MNE-CPP
beta 1.0
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The RapMusic class provides the RAP MUSIC Algorithm CPU implementation. ToDo: Paper references. More...
#include <rapmusic.h>
Public Types | |
typedef QSharedPointer< RapMusic > | SPtr |
typedef QSharedPointer< const RapMusic > | ConstSPtr |
typedef Eigen::Matrix< double, Eigen::Dynamic, Eigen::Dynamic > | MatrixXT |
typedef Eigen::Matrix< double, Eigen::Dynamic, 6 > | MatrixX6T |
typedef Eigen::Matrix< double, 6, Eigen::Dynamic > | Matrix6XT |
typedef Eigen::Matrix< double, 6, 6 > | Matrix6T |
typedef Eigen::Matrix< double, Eigen::Dynamic, 1 > | VectorXT |
typedef Eigen::Matrix< double, 6, 1 > | Vector6T |
Public Member Functions | |
RapMusic () | |
RapMusic (MNEForwardSolution &p_pFwd, bool p_bSparsed, int p_iN=2, double p_dThr=0.5) | |
bool | init (MNEForwardSolution &p_pFwd, bool p_bSparsed=false, int p_iN=2, double p_dThr=0.5) |
virtual MNESourceEstimate | calculateInverse (const FiffEvoked &p_fiffEvoked, bool pick_normal=false) |
virtual MNESourceEstimate | calculateInverse (const MatrixXd &data, float tmin, float tstep) const |
virtual MNESourceEstimate | calculateInverse (const MatrixXd &p_matMeasurement, QList< DipolePair< double > > &p_RapDipoles) const |
virtual const char * | getName () const |
virtual const MNESourceSpace & | getSourceSpace () const |
void | setStcAttr (int p_iSampStcWin, float p_fStcOverlap) |
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virtual | ~IInverseAlgorithm () |
Protected Member Functions | |
int | calcPhi_s (const MatrixXT &p_matMeasurement, MatrixXT *&p_pMatPhi_s) const |
void | calcOrthProj (const MatrixXT &p_matA_k_1, MatrixXT &p_matOrthProj) const |
void | calcPairCombinations (const int p_iNumPoints, const int p_iNumCombinations, Pair **p_ppPairIdxCombinations) const |
Static Protected Member Functions | |
static double | subcorr (MatrixX6T &p_matProj_G, const MatrixXT &p_pMatU_B) |
static double | subcorr (MatrixX6T &p_matProj_G, const MatrixXT &p_matU_B, Vector6T &p_vec_phi_k_1) |
static void | calcA_k_1 (const MatrixX6T &p_matG_k_1, const Vector6T &p_matPhi_k_1, const int p_iIdxk_1, MatrixXT &p_matA_k_1) |
static void | getPointPair (const int p_iPoints, const int p_iCurIdx, int &p_iIdx1, int &p_iIdx2) |
static void | getGainMatrixPair (const MatrixXT &p_matGainMarix, MatrixX6T &p_matGainMarix_Pair, int p_iIdx1, int p_iIdx2) |
static void | insertSource (int p_iDipoleIdx1, int p_iDipoleIdx2, const Vector6T &p_vec_phi_k_1, double p_valCor, QList< DipolePair< double > > &p_RapDipoles) |
static int | getRank (const MatrixXT &p_matSigma) |
static int | useFullRank (const MatrixXT &p_Mat, const MatrixXT &p_matSigma_src, MatrixXT &p_matFull_Rank, int type=NOT_TRANSPOSED) |
static MatrixXT | makeSquareMat (const MatrixXT &p_matF) |
Protected Attributes | |
MNEForwardSolution | m_ForwardSolution |
int | m_iN |
double | m_dThreshold |
int | m_iNumGridPoints |
int | m_iNumChannels |
int | m_iNumLeadFieldCombinations |
Pair ** | m_ppPairIdxCombinations |
int | m_iMaxNumThreads |
bool | m_bIsInit |
int | m_iSamplesStcWindow |
float | m_fStcOverlap |
The RapMusic class provides the RAP MUSIC Algorithm CPU implementation. ToDo: Paper references.
ToDo Detailed description
Definition at line 109 of file rapmusic.h.
typedef QSharedPointer<const RapMusic> INVERSELIB::RapMusic::ConstSPtr |
Const shared pointer type for RapMusic.
Definition at line 113 of file rapmusic.h.
typedef Eigen::Matrix<double, 6, 6> INVERSELIB::RapMusic::Matrix6T |
Defines Eigen::Matrix<T, 6, 6> as Matrix6T type.
