Data Analysis and Processing

Data analysis pipelines are inspired by the well established and feature-rich MATLAB toolbox FieldTrip. Syncopy aims to emulate FieldTrip’s basic usage concepts.

Syncopy Meta-Functions

All of Syncopy’s computing managers (like freqanalysis()) can be either called using positional/keyword arguments following standard Python syntax, e.g.,

spec = spy.freqanalysis(data, method="mtmfft", foilim=[1, 150], output="pow", taper="dpss", tapsmofrq=10)

or using a cfg configuration structure:

cfg = spy.get_defaults(spy.freqanalysis)
cfg.method = 'mtmfft';
cfg.foilim = [1, 150];
cfg.output = 'pow';
cfg.taper = 'dpss';
cfg.tapsmofrq = 10;
spec = spy.freqanalysis(cfg, data)

Serial and Parallel Processing

By default, all computations in Syncopy are executed sequentially relying solely on low-level built-in parallelization offered by external libraries like NumPy. The simplest way to enable full concurrency for a given Syncopy calculation is by using the parallel keyword supported by all Syncopy meta-functions, i.e.,

spec = spy.freqanalysis(data, method="mtmfft", foilim=[1, 150], output="pow", taper="dpss", tapsmofrq=10, parallel=True)

or

cfg = spy.get_defaults(spy.freqanalysis)
cfg.method = 'mtmfft'
cfg.foilim = [1, 150]
cfg.output = 'pow'
cfg.taper = 'dpss'
cfg.tapsmofrq = 10
cfg.parallel = True
spec = spy.freqanalysis(cfg, data)

More fine-grained control over allocated resources and load-balancer options is available via the routine esi_cluster_setup(). It permits to launch a custom-tailored “cluster” of parallel workers (corresponding to CPU cores if run on a single machine, i.e., laptop or workstation, or compute jobs if run on a cluster computing manager such as SLURM). Thus, instead of simply “turning on” parallel computing via a keyword and letting Syncopy choose an optimal setup for the computation at hand, more fine-grained control over resource allocation and management can be achieved via running esi_cluster_setup() before launching the actual calculation. For example,

spyClient = spy.esi_cluster_setup(partition="16GBXL", n_jobs=10)

starts 10 concurrent SLURM workers in the 16GBXL queue if run on the ESI HPC cluster. All subsequent invocations of Syncopy analysis routines will automatically pick up spyClient and distribute any occurring computational payload across the workers collected in spyClient.

Visualization

Syncopy offers convenience functions for quick visual inspection of its data objects:

import matplotlib.pyplot as plt
plt.ion() # enable "pop-out" figures

# generate synthetic data
from syncopy.tests.misc import generate_artificial_data
adata = generate_artificial_data(nChannels=12)

# plot each channel in `adata` inside one panel
spy.singlepanelplot(adata, avg_channels=False)

# compute dummy spectrum of `adata` and have a look at it
spec = spy.freqanalysis(adata, method="mtmfft", output="pow", keeptrials=False)
spy.singlepanelplot(spec)

For more information, please refer to the documentation of singlepanelplot() and multipanelplot().