From 2b90b292d2431e4bc8357071529b42d7d5107478 Mon Sep 17 00:00:00 2001
From: William T Clarke <william.clarke@ndcn.ox.ac.uk>
Date: Thu, 7 Dec 2023 08:35:36 +0000
Subject: [PATCH] Enh: Automatically add spectralwidth to header extension
 (#120)

* Automatically add spectralwidth

* Better handling of existing spectralWidth field
---
 CHANGELOG.md                |  5 +++++
 requirements.yml            |  2 +-
 spec2nii/spec2nii.py        | 16 ++++++++++++++++
 tests/test_spectralwidth.py | 29 +++++++++++++++++++++++++++++
 4 files changed, 51 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_spectralwidth.py

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 62e8984..b6442ec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,10 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.7.2 (WIP)
+---------------------------------
+- SpectralWidth now added to header extension automatically to match bids specification.
+- NIfTI-MRS V0.8 now generated.
+
 0.7.1 (Tuesday 7th November 2023)
 ---------------------------------
 - The --anon flag can be passed with any call to anonymise after writing files.
diff --git a/requirements.yml b/requirements.yml
index 09d716f..4e0f419 100644
--- a/requirements.yml
+++ b/requirements.yml
@@ -6,4 +6,4 @@ dependencies:
  - scipy
  - brukerapi>=0.1.8
  - pandas
- - nifti-mrs>=1.0.2
+ - nifti-mrs>=1.1.1
diff --git a/spec2nii/spec2nii.py b/spec2nii/spec2nii.py
index 56742e0..9ea7897 100644
--- a/spec2nii/spec2nii.py
+++ b/spec2nii/spec2nii.py
@@ -13,6 +13,7 @@
 import json
 from nibabel.nifti2 import Nifti2Image
 from spec2nii import __version__ as spec2nii_ver
+from numpy import isclose
 # There are case specific imports below
 
 
@@ -291,6 +292,8 @@ def add_common_parameters(subparser):
         if self.imageOut:
             self.implement_overrides(args)
 
+            self.insert_spectralwidth()
+
             if args.anon:
                 from spec2nii.anonymise import anon_nifti_mrs
                 for idx, nifti_mrs_img in enumerate(self.imageOut):
@@ -325,6 +328,19 @@ def implement_overrides(self, args):
                 nifti_mrs_img.header.extensions.clear()
                 nifti_mrs_img.header.extensions.append(new_ext)
 
+    def insert_spectralwidth(self):
+        """Ensure that the correct spectral width is inserted into the header extension"""
+        for nifti_mrs_img in self.imageOut:
+            if 'SpectralWidth' in nifti_mrs_img.hdr_ext\
+                    and not isclose(
+                        nifti_mrs_img.hdr_ext['SpectralWidth'],
+                        1 / nifti_mrs_img.dwelltime,
+                        atol=1E-2):
+                nifti_mrs_img.remove_hdr_field('SpectralWidth')
+                nifti_mrs_img.add_hdr_field('SpectralWidth', 1 / nifti_mrs_img.dwelltime)
+            else:
+                nifti_mrs_img.add_hdr_field('SpectralWidth', 1 / nifti_mrs_img.dwelltime)
+
     def validate_output(self):
         """Run NIfTI MRS validation on output."""
         import nifti_mrs.validator as validate
diff --git a/tests/test_spectralwidth.py b/tests/test_spectralwidth.py
new file mode 100644
index 0000000..4e548d7
--- /dev/null
+++ b/tests/test_spectralwidth.py
@@ -0,0 +1,29 @@
+'''Simple test for SpectralWidth compliance'''
+
+import subprocess
+from pathlib import Path
+import json
+
+import numpy as np
+
+from .io_for_tests import read_nifti_mrs
+
+# Data paths
+siemens_path = Path(__file__).parent / 'spec2nii_test_data' / 'Siemens'
+vb_path = siemens_path / 'VBData' / 'Twix/meas_MID151_svs_se_C_T15_S10_10_FID108741.dat'
+
+
+def test_insertion_spectralwidth(tmp_path):
+    subprocess.check_call(['spec2nii', 'twix',
+                           '-e', 'image',
+                           '-f', 'vb',
+                           '-o', tmp_path,
+                           '-j', str(vb_path)])
+
+    img_t = read_nifti_mrs(tmp_path / 'vb.nii.gz')
+
+    hdr_ext_codes = img_t.header.extensions.get_codes()
+    hdr_ext = json.loads(img_t.header.extensions[hdr_ext_codes.index(44)].get_content())
+
+    assert 'SpectralWidth' in hdr_ext
+    assert np.isclose(hdr_ext['SpectralWidth'], 1 / img_t.header['pixdim'][4])