def tree(grp, expand=False, level=None):
"""Provide a ``print``-able display of the hierarchy. This function is provided
mainly as a convenience for obtaining a tree view of an h5py group - zarr groups
have a ``.tree()`` method.
Parameters
----------
grp : Group
Zarr or h5py group.
expand : bool, optional
Only relevant for HTML representation. If True, tree will be fully expanded.
level : int, optional
Maximum depth to descend into hierarchy.
Examples
--------
>>> import zarr
>>> g1 = zarr.group()
>>> g2 = g1.create_group('foo')
>>> g3 = g1.create_group('bar')
>>> g4 = g3.create_group('baz')
>>> g5 = g3.create_group('qux')
>>> d1 = g5.create_dataset('baz', shape=100, chunks=10)
>>> g1.tree()
/
├── bar
│ ├── baz
│ └── qux
│ └── baz (100,) float64
└── foo
>>> import h5py
>>> h5f = h5py.File('data/example.h5', mode='w')
>>> zarr.copy_all(g1, h5f)
(5, 0, 800)
>>> zarr.tree(h5f)
/
├── bar
│ ├── baz
│ └── qux
│ └── baz (100,) float64
└── foo
See Also
--------
zarr.hierarchy.Group.tree
Notes
-----
Please note that this is an experimental feature. The behaviour of this
function is still evolving and the default output and/or parameters may change
in future versions.
"""
return TreeViewer(grp, expand=expand, level=level)
def tree(self, expand=False, level=None):
"""Provide a ``print``-able display of the hierarchy.
Parameters
----------
expand : bool, optional
Only relevant for HTML representation. If True, tree will be fully expanded.
level : int, optional
Maximum depth to descend into hierarchy.
Examples
--------
>>> import zarr
>>> g1 = zarr.group()
>>> g2 = g1.create_group('foo')
>>> g3 = g1.create_group('bar')
>>> g4 = g3.create_group('baz')
>>> g5 = g3.create_group('quux')
>>> d1 = g5.create_dataset('baz', shape=100, chunks=10)
>>> g1.tree()
/
├── bar
│ ├── baz
│ └── quux
│ └── baz (100,) float64
└── foo
>>> g1.tree(level=2)
/
├── bar
│ ├── baz
│ └── quux
└── foo
>>> g3.tree()
bar
├── baz
└── quux
└── baz (100,) float64
Notes
-----
Please note that this is an experimental feature. The behaviour of this
function is still evolving and the default output and/or parameters may change
in future versions.
"""
return TreeViewer(self, expand=expand, level=level)
def tree(self, expand=False, level=None):
"""Provide a ``print``-able display of the hierarchy.
Parameters
----------
expand : bool, optional
Only relevant for HTML representation. If True, tree will be fully expanded.
level : int, optional
Maximum depth to descend into hierarchy.
Examples
--------
>>> import zarr
>>> g1 = zarr.group()
>>> g2 = g1.create_group('foo')
>>> g3 = g1.create_group('bar')
>>> g4 = g3.create_group('baz')
>>> g5 = g3.create_group('quux')
>>> d1 = g5.create_dataset('baz', shape=100, chunks=10)
>>> g1.tree()
/
├── bar
│ ├── baz
│ └── quux
│ └── baz (100,) float64
└── foo
>>> g1.tree(level=2)
/
├── bar
│ ├── baz
│ └── quux
└── foo
>>> g3.tree()
bar
├── baz
└── quux
└── baz (100,) float64
"""
return TreeViewer(self, expand=expand, level=level)
def __str__(self):
""" Generate the string for printing """
affine = np.array(self.voxel_to_rasmm, dtype=np.float32)
dimensions = np.array(self.dimensions, dtype=np.uint16)
vox_sizes = np.array(voxel_sizes(affine), dtype=np.float32)
vox_order = ''.join(aff2axcodes(affine))
text = 'VOXEL_TO_RASMM: \n{}'.format(
np.array2string(affine,
formatter={'float_kind': lambda x: "%.6f" % x}))
text += '\nDIMENSIONS: {}'.format(np.array2string(dimensions))
text += '\nVOX_SIZES: {}'.format(
np.array2string(vox_sizes,
formatter={'float_kind': lambda x: "%.2f" % x}))
text += '\nVOX_ORDER: {}'.format(vox_order)
text += '\nNB_STREAMLINES: {}'.format(self.nb_streamlines)
text += '\nNB_POINTS: {}'.format(self.nb_points)
text += '\n' + TreeViewer(self._zcontainer).__unicode__()
return text
