Merge pull request #65 from effigies/fix/lta_missing_fields

FIX: Improve handling of optional fields in LTA

Author: oesteban

nitransforms/io/lta.py

@@ -266,21 +266,20 @@ def from_string(klass, string):
                 klass._inner_type.from_string('\n'.join(lines[:25])))
             lta._xforms[-1].structarr['type'] = sa['type']
             lines = lines[25:]
-        if lines:
-            for key in ('subject', 'fscale'):
-                # Optional keys
-                if not lines[0].startswith(key):
-                    continue
-                try:
-                    label, valstring = lines.pop(0).split(' ')
-                except ValueError:
-                    sa[key] = ''
-                else:
-                    assert label.strip() == key
-
-                    val = np.genfromtxt([valstring.encode()],
-                                        dtype=klass.dtype[key])
-                    sa[key] = val.reshape(sa[key].shape) if val.size else ''
+        for key in ('subject', 'fscale'):
+            # Optional keys
+            if not (lines and lines[0].startswith(key)):
+                continue
+            try:
+                label, valstring = lines.pop(0).split(' ')
+            except ValueError:
+                sa[key] = ''
+            else:
+                assert label.strip() == key
+
+                val = np.genfromtxt([valstring.encode()],
+                                    dtype=klass.dtype[key])
+                sa[key] = val.reshape(sa[key].shape) if val.size else ''
 
         assert len(lta._xforms) == sa['nxforms']
         return lta

nitransforms/tests/data/regressions/robust_register.lta

@@ -0,0 +1,30 @@
+# transform file /home/oesteban/tmp/fmriprep-ds005/fprep-work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta
+# created by oesteban on Sat Mar 14 19:28:37 2020
+
+type      = 1 # LINEAR_RAS_TO_RAS
+nxforms   = 1
+mean      = 129.0000 157.0000 132.0000
+sigma     = 10000.0000
+1 4 4
+9.999999403953552e-01 -1.698292035143822e-04 1.542967074783519e-04 -1.678466796875000e-04 
+1.698438863968477e-04 9.999999403953552e-01 -9.513227996649221e-05 -1.318359375000000e-02 
+-1.542805403005332e-04 9.515848068986088e-05 9.999999403953552e-01 -6.271362304687500e-03 
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999403953552e-01 
+src volume info
+valid = 1  # volume info valid
+filename = /oak/stanford/groups/russpold/data/openfmri/derivatives/ds000005/freesurfer-6.0.1/sub-01/mri/T1.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -9.999999403953552e-01
+zras   = 0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00
+cras   = -9.999847412109375e-01 -5.000015258789062e+00 -1.000038146972656e+00
+dst volume info
+valid = 1  # volume info valid
+filename = /oak/stanford/groups/russpold/data/openfmri/ds000005/sub-01/anat/sub-01_T1w.nii.gz
+volume = 160 192 192
+voxelsize = 1.000000000000000e+00 1.333333015441895e+00 1.333333015441895e+00
+xras   = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+zras   = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+cras   = -1.000000000000000e+00 -5.000030517578125e+00 -1.000030517578125e+00

nitransforms/tests/test_io.py

@@ -340,3 +340,8 @@ def test_Displacements(sw_tool):
         field = nb.Nifti1Image(np.zeros((10, 10, 10, 1, 4)), None, None)
         with pytest.raises(TransformFileError):
             afni.AFNIDisplacementsField.from_image(field)
+
+
+@pytest.mark.parametrize('file_type, test_file', [(LTA, 'robust_register.lta')])
+def test_regressions(file_type, test_file, data_path):
+    file_type.from_filename(data_path / 'regressions' / test_file)

setup.cfg

@@ -7,7 +7,7 @@ python_requires = >= 3.5
 install_requires =
     numpy
     scipy
-    nibabel @ git+https://github.com/nipy/nibabel@cd48bf05bc567387afe4504eda1da15324bb616f
+    nibabel >= 3.0
     h5py
 test_requires =
     pytest