Working with big data

New in version 1.2.

HyperSpy makes it possible to analyse data larger than the available memory by providing “lazy” versions of most of its signals and functions. In most cases the syntax remains the same. This chapter describes how to work with data larger than memory using the LazySignal class and its derivatives.

Creating Lazy Signals

Lazy Signals from external data

If the data is large and not loaded by HyperSpy (for example a hdf5.Dataset or similar), first wrap it in dask.array.Array as shown here and then pass it as normal and call as_lazy():

>>> import h5py
>>> f = h5py.File("myfile.hdf5")           # Load the file
>>> data = f['/data/path']                 # Get the data
>>> import dask.array as da                # Import dask to wrap
>>> chunks = (1000,100)                    # Chunk as appropriate
>>> x = da.from_array(data, chunks=chunks) # Wrap the data in dask
>>> s = hs.signals.Signal1D(x).as_lazy() # Create the lazy signal

Loading lazily

To load the data lazily, pass the keyword lazy=True. As an example, loading a 34.9 GB .blo file on a regular laptop might look like:

>>> s = hs.load("shish26.02-6.blo", lazy=True)
>>> s
<LazySignal2D, title: , dimensions: (400, 333|512, 512)>
>>> s.data
dask.array<array-e..., shape=(333, 400, 512, 512), dtype=uint8, chunksize=(20, 12, 512, 512)>
>>> print(s.data.dtype, s.data.nbytes / 1e9)
uint8 34.9175808
>>> s.change_dtype("float") # To be able to perform decomposition, etc.
>>> print(s.data.dtype, s.data.nbytes / 1e9)
float64 279.3406464

Loading the dataset in the original unsigned integer format would require around 35GB of memory. To store it in a floating-point format one would need almost 280GB of memory. However, with the lazy processing both of these steps are near-instantaneous and require very little computational resources.

Lazy stacking

Occasionally the full dataset consists of many smaller files. To combine them into a one large LazySignal, we can stack them lazily (both when loading or afterwards):

>>> siglist = hs.load("*.hdf5")
>>> s = hs.stack(siglist, lazy=True)
>>> # Or load lazily and stack afterwards:
>>> siglist = hs.load("*.hdf5", lazy=True)
>>> s = hs.stack(siglist) # no need to pass 'lazy', as signals already lazy
>>> # Or do everything in one go:
>>> s = hs.load("*.hdf5", lazy=True, stack=True)

Casting signals as lazy

To convert a regular HyperSpy signal to a lazy one such that any future operations are only performed lazily, use the as_lazy() method:

>>> s = hs.signals.Signal1D(np.arange(150.).reshape((3, 50)))
>>> s
<Signal1D, title: , dimensions: (3|50)>
>>> sl = s.as_lazy()
>>> sl
<LazySignal1D, title: , dimensions: (3|50)>

Practical tips

Despite the limitations detailed below, most HyperSpy operations can be performed lazily. Important points of note are:

Computing lazy signals

Upon saving lazy signals, the result of computations is stored on disk.

In order to store the lazy signal in memory (i.e. make it a normal HyperSpy signal) it has a compute() method:

>>> s
<LazySignal2D, title: , dimensions: (|512, 512)>
>>> s.compute()
[########################################] | 100% Completed |  0.1s
>>> s
<Signal2D, title: , dimensions: (|512, 512)>

Limitations

Most operations can be performed lazily. However, lazy operations come with a few limitations and constraints that we detail below.

Immutable signals

An important limitation when using LazySignal is the inability to modify existing data (immutability). This is a logical consequence of the DAG (tree structure, explained in Behind the scenes –technical details), where a complete history of the processing has to be stored to traverse later.

In fact, lazy evaluation removes the need for such operation, since only additional tree branches are added, requiring very little resources. In practical terms the following fails with lazy signals:

>>> s = hs.signals.BaseSignal([0]).as_lazy()
>>> s += 1
Traceback (most recent call last):
  File "<ipython-input-6-1bd1db4187be>", line 1, in <module>
    s += 1
  File "<string>", line 2, in __iadd__
  File "/home/fjd29/Python/hyperspy3/hyperspy/signal.py", line 1591, in _binary_operator_ruler
    getattr(self.data, op_name)(other)
AttributeError: 'Array' object has no attribute '__iadd__'

However, when operating lazily there is no clear benefit to using in-place operations. So, the operation above could be rewritten as follows:

>>> s = hs.signals.BaseSignal([0]).as_lazy()
>>> s = s + 1

Or even better:

>>> s = hs.signals.BaseSignal([0]).as_lazy()
>>> s1 = s + 1

Machine learning (decomposition)

Decomposition algorithms often performs large matrix manipulations, requiring significantly more memory than the data size. To perform decomposition operation lazily HyperSpy provides several “online” algorithms. These algorithms perform the decomposition by operating serially on chunks of data, enabling the lazy decomposition of large datasets.

In line with the standard HyperSpy signals, decomposition() offers the following implementations:

  • PCA (algorithm='PCA'): performs IncrementalPCA from scikit-learn.
  • ORPCA (algorithm='ORPCA'): performs Online Robust PCA. (It is also available for regular signals.)
  • NMF (algorithm='ONMF'): performs Online Robust NMF, as per “OPGD” algorithm in [Zhao2016].

Other minor differences

  • Histograms for a LazySignal do not support knuth and blocks binning algorithms.
  • CircleROI sets the elements outside the ROI to np.nan instead of using a masked array, because dask does not support masking. As a convenience, nansum, nanmean and other nan* signal methods were added to mimic the workflow as closely as possible.

Behind the scenes –technical details

Standard HyperSpy signals load the data into memory for fast access and processing. While this behaviour gives good performance in terms of speed, it obviously requires at least as much computer memory as the dataset, and often twice that to store the results of subsequent computations. This can become a significant problem when processing very large datasets on consumer-oriented hardware.

HyperSpy offers a solution for this problem by including LazySignal and its derivatives. The main idea of these classes is to perform any operation (as the name suggests) lazily (delaying the execution until the result is requested (e.g. saved, plotted)) and in a blocked fashion. This is achieved by building a “history tree” (formally called a Directed Acyclic Graph (DAG)) of the computations, where the original data is at the root, and any further operations branch from it. Only when a certain branch result is requested, the way to the root is found and evaluated in the correct sequence on the correct blocks.

The “magic” is performed by (for the sake of simplicity) storing the data not as numpy.ndarray, but dask.array.Array (more information here). dask offers a couple of advantages:

  • Arbitrary-sized data processing is possible. By only loading a couple of chunks at a time, theoretically any signal can be processed, albeit slower. In practice, this may be limited: (i) some operations may require certain chunking pattern, which may still saturate memory; (ii) many chunks should fit into the computer memory comfortably at the same time.
  • Loading only the required data. If a certain part (chunk) of the data is not required for the final result, it will not be loaded at all, saving time and resources.
  • Able to extend to a distributed computing environment (clusters). dask.distributed (documentation here) offers a straightforward way to expand the effective memory for computations to that of a cluster, which allows performing the operations significantly faster than on a single machine.