TEST: Parametrize all DerivativesDataSink tests

Author: effigies

niworkflows/interfaces/tests/test_bids.py

@@ -47,6 +47,34 @@
 BOLD_PATH = "ds054/sub-100185/func/sub-100185_task-machinegame_run-01_bold.nii.gz"
 
 
+def make_prep_and_save(
+    prep_interface,
+    base_directory,
+    out_path_base=None,
+    **kwargs,
+):
+    if prep_interface is bintfs.DerivativesDataSink:
+        kwargs.update(out_path_base=out_path_base, base_directory=base_directory)
+
+    prep = save = prep_interface(**kwargs)
+
+    if prep_interface is not bintfs.DerivativesDataSink:
+        save = bintfs.SaveDerivative(base_directory=base_directory)
+
+    return prep, save
+
+
+def connect_and_run_save(prep_result, save):
+    if prep_result.interface is bintfs.DerivativesDataSink:
+        return prep_result
+
+    save.inputs.in_file = prep_result.outputs.out_file
+    save.inputs.relative_path = prep_result.outputs.out_path
+    save.inputs.metadata = prep_result.outputs.out_meta
+
+    return save.run()
+
+
 @pytest.mark.parametrize("interface", [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
 @pytest.mark.parametrize("out_path_base", [None, "fmriprep"])
 @pytest.mark.parametrize(
@@ -296,36 +324,26 @@ def test_DerivativesDataSink_build_path(
         ds_inputs.append(str(fname))
 
     base_directory = tmp_path / "output"
-    work_dir = tmp_path / "work"
     base_directory.mkdir()
-    work_dir.mkdir()
 
-    prep = save = interface(
+    prep, save = make_prep_and_save(
+        interface,
+        base_directory=str(base_directory),
+        out_path_base=out_path_base,
         in_file=ds_inputs,
         source_file=source,
         dismiss_entities=dismiss_entities,
         **entities,
-        **({"out_path_base": out_path_base} if interface == bintfs.DerivativesDataSink else {}),
     )
-    if interface == bintfs.DerivativesDataSink:
-        prep.inputs.base_directory = str(base_directory)
-    else:
-        save = bintfs.SaveDerivative(base_directory=str(base_directory))
-
     if isinstance(expectation, type):
         with pytest.raises(expectation):
             prep.run()
         return
 
-    prep_outputs = save_outputs = prep.run().outputs
-
-    if save is not prep:
-        save.inputs.in_file = prep_outputs.out_file
-        save.inputs.relative_path = prep_outputs.out_path
-        save.inputs.metadata = prep_outputs.out_meta
-        save_outputs = save.run().outputs
+    prep_result = prep.run()
+    save_result = connect_and_run_save(prep_result, save)
 
-    output = save_outputs.out_file
+    output = save_result.outputs.out_file
     if isinstance(expectation, str):
         expectation = [expectation]
         output = [output]
@@ -363,7 +381,8 @@ def test_DerivativesDataSink_build_path(
         assert sha1(Path(out).read_bytes()).hexdigest() == chksum
 
 
-def test_DerivativesDataSink_dtseries_json(tmp_path):
+@pytest.mark.parametrize("interface", [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
+def test_DerivativesDataSink_dtseries_json(tmp_path, interface):
     cifti_fname = str(tmp_path / "test.dtseries.nii")
 
     axes = (nb.cifti2.SeriesAxis(start=0, step=2, size=20),
@@ -378,20 +397,22 @@ def test_DerivativesDataSink_dtseries_json(tmp_path):
     source_file.parent.mkdir(parents=True)
     source_file.touch()
 
-    dds = bintfs.DerivativesDataSink(
-        in_file=cifti_fname,
+    prep, save = make_prep_and_save(
+        interface,
         base_directory=str(tmp_path),
+        out_path_base="",
+        in_file=cifti_fname,
         source_file=str(source_file),
         compress=False,
-        out_path_base="",
         space="fsLR",
         grayordinates="91k",
         RepetitionTime=2.0,
     )
 
-    res = dds.run()
+    prep_result = prep.run()
+    save_result = connect_and_run_save(prep_result, save)
 
