fix: itk text transform file indices start from zero

Author: oesteban

nitransforms/io/itk.py

@@ -2,7 +2,7 @@
 import numpy as np
 from scipy.io import savemat as _save_mat
 from nibabel.affines import from_matvec
-from .base import StringBasedStruct, _read_mat
+from .base import StringBasedStruct, _read_mat, TransformFileError
 
 LPS = np.diag([-1, -1, 1, 1])
 
@@ -23,7 +23,7 @@ class ITKLinearTransform(StringBasedStruct):
     def __init__(self, parameters=None, offset=None):
         """Initialize with default offset and index."""
         super().__init__()
-        self.structarr['index'] = 1
+        self.structarr['index'] = 0
         self.structarr['offset'] = offset or [0, 0, 0]
         self.structarr['parameters'] = np.eye(4)
         if parameters is not None:
@@ -76,7 +76,7 @@ def to_string(self, banner=None):
         string = '%s'
 
         if banner is None:
-            banner = self.structarr['index'] == 1
+            banner = self.structarr['index'] == 0
 
         if banner:
             string = '#Insight Transform File V1.0\n%s'
@@ -103,7 +103,7 @@ def from_matlab_dict(cls, mdict, index=None):
         if index is not None:
             raise NotImplementedError
 
-        sa['index'] = 1
+        sa['index'] = 0
         parameters = np.eye(4, dtype='f4')
         parameters[:3, :3] = mdict['AffineTransform_float_3_3'][:-3].reshape((3, 3))
         parameters[:3, 3] = mdict['AffineTransform_float_3_3'][-3:].flatten()
@@ -116,7 +116,7 @@ def from_ras(cls, ras, index=0):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         tf = cls()
         sa = tf.structarr
-        sa['index'] = index + 1
+        sa['index'] = index
         sa['parameters'] = LPS.dot(ras.dot(LPS))
         return tf
 
@@ -171,7 +171,7 @@ def xforms(self, value):
 
         # Update indexes
         for i, val in enumerate(self._xforms):
-            val['index'] = i + 1
+            val['index'] = i
 
     def __getitem__(self, idx):
         """Allow dictionary access to the transforms."""
@@ -197,7 +197,7 @@ def to_string(self):
         """Convert to a string directly writeable to file."""
         strings = []
         for i, xfm in enumerate(self.xforms):
-            xfm.structarr['index'] = i + 1
+            xfm.structarr['index'] = i
             strings.append(xfm.to_string())
         return '\n'.join(strings)
 

nitransforms/tests/data/itktflist.tfm

@@ -1,45 +1,45 @@
 #Insight Transform File V1.0
-#Transform 1
+#Transform 0
 Transform: AffineTransform_float_3_3
 Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
 FixedParameters: 10 10 10
 
-#Transform 2
+#Transform 1
 Transform: AffineTransform_float_3_3
 Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
 FixedParameters: 10 10 10
 
-#Transform 3
+#Transform 2
 Transform: AffineTransform_float_3_3
 Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
 FixedParameters: 10 10 10
 
-#Transform 4
+#Transform 3
 Transform: AffineTransform_float_3_3
 Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
 FixedParameters: 10 10 10
 
-#Transform 5
+#Transform 4
 Transform: AffineTransform_float_3_3
 Parameters: -1.53626 0.71973 -0.639856 -0.190759 -1.80082 -0.915885 0.502537 1.12532 0.275748 0.393413 1.13855 0.761131
 FixedParameters: -0.0993171 0.364984 1.99264
 
-#Transform 6
+#Transform 5
 Transform: AffineTransform_float_3_3
 Parameters: -0.130507 -1.03017 2.08189 -1.51723 1.37849 -0.0890962 -0.656323 0.242694 2.15801 -1.26689 0.367131 1.23616
 FixedParameters: 0.626607 0.15351 1.24982
 
-#Transform 7
+#Transform 6
 Transform: AffineTransform_float_3_3
 Parameters: -1.55395 -0.36383 -0.17749 1.3387 -0.384534 -0.901462 -1.06598 -0.448228 -1.07535 1.92599 0.454696 0.576697
 FixedParameters: -0.425602 0.333406 -1.14957
 
-#Transform 8
+#Transform 7
 Transform: AffineTransform_float_3_3
 Parameters: 0.723719 -1.05617 -0.800562 -2.47048 -1.76301 -1.4447 -0.749896 1.29774 -1.48893 1.02789 0.65017 -1.48326
 FixedParameters: 0.800882 -1.20202 1.25495
 
-#Transform 9
+#Transform 8
 Transform: AffineTransform_float_3_3
 Parameters: 1.24025 -0.77628 0.618013 -0.523829 1.09471 1.66921 0.73753 -1.33588 -0.627659 -0.449913 -0.00124181 0.21433
 FixedParameters: -0.226504 -0.877893 0.2608

nitransforms/tests/test_io.py

@@ -113,7 +113,7 @@ def test_ITKLinearTransformArray(tmpdir, data_path):
                 for _ in range(4)])
 
     assert itklist['nxforms'] == 4
-    assert itklist['xforms'][1].structarr['index'] == 2
+    assert itklist['xforms'][1].structarr['index'] == 1
 
     with pytest.raises(KeyError):
         itklist['invalid_key']