Definition at line 126 of file rapmusic.h.
typedef Eigen::Matrix<double, 6, Eigen::Dynamic> INVERSELIB::RapMusic::Matrix6XT |
Defines Eigen::Matrix<T, 6, Eigen::Dynamic> as Matrix6XT type.
Definition at line 124 of file rapmusic.h.
typedef Eigen::Matrix<double, Eigen::Dynamic, 6> INVERSELIB::RapMusic::MatrixX6T |
Defines Eigen::Matrix<T, Eigen::Dynamic, 6> as MatrixX6T type.
Definition at line 122 of file rapmusic.h.
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> INVERSELIB::RapMusic::MatrixXT |
Defines Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic> as MatrixXT type.
Definition at line 120 of file rapmusic.h.
typedef QSharedPointer<RapMusic> INVERSELIB::RapMusic::SPtr |
Shared pointer type for RapMusic.
Definition at line 112 of file rapmusic.h.
typedef Eigen::Matrix<double, 6, 1> INVERSELIB::RapMusic::Vector6T |
Defines Eigen::Matrix<T, 6, 1> as Vector6T type.
Definition at line 130 of file rapmusic.h.
typedef Eigen::Matrix<double, Eigen::Dynamic, 1> INVERSELIB::RapMusic::VectorXT |
Defines Eigen::Matrix<T, Eigen::Dynamic, 1> as VectorXT type.
Definition at line 128 of file rapmusic.h.
RapMusic::RapMusic | ( | ) |
Default constructor creates an empty RapMusic algorithm which still needs to be initialized.
Definition at line 62 of file rapmusic.cpp.
RapMusic::RapMusic | ( | MNEForwardSolution & | p_pFwd, |
bool | p_bSparsed, | ||
int | p_iN = 2 , |
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double | p_dThr = 0.5 |
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Constructor which initializes the RapMusic algorithm with the given model.
[in] | p_Fwd | The model which contains the gain matrix and its corresponding grid matrix. |
[in] | p_bSparsed | True when sparse matrices should be used. |
[in] | p_iN | The number (default 2) of uncorrelated sources, which should be found. Starting with the strongest. |
[in] | p_dThr | The correlation threshold (default 0.5) at which the search for sources stops. |
Definition at line 79 of file rapmusic.cpp.
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staticprotected |
Calculates the accumulated manifold vectors A_{k1}
[in] | p_matG_k_1 | The Lead Field combination for the currently best correlated pair. |
[in] | p_matPhi_k_1 | Is equal to u_k_1 in the paper and it is the direction of the currently best correlated pair. |
[in] | p_iIdxk_1 | The current position in the manifold vector array A_k_1 |
[out] | p_matA_k_1 | The array of the manifold vectors. |
Definition at line 756 of file rapmusic.cpp.
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Calculates the orthogonal projector Phi_A_k_1 like in the paper Mosher 1999 (13)
[in] | p_matA_k_1 | The array of the manifold vectors. |
[out] | p_matOrthProj | The orthogonal projector. |
Definition at line 772 of file rapmusic.cpp.
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Pre-Calculates the gain matrix index combinations to search for a two dipole independent topography (IT = source).
[in] | p_iNumPoints | The number of Lead Field points -> for dimension check |
[in] | p_iNumCombinations | The number of pair index combinations. |
[out] | p_ppPairIdxCombinations | The destination which contains pointer to pointer of index combinations of Lead Field indices -> Number of pointers = Combination (number of grid points over 2 = Num + 1 C 2) |
Definition at line 815 of file rapmusic.cpp.
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Computes the signal subspace Phi_s out of the measurement F.
[in] | p_pMatMeasurement | The current measured data to process (for best performance it should have the dimension channels x samples with samples = number of channels) |
[out] | p_pMatPhi_s | The calculated signal subspace. |
Definition at line 593 of file rapmusic.cpp.
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virtual |
Applies the inverse algorithm to input data and returns a source estimate.
[in] | p_fiffEvoked | Evoked data. |
[in] | pick_normal | If True, rather than pooling the orientations by taking the norm, only the radial component is kept. This is only applied when working with loose orientations. |
Implements INVERSELIB::IInverseAlgorithm.
Reimplemented in INVERSELIB::PwlRapMusic.
Definition at line 208 of file rapmusic.cpp.
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virtual |
Applies the inverse algorithm to input data and returns a source estimate.
[in] | p_fiffEvoked | Evoked data. |
[in] | tmin | Minimal time point |
[in] | tmin | Time between two samples |
Implements INVERSELIB::IInverseAlgorithm.
