Smart Adaptive Multi-dimensional Fitting (SAMFire)#

SAMFire (Smart Adaptive Multi-dimensional Fitting) is an algorithm created to reduce the starting value (or local / false minima) problem, which often arises when fitting multi-dimensional datasets.

The algorithm is described in Tomas Ostasevicius’ PhD thesis, entitled “Multi-dimensional Data Analysis in Electron Microscopy”.

The idea#

The main idea of SAMFire is to change two things compared to the traditional way of fitting datasets with many dimensions in the navigation space:

  1. Pick a more sensible pixel fitting order.

  2. Calculate the pixel starting parameters from already fitted parts of the dataset.

Both of these aspects are linked one to another and are represented by two different strategy families that SAMFfire uses while operating.

Strategies#

During operation SAMFire uses a list of strategies to determine how to select the next pixel and estimate its starting parameters. Only one strategy is used at a time. Next strategy is chosen when no new pixels can be fitted with the current strategy. Once either the strategy list is exhausted or the full dataset fitted, the algorithm terminates.

There are two families of strategies. In each family there may be many strategies, using different statistical or significance measures.

As a rule of thumb, the first strategy in the list should always be from the local family, followed by a strategy from the global family.

Local strategy family#

These strategies assume that locally neighbouring pixels are similar. As a result, the pixel fitting order seems to follow data-suggested order, and the starting values are computed from the surrounding already fitted pixels.

More information about the exact procedure will be available once the accompanying paper is published.

Global strategy family#

Global strategies assume that the navigation coordinates of each pixel bear no relation to it’s signal (i.e. the location of pixels is meaningless). As a result, the pixels are selected at random to ensure uniform sampling of the navigation space.

A number of candidate starting values are computed form global statistical measures. These values are all attempted in order until a satisfactory result is found (not necessarily testing all available starting guesses). As a result, on average each pixel requires significantly more computations when compared to a local strategy.

More information about the exact procedure will be available once the accompanying paper is published.

Seed points#

Due to the strategies using already fitted pixels to estimate the starting values, at least one pixel has to be fitted beforehand by the user.

The seed pixel(s) should be selected to require the most complex model present in the dataset, however in-built goodness of fit checks ensure that only sufficiently well fitted values are allowed to propagate.

If the dataset consists of regions (in the navigation space) of highly dissimilar pixels, often called “domain structures”, at least one seed pixel should be given for each unique region.

If the starting pixels were not optimal, only part of the dataset will be fitted. In such cases it is best to allow the algorithm terminate, then provide new (better) seed pixels by hand, and restart SAMFire. It will use the new seed together with the already computed parts of the data.

Usage#

After creating a model and fitting suitable seed pixels, to fit the rest of the multi-dimensional dataset using SAMFire we must create a SAMFire instance as follows:

>>> samf = m.create_samfire(workers=None, ipyparallel=False)

By default SAMFire will look for an ipyparallel cluster for the workers for around 30 seconds. If none is available, it will use multiprocessing instead. However, if you are not planning to use ipyparallel, it’s recommended specify it explicitly via the ipyparallel=False argument, to use the fall-back option of multiprocessing.

By default a new SAMFire object already has two (and currently only) strategies added to its strategies list:

>>> samf.strategies 
  A |    # | Strategy
 -- | ---- | -------------------------
  x |    0 | Reduced chi squared strategy
    |    1 | Histogram global strategy

The currently active strategy is marked by an ‘x’ in the first column.

If a new datapoint (i.e. pixel) is added manually, the “database” of the currently active strategy has to be refreshed using the refresh_database() call.

The current strategy “database” can be plotted using the plot() method.

Whilst SAMFire is running, each pixel is checked by a goodness_test, which is by default red_chisq_test, checking the reduced chi-squared to be in the bounds of [0, 2].

This tolerance can (and most likely should!) be changed appropriately for the data as follows:

>>> # use a sensible value
>>> samf.metadata.goodness_test.tolerance = 0.3

The SAMFire managed multi-dimensional fit can be started using the start() method. All keyword arguments are passed to the underlying (i.e. usual) fit() call:

>>> samf.start(optimizer='lm', bounded=True)