enh: add unit tests

Author: oesteban

nitransforms/io/__init__.py

@@ -9,12 +9,12 @@
 """
 Read and write transforms.
 
-.. currentmodule:: nitransforms
+.. currentmodule:: nitransforms.io
 
 .. autosummary::
    :toctree: ../generated
 
-   transform
+   io
 """
 from .lta import LinearTransform, LinearTransformArray, VolumeGeometry
 

nitransforms/io/itk.py

@@ -90,9 +90,10 @@ def __init__(self,
         """Initialize with (optionally) a list of transforms."""
         super().__init__(binaryblock, endianness, check)
         self._xforms = []
-        for mat in xforms or []:
+        for i, mat in enumerate(xforms or []):
             xfm = ITKLinearTransform()
             xfm['parameters'] = mat
+            xfm['index'] = i + 1
             self._xforms.append(xfm)
 
     def __getitem__(self, idx):

nitransforms/tests/data/itktflist.tfm

@@ -0,0 +1,45 @@
+#Insight Transform File V1.0
+#Transform 1
+Transform: MatrixOffsetTransformBase_double_3_3
+Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
+FixedParameters: 10 10 10
+
+#Transform 2
+Transform: MatrixOffsetTransformBase_double_3_3
+Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
+FixedParameters: 10 10 10
+
+#Transform 3
+Transform: MatrixOffsetTransformBase_double_3_3
+Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
+FixedParameters: 10 10 10
+
+#Transform 4
+Transform: MatrixOffsetTransformBase_double_3_3
+Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
+FixedParameters: 10 10 10
+
+#Transform 5
+Transform: MatrixOffsetTransformBase_double_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: MatrixOffsetTransformBase_double_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: MatrixOffsetTransformBase_double_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: MatrixOffsetTransformBase_double_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: MatrixOffsetTransformBase_double_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

@@ -4,12 +4,12 @@
 import numpy as np
 
 from ..io import (
+    itk,
     VolumeGeometry as VG,
     LinearTransform as LT,
     LinearTransformArray as LTA,
 )
 
-
 def test_VolumeGeometry(tmpdir, get_testdata):
     vg = VG()
     assert vg['valid'] == 0
@@ -55,3 +55,32 @@ def test_LinearTransformArray(tmpdir, data_path):
     with open(outlta) as fp:
         lta2 = LTA.from_fileobj(fp)
     assert np.allclose(lta['xforms'][0]['m_L'], lta2['xforms'][0]['m_L'])
+
+
+def test_ITKLinearTransformArray(tmpdir, data_path):
+    tmpdir.chdir()
+
+    with open(str(data_path / 'itktflist.tfm')) as f:
+        text = f.read()
+        f.seek(0)
+        itklist = itk.ITKLinearTransformArray.from_fileobj(f)
+
+    assert itklist['nxforms'] == 9
+    assert text == itklist.to_string()
+
+    itklist = itk.ITKLinearTransformArray(
+        xforms=[np.around(np.random.normal(size=(4, 4)), decimals=5)
+                for _ in range(4)])
+
+    assert itklist['nxforms'] == 4
+    assert itklist['xforms'][1].structarr['index'] == 2
+
+    xfm = itklist['xforms'][1]
+    xfm['index'] = 1
+    with open('extracted.tfm', 'w') as f:
+        f.write(xfm.to_string())
+
+    with open('extracted.tfm') as f:
+        xfm2 = itk.ITKLinearTransform.from_fileobj(f)
+    assert np.allclose(xfm.structarr['parameters'][:3, ...],
+                       xfm2.structarr['parameters'][:3, ...])