RF (not backward compatible): embed_nifti -> embed_dicom_and_nifti_metadata

That function was returning a new nifti constructed from dicoms if nifti file
did not exist before.  That lead to also different returns in comparison to
operation whenever used on an existing nifti file.
All conversions to nifti should be done centrally, using dcm2niix (via nipype_convert)
and we should avoid possible other tool to create nifti files -- could lead to
inconsistencies etc.

Now that the function does not produce those files or changes those passed
names, there is no need for it to return anything.  So it would return None.

Test adjusted accordingly to use nipype_convert

Author: yarikoptic

heudiconv/dicoms.py

@@ -386,14 +386,10 @@ def _assign_dicom_time(ti):
     return outtar
 
 
-def embed_nifti(dcmfiles, niftifile, infofile, bids_info):
-    """
-
-    If `niftifile` doesn't exist, it gets created out of the `dcmfiles` stack,
-    and json representation of its meta_ext is returned (bug since should return
-    both niftifile and infofile?)
+def embed_dicom_and_nifti_metadata(dcmfiles, niftifile, infofile, bids_info):
+    """Embed metadata from nifti (affine etc) and dicoms into infofile (json)
 
-    if `niftifile` exists, its affine's orientation information is used while
+    `niftifile` should exist. Its affine's orientation information is used while
     establishing new `NiftiImage` out of dicom stack and together with `bids_info`
     (if provided) is dumped into json `infofile`
 
@@ -402,11 +398,11 @@ def embed_nifti(dcmfiles, niftifile, infofile, bids_info):
     dcmfiles
     niftifile
     infofile
-    bids_info
-
-    Returns
-    -------
-    niftifile, infofile
+    bids_info: dict
+      Additional metadata to be embedded. `infofile` is overwritten if exists,
+      so here you could pass some metadata which would overload (at the first
+      level of the dict structure, no recursive fancy updates) what is obtained
+      from nifti and dicoms
 
     """
     # imports for nipype
@@ -422,18 +418,21 @@ def embed_nifti(dcmfiles, niftifile, infofile, bids_info):
     # may be odict now - iter to be safe
     stack = next(iter(stack))
 
-    # Create the nifti image using the data array
     if not op.exists(niftifile):
-        nifti_image = stack.to_nifti(embed_meta=True)
-        nifti_image.to_filename(niftifile)
-        return ds.NiftiWrapper(nifti_image).meta_ext.to_json()
+        raise NotImplementedError(
+            "%s does not exist. "
+            "We are not producing new nifti files here any longer. "
+            "Use dcm2niix directly or .convert.nipype_convert helper ."
+            % niftifile
+        )
 
     orig_nii = nb.load(niftifile)
     aff = orig_nii.affine
     ornt = nb.orientations.io_orientation(aff)
     axcodes = nb.orientations.ornt2axcodes(ornt)
     new_nii = stack.to_nifti(voxel_order=''.join(axcodes), embed_meta=True)
     meta_info = ds.NiftiWrapper(new_nii).meta_ext.to_json()
+    meta_info = json.loads(meta_info)
 
     if bids_info:
         # make nice with python 3 - same behavior?
@@ -444,8 +443,6 @@ def embed_nifti(dcmfiles, niftifile, infofile, bids_info):
     with open(infofile, 'wt') as fp:
         json.dump(meta_info, fp, indent=3, sort_keys=True)
 
-    return niftifile, infofile
-
 
 def embed_metadata_from_dicoms(bids_options, item_dicoms, outname, outname_bids,
                                prov_file, scaninfo, tempdirs, with_prov):
@@ -476,7 +473,7 @@ def embed_metadata_from_dicoms(bids_options, item_dicoms, outname, outname_bids,
     embedfunc = Node(Function(input_names=['dcmfiles', 'niftifile', 'infofile',
                                            'bids_info',],
                               output_names=['outfile', 'meta'],
-                              function=embed_nifti),
+                              function=embed_dicom_and_nifti_metadata),
                      name='embedder')
     embedfunc.inputs.dcmfiles = item_dicoms
     embedfunc.inputs.niftifile = op.abspath(outname)

heudiconv/tests/test_dicoms.py

@@ -5,7 +5,8 @@
 
 from heudiconv.external.pydicom import dcm
 from heudiconv.cli.run import main as runner
-from heudiconv.dicoms import parse_private_csa_header, embed_nifti
+from heudiconv.convert import nipype_convert
+from heudiconv.dicoms import parse_private_csa_header, embed_dicom_and_nifti_metadata
 from .utils import TESTS_DATA_PATH
 
 # Public: Private DICOM tags
@@ -26,35 +27,33 @@ def test_private_csa_header(tmpdir):
         runner(['--files', dcm_file, '-c' 'none', '-f', 'reproin'])
 
 
-def test_nifti_embed(tmpdir):
+def test_embed_dicom_and_nifti_metadata(tmpdir):
     """Test dcmstack's additional fields"""
     tmpdir.chdir()
     # set up testing files
     dcmfiles = [op.join(TESTS_DATA_PATH, 'axasc35.dcm')]
     infofile = 'infofile.json'
 
-    # 1) nifti does not exist
-    out = embed_nifti(dcmfiles, 'nifti.nii', 'infofile.json', None, False)
-    # string -> json
-    out = json.loads(out)
-    # should have created nifti file
-    assert op.exists('nifti.nii')
+    # 1) nifti does not exist -- no longer supported
+    # we should produce nifti using our "standard" ways
+    out_prefix = str(tmpdir / "nifti")
+    nipype_out, prov_file = nipype_convert(
+        dcmfiles, prefix=out_prefix, with_prov=False,
+        bids_options=None, tmpdir=str(tmpdir))
+    niftifile = nipype_out.outputs.converted_files
 
+    assert op.exists(niftifile)
     # 2) nifti exists
-    nifti, info = embed_nifti(dcmfiles, 'nifti.nii', 'infofile.json', None, False)
-    assert op.exists(nifti)
-    assert op.exists(info)
-    with open(info) as fp:
+    embed_dicom_and_nifti_metadata(dcmfiles, niftifile, infofile, None)
+    assert op.exists(infofile)
+    with open(infofile) as fp:
         out2 = json.load(fp)
 
-    assert out == out2
-
     # 3) with existing metadata
     bids = {"existing": "data"}
-    nifti, info = embed_nifti(dcmfiles, 'nifti.nii', 'infofile.json', bids, False)
-    with open(info) as fp:
+    embed_dicom_and_nifti_metadata(dcmfiles, niftifile, infofile, bids)
+    with open(infofile) as fp:
         out3 = json.load(fp)
 
-    assert out3["existing"]
-    del out3["existing"]
-    assert out3 == out2 == out
+    assert out3.pop("existing") == "data"
+    assert out3 == out2