Modify an element in a matrix

Engineering
1

Hi, if I want to modify an element in a matrix, in ITK 4.13.3, I can code like

image
image1261×114 5.04 KB

But in ITK 5.2.1, the same code seems fail to change the element.
image
image1612×134 6.78 KB

I’d like to know what’s the way to do this in ITK 5. Thanks in advance.

2

@matt.mccormick, trying the above code on my computer also gives me an error, in two different environments:

Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 05:59:45) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import itk
>>> a=itk.Matrix[itk.D,3,3]
>>> a.GetVnlMatrix().set(0,0,1)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: GetVnlMatrix() missing 1 required positional argument: 'self'
>>> itk.__file__
'C:\\Users\\Dzenan\\miniconda3\\envs\\deep_learning\\lib\\site-packages\\itk\\__init__.py'
>>> itk.__version__
'5.2.1'

Python 3.9.13 (tags/v3.9.13:6de2ca5, May 17 2022, 16:36:42) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import itk
>>> a=itk.Matrix[itk.D,3,3]
>>> a.GetVnlMatrix().set(0,0,1)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: GetVnlMatrix() missing 1 required positional argument: 'self'
>>> itk.__file__
'M:\\a\\ITK-py\\Wrapping\\Generators\\Python\\itk\\__init__.py'
>>> itk.__version__
'5.3.0'
3

Ooops, I forgot instantiation parentheses. With that I get the same output as @zhuangming.shen in both of these enviroments.

4

I think the use of set was incorrect originally. vnl_matrix has a set method, but it’s not doing what you are trying to do there.

  //: Fills (laminates) this matrix with the given data, then returns it.
  // A synonym for copy_in()
  vnl_matrix& set(T const *d) { return copy_in(d); }

If you want to set a pixel in a vnl_matrix, you need to use put instead of set. Or probably easier, use itk.GetArrayViewFromVnlMatrix. And use numpy operator [] to manipulate it.

I am not sure if the ITK4 code is calling a constructor on-the-fly with arguments (0, 0, 1) and passing it to set?

5

I tried “put” instead of “set”, but still fail to change the element in ITK 5.2.1.

image
image963×215 5.35 KB

6

Umm, the problem is that the GetVnlMatrix() returns a copy, instead of a reference.

In [2]: m = itk.Matrix[itk.D, 3,3]()

In [3]: m
Out[3]: itkMatrixD33 ([[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]])

In [4]: m.GetVnlMatrix()
Out[4]: <itk.vnl_matrix_fixedPython.vnl_matrix_fixedD_3_3; proxy of <Swig Object of type 'vnl_matrix_fixedD_3_3 *' at 0x7fb3662bdb90> >

In [5]: m.GetVnlMatrix()
Out[5]: <itk.vnl_matrix_fixedPython.vnl_matrix_fixedD_3_3; proxy of <Swig Object of type 'vnl_matrix_fixedD_3_3 *' at 0x7fb423e87240> >

It was changed here:

2 Likes
7

Opened an issue here:

Thanks for reporting it @zhuangming.shen
I am not sure right now how to modify an element from an itk.Matrix in python.

8

Since ITK can now convert matrices from / to NumPy arrays, I think the best is to do something like

>>> import itk
>>> import numpy as np
>>> m = itk.Matrix[itk.D, 3,3]()
>>> m.GetVnlMatrix().get(0,0)
0.0
>>> a=itk.array_from_matrix(m)
>>> a[0,0]=1
>>> m=itk.matrix_from_array(a)
>>> m.GetVnlMatrix().get(0,0)
1.0
4 Likes