Which attributes does torchio.Subject check for?

[sarthakpati]

Hey,

I was curious which attributes other than shape does torchio.Subject check for? Specifically, does it check for the spacing attribute? For example, if shapes of 2 modalities in a subject are same but spacing is different, will that trigger an exception?

Cheers,
Sarthak

[fepegar]

Hi, @sarthakpati.

I was curious which attributes other than shape does torchio.Subject check for?

You can take a look at the code for Subject:

https://github.com/fepegar/torchio/blob/8b8791af3e9cd7e6bc45cc3bde3c124a3354c87b/torchio/data/subject.py#L218-L229

Specifically, does it check for the spacing attribute?

It can:

https://github.com/fepegar/torchio/blob/8b8791af3e9cd7e6bc45cc3bde3c124a3354c87b/torchio/data/subject.py#L121-L135

For example, if shapes of 2 modalities in a subject are same but spacing is different, will that trigger an exception?

If that's what you're checking for, yes.

In [1]: import torch

In [2]: import torchio as tio

In [3]: import numpy as np

In [4]: x = torch.rand(1, 2, 3, 4)

In [5]: t1 = tio.ScalarImage(tensor=x, affine=np.diag((1, 1, 1, 1)))

In [6]: t2 = tio.ScalarImage(tensor=x, affine=np.diag((1, 1, 1.5, 1)))

In [7]: subject = tio.Subject(t1=t1, t2=t2)

In [8]: subject.shape
Out[8]: (1, 2, 3, 4)

In [9]: subject.spacing
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-9-08ec10953581> in <module>
----> 1 subject.spacing

~/git/torchio/torchio/data/subject.py in spacing(self)
    132             (1.0, 1.0, 1.2999954223632812)
    133         """
--> 134         self.check_consistent_attribute('spacing')
    135         return self.get_first_image().spacing
    136

~/git/torchio/torchio/data/subject.py in check_consistent_attribute(self, attribute)
    227                 f'\n{pprint.pformat(values_dict)}'
    228             )
--> 229             raise RuntimeError(message)
    230
    231     def check_consistent_spatial_shape(self) -> None:

RuntimeError: More than one spacing found in subject images:
{'t1': (1.0, 1.0, 1.0), 't2': (1.0, 1.0, 1.5)}

[sarthakpati]

Thanks!