enh: more tests on io.afni and io.fsl modules

Author: oesteban

nitransforms/io/afni.py

@@ -59,11 +59,13 @@ def from_string(cls, string):
         tf = cls()
         sa = tf.structarr
         lines = [l for l in string.splitlines()
-                 if l.strip()]
+                 if l.strip() and not l.startswith('#')]
 
         if '3dvolreg matrices' in lines[0]:
             lines = lines[1:]  # Drop header
 
+        if not lines:
+            raise ValueError('String "%s"' % string)
         parameters = np.vstack((
             np.genfromtxt([lines[0].encode()],
                           dtype='f8').reshape((3, 4)),
@@ -86,7 +88,11 @@ def to_string(self):
         """Convert to a string directly writeable to file."""
         strings = []
         for i, xfm in enumerate(self.xforms):
-            strings.append(xfm.to_string(banner=(i == 0)))
+            lines = [
+                l.strip()
+                for l in xfm.to_string(banner=(i == 0)).splitlines()
+                if l.strip()]
+            strings += lines
         return '\n'.join(strings)
 
     @classmethod
@@ -103,7 +109,8 @@ def from_string(cls, string):
         """Read the struct from string."""
         _self = cls()
         _self.xforms = [cls._inner_type.from_string(l.strip())
-                        for l in string.splitlines() if l.strip()]
+                        for l in string.splitlines()
+                        if l.strip() and not l.startswith('#')]
         return _self
 
 

nitransforms/io/fsl.py

@@ -1,4 +1,5 @@
 """Read/write FSL's transforms."""
+import os
 import numpy as np
 from nibabel.affines import voxel_sizes
 
@@ -95,6 +96,26 @@ def from_string(cls, string):
                         for l in string.splitlines() if l.strip()]
         return _self
 
+    @classmethod
+    def from_filename(cls, filename):
+        """Read the struct from a file given its path."""
+        if os.path.exists(str(filename)):
+            return super().from_filename(filename)
+
+        _xforms = []
+        index = 0
+        while os.path.exists('%s.%03d' % (filename, index)):
+            with open('%s.%03d' % (filename, index)) as f:
+                string = f.read()
+            _xforms.append(cls._inner_type.from_string(string))
+            index += 1
+
+        if index == 0:
+            raise FileNotFoundError(str(filename))
+        _self = cls()
+        _self.xforms = _xforms
+        return _self
+
 
 def _fsl_aff_adapt(space):
     """

nitransforms/tests/test_io.py

@@ -137,6 +137,38 @@ def test_Linear_common(tmpdir, data_path, sw, image_orientation,
     assert np.allclose(xfm.to_ras(reference=reference, moving=moving), RAS)
 
 
+@pytest.mark.parametrize('image_orientation', [
+    'RAS', 'LAS', 'LPS', 'oblique',
+])
+@pytest.mark.parametrize('sw', ['afni', 'fsl', 'itk'])
+def test_LinearList_common(tmpdir, data_path, sw, image_orientation,
+                       get_testdata):
+    tmpdir.chdir()
+
+    angles = np.random.uniform(low=-3.14, high=3.14, size=(5, 3))
+    translation = np.random.uniform(low=-5., high=5., size=(5, 3))
+    mats = [from_matvec(euler2mat(*a), t)
+            for a, t in zip(angles, translation)]
+
+    ext = ''
+    if sw == 'afni':
+        factory = afni.AFNILinearTransformArray
+    elif sw == 'fsl':
+        factory = fsl.FSLLinearTransformArray
+    elif sw == 'itk':
+        ext = '.tfm'
+        factory = itk.ITKLinearTransformArray
+
+    tflist1 = factory(mats)
+
+    fname = 'affine-%s.%s%s' % (image_orientation, sw, ext)
+    tflist1.to_filename(fname)
+    tflist2 = factory.from_filename(fname)
+
+    assert tflist1['nxforms'] == tflist2['nxforms']
+    assert all([np.allclose(x1['parameters'], x2['parameters'])
+                for x1, x2 in zip(tflist1.xforms, tflist2.xforms)])
+
 def test_ITKLinearTransform(tmpdir, data_path):
     tmpdir.chdir()