Add validation of SpectralWidth

CHANGELOG.md

@@ -1,5 +1,9 @@
 This document contains the nifti_mrs_tools release history in reverse chronological order.
 
+1.1.1 (Wednesday 6th December 2023)
+-----------------------------------
+- Validator checks consistency of any `SpectraWidth` header extension value with the dwell time in `pixdim[4]`.
+
 1.1.0 (Wednesday 6th December 2023)
 -----------------------------------
 - Update definitions to NIfTI-MRS V0.8

src/nifti_mrs/nifti_mrs.py

@@ -132,12 +132,18 @@ def __init__(self, *args, validate_on_creation=True, **kwargs):
                 self._hdr_ext.to_json(),
                 self.image.shape,
                 np.max((self._hdr_ext.ndim, self.image.ndim)))
+            validator.validate_spectralwidth(
+                self._hdr_ext.to_json(),
+                self.dwelltime)
         else:
             try:
                 validator.validate_hdr_ext(
                     self._hdr_ext.to_json(),
                     self.image.shape,
                     np.max((self._hdr_ext.ndim, self.image.ndim)))
+                validator.validate_spectralwidth(
+                    self._hdr_ext.to_json(),
+                    self.dwelltime)
             except validator.headerExtensionError as exc:
                 print(f"This file's header extension is currently invalid. Reason: {str(exc)}")
 
@@ -278,9 +284,11 @@ def hdr_ext(self, new_hdr):
         '''Update MRS JSON header extension from python dict or Hdr_Ext object'''
         if isinstance(new_hdr, dict):
             validator.validate_hdr_ext(json.dumps(new_hdr), self.shape)
+            validator.validate_spectralwidth(json.dumps(new_hdr), self.dwelltime)
             self._hdr_ext = Hdr_Ext.from_header_ext(new_hdr)
         elif isinstance(new_hdr, Hdr_Ext):
             validator.validate_hdr_ext(new_hdr.to_json(), self.shape)
+            validator.validate_spectralwidth(new_hdr.to_json(), self.dwelltime)
             self._hdr_ext = new_hdr
         else:
             raise TypeError('Passed header extension must be a dict or Hdr_Ext object')

src/nifti_mrs/validator.py

@@ -38,6 +38,11 @@ def validate_nifti_mrs(nifti_mrs):
         nifti_mrs.header.extensions[0].get_content(),
         nifti_mrs.shape)
 
+    # Validate that any SpectralWidth definition matches pixdim[4]
+    validate_spectralwidth(
+        nifti_mrs.header.extensions[0].get_content(),
+        nifti_mrs.header['pixdim'][4])
+
 
 def validate_nifti_data(nifti_img_data):
     """Validate the data inside a nibabel nifti image
@@ -230,3 +235,23 @@ def check_type(value, json_type):
         if isinstance(value, json_type):
             return True
     return False
+
+
+def validate_spectralwidth(header_ex, dwelltime):
+    """If a SpectralWidth field is present, check that it matches the dwell time
+
+    Dwell time is stored in pixdim[4].
+
+    :param header_ex: NIfTI-MRS header extensions as a json deserialisable string
+    :type header_ex: str
+    :param dwelltime: Dwell time as stored in pixdim[4] to check against any SpectralWidth definition. In seconds.
+    :type dwelltime: float
+    """
+
+    json_dict = json.loads(header_ex)
+    # check that (if present) SpectralWidth is consistent with pixdim[4]
+    if 'SpectralWidth' in json_dict:
+        if not np.isclose(json_dict['SpectralWidth'], 1 / dwelltime, atol=1E-2):
+            raise headerExtensionError(
+                f'SpectralWidth ({json_dict["SpectralWidth"]:0.2f} Hz) does not match'
+                f' 1 / dwelltime ({1 / dwelltime:0.2f} Hz).')

tests/test_validator.py

@@ -214,3 +214,41 @@ def test_dynamic_header_size():
         dim_5_header={'test': {'Value': [0, 1, 3, 4], 'Description': 'test'}}
     )
     validator.validate_hdr_ext(json.dumps(test_dict), (1, 1, 1, 512, 4), data_dimensions=5)
+
+
+def test_spectralwidth():
+    # Wrong value
+    test_dict = dict(
+        SpectrometerFrequency=[123.2, ],
+        ResonantNucleus=["1H", ],
+        SpectralWidth=500
+    )
+
+    with raises(
+            validator.headerExtensionError,
+            match=r'SpectralWidth \(500\.00 Hz\) does not match 1 / dwelltime \(1000\.00 Hz\).'):
+        validator.validate_spectralwidth(
+            json.dumps(test_dict),
+            0.001)
+
+    # Right value
+    test_dict = dict(
+        SpectrometerFrequency=[123.2, ],
+        ResonantNucleus=["1H", ],
+        SpectralWidth=1000
+    )
+
+    validator.validate_spectralwidth(
+        json.dumps(test_dict),
+        0.001)
+
+    # No value
+    test_dict = dict(
+        SpectrometerFrequency=[123.2, ],
+        ResonantNucleus=["1H", ],
+    )
+
+    validator.validate_spectralwidth(
+        json.dumps(test_dict),
+        0.001)
+