feat(io.reader): draft implementation of ITK/ANTs' composite HDF5 transforms

Uses ``h5py`` to browse the transforms group, and concatenates them in a list
ready for nitransforms' wrapping into a ``TransformsChain``.

The writer is not included in this PR.

The implementation takes into account the misspelling of "Tranforms" present
in transforms generated with older versions of ITK.

This implementation only accepts the composite transforms generated by ANTs.

Resolves: #4

Author: oesteban

nitransforms/io/itk.py

@@ -2,6 +2,7 @@
 import warnings
 import numpy as np
 from scipy.io import savemat as _save_mat
+from nibabel import Nifti1Header, Nifti1Image
 from nibabel.affines import from_matvec
 from .base import (
     BaseLinearTransformList,
@@ -280,3 +281,64 @@ def from_image(cls, imgobj):
         field[..., (0, 1)] *= -1.0
 
         return imgobj.__class__(field, imgobj.affine, hdr)
+
+
+class ITKCompositeH5:
+    """A data structure for ITK's HDF5 files."""
+
+    @classmethod
+    def from_filename(cls, filename):
+        """Read the struct from a file given its path."""
+        from h5py import File as H5File
+        if not str(filename).endswith('.h5'):
+            raise RuntimeError("Extension is not .h5")
+
+        with H5File(str(filename)) as f:
+            return cls.from_h5obj(f)
+
+    @classmethod
+    def from_h5obj(cls, fileobj, check=True):
+        """Read the struct from a file object."""
+        xfm_list = []
+        h5group = fileobj["TransformGroup"]
+        typo_fallback = "Transform"
+        try:
+            h5group['1'][f"{typo_fallback}Parameters"]
+        except KeyError:
+            typo_fallback = "Tranform"
+
+        for xfm in reversed(h5group.keys())[:-1]:
+            if h5group[xfm]["TransformType"][0].startswith(b"AffineTransform"):
+                xfm_list.append(
+                    ITKLinearTransform(
+                        parameters=np.asanyarray(h5group[xfm][f"{typo_fallback}Parameters"]),
+                        offset=np.asanyarray(h5group[xfm][f"{typo_fallback}FixedParameters"])
+                    )
+                )
+                continue
+            if h5group[xfm]["TransformType"][0].startswith(b"DisplacementFieldTransform"):
+                _fixed = np.asanyarray(h5group[xfm][f"{typo_fallback}FixedParameters"])
+                shape = _fixed[:3].astype('uint16').tolist()
+                offset = _fixed[3:6].astype('uint16')
+                zooms = _fixed[6:9].astype('float')
+                directions = _fixed[9:].astype('float').reshape((3, 3))
+                affine = from_matvec(directions * zooms, offset)
+                field = np.asanyarray(h5group[xfm][f"{typo_fallback}Parameters"]).reshape(
+                    tuple(shape + [-1])
+                )
+                hdr = Nifti1Header()
+                hdr.set_intent("vector")
+                hdr.set_data_dtype("float")
+
+                xfm_list.append(
+                    ITKDisplacementsField.from_image(
+                        Nifti1Image(field.astype("float"), affine, hdr)
+                    )
+                )
+                continue
+
+            raise NotImplementedError(
+                f"Unsupported transform type {h5group[xfm]['TransformType'][0]}"
+            )
+
+        return xfm_list