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FiffProj

Namespace: FIFFLIB  ·  Library: FIFF Library

Python equivalent

mne.Projection in MNE-Python.

#include <fiff/fiff_proj.h>

class FIFFLIB::FiffProj

Single SSP projection item: kind, active flag, desired flag and the named projection vector matrix.

Maps one FIFFB_PROJ_ITEM block to a C++ value: description, kind, nvec, active, plus a FiffNamedMatrix whose row names are the channels the projector acts on. Multiple FiffProj instances form the info['projs'] list and are combined into one projection operator by make_projector when raw / evoked data is loaded.

src/examples/ex_fiff_api/main.cpp
const FiffProj& pca = info.projs[0]; // "PCA-v1", 1 vector over 102 magnetometers, inactive
QList<FiffProj> projs = info.projs;
FiffProj::activate_projs(projs);

Public Methods​

FiffProj()​

Default constructor.

FiffProj(p_FiffProj)​

Copy constructor.

Parameters:

  • p_FiffProj : const FiffProj & SSP projector data which should be copied.

operator=(other)​

Copy assignment.

Every member has value semantics, so the compiler-generated member-wise assignment is correct. It is declared explicitly because declaring a copy constructor and/or a destructor deprecates the implicitly generated one.

Parameters:

  • other : const FiffProj & Object to assign from.

Returns:

  • FiffProj & — reference to this object.

FiffProj(p_kind, p_active, p_desc, p_data)​

Constructor.

Parameters:

  • p_kind : fiff_int_t Projection kind (FIFFV_PROJ_ITEM_* constant).

  • p_active : bool Whether the projector is already applied to the data.

  • p_desc : QString Human-readable description of the projector.

  • p_data : FiffNamedMatrix & Projection vectors with channel names; a deep copy is stored.

~FiffProj()​

Destroys the FiffProj.

Static Methods​

activate_projs(p_qListFiffProj)​

Set all projections to active.

Parameters:

  • p_qListFiffProj : QList< FiffProj > & activates projectors in place.

make_projector(projs, ch_names, proj, bads, U)​

mne_make_projector

ToDo move this to fiff_proj; Before: check if info is needed and if make_projector_info should be also moved.

Make an SSP operator

Parameters:

  • projs : const QList< FiffProj > & A set of projection vectors.

  • ch_names : const QStringList & A cell array of channel names.

  • proj : Eigen::MatrixXd & The projection operator to apply to the data.

  • bads : const QStringList & Bad channels to exclude.

  • U : Eigen::MatrixXd & The orthogonal basis of the projection vectors (optional).

Returns:

  • fiff_int_t — nproj - How many items in the projector.

compute_from_raw(raw, events, eventCode, tmin, tmax, nGrad, nMag, nEeg, mapReject)​

compute_from_raw

Create SSP (Signal-Space Projection) operators from raw data via SVD. Ported from make_ssp.c (MNE-C).

Parameters:

  • raw : const FiffRawData & The raw data.

  • events : const Eigen::MatrixXi & Event matrix (nEvents x 3).

  • eventCode : int Which event code to select epochs for.

  • tmin : float Start of epoch relative to event (seconds).

  • tmax : float End of epoch relative to event (seconds).

  • nGrad : int Number of gradiometer projection vectors.

  • nMag : int Number of magnetometer projection vectors.

  • nEeg : int Number of EEG projection vectors.

  • mapReject : const QMap< QString, double > & Rejection thresholds (key = channel type string, value = threshold).

Returns:

compute_from_evoked(evoked, nGrad, nMag, nEeg)​

Create SSP operators from averaged artifact data (mne.compute_proj_evoked).

For each of gradiometers, magnetometers and EEG (bad channels excluded) the leading left singular vectors of the evoked data become inactive projectors named like "planar-<tmin>-<tmax>-PCA-01", "axial-..." and "eeg-...".

Parameters:

  • evoked : const FiffEvoked & The averaged artifact.

  • nGrad : int Number of gradiometer projection vectors.

  • nMag : int Number of magnetometer projection vectors.

  • nEeg : int Number of EEG projection vectors.

Returns:

  • QList< FiffProj > — List of FiffProj items (all channels as columns), or empty list for empty data.

Example​

Used in examples​

ex_fiff_api​

FIFF library: measurement info, channels, digitizer, transforms, projectors, covariance, events,.

src/examples/ex_fiff_api/main.cpp, line 157
const FiffProj& pca = info.projs[0]; // "PCA-v1", 1 vector over 102 magnetometers, inactive
QList<FiffProj> projs = info.projs;
FiffProj::activate_projs(projs);
ok &= expect(pca.desc == "PCA-v1" && !pca.active && pca.data->nrow == 1 && pca.data->ncol == 102 && projs[0].active,
             "FiffProj/FiffNamedMatrix: PCA-v1 is 1 x 102 and inactive until activated");

ex_mne_api​

MNE library: BEM surfaces, surface projection, ICP, source spaces and epochs.

src/examples/ex_mne_api/main.cpp, line 451
MatrixXi eventsBack;
MNE::read_events(eveName, rawFile.fileName(), eventsBack);
QList<FiffProj> projs = raw.info.projs; // stored inactive in the raw file
FiffProj::activate_projs(projs);
MatrixXd ssp; // like mne._fiff.proj.make_projector(info['projs'], ch_names, bads)
const int nProj = MNE::make_projector(projs, raw.info.ch_names, ssp, raw.info.bads);
// mne.find_events: 25 events, first at sample 13988 with code 2; make_projector: 4 vectors, trace 372 of 376
ok &= expect(eventsBack.rows() == 25 && eventsBack(0, 0) == 13988 && eventsBack(0, 2) == 2 && nProj == 4 && near(ssp.trace(), 372.0, 1e-9) && near(ssp.norm(), 19.28730152198591, 1e-9),
             "MNE: event file round trip and SSP projector like mne.find_events / make_projector");

ex_dsp_rt​

DSP real-time workers: averaging, covariance, noise spectrum, connectivity, HPI fitting and inverse operators.

src/examples/ex_dsp_rt/main.cpp, line 281
ok &= hpiRaw.read_raw_segment(hpiData, hpiTimes, hpiRaw.first_samp, hpiRaw.first_samp + 399);
MatrixXd projectors = MatrixXd::Identity(hpiInfo->nchan, hpiInfo->nchan);
FiffInfo projInfo = *hpiInfo;
for (FiffProj& proj : projInfo.projs) {
    proj.active = true;
}
projInfo.make_projector(projectors);

Authors of this file​