Nov 23, 2013 · Nov 28, 2013 · Nov 28, 2013
diff --git a/nibabel/hdfloadsave.py b/nibabel/hdfloadsave.py
    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 = 'r+'

    f = h5py.File(fname, mode)

    h5img = f.create_group(h5path)
    h5img['data']   = spatial_img.get_data()
    h5img['extra']  = spatial_img.get_extra()
    h5img['affine'] = spatial_img.get_affine()
        mode = 'a'

    hdr = spatial_img.get_header()
    for k in hdr.keys():
        h5img['data'].attrs[k] = hdr[k]
    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()

    f.close()
        hdr = spatial_img.get_header()
        for k in hdr.keys():
            h5img['data'].attrs[k] = hdr[k]


 def hdfgroup_to_nifti1image(fname, h5path):

    @return: nibabel Nifti1Image
    """
    f = h5py.File(fname, 'r')

    h5img  = f[h5path]
    data   = h5img['data'].value
    extra  = h5img['extra'].value
    affine = h5img['affine'].value

    header = get_nifti1hdr_from_h5attrs(h5img['data'].attrs)
    with h5py.File(fname, 'r') as f:
        h5img  = f[h5path]
        data   = h5img['data'][()]
        extra  = h5img['extra'][()]
        affine = h5img['affine'][()]

 f.close()
    header = get_nifti1hdr_from_h5attrs(h5img['data'].attrs)

    img = Nifti1Image(data, affine, header=header, extra=extra)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -38,23 +38,28 @@ def nifti1img_to_hdf(fname, spatial_img, h5path='/img', append=True):
		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 = 'r+'

		f = h5py.File(fname, mode)

		h5img = f.create_group(h5path)
		h5img['data'] = spatial_img.get_data()
		h5img['extra'] = spatial_img.get_extra()
		h5img['affine'] = spatial_img.get_affine()
		mode = 'a'

		hdr = spatial_img.get_header()
		for k in hdr.keys():
		h5img['data'].attrs[k] = hdr[k]
		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()

		f.close()
		hdr = spatial_img.get_header()
		for k in hdr.keys():
		h5img['data'].attrs[k] = hdr[k]


		def hdfgroup_to_nifti1image(fname, h5path):
Expand All		@@ -69,16 +74,13 @@ def hdfgroup_to_nifti1image(fname, h5path):

		@return: nibabel Nifti1Image
		"""
		f = h5py.File(fname, 'r')

		h5img = f[h5path]
		data = h5img['data'].value
		extra = h5img['extra'].value
		affine = h5img['affine'].value

		header = get_nifti1hdr_from_h5attrs(h5img['data'].attrs)
		with h5py.File(fname, 'r') as f:
		h5img = f[h5path]
		data = h5img['data'][()]
		extra = h5img['extra'][()]
		affine = h5img['affine'][()]

		f.close()
		header = get_nifti1hdr_from_h5attrs(h5img['data'].attrs)

		img = Nifti1Image(data, affine, header=header, extra=extra)

Expand Down