ITK Python [1]
Hope this helps,
Francois
[1] https://github.com/InsightSoftwareConsortium/ITKPythonPackage
On Fri, Apr 28, 2017 at 12:05 PM, D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>> wrote:
Thank you for your reply.
1) I have tried as a first step the following:
DRRPhy = itk.PhysicalPointImageSource[itk.Image[itk.Point[itk.F, Dimension], Dimension]].New()
But I get the error:
KeyError: "itkTemplate : No template (<class 'itkPointPython.itkPointF3'>, 3) for the itk::Image class"
So I guess I can’t generate an image with itk.Points as PixelType. Therefore I chose to use a VectorImage as ImageType in Input to the PhysicalPointImageSource.
sourceImage = itk.PhysicalPointImageSource[itk.VectorImage[itk.F, Dimension]].New()
sourceImage.SetSize(size)
sourceImage.SetSpacing(spacing)
sourceImage.SetOrigin(origin)
#DRRPhy.SetIndex(start) it does not work, how to set the start index?
DRRPhy.SetDirection(direction)
2) However, using PyBuffer to get a numpy array form that does not work:
sourceImageArray = itk. PyBuffer[ImageType].GetArrayFromImage(sourceImage)
I get the error:
AttributeError: 'itkPhysicalPointImageSourceVIF3' object has no attribute 'GetLargestPossibleRegion'
Am I doing the right thing in point 1) ?
How could I solve point 2) ?
Thank you !
Fabio.
From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>]
Sent: Donnerstag, 27. April 2017 23:16
To: D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>>
Cc: insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK] [ITK-users] ITK PyBuffer get physical point coordinates
Hi!
You can generate an image of the physical locations of each pixel with the PhysicalPointImageSource filter:
https://itk.org/Doxygen/html/classitk_1_1PhysicalPointImageSource.html
Very recently added is the SetReferenceImage, which can be use to copy the meta data from one image to the parameters of this filter. If your version is not super recent then you can manually set the Size, Spacing, Origin, Direction and StartIndex.
After you generate the point image you should be able to convert to with the same method.
HTH,
Brad
On Apr 27, 2017, at 4:58 PM, D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>> wrote:
Hallo,
I know it’s possible to get a numpy array of an itk image with:
itk.PyBuffer[ImageType].GetArrayFromImage(Image)
Is it by any chance also possible to obtain a (flattended) numpy array of the physical coordinates of the image pixels too?
Thank you!
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