@@ -0,0 +1,104 @@
+# 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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+
+import numpy as np
+import h5py
+
+from .nifti1 import Nifti1Image, Nifti1Header
+
+#from .spm2analyze import Spm2AnalyzeImage
+#from .nifti1 import Nifti1Image, Nifti1Pair, Nifti1Header, header_dtype as ni1_hdr_dtype
+#from .nifti2 import Nifti2Image, Nifti2Pair
+#from .minc1 import Minc1Image
+#from .minc2 import Minc2Image
+#from .freesurfer import MGHImage
+
+def nifti1img_to_hdf(fname, spatial_img, h5path='/img', append=True):
+"""
+Saves a Nifti1Image into an HDF5 file.
+
+fname: string
+Output HDF5 file path
+
+spatial_img: nibabel SpatialImage
+Image to be saved
+
+h5path: string
+HDF5 group path where the image data will be saved.
+Datasets will be created inside the given group path:
+'data', 'extra', 'affine', the header information will
+be set as attributes of the 'data' dataset.
+
+append: bool
+True if you don't want to erase the content of the file
+if it already exists, False otherwise.
+
+@note:
+HDF5 open modes
+>>> 'r' Readonly, file must exist
+>>> 'r+' Read/write, file must exist
+>>> 'w' Create file, truncate if exists
+>>> 'w-' Create file, fail if exists
+>>> 'a' Read/write if exists, create otherwise (default)
+"""
+mode = 'w'
+if append:
+mode = 'a'
+
+with h5py.File(fname, mode) as f:
+h5img = f.create_group(h5path)
+h5img['data'] = spatial_img.get_data()
+h5img['extra'] = spatial_img.get_extra()
+h5img['affine'] = spatial_img.get_affine()
+
+hdr = spatial_img.get_header()
+for k in hdr.keys():
+h5img['data'].attrs[k] = hdr[k]
+
+
+def hdfgroup_to_nifti1image(fname, h5path):
+"""
+Returns a nibabel Nifti1Image from an HDF5 group datasets
+
+@param fname: string
+HDF5 file path
+
+@param h5path:
+HDF5 group path in fname
+
+@return: nibabel Nifti1Image
+"""
+with h5py.File(fname, 'r') as f:
+h5img = f[h5path]
+data = h5img['data'][()]
+extra = h5img['extra'][()]
+affine = h5img['affine'][()]
+
+header = get_nifti1hdr_from_h5attrs(h5img['data'].attrs)
+
+img = Nifti1Image(data, affine, header=header, extra=extra)
+
+return img
+
+
+def get_nifti1hdr_from_h5attrs(h5attrs):
+"""
+Transforms an H5py Attributes set to a dict.
+Converts unicode string keys into standard strings
+and each value into a numpy array.
+
+@param h5attrs: H5py Attributes
+
+@return: dict
+"""
+hdr = Nifti1Header()
+for k in h5attrs.keys():
+hdr[str(k)] = np.array(h5attrs[k])
+
+return hdr