ENH: Implement BIDS X5 io module

nitransforms/io/__init__.py

@@ -1,7 +1,8 @@
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Read and write transforms."""
-from nitransforms.io import afni, fsl, itk, lta
+
+from nitransforms.io import afni, fsl, itk, lta, x5
 from nitransforms.io.base import TransformIOError, TransformFileError
 
 __all__ = [
@@ -22,6 +23,7 @@
     "fs": (lta, "FSLinearTransform"),
     "fsl": (fsl, "FSLLinearTransform"),
     "afni": (afni, "AFNILinearTransform"),
+    "x5": (x5, "X5LinearTransform"),
 }
 
 

nitransforms/io/x5.py

@@ -0,0 +1,39 @@
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""Read/write x5 transforms."""
+
+import numpy as np
+from h5py import File as H5File
+
+
+def to_filename(fname, xfm, moving=None):
+    """Store the transform in BIDS-Transforms HDF5 file format (.x5)."""
+    with H5File(fname, "w") as out_file:
+        out_file.attrs["Format"] = "X5"
+        out_file.attrs["Version"] = np.uint16(1)
+        x5_root = out_file.create_group("/0")
+
+        # Serialize this object into the x5 file format.
+        transform_group = x5_root.create_group("TransformGroup")
+
+        # Group '0' containing Affine transform
+        transform_0 = transform_group.create_group("0")
+
+        transform_0.attrs["Type"] = "Affine"
+        transform_0.create_dataset("Transform", data=xfm.matrix)
+        transform_0.create_dataset("Inverse", data=~xfm)
+
+        metadata = {"key": "value"}
+        transform_0.attrs["Metadata"] = str(metadata)
+
+        # sub-group 'Domain' contained within group '0'
+        transform_0.create_group("Domain")
+        # domain_group.attrs["Grid"] = self._grid
+        # domain_group.create_dataset("Size", data=_as_homogeneous(self._reference.shape))
+        # domain_group.create_dataset("Mapping", data=self.mapping)