Getting your data in Fuel


We’re still in the process of figuring out the interface, which means the “preferred” way of getting your data in Fuel may change in the future.

Built-in datasets are convenient for training on common benchmark tasks, but what if you want to train a model on your own data?

This section shows how to accomplish the common task of loading into Fuel a bunch of data sources (e.g. features, targets) split into different sets.

A toy example

We’ll start this tutorial by creating bogus data sources that could be lying around on disk.

>>> import numpy
...     'train_vector_features.npy',
...     numpy.random.normal(size=(90, 10)).astype('float32'))
...     'test_vector_features.npy',
...     numpy.random.normal(size=(10, 10)).astype('float32'))
...     'train_image_features.npy',
...     numpy.random.randint(2, size=(90, 3, 5, 5)).astype('uint8'))
...     'test_image_features.npy',
...     numpy.random.randint(2, size=(10, 3, 5, 5)).astype('uint8'))
...     'train_targets.npy',
...     numpy.random.randint(10, size=(90, 1)).astype('uint8'))
...     'test_targets.npy',
...     numpy.random.randint(10, size=(10, 1)).astype('uint8'))

Our goal is to process these files into a format that can be natively imported in Fuel.

HDF5 datasets

The best-supported way to load data in Fuel is through the H5PYDataset class, which wraps HDF5 files using h5py.

This is the class that’s used for most built-in datasets. It makes a series of assumptions about the structure of the HDF5 file which greatly simplify things if your data happens to meet these assumptions:

  • All data is stored into a single HDF5 file.
  • Data sources reside in the root group, and their names define the source names.
  • Data sources are not explicitly split into separate HDF5 datasets or separate HDF5 files. Instead, splits are defined in the split attribute of the root group. It’s expected to be a 1D numpy array of compound dtype with seven fields, organized as follows:
    1. split : string identifier for the split name
    2. source : string identifier for the source name
    3. start : start index (inclusive) of the split in the source array, used if indices is a null reference.
    4. stop : stop index (exclusive) of the split in the source array, used if indices is a null reference.
    5. indices : h5py.Reference, reference to a dataset containing subset indices for this split/source pair. If it’s a null reference, start and stop are used.
    6. available : boolean, False is this split is not available for this source
    7. comment : comment string


Some of you may wonder if this means all data has to be read off disk all the time. Rest assured, H5PYDataset has an option to load things into memory which we will be covering soon.

Converting the toy example

Let’s now convert our bogus files into a format that’s digestible by H5PYDataset.

We first load the data from disk.

>>> train_vector_features = numpy.load('train_vector_features.npy')
>>> test_vector_features = numpy.load('test_vector_features.npy')
>>> train_image_features = numpy.load('train_image_features.npy')
>>> test_image_features = numpy.load('test_image_features.npy')
>>> train_targets = numpy.load('train_targets.npy')
>>> test_targets = numpy.load('test_targets.npy')

We then open an HDF5 file for writing and create three datasets in the root group, one for each data source. We name them after their source name.

>>> import h5py
>>> f = h5py.File('dataset.hdf5', mode='w')
>>> vector_features = f.create_dataset(
...     'vector_features', (100, 10), dtype='float32')
>>> image_features = f.create_dataset(
...     'image_features', (100, 3, 5, 5), dtype='uint8')
>>> targets = f.create_dataset(
...     'targets', (100, 1), dtype='uint8')

Notice how the number of examples we specify (100) in the shapes is the sum of the number of training and test examples. We’ll be filling the first 90 rows with training examples and the last 10 rows with test examples.

>>> vector_features[...] = numpy.vstack(
...     [train_vector_features, test_vector_features])
>>> image_features[...] = numpy.vstack(
...     [train_image_features, test_image_features])
>>> targets[...] = numpy.vstack([train_targets, test_targets])

H5PYDataset allows us to label axes with semantic information. We record that information in the HDF5 file through dimension scales.

>>> vector_features.dims[0].label = 'batch'
>>> vector_features.dims[1].label = 'feature'
>>> image_features.dims[0].label = 'batch'
>>> image_features.dims[1].label = 'channel'
>>> image_features.dims[2].label = 'height'
>>> image_features.dims[3].label = 'width'
>>> targets.dims[0].label = 'batch'
>>> targets.dims[1].label = 'index'

This particular choice of label is arbitrary. Nothing in Fuel forces you to adopt any labeling convention. Note, however, that certain external frameworks that rely on Fuel may impose some restrictions on the choice of labels.