-    out_path = Path(res.outputs.out_file)
+    out_path = Path(save_result.outputs.out_file)
 
     assert out_path.name == "sub-01_task-rest_space-fsLR_bold.dtseries.nii"
     old_sidecar = out_path.with_name("sub-01_task-rest_space-fsLR_bold.dtseries.json")
@@ -402,6 +423,7 @@ def test_DerivativesDataSink_dtseries_json(tmp_path):
     assert "RepetitionTime" in json.loads(new_sidecar.read_text())
 
 
+@pytest.mark.parametrize("interface", [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
 @pytest.mark.parametrize(
     "space, size, units, xcodes, zipped, fixed, data_dtype",
     [
@@ -427,7 +449,7 @@ def test_DerivativesDataSink_dtseries_json(tmp_path):
     ],
 )
 def test_DerivativesDataSink_bold(
-    tmp_path, space, size, units, xcodes, zipped, fixed, data_dtype
+    tmp_path, interface, space, size, units, xcodes, zipped, fixed, data_dtype
 ):
     fname = str(tmp_path / "source.nii") + (".gz" if zipped else "")
 
@@ -438,25 +460,29 @@ def test_DerivativesDataSink_bold(
     nb.Nifti1Image(np.zeros(size), np.eye(4), hdr).to_filename(fname)
 
     # BOLD derivative in T1w space
-    dds = bintfs.DerivativesDataSink(
+    prep, _ = make_prep_and_save(
+        interface,
         base_directory=str(tmp_path),
         keep_dtype=True,
         data_dtype=data_dtype or Undefined,
         desc="preproc",
         source_file=BOLD_PATH,
         space=space or Undefined,
         in_file=fname,
-    ).run()
+    )
+
+    prep_result = prep.run()
 
-    nii = nb.load(dds.outputs.out_file)
-    assert dds.outputs.fixed_hdr == fixed
+    nii = nb.load(prep_result.outputs.out_file)
+    assert prep_result.outputs.fixed_hdr == fixed
     if data_dtype:
         assert nii.get_data_dtype() == np.dtype(data_dtype)
     assert int(nii.header["qform_code"]) == XFORM_CODES[space]
     assert int(nii.header["sform_code"]) == XFORM_CODES[space]
     assert nii.header.get_xyzt_units() == ("mm", "sec")
 
 
+@pytest.mark.parametrize("interface", [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
 @pytest.mark.parametrize(
     "space, size, units, xcodes, fixed",
     [
@@ -480,7 +506,7 @@ def test_DerivativesDataSink_bold(
         (None, (30, 30, 30), (None, "sec"), (0, 0), [True]),
     ],
 )
-def test_DerivativesDataSink_t1w(tmp_path, space, size, units, xcodes, fixed):
+def test_DerivativesDataSink_t1w(tmp_path, interface, space, size, units, xcodes, fixed):
     fname = str(tmp_path / "source.nii.gz")
 
     hdr = nb.Nifti1Header()
@@ -490,22 +516,26 @@ def test_DerivativesDataSink_t1w(tmp_path, space, size, units, xcodes, fixed):
     nb.Nifti1Image(np.zeros(size), np.eye(4), hdr).to_filename(fname)
 
     # BOLD derivative in T1w space
-    dds = bintfs.DerivativesDataSink(
+    prep, _ = make_prep_and_save(
+        interface,
         base_directory=str(tmp_path),
         keep_dtype=True,
         desc="preproc",
         source_file=T1W_PATH,
         space=space or Undefined,
         in_file=fname,
-    ).run()
+    )
 
-    nii = nb.load(dds.outputs.out_file)
-    assert dds.outputs.fixed_hdr == fixed
+    prep_result = prep.run()
+
+    nii = nb.load(prep_result.outputs.out_file)
+    assert prep_result.outputs.fixed_hdr == fixed
     assert int(nii.header["qform_code"]) == XFORM_CODES[space]
     assert int(nii.header["sform_code"]) == XFORM_CODES[space]
     assert nii.header.get_xyzt_units() == ("mm", "unknown")
 
