Working with big data

Warning

All the features described in this chapter are in beta state. Although most of them work, their opearation may not always be optimal, well documented and/or consistent with their in-memory counterparts. Therefore, although efforts will be taken to minimise major disruptions, the syntax and features described here may change in patch and minor HyperSpy releases. If you experience issues with HyperSpy’s lazy features please report them to the developers.

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.

New in version 1.4: close_file()

Currently when loading an hdf5 file lazily the file remains open at least while the signal exists. In order to close it explicitly, use the close_file() method. Alternatively, you could close it on calling compute() by passing the keyword argument close_file=True e.g.:

>>> s = hs.load("file.hspy", lazy=True)
>>> ssum = s.sum(axis=0)
>>> ssum.compute(close_file=True) # closes the file.hspy file

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:

Chunking

New in version 1.3.2.

By default, HyperSpy tries to optimize the chunking for most operations. However, it is sometimes possible to manually set a more optimal chunking manually. Therefore, many operations take a rechunk or optimize keyword argument to disable automatic rechunking.

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)>

Lazy operations that affect the axes

When using lazy signals the computation of the data is delayed until requested. However, the changes to the axes properties are performed when running a given function that modfies them i.e. they are not performed lazily. This can lead to hard to debug issues when the result of a given function that is computed lazily depends on the value of the axes parameters that may have changed before the computation is requested. Therefore, in order to avoid such issues, it is reccomended to explicitly compute the result of all functions that are affected by the axes paramters. This is the reason why e.g. the result of shift1D() is not lazy.

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 and dask’s lazy SVD algorithm. Online 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 online algorithms:

  • PCA (algorithm='PCA'): performs IncrementalPCA from scikit-learn. Please refer to its documentation for a description of the several keyword arguments taken by its :meth:fit method.
  • ORPCA (algorithm='ORPCA'): performs Online Robust PCA. Please refer to the docstring of ORPCA() for details on usage and keyword arguments.
  • NMF (algorithm='ONMF'): performs Online Robust NMF, as per “OPGD” algorithm in [Zhao2016]. Please refer to the docstring of ONMF() for details on usage and keyword arguments.

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.