The last thing we need to do is to give H5PYDataset a way to recover what the splits are. This is done by setting the split attribute of the root group.

>>> split_array = numpy.empty(
...     6,
...     dtype=numpy.dtype([
...         ('split', 'a', 5),
...         ('source', 'a', 15),
...         ('start', numpy.int64, 1),
...         ('stop', numpy.int64, 1),
...         ('indices', h5py.special_dtype(ref=h5py.Reference)),
...         ('available', numpy.bool, 1),
...         ('comment', 'a', 1)]))
>>> split_array[0:3]['split'] = 'train'.encode('utf8')
>>> split_array[3:6]['split'] = 'test'.encode('utf8')
>>> split_array[0:6:3]['source'] = 'vector_features'.encode('utf8')
>>> split_array[1:6:3]['source'] = 'image_features'.encode('utf8')
>>> split_array[2:6:3]['source'] = 'targets'.encode('utf8')
>>> split_array[0:3]['start'] = 0
>>> split_array[0:3]['stop'] = 90
>>> split_array[3:6]['start'] = 90
>>> split_array[3:6]['stop'] = 100
>>> split_array[:]['indices'] = h5py.Reference()
>>> split_array[:]['available'] = True
>>> split_array[:]['comment'] = '.'.encode('utf8')
>>> f.attrs['split'] = split_array

We created a 1D numpy array with six elements. The dtype for this array is a compound type: every element of the array is a tuple of (str, str, int, int, h5py.Reference, bool, str). The length of each string element has been chosen to be the maximum length we needed to store: that’s 5 for the split element ('train' being the longest split name) and 15 for the source element ('vector_features' being the longest source name). We didn’t include any comment, so the length for that element was set to 1. Due to a quirk in pickling empty strings, we put '.' as the comment value.


Due to limitations in h5py, you must make sure to use bytes for split, source and comment.

H5PYDataset expects the split attribute of the root node to contain as many elements as the cartesian product of all sources and all splits, i.e. all possible split/source combinations. Sometimes, no data is available for some source/split combination: for instance, the test set may not be labeled, and the ('test', 'targets') combination may not exist. In that case, you can set the available element for that combination to False, and H5PYDataset will ignore it.

Don’t worry too much about indices; we’ll get back to that later. For the moment, all you need to know is that since our splits are contiguous, we don’t need that feature and therefore put empty references.

The method described above does the job, but it’s not very convenient. An even simpler way of achieving the same result is to call create_split_array().

>>> from fuel.datasets.hdf5 import H5PYDataset
>>> split_dict = {
...     'train': {'vector_features': (0, 90), 'image_features': (0, 90),
...               'targets': (0, 90)},
...     'test': {'vector_features': (90, 100), 'image_features': (90, 100),
...              'targets': (90, 100)}}
>>> f.attrs['split'] = H5PYDataset.create_split_array(split_dict)

The create_split_array() method expects a dictionary mapping split names to dictionaries. Those dictionaries map source names to tuples of length 2, 3 or 4. The first two elements correspond to the start and stop indexes. The other two elements are optional and correspond to the indices reference and the comment, respectively. The method will create the array behind the scenes, choose the string lengths automatically and populate it with the information in the split dictionary. If a particular split/source combination isn’t present, its available attribute is set to False, which allows us to specify only what’s actually present in the HDF5 file we created.


By default, H5PYDataset sorts sources in alphabetical order, and data requests are also returned in that order. If sources is passed as argument upon instantiation, H5PYDataset will use the order of sources instead. This means that if you want to force a particular source order, you can do so by explicitly passing the sources argument with the desired ordering. For example, if your dataset has two sources named 'features' and 'targets' and you’d like the targets to be returned first, you need to pass sources=('targets', 'features') as a constructor argument.

We flush, close the file and voilà!

>>> f.flush()
>>> f.close()

Playing with H5PYDataset datasets

Let’s explore what we can do with the dataset we just created.

The simplest thing is to load it by giving its path and a tuple of split names:

>>> train_set = H5PYDataset('dataset.hdf5', which_sets=('train',))
>>> print(train_set.num_examples)
>>> test_set = H5PYDataset('dataset.hdf5', which_sets=('test',))
>>> print(test_set.num_examples)

Passing more than one split name would cause the splits to be concatenated. The available data sources would be the intersection of the sources provided by each split.

You can further restrict which examples are used by providing a slice object or a list of indices as the subset argument.

