ENH: spec2nii insert handles non-compliant NIfTI files. (#70)

* spec2nii insert handles non-compliant nifti files.

* Correct date in changelog.

CHANGELOG.md

@@ -1,5 +1,10 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.6.7 (Wednesday 15th March 2023)
+---------------------------------
+- `spec2nii insert` can now insert a compliant header object into a non-compliant NIfTI file to generate a new NIfTI-MRS file.
+- `spec2nii insert` can now update dwelltime using the optional `--dwelltime` argument.
+
 0.6.6 (Thursday 9th March 2023)
 -------------------------------
 - Added in ability to generate empty NIfTI-MRS for twix-pathway MRSI scans.

spec2nii/other.py

@@ -6,7 +6,7 @@
 import json
 import pprint
 
-from nifti_mrs.nifti_mrs import NIFTI_MRS
+from nifti_mrs.nifti_mrs import NIFTI_MRS, NotNIFTI_MRS
 
 
 def dump_headers(args):
@@ -52,13 +52,31 @@ def insert_hdr_ext(args):
     :return: List of output names
     :rtype: [str,]
     """
-    # Load data
-    nifti_mrs_img = NIFTI_MRS(args.file)
 
     with open(args.json_file) as jf:
         new_hdr = json.load(jf)
 
-    nifti_mrs_img.hdr_ext = new_hdr
+    # Load data
+    try:
+        nifti_mrs_img = NIFTI_MRS(args.file)
+        nifti_mrs_img.hdr_ext = new_hdr
+
+    except NotNIFTI_MRS:
+        print(f'{args.file} is not compliant with the NIfTI-MRS standard, attempting to convert')
+        from fsl.data.image import Image
+        from nifti_mrs.create_nmrs import gen_nifti_mrs_hdr_ext
+        from nifti_mrs.hdr_ext import Hdr_Ext
+
+        nimg = Image(args.file)
+        hdr_ext = Hdr_Ext.from_header_ext(new_hdr, dimensions=nimg.ndim)
+        nifti_mrs_img = gen_nifti_mrs_hdr_ext(
+            nimg[:],
+            nimg.header['pixdim'][4],
+            hdr_ext,
+            affine=nimg.getAffine('voxel', 'world'))
+
+    if args.dwelltime is not None:
+        nifti_mrs_img.dwelltime = args.dwelltime
 
     # Process output name.
     if args.fileout:

spec2nii/spec2nii.py

@@ -252,6 +252,8 @@ def add_common_parameters(subparser):
         parser_insert = subparsers.add_parser('insert', help='Insert json formatted file into existing NIfTI-MRS file.')
         parser_insert.add_argument('file', help='NIFTI-MRS file', type=Path)
         parser_insert.add_argument('json_file', help='JSON file to insert', type=Path)
+        parser_insert.add_argument("--dwelltime", type=float,
+                                   help="Specify a new dwelltime (1/bandwidth, pixdim[4]) value in seconds.")
         parser_insert.add_argument("-f", "--fileout", type=str,
                                    help="Output file base name (default = input file name)")
         parser_insert.add_argument("-o", "--outdir", type=Path,

tests/test_other_func.py

@@ -5,10 +5,14 @@
 '''
 
 import subprocess
-from .io_for_tests import read_nifti_mrs
 from pathlib import Path
 import json
 
+import numpy as np
+from fsl.data.image import Image
+
+from .io_for_tests import read_nifti_mrs
+
 # Data paths
 siemens_path = Path(__file__).parent / 'spec2nii_test_data' / 'Siemens'
 data_path = siemens_path / 'VBData' / 'Twix' / 'meas_MID151_svs_se_C_T15_S10_10_FID108741.dat'
@@ -74,6 +78,7 @@ def test_insert(tmp_path):
     subprocess.check_call(['spec2nii', 'insert',
                            '-o', tmp_path,
                            '-f', 'new',
+                           '--dwelltime', '0.0005',
                            str(tmp_path / 'original.nii.gz'),
                            str(tmp_path / 'new.json')])
 
@@ -82,3 +87,52 @@ def test_insert(tmp_path):
     hdr_ext = json.loads(img.header.extensions[hdr_ext_codes.index(44)].get_content())
 
     assert extracted_hdr == hdr_ext
+    assert np.isclose(img.header['pixdim'][4], 0.0005)
+
+
+def test_insert_not_nmrs(tmp_path):
+    # Create a small dummy file that doesn't conform to the standard
+
+    affine = np.random.random((4, 4))
+    affine[3, 0] = 0.0
+    affine[3, 1] = 0.0
+    affine[3, 2] = 0.0
+    affine[3, 3] = 1.0
+
+    data = np.ones((3, 3, 3, 256), dtype=float) + 1j * np.ones((3, 3, 3, 256), dtype=float)
+
+    non_compliant = Image(data, header=None, xform=affine)
+    non_compliant.header['pixdim'][4] = 1 / 1000
+    non_compliant.save(tmp_path / 'noncompliant.nii.gz')
+
+    newhd = {
+        'SpectrometerFrequency': 123.456789,
+        'ResonantNucleus': '1H'}
+
+    with open(tmp_path / 'new.json', 'w') as jf:
+        json.dump(newhd, jf)
+
+    subprocess.check_call(['spec2nii', 'insert',
+                           '-o', tmp_path,
+                           '-f', 'compliant',
+                           str(tmp_path / 'noncompliant.nii.gz'),
+                           str(tmp_path / 'new.json')])
+
+    img = read_nifti_mrs(tmp_path / 'compliant.nii.gz')
+    hdr_ext_codes = img.header.extensions.get_codes()
+    hdr_ext = json.loads(img.header.extensions[hdr_ext_codes.index(44)].get_content())
+
+    assert hdr_ext['ResonantNucleus'][0] == '1H'
+    assert img.header.get_intent()[2].split('_')[0] == 'mrs'
+    assert np.allclose(img.affine, affine)
+    assert np.isclose(img.header['pixdim'][4], 1 / 1000)
+
+    subprocess.check_call(['spec2nii', 'insert',
+                           '-o', tmp_path,
+                           '-f', 'compliant_dt',
+                           '--dwelltime', '0.0005',
+                           str(tmp_path / 'noncompliant.nii.gz'),
+                           str(tmp_path / 'new.json')])
+
+    img = read_nifti_mrs(tmp_path / 'compliant_dt.nii.gz')
+    assert np.isclose(img.header['pixdim'][4], 0.0005)