Updates for GE HBCD Sequence

[agudmundson]

More updates for the GE HBCD ISTHMUS sequence. Resolves issues with multichannel data, handles separated short TE and long TE scans that have the same PSD, and correctly uses HERCULES vs. ISTHMUS specific processing routines.

[agudmundson]

@wtclarke Getting a failure in the validation.py from the dimensions. The data is correctly shaped (you can see from my log statements just above the error.. Can you see an obvious reason as to why this might be having an issue?

[wtclarke]

Just looks like the dimensions are changed. Did you change the order? If so you will need to update the tests.

[agudmundson]

@wtclarke Thanks for getting back to me! I thought this was the issue as well, so I went back and made sure that it was ordered the same as before. Still received the same error regardless unfortunately.

[wtclarke]

But it clearly has. The test which was passing before these changes checks for

img = NIFTI_MRS(tmp_path / 'hbcd_edited.nii.gz')
assert img.shape == (1, 1, 1, 2048, 56, 8, 4)

but now that line is failing in the test here

    00 _edited         (1, 1, 1, 2048, 56, 4, 8)
...
FAILED tests/test_ge_pfile.py::test_hbcd_isthmus - assert (1, 1, 1, 2048, 56, 4, ...) == (1, 1, 1, 2048, 56, 8, ...)

and your changes have swapped the last two dimensions.

[agudmundson]

@wtclarke I thought I switched them back after I received the error. Let me ensure I pushed those changes up.

[wtclarke]

Right, but that's just the labelling of the dimensions, the actual sizes are dictated by the data shape you've constructed.

[wtclarke]

Does new_shape.insert(5, edit_cases) insert in the right place?

[agudmundson]

@wtclarke ahh you're right, I forgot to update the reshaping. Looks to have passed now. Thank you!

[agudmundson]

@wtclarke Hi Will, did we need anything else or can we close this out?