>>> train_set = H5PYDataset(
...     'dataset.hdf5', which_sets=('train',), subset=slice(0, 80))
>>> print(train_set.num_examples)
>>> valid_set = H5PYDataset(
...     'dataset.hdf5', which_sets=('train',), subset=slice(80, 90))
>>> print(valid_set.num_examples)

The available data sources are defined by the names of the datasets in the root node of the HDF5 file, and H5PYDataset automatically picked them up for us:

>>> print(train_set.provides_sources)
('image_features', 'targets', 'vector_features')

It also parsed axis labels, which are accessible through the axis_labels property, which is a dict mapping source names to a tuple of axis labels:

>>> print(train_set.axis_labels['image_features'])
('batch', 'channel', 'height', 'width')
>>> print(train_set.axis_labels['vector_features'])
('batch', 'feature')
>>> print(train_set.axis_labels['targets'])
('batch', 'index')

We can request data as usual:

>>> handle =
>>> data = train_set.get_data(handle, slice(0, 10))
>>> print((data[0].shape, data[1].shape, data[2].shape))
((10, 3, 5, 5), (10, 1), (10, 10))
>>> train_set.close(handle)

We can also request just the vector features:

>>> train_vector_features = H5PYDataset(
...     'dataset.hdf5', which_sets=('train',), subset=slice(0, 80),
...     sources=['vector_features'])
>>> handle =
>>> data, = train_vector_features.get_data(handle, slice(0, 10))
>>> print(data.shape)
(10, 10)
>>> train_vector_features.close(handle)

Loading data in memory

Reading data off disk is inefficient compared to storing it in memory. Large datasets make it inevitable, but if your dataset is small enough that it fits into memory, you should take advantage of it.

In H5PYDataset, this is accomplished via the load_in_memory constructor argument. It has the effect of loading just what you requested, and nothing more.

>>> in_memory_train_vector_features = H5PYDataset(
...     'dataset.hdf5', which_sets=('train',), subset=slice(0, 80),
...     sources=['vector_features'], load_in_memory=True)
>>> data, = in_memory_train_vector_features.data_sources
>>> print(type(data)) 
<... 'numpy.ndarray'>
>>> print(data.shape)
(80, 10)

Non-contiguous splits

Sometimes it’s not possible to store the different splits contiguously. In that case, you’ll want to use the indices field of the H5PYDataset split array. A non-empty reference in that field overrides the start and stop fields, and the dataset the reference points to is used to determine the indices for that split/source pair.

Suppose that you’d like to use the even examples as your training set and the odd examples as your test set. We’ll start with the HDF5 file we populated earlier and manipulate its split attribute.

>>> f = h5py.File('dataset.hdf5', mode='a')
>>> f['train_indices'] = numpy.arange(0, 100, 2)
>>> train_ref = f['train_indices'].ref
>>> f['test_indices'] = numpy.arange(1, 100, 2)
>>> test_ref = f['test_indices'].ref
>>> split_dict = {
...     'train': {'vector_features': (-1, -1, train_ref),
...               'image_features': (-1, -1, train_ref),
...               'targets': (-1, -1, train_ref)},
...     'test': {'vector_features': (-1, -1, test_ref),
...              'image_features': (-1, -1, test_ref),
...              'targets': (-1, -1, test_ref)}}
>>> f.attrs['split'] = H5PYDataset.create_split_array(split_dict)
>>> f.flush()
>>> f.close()

We created two new datasets containing even and odd indices from 0 to 99, respectively, and passed references to these datasets in the split dict. In that case, the value we pass to start and stop really doesn’t matter, so we arbitrarily chose -1 for both.

Let’s check that the training and test set do contain even and odd examples:

>>> train_set = H5PYDataset(
...     'dataset.hdf5', which_sets=('train',), sources=('vector_features',))
>>> handle =
>>> print(
...     numpy.array_equal(
...         train_set.get_data(handle, slice(0, 50))[0],
...         numpy.vstack(
...             [numpy.load('train_vector_features.npy'),
...              numpy.load('test_vector_features.npy')])[::2]))
>>> train_set.close(handle)
>>> test_set = H5PYDataset(
...     'dataset.hdf5', which_sets=('test',), sources=('vector_features',))
>>> handle =
>>> print(
...     numpy.array_equal(
...         test_set.get_data(handle, slice(0, 50))[0],
...         numpy.vstack(
...             [numpy.load('train_vector_features.npy'),
...              numpy.load('test_vector_features.npy')])[1::2]))
>>> test_set.close(handle)

Variable-length data

H5PYDataset also supports variable length data. Let’s update the image features to reflect that:

>>> sizes = numpy.random.randint(3, 9, size=(100,))
>>> train_image_features = [
...     numpy.random.randint(256, size=(3, size, size)).astype('uint8')
...     for size in sizes[:90]]
>>> test_image_features = [
...     numpy.random.randint(256, size=(3, size, size)).astype('uint8')
...     for size in sizes[90:]]

In this new example, images have random shapes ranging from 3x3 pixels to 8x8 pixels.