 
+@pytest.mark.parametrize("interface", [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
 @pytest.mark.parametrize(
     "source_file",
     [
@@ -517,7 +547,7 @@ def test_DerivativesDataSink_t1w(tmp_path, space, size, units, xcodes, fixed):
 @pytest.mark.parametrize("source_dtype", ["<i4", "<f4"])
 @pytest.mark.parametrize("in_dtype", ["<i4", "<f4"])
 def test_DerivativesDataSink_data_dtype_source(
-    tmp_path, source_file, source_dtype, in_dtype
+    tmp_path, interface, source_file, source_dtype, in_dtype
 ):
 
     def make_empty_nii_with_dtype(fname, dtype):
@@ -539,19 +569,23 @@ def make_empty_nii_with_dtype(fname, dtype):
         for s in source_file:
             make_empty_nii_with_dtype(s, source_dtype)
 
-    dds = bintfs.DerivativesDataSink(
+    prep, save = make_prep_and_save(
+        interface,
         base_directory=str(tmp_path),
         data_dtype="source",
         desc="preproc",
         source_file=source_file,
         in_file=in_file,
-    ).run()
+    )
+
+    prep_result = prep.run()
 
-    nii = nb.load(dds.outputs.out_file)
+    nii = nb.load(prep_result.outputs.out_file)
     assert nii.get_data_dtype() == np.dtype(source_dtype)
 
 
-def test_DerivativesDataSink_fmapid(tmp_path):
+@pytest.mark.parametrize("interface", [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
+def test_DerivativesDataSink_fmapid(tmp_path, interface):
     """Ascertain #637 is not regressing."""
     source_file = [
         (tmp_path / s)
@@ -569,7 +603,8 @@ def test_DerivativesDataSink_fmapid(tmp_path):
     in_file = tmp_path / "report.svg"
     in_file.write_text("")
 
-    dds = bintfs.DerivativesDataSink(
+    prep, save = make_prep_and_save(
+        interface,
         base_directory=str(tmp_path),
         datatype="figures",
         suffix="fieldmap",
@@ -579,12 +614,19 @@ def test_DerivativesDataSink_fmapid(tmp_path):
         fmapid="auto00000",
         source_file=[str(s.absolute()) for s in source_file],
         in_file=str(in_file),
-    ).run()
-    assert dds.outputs.out_file.endswith("sub-36_fmapid-auto00000_desc-pepolar_fieldmap.svg")
+    )
 
+    prep_result = prep.run()
+    save_result = connect_and_run_save(prep_result, save)
 
+    assert save_result.outputs.out_file.endswith(
+        "sub-36_fmapid-auto00000_desc-pepolar_fieldmap.svg"
+    )
+
+
+@pytest.mark.parametrize("interface", [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
 @pytest.mark.parametrize("dtype", ("i2", "u2", "f4"))
-def test_DerivativesDataSink_values(tmp_path, dtype):
+def test_DerivativesDataSink_values(tmp_path, interface, dtype):
     # We use static checksums above, which ensures we don't break things, but
     # pins the tests to specific values.
     # Here we use random values, check that the values are preserved, and then
@@ -599,16 +641,19 @@ def test_DerivativesDataSink_values(tmp_path, dtype):
     orig_data = np.asanyarray(nb.load(fname).dataobj)
     expected = np.rint(orig_data) if dtype[0] in "iu" else orig_data
 
-    dds = bintfs.DerivativesDataSink(
+    prep, _ = make_prep_and_save(
+        interface,
         base_directory=str(tmp_path),
         keep_dtype=True,
         data_dtype=dtype,
         desc="preproc",
         source_file=T1W_PATH,
         in_file=fname,
-    ).run()
+    )
+
+    prep_result = prep.run()
 
-    out_file = Path(dds.outputs.out_file)
+    out_file = Path(prep_result.outputs.out_file)
 
     nii = nb.load(out_file)
     assert np.allclose(nii.dataobj, expected)
@@ -617,14 +662,17 @@ def test_DerivativesDataSink_values(tmp_path, dtype):
     out_file.unlink()
 
     # Rerun to ensure determinism with non-zero data
-    dds = bintfs.DerivativesDataSink(
+    prep, _ = make_prep_and_save(
+        interface,
         base_directory=str(tmp_path),
         keep_dtype=True,
         data_dtype=dtype,
         desc="preproc",
         source_file=T1W_PATH,
         in_file=fname,
-    ).run()
+    )
+
+    prep_result = prep.run()
 
     assert sha1(out_file.read_bytes()).hexdigest() == checksum