Implement ndim

Tranformbase -> now raises TypeError; Affine -> overshadows TransformBase's property and returns self._matrix.ndim + 1. To be applied to LinearTransformMapping (Currently TypeError)

Author: Julien Marabotto

commandline_for_tests.txt

@@ -0,0 +1,7 @@
+Terminal command line to test code:
+
+>>> TEST_DATA_HOME=$HOME/Desktop/nitransforms-tests python3 -m pytest
+
+Also works for a path to a specific test, eg:
+
+>>> TEST_DATA_HOME=$HOME/Desktop/nitransforms-tests python3 -m pytest ~/workspace/nitransforms/nitransforms/tests/test_base.py::test_TransformBase 

nitransforms/.DS_Store

@@ -15,6 +15,7 @@
 from nibabel import funcs as _nbfuncs
 from nibabel.nifti1 import intent_codes as INTENT_CODES
 from nibabel.cifti2 import Cifti2Image
+from nitransforms import linear as nitl
 
 EQUALITY_TOL = 1e-5
 
@@ -177,7 +178,8 @@ def __ne__(self, other):
 class TransformBase:
     """Abstract image class to represent transforms."""
 
-    __slots__ = ("_reference",)
+    __slots__ = ("_reference", "_ndim",)
+
 
     def __init__(self, reference=None):
         """Instantiate a transform."""
@@ -211,6 +213,13 @@ def reference(self):
         if self._reference is None:
             warnings.warn("Reference space not set")
         return self._reference
+    
+    @property
+    def reference(_ndim):
+        """Access a reference space where data will be resampled onto."""
+        if _ndim._reference is None:
+            warnings.warn("Reference space not set")
+        return _ndim._reference
 
     @reference.setter
     def reference(self, image):
@@ -219,7 +228,8 @@ def reference(self, image):
     @property
     def ndim(self):
         """Access the dimensions of the reference space."""
-        return self.reference.ndim
+        #return self.reference.ndim
+        raise TypeError("TransformBase has no dimensions")
 
     def map(self, x, inverse=False):
         r"""
@@ -287,3 +297,5 @@ def _as_homogeneous(xyz, dtype="float32", dim=3):
 def _apply_affine(x, affine, dim):
     """Get the image array's indexes corresponding to coordinates."""
     return affine.dot(_as_homogeneous(x, dim=dim).T)[:dim, ...].T
+
+#import pdb; pdb.set_trace()

nitransforms/base.py

@@ -143,6 +143,11 @@ def matrix(self):
         """Access the internal representation of this affine."""
         return self._matrix
 
+    @property
+    def ndim(self):
+        """Access the internal representation of this affine."""
+        return self._matrix.ndim + 1
+    
     def map(self, x, inverse=False):
         r"""
         Apply :math:`y = f(x)`.
@@ -270,7 +275,7 @@ def __repr__(self):
 
         """
         return repr(self.matrix)
-
+    
 
 class LinearTransformsMapping(Affine):
     """Represents a series of linear transforms."""
@@ -533,4 +538,4 @@ def load(filename, fmt=None, reference=None, moving=None):
     if isinstance(xfm, LinearTransformsMapping) and len(xfm) == 1:
         xfm = xfm[0]
 
-    return xfm
+    return xfm

nitransforms/io/.DS_Store

@@ -95,7 +95,8 @@ def _to_hdf5(klass, x5_root):
     # Test identity transform
     xfm = TransformBase()
     xfm.reference = fname
-    assert xfm.ndim == 3
+    with pytest.raises(TypeError):
+        _ = xfm.ndim
     moved = apply(xfm, fname, order=0)
     assert np.all(
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
@@ -104,12 +105,18 @@ def _to_hdf5(klass, x5_root):
     # Test identity transform - setting reference
     xfm = TransformBase()
     xfm.reference = fname
-    assert xfm.ndim == 3
+    with pytest.raises(TypeError):
+        _ = xfm.ndim
     moved = apply(xfm, str(fname), reference=fname, order=0)
     assert np.all(
         imgdata == np.asanyarray(moved.dataobj, dtype=moved.get_data_dtype())
     )
 
+    #Test ndim returned by affine
+    #breakpoint()
+    assert nitl.Affine().ndim == 3
+    assert nitl.LinearTransformsMapping(xfm.matrix).ndim == 4
+
     # Test applying to Gifti
     gii = nb.gifti.GiftiImage(
         darrays=[