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Expose chunk shape in write nodes #160

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Expose chunk shape in write nodes #160

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20 changes: 15 additions & 5 deletions gunpowder/nodes/hdf5like_write_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,12 @@ class Hdf5LikeWrite(BatchFilter):
A dictionary from array keys to datatype (eg. ``np.int8``). If
given, arrays are stored using this type. The original arrays
within the pipeline remain unchanged.

chunks (``tuple`` of ``int``, or ``bool``):

Chunk shape for output datasets. Set to ``True`` for auto-chunking,
set to ``False`` to obtain a chunk equal to the dataset size.
Defaults to ``True``.
'''

def __init__(
Expand All @@ -49,7 +55,8 @@ def __init__(
output_dir='.',
output_filename='output.hdf',
compression_type=None,
dataset_dtypes=None):
dataset_dtypes=None,
chunks=True):

self.dataset_names = dataset_names
self.output_dir = output_dir
Expand All @@ -59,6 +66,7 @@ def __init__(
self.dataset_dtypes = {}
else:
self.dataset_dtypes = dataset_dtypes
self.chunks = chunks

self.dataset_offsets = {}

Expand Down Expand Up @@ -149,10 +157,12 @@ def init_datasets(self, batch):
offset, voxel_size)

dataset = data_file.create_dataset(
name=dataset_name,
shape=data_shape,
compression=self.compression_type,
dtype=dtype)
name=dataset_name,
shape=data_shape,
compression=self.compression_type,
dtype=dtype,
chunks=self.chunks
)

self._set_offset(dataset, offset)
self._set_voxel_size(dataset, voxel_size)
Expand Down