Compatibility with nibabel changes to header extension access.

CHANGELOG.md

@@ -1,5 +1,9 @@
 This document contains the nifti_mrs_tools release history in reverse chronological order.
 
+1.3.1 (Monday 21st October 2024)
+--------------------------------
+- Fix compatibility issue with nibabel > 5.3
+
 1.3.0 (Wednesday 26th June 2024)
 --------------------------------
 - Added `--full-hdr` argumet to `mrs_tools info` which enables printing of the full header extension.

setup.cfg

@@ -19,7 +19,7 @@ author_email = william.clarke@ndcn.ox.ac.uk
 [options]
 install_requires =
     numpy
-    nibabel
+    nibabel>=5.3
     fslpy
     importlib_resources;python_version<'3.10'
 python_requires = >=3.8

src/nifti_mrs/nifti_mrs.py

@@ -118,8 +118,7 @@ def __init__(self, *args, validate_on_creation=True, **kwargs):
                 raise NotNIFTI_MRS('NIFTI-MRS must have a header extension.')
 
             self._hdr_ext = Hdr_Ext.from_header_ext(
-                json.loads(
-                    self.header.extensions[hdr_ext_codes.index(44)].get_content()))
+                self.header.extensions[hdr_ext_codes.index(44)].json())
 
         # Some validation upon creation
         if validate_on_creation:

src/nifti_mrs/validator.py

@@ -35,12 +35,12 @@ def validate_nifti_mrs(nifti_mrs):
 
     # Validate header extension
     validate_hdr_ext(
-        nifti_mrs.header.extensions[0].get_content(),
+        nifti_mrs.header.extensions[0],
         nifti_mrs.shape)
 
     # Validate that any SpectralWidth definition matches pixdim[4]
     validate_spectralwidth(
-        nifti_mrs.header.extensions[0].get_content(),
+        nifti_mrs.header.extensions[0].json(),
         nifti_mrs.header['pixdim'][4])
 
 
@@ -97,7 +97,7 @@ def validate_hdr_ext(header_ex, dimension_sizes, data_dimensions=None):
     """
     # 1. Check that header_ext is json
     try:
-        json_dict = json.loads(header_ex)
+        json_dict = header_ex.json()
     except json.JSONDecodeError as exc:
         raise headerExtensionError("Header extension is not json deserialisable.") from exc
 

tests/test_script_mrs_tools.py

@@ -7,7 +7,6 @@
 # Imports
 import subprocess
 from pathlib import Path
-import json
 
 import nibabel as nib
 import pytest
@@ -163,8 +162,7 @@ def test_merge(tmp_path):
     assert (tmp_path / 'test_newaxis_merge.nii.gz').exists()
     fna = nib.load(tmp_path / 'test_newaxis_merge.nii.gz')
     hdr_ext_codes = fna.header.extensions.get_codes()
-    hdr_ext = json.loads(
-        fna.header.extensions[hdr_ext_codes.index(44)].get_content())
+    hdr_ext = fna.header.extensions[hdr_ext_codes.index(44)].json()
 
     assert fna.ndim == 7
     assert fna.shape == (1, 1, 1, 4096, 4, 2, 2)
@@ -267,8 +265,7 @@ def test_reshape(tmp_path):
     assert f1.shape == (1, 1, 1, 4096, 4, 4, 4)
 
     hdr_ext_codes = f1.header.extensions.get_codes()
-    hdr_ext = json.loads(
-        f1.header.extensions[hdr_ext_codes.index(44)].get_content())
+    hdr_ext = f1.header.extensions[hdr_ext_codes.index(44)].json()
 
     assert hdr_ext['dim_5'] == 'DIM_COIL'
     assert hdr_ext['dim_6'] == 'DIM_DYN'
@@ -287,8 +284,7 @@ def test_reshape(tmp_path):
     assert f2.shape == (1, 1, 1, 4096, 8, 8)
 
     hdr_ext_codes = f2.header.extensions.get_codes()
-    hdr_ext = json.loads(
-        f2.header.extensions[hdr_ext_codes.index(44)].get_content())
+    hdr_ext = f2.header.extensions[hdr_ext_codes.index(44)].json()
 
     assert hdr_ext['dim_5'] == 'DIM_COIL'
     assert hdr_ext['dim_6'] == 'DIM_DYN'