FIX: Check for valid qform before calculating change

niworkflows/interfaces/images.py

@@ -420,25 +420,28 @@ def _run_interface(self, runtime):
         elif (valid_sform and sform_code > 0) and (not matching_affines or qform_code == 0):
             img.set_qform(sform, sform_code)
             new_qform = img.get_qform()
-            if np.allclose(new_qform, qform) and qform_code > 0:
-                # False alarm
-                self._results['out_file'] = self.inputs.in_file
-                open(out_report, 'w').close()
-                self._results['out_report'] = out_report
-                return runtime
-            diff = np.linalg.inv(qform) @ new_qform
-            trans, rot, _, _ = transforms3d.affines.decompose44(diff)
-            angle = transforms3d.axangles.mat2axangle(rot)[1]
-            total_trans = np.sqrt(np.sum(trans * trans))  # Add angle and total_trans to report
-            warning_txt = 'Note on orientation: qform matrix overwritten'
-            description = """\
+            if valid_qform:
+                # False alarm - the difference is due to precision loss of qform
+                if np.allclose(new_qform, qform) and qform_code > 0:
+                    self._results['out_file'] = self.inputs.in_file
+                    open(out_report, 'w').close()
+                    self._results['out_report'] = out_report
+                    return runtime
+                # Replacing an existing, valid qform. Report magnitude of change.
+                diff = np.linalg.inv(qform) @ new_qform
+                trans, rot, _, _ = transforms3d.affines.decompose44(diff)
+                angle = transforms3d.axangles.mat2axangle(rot)[1]
+                total_trans = np.sqrt(np.sum(trans * trans))  # Add angle and total_trans to report
+                warning_txt = 'Note on orientation: qform matrix overwritten'
+                description = """\
     <p class="elem-desc">
     The qform has been copied from sform.
     The difference in angle is {angle:.02g}.
     The difference in translation is {total_trans:.02g}.
     </p>
     """.format(angle=angle, total_trans=total_trans)
-            if not valid_qform and qform_code > 0:
+            elif qform_code > 0:
+                # qform code indicates the qform is supposed to be valid. Use more stridency.
                 warning_txt = 'WARNING - Invalid qform information'
                 description = """\
 <p class="elem-desc">
@@ -448,6 +451,10 @@ def _run_interface(self, runtime):
     by the scanner is advised.
 </p>
 """
+            else:  # qform_code == 0
+                # qform is not expected to be valids. Simple note.
+                warning_txt = 'Note on orientation: qform matrix overwritten'
+                description = '<p class="elem-desc">The qform has been copied from sform.</p>'
         # Rows 5-6:
         else:
             affine = img.header.get_base_affine()

niworkflows/interfaces/tests/test_images.py

@@ -34,11 +34,51 @@ def test_qformsform_warning(tmp_path, qform_add, sform_add, expectation):
     validate = pe.Node(im.ValidateImage(), name='validate', base_dir=str(tmp_path))
     validate.inputs.in_file = fname
     res = validate.run()
+    out_report = Path(res.outputs.out_report).read_text()
     if expectation == 'warn':
-        assert "Note on" in Path(res.outputs.out_report).read_text()
-        assert len(Path(res.outputs.out_report).read_text()) > 0
+        assert "Note on" in out_report
     elif expectation == 'no_warn':
-        assert len(Path(res.outputs.out_report).read_text()) == 0
+        assert len(out_report) == 0
+
+
+@pytest.mark.parametrize('qform_code, warning_text', [
+    (0, "Note on orientation"),
+    (1, "WARNING - Invalid qform"),
+])
+def test_bad_qform(tmp_path, qform_code, warning_text):
+    fname = str(tmp_path / 'test.nii')
+
+    # make a random image
+    random_data = np.random.random(size=(5, 5, 5) + (5,))
+    img = nb.Nifti1Image(random_data, np.eye(4))
+
+    # Some magic terms from a bad qform in the wild
+    img.header['qform_code'] = qform_code
+    img.header['quatern_b'] = 0
+    img.header['quatern_c'] = 0.998322
+    img.header['quatern_d'] = -0.0579125
+    img.to_filename(fname)
+
+    validate = pe.Node(im.ValidateImage(), name='validate', base_dir=str(tmp_path))
+    validate.inputs.in_file = fname
+    res = validate.run()
+    assert warning_text in Path(res.outputs.out_report).read_text()
+
+
+def test_no_good_affines(tmp_path):
+    fname = str(tmp_path / 'test.nii')
+
+    # make a random image
+    random_data = np.random.random(size=(5, 5, 5) + (5,))
+    img = nb.Nifti1Image(random_data, None)
+    img.header['qform_code'] = 0
+    img.header['sform_code'] = 0
+    img.to_filename(fname)
+
+    validate = pe.Node(im.ValidateImage(), name='validate', base_dir=str(tmp_path))
+    validate.inputs.in_file = fname
+    res = validate.run()
+    assert 'WARNING - Missing orientation information' in Path(res.outputs.out_report).read_text()
 
 
 @pytest.mark.parametrize('nvols, nmasks, ext, factor', [