Add option to supress conjugation on creation from numpy

.gitignore

@@ -2,3 +2,5 @@ __pycache__/
 *.egg-info/
 .vscode
 tmp_notes
+build
+

CHANGELOG.md

@@ -1,5 +1,9 @@
 This document contains the nifti_mrs_tools release history in reverse chronological order.
 
+0.1.2 (Thursday 12th January 2023)
+----------------------------------
+- Add option to prevent conjugation with numpy data. For spec2nii compatibility.
+
 0.1.1 (Wednesday 11th January 2023)
 -----------------------------------
 - Make compliant with NIfTI-MRS V0.6

src/nifti_mrs/create_nmrs.py

@@ -37,7 +37,15 @@ def _default_affine():
     return default
 
 
-def gen_nifti_mrs(data, dwelltime, spec_freq, nucleus='1H', affine=None, dim_tags=[None, None, None], nifti_version=2):
+def gen_nifti_mrs(
+        data,
+        dwelltime,
+        spec_freq,
+        nucleus='1H',
+        affine=None,
+        dim_tags=[None, None, None],
+        nifti_version=2,
+        no_conj=False):
     """Generate NIfTI-MRS from data and required metadata
 
     :param data: Complex-typed numpy array of at least 4 dimensions (max 7)
@@ -54,6 +62,8 @@ def gen_nifti_mrs(data, dwelltime, spec_freq, nucleus='1H', affine=None, dim_tag
     :type dim_tags: list, optional
     :param nifti_version: Version of NIfTI header format, defaults to 2
     :type nifti_version: int, optional
+    :param no_conj: If true stops conjugation of data on creation, defaults to False
+    :type no_conj: bool, optional
     :return: NIfTI-MRS object
     :rtype: nifti_mrs.nifti_mrs.NIFTI_MRS
     """
@@ -74,10 +84,11 @@ def gen_nifti_mrs(data, dwelltime, spec_freq, nucleus='1H', affine=None, dim_tag
         dwelltime,
         hdr_ext,
         affine=affine,
-        nifti_version=nifti_version)
+        nifti_version=nifti_version,
+        no_conj=no_conj)
 
 
-def gen_nifti_mrs_hdr_ext(data, dwelltime, hdr_ext, affine=None, nifti_version=2):
+def gen_nifti_mrs_hdr_ext(data, dwelltime, hdr_ext, affine=None, nifti_version=2, no_conj=False):
     """Generate NIfTI-MRS from data and header extension object
 
     :param data: Complex-typed numpy array of at least 4 dimensions (max 7)
@@ -92,6 +103,8 @@ def gen_nifti_mrs_hdr_ext(data, dwelltime, hdr_ext, affine=None, nifti_version=2
     :type dim_tags: list, optional
     :param nifti_version: Version of NIfTI header format, defaults to 2
     :type nifti_version: int, optional
+    :param no_conj: If true stops conjugation of data on creation, defaults to False
+    :type no_conj: bool, optional
     :return: NIfTI-MRS object
     :rtype: nifti_mrs.nifti_mrs.NIFTI_MRS
     """
@@ -133,4 +146,7 @@ def gen_nifti_mrs_hdr_ext(data, dwelltime, hdr_ext, affine=None, nifti_version=2
     extension = nib.nifti1.Nifti1Extension(44, json_s.encode('UTF-8'))
     header.extensions.append(extension)
 
-    return NIFTI_MRS(data, header=header)
+    if no_conj:
+        return NIFTI_MRS(data.conj(), header=header)
+    else:
+        return NIFTI_MRS(data, header=header)

tests/test_create_nmrs.py

@@ -72,3 +72,11 @@ def test_gen_new_nifti_mrs_conj(tmp_path):
                          nucleus='1H')
 
     assert np.allclose(nmrs[:], obj_in[:])
+
+    nmrs = gen_nifti_mrs(obj_in[:],
+                         obj_in.dwelltime,
+                         obj_in.spectrometer_frequency[0],
+                         nucleus='1H',
+                         no_conj=True)
+
+    assert np.allclose(nmrs[:], obj_in[:].conj())