From 2c26fa57b948eebb44bcc9a44ba64f1eaf477202 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sun, 9 Jun 2024 11:10:12 -0400
Subject: [PATCH 1/3] MNT: Fix ruff pre-commit arguments

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 354bd3da1..b348393a4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -16,7 +16,7 @@ repos:
     rev: v0.3.4
     hooks:
       - id: ruff
-        args: [--fix, --show-fix, --exit-non-zero-on-fix]
+        args: [--fix, --show-fixes, --exit-non-zero-on-fix]
         exclude: = ["doc", "tools"]
       - id: ruff-format
         exclude: = ["doc", "tools"]

From 63f0647da9bbd0b584b09a8edc7cbac01deff608 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sun, 9 Jun 2024 11:10:28 -0400
Subject: [PATCH 2/3] ENH: Update Nifti extension codes, implement JSON type

---
 nibabel/nifti1.py | 32 +++++++++++++++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/nibabel/nifti1.py b/nibabel/nifti1.py
index d07e54de1..cc89113df 100644
--- a/nibabel/nifti1.py
+++ b/nibabel/nifti1.py
@@ -13,6 +13,7 @@
 
 from __future__ import annotations
 
+import json
 import warnings
 from io import BytesIO
 
@@ -377,7 +378,7 @@ def __repr__(self):
             # deal with unknown codes
             code = self._code
 
-        s = f"Nifti1Extension('{code}', '{self._content}')"
+        s = f"{self.__class__.__name__}('{code}', '{self._content}')"
         return s
 
     def __eq__(self, other):
@@ -505,6 +506,20 @@ def _mangle(self, dataset):
         return dio.read(ds_len)
 
 
+class NiftiJSONExtension(Nifti1Extension):
+    """Generic JSON-based NIfTI header extension
+
+    This class handles serialization and deserialization of JSON contents
+    without any further validation or processing.
+    """
+
+    def _unmangle(self, value: bytes) -> dict:
+        return json.loads(value.decode('utf-8'))
+
+    def _mangle(self, value: dict) -> bytes:
+        return json.dumps(value).encode('utf-8')
+
+
 # NIfTI header extension type codes (ECODE)
 # see nifti1_io.h for a complete list of all known extensions and
 # references to their description or contacts of the respective
@@ -520,6 +535,21 @@ def _mangle(self, dataset):
         (12, 'workflow_fwds', Nifti1Extension),
         (14, 'freesurfer', Nifti1Extension),
         (16, 'pypickle', Nifti1Extension),
+        (18, 'mind_ident', Nifti1Extension),
+        (20, 'b_value', Nifti1Extension),
+        (22, 'spherical_direction', Nifti1Extension),
+        (24, 'dt_component', Nifti1Extension),
+        (26, 'shc_degreeorder', Nifti1Extension),
+        (28, 'voxbo', Nifti1Extension),
+        (30, 'caret', Nifti1Extension),
+        ## Defined in nibabel.cifti2.parse_cifti2
+        # (32, 'cifti', Cifti2Extension),
+        (34, 'variable_frame_timing', Nifti1Extension),
+        (36, 'unassigned', Nifti1Extension),
+        (38, 'eval', Nifti1Extension),
+        (40, 'matlab', Nifti1Extension),
+        (42, 'quantiphyse', Nifti1Extension),
+        (44, 'mrs', NiftiJSONExtension),
     ),
     fields=('code', 'label', 'handler'),
 )

From 9afa0be1f33ab7fb276e4cc3d13d87d19e1004bf Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 11 Jun 2024 22:32:37 -0400
Subject: [PATCH 3/3] TEST: Test NiftiJSONExtension

---
 nibabel/tests/test_nifti1.py | 51 ++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/nibabel/tests/test_nifti1.py b/nibabel/tests/test_nifti1.py
index 5ee4fb3c1..e9f79319e 100644
--- a/nibabel/tests/test_nifti1.py
+++ b/nibabel/tests/test_nifti1.py
@@ -30,6 +30,7 @@
     Nifti1Image,
     Nifti1Pair,
     Nifti1PairHeader,
+    NiftiJSONExtension,
     data_type_codes,
     extension_codes,
     load,
@@ -1388,6 +1389,56 @@ def test_nifti_dicom_extension():
         Nifti1DicomExtension(2, 0)
 
 
+def test_json_extension(tmp_path):
+    nim = load(image_file)
+    hdr = nim.header
+    exts_container = hdr.extensions
+
+    # Test basic functionality
+    json_ext = NiftiJSONExtension('ignore', b'{"key": "value"}')
+    assert json_ext.get_content() == {'key': 'value'}
+    byte_content = json_ext._mangle(json_ext.get_content())
+    assert byte_content == b'{"key": "value"}'
+    json_obj = json_ext._unmangle(byte_content)
+    assert json_obj == {'key': 'value'}
+    size = 16 * ((len(byte_content) + 7) // 16 + 1)
+    assert json_ext.get_sizeondisk() == size
+
+    def ext_to_bytes(ext, byteswap=False):
+        bio = BytesIO()
+        ext.write_to(bio, byteswap)
+        return bio.getvalue()
+
+    # Check serialization
+    bytestring = ext_to_bytes(json_ext)
+    assert bytestring[:8] == struct.pack('<2I', size, extension_codes['ignore'])
+    assert bytestring[8:].startswith(byte_content)
+    assert len(bytestring) == size
+
+    # Save to file and read back
+    exts_container.append(json_ext)
+    nim.to_filename(tmp_path / 'test.nii')
+
+    # We used ignore, so it comes back as a Nifti1Extension
+    rt_img = Nifti1Image.from_filename(tmp_path / 'test.nii')
+    assert len(rt_img.header.extensions) == 3
+    rt_ext = rt_img.header.extensions[-1]
+    assert rt_ext.get_code() == extension_codes['ignore']
+    assert rt_ext.get_content() == byte_content
+
+    # MRS is currently the only JSON extension
+    json_ext._code = extension_codes['mrs']
+    nim.to_filename(tmp_path / 'test.nii')
+
+    # Check that the extension is read back as a NiftiJSONExtension
+    rt_img = Nifti1Image.from_filename(tmp_path / 'test.nii')
+    assert len(rt_img.header.extensions) == 3
+    rt_ext = rt_img.header.extensions[-1]
+    assert rt_ext.get_code() == extension_codes['mrs']
+    assert isinstance(rt_ext, NiftiJSONExtension)
+    assert rt_ext.get_content() == json_obj
+
+
 class TestNifti1General:
     """Test class to test nifti1 in general