# ITK 5.1.2 Python XArray to image bug
**URL:** https://discourse.itk.org/t/itk-5-1-2-python-xarray-to-image-bug/3760
**Category:** Uncategorized
**Created:** [January 14, 2021, 10:47pm UTC](https://discourse.itk.org/t/itk-5-1-2-python-xarray-to-image-bug/3760 "2021-01-14T22:47:50Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)
#### Post date: [January 14, 2021, 10:47pm UTC](https://discourse.itk.org/t/itk-5-1-2-python-xarray-to-image-bug/3760/1 "2021-01-14T22:47:50Z")
Hi message board,
I’m trying to create a script in Python where I create a cine clip of a 3D volume. I want to make an itk image out of a 4D x array with data labels ‘x’, ‘y’, ‘z’, ‘t’.
I made a simple script where I repeat an image volume of a sphere at each time point. When I try to create the itk image I get an error message. My python script and error messages are below. Are there any suggestions for what the problem could be?
Code:
```
import numpy as np
import xarray as xr
import itk
###3D sphere
npim = np.zeros( (101,101,101) )
xx, yy, zz = np.mgrid[0:101, 0:101, 0:101]
rr = np.sqrt( (xx-50)**2 + (yy-50)**2 + (zz-50)**2 )
npim[rr < 15] = 1
###Replicate across t dimension
fourd = npim
fourd.shape = ( 101, 101,101, 1)
fourd = np.tile(fourd, [1,1,1,5])
fourdxr = xr.DataArray(fourd, dims=['x','y','z','t'])
###Create an itk image
print('Creating a 4D image')
itkim = itk.image_from_xarray(fourdxr)
```
Error Message:
Traceback (most recent call last):
File “testScript.py”, line 24, in
itkim = itk.image\_from\_xarray(fourdxr)
File “/home/nick/Software/InsightToolkit-5.1.2/build/Wrapping/Generators/Python/itkExtras.py”, line 453, in image\_from\_xarray
origin.reverse()
TypeError: Expecting an itkVectorD4, an int, a float, a sequence of int or a sequence of float.
Additional information:
Wrong number or type of arguments for overloaded function ‘itkImageBase4\_SetSpacing’.
Possible C/C++ prototypes are:
itkImageBase4::SetSpacing(itkVectorD4 const &)
itkImageBase4::SetSpacing(double const \*)
itkImageBase4::SetSpacing(float const \*)
ITK script where my code sample errors out:
```
def image_from_xarray(data_array):
"""Convert an xarray.DataArray to an itk.Image.
Metadata encoded with xarray_from_image is applied to the itk.Image.
This interface is and behavior is experimental and is subject to possible
future changes."""
import numpy as np
import itk
spatial_dims = list({'z', 'y', 'x'}.intersection(set(data_array.dims)))
spatial_dims.sort(reverse=True)
spatial_dimension = len(spatial_dims)
ordered_dims = ('z', 'y', 'x')[-spatial_dimension:]
if ordered_dims != tuple(spatial_dims):
raise ValueError('Spatial dimensions do not have the required order: ' + str(ordered_dims))
is_vector = 'c' in data_array.dims
itk_image = itk.image_view_from_array(data_array.values, is_vector=is_vector)
origin = [0.0]*spatial_dimension
spacing = [1.0]*spatial_dimension
for index, dim in enumerate(spatial_dims):
coords = data_array.coords[dim]
if coords.shape[0] > 1:
origin[index] = float(coords[0])
spacing[index] = float(coords[1]) - float(coords[0])
spacing.reverse()
itk_image.SetSpacing(spacing)
origin.reverse()
itk_image.SetOrigin(origin)
if 'direction' in data_array.attrs:
direction = data_array.attrs['direction']
itk_image.SetDirection(np.flip(direction))
return itk_image
```
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [January 15, 2021, 10:18pm UTC](https://discourse.itk.org/t/itk-5-1-2-python-xarray-to-image-bug/3760/2 "2021-01-15T22:18:02Z")
Before version 5.2RC1, ITK’s python wrapping was compiled with dimensions 2 and 3, but not 4. That is probably the issue, which should be resolved by `itk5.2rc1`. Give the new version a try and report back.
---
### Author:  [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)
#### Post date: [January 15, 2021, 11:07pm UTC](https://discourse.itk.org/t/itk-5-1-2-python-xarray-to-image-bug/3760/3 "2021-01-15T23:07:27Z")
I did turn on 4d wrapping in the cmake options when compiling ITK. Are issues with 4d images expected in 5.1 even when the CMake option to wrap 2;3;4 dimensional images is turned on?
I will try downloading the 5.2 version.
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [January 15, 2021, 11:17pm UTC](https://discourse.itk.org/t/itk-5-1-2-python-xarray-to-image-bug/3760/4 "2021-01-15T23:17:31Z")
If you compiled yourself and turned on 4th dimension, that should have been enough. As a recent addition, `image_from_xarray` is not thoroughly tested.
In `spacing[index] = float(coords[1]) - float(coords[0])` the `float` might need to be `double`. Or `spacing` somehow else adjusted to be accepted by `itk_image.SetSpacing()`.
---
### Author:  [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [February 9, 2021, 2:48pm UTC](https://discourse.itk.org/t/itk-5-1-2-python-xarray-to-image-bug/3760/5 "2021-02-09T14:48:03Z")
Hello @Nick_Rubert! 👋
As @dzenanz, support was not yet added for a `t` dimension. This is added in this PR:
>