First, we put the vector features and the targets inside the HDF5 file as before:

>>> f = h5py.File('dataset.hdf5', mode='w')
>>> f['vector_features'] = numpy.vstack(
...     [numpy.load('train_vector_features.npy'),
...      numpy.load('test_vector_features.npy')])
>>> f['targets'] = numpy.vstack(
...     [numpy.load('train_targets.npy'),
...      numpy.load('test_targets.npy')])
>>> f['vector_features'].dims[0].label = 'batch'
>>> f['vector_features'].dims[1].label = 'feature'
>>> f['targets'].dims[0].label = 'batch'
>>> f['targets'].dims[1].label = 'index'

We now have to put the variable-length images inside the HDF5 file. We can’t do that directly, since HDF5 and h5py don’t support multi-dimensional ragged arrays. However, there is support for 1D ragged arrays. Instead, we’ll flatten the images before putting them in the HDF5 file:

>>> all_image_features = train_image_features + test_image_features
>>> dtype = h5py.special_dtype(vlen=numpy.dtype('uint8'))
>>> image_features = f.create_dataset('image_features', (100,), dtype=dtype)
>>> image_features[...] = [image.flatten() for image in all_image_features]
>>> image_features.dims[0].label = 'batch'

If you’re feeling lost, have a look at the dedicated tutorial on variable-length data.

The images are now in the HDF5 file, but that doesn’t help us unless we can recover their original shape. For that, we’ll create a dimension scale that we’ll attach to the 'image_features' dataset using the name 'shapes' (use this exact name):

>>> image_features_shapes = f.create_dataset(
...     'image_features_shapes', (100, 3), dtype='int32')
>>> image_features_shapes[...] = numpy.array(
...     [image.shape for image in all_image_features])
>>> image_features.dims.create_scale(image_features_shapes, 'shapes')
>>> image_features.dims[0].attach_scale(image_features_shapes)

We’d also like to tag those variable-length dimensions with semantic information. We’ll create another dimension scale that we’ll attach to the 'image_features' dataset using the name 'shape_labels' (use this exact name):

>>> image_features_shape_labels = f.create_dataset(
...     'image_features_shape_labels', (3,), dtype='S7')
>>> image_features_shape_labels[...] = [
...     'channel'.encode('utf8'), 'height'.encode('utf8'),
...     'width'.encode('utf8')]
>>> image_features.dims.create_scale(
...     image_features_shape_labels, 'shape_labels')
>>> image_features.dims[0].attach_scale(image_features_shape_labels)

The H5PYDataset class will handle things from there on. When image features are loaded, it will retrieve their shapes and do the reshape automatically.

Lastly, we create the split dictionary exactly as before:

>>> split_dict = {
...     'train': {'vector_features': (0, 90), 'image_features': (0, 90),
...               'targets': (0, 90)},
...     'test': {'vector_features': (90, 100), 'image_features': (90, 100),
...              'targets': (90, 100)}}
>>> f.attrs['split'] = H5PYDataset.create_split_array(split_dict)
>>> f.flush()
>>> f.close()

That’s it. Now let’s kick the tires a little. The axis labels appear as they should:

>>> train_set = H5PYDataset(
...     'dataset.hdf5', which_sets=('train',), sources=('image_features',))
>>> print(train_set.axis_labels['image_features'])
('batch', 'channel', 'height', 'width')

H5PYDataset retrieves images of different shapes and automatically unflattens them:

>>> handle =
>>> images, = train_set.get_data(handle, slice(0, 10))
>>> train_set.close(handle)
>>> print(images[0].shape, images[1].shape)
(3, 6, 6) (3, 8, 8)

The object returned by get_data is a 1D numpy array of objects:

>>> print(type(images), images.dtype, images.shape) 
<... 'numpy.ndarray'> object (10,)