Reimplemented in INVERSELIB::PwlRapMusic.
Definition at line 331 of file rapmusic.cpp.
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staticprotected |
Returns a gain matrix pair for the given indices
[in] | p_matGainMarix | The Lead Field matrix. |
[out] | p_matGainMarix_Pair | Lead Field combination (dimension: m x 6) |
[in] | p_iIdx1 | first Lead Field index point |
[in] | p_iIdx2 | second Lead Field index point |
Definition at line 859 of file rapmusic.cpp.
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Returns the algorithm name
Implements INVERSELIB::IInverseAlgorithm.
Reimplemented in INVERSELIB::PwlRapMusic.
Definition at line 192 of file rapmusic.cpp.
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staticprotected |
Calculates the combination indices Idx1 and Idx2 of n points.
[ (0,0) (0,1) (0,2) ... (0,n-1) (0,n)
(1,1) (1,2) ... (1,n-1) (1,n)
(2,2) ... (2,n-1) (2,n)
(n-1,n-1) (n-1,n)
(n,n)]
[in] | p_iPoints | The number of points n which are combined with each other. |
[in] | p_iCurIdx | The current combination index (between 0 and nchoosek(n+1,2)) |
[out] | p_iIdx1 | The resulting index 1. |
[out] | p_iIdx2 | The resulting index 2. |
Definition at line 846 of file rapmusic.cpp.
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inlinestaticprotected |
Returns the rank r of a singular value matrix based on non-zero singular values (singular value > epsilon = 10^-5)
[in] | p_matSigma | diagonal matrix which contains the Singular values (Dimension n x n) |
Definition at line 377 of file rapmusic.h.
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virtual |
Returns the current mne source space on which the inverse algorithm is performing on. Either from inverse operator (minimum norm estimate), or from forward solution (beamformers)
Implements INVERSELIB::IInverseAlgorithm.
Definition at line 200 of file rapmusic.cpp.
bool RapMusic::init | ( | MNEForwardSolution & | p_pFwd, |
bool | p_bSparsed = false , |
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int | p_iN = 2 , |
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double | p_dThr = 0.5 |
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Initializes the RAP MUSIC algorithm with the given model.
[in] | p_Fwd | The model which contains the gain matrix and its corresponding Grid matrix. |
[in] | p_bSparsed | True when sparse matrices should be used. |
[in] | p_iN | The number (default 2) of uncorrelated sources, which should be found. Starting with the strongest. |
[in] | p_dThr | The correlation threshold (default 0.5) at which the search for sources stops. |
Definition at line 107 of file rapmusic.cpp.
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staticprotected |
Adds a new correlated dipole pair to th RapDipoles. This function is called by the RAP MUSIC Algorithm.
[in] | p_iDipoleIdx1 | Index (Lead Field grid index) of the first dipole. |
[in] | p_iDipoleIdx2 | Index (Lead Field grid index) of the second dipole. |
[in] | p_vec_phi_k_1 | Array of the dipole directories (phi_x1, phi_y1, phi_z1, phi_x2, phi_y2, phi_z2). |
[in] | p_valCor | Correlation value of the dipole pair. |
[out] | p_RapDipoles | the list of dipole pairs. |
Definition at line 871 of file rapmusic.cpp.
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inlinestaticprotected |
Performs F * F^Transposed, is used when n > m
[in] | p_matF | The matrix which should be transformed. |
Definition at line 412 of file rapmusic.h.
void RapMusic::setStcAttr | ( | int | p_iSampStcWin, |
float | p_fStcOverlap | ||
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Sets the source estimate attributes.
[in] | p_iSampStcWin | Samples per source localization window (default - 1 = not set) |
[in] | p_fStcOverlap | Percentage of localization window overlap |
Definition at line 905 of file rapmusic.cpp.
Computes the subspace correlation between the projected G_rho and the projected signal subspace Phi_s. For speed-up: we calculate the decomposition of the projected Phi_s before this function. So the argument for this function is U_B instead of Phi_s.
[in] | p_matProj_G | The projected Lead Field combination. This is a m x 6 matrix composed of the Lead Field combination of two Points for all m channels and 3 orthogonal components (x y z). |
[in] | p_matU_B | The matrix U is the subspace projection of the orthogonal projected Phi_s |
Definition at line 623 of file rapmusic.cpp.
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staticprotected |
Computes the subspace correlation between the projected G_rho and the projected signal subspace Phi_s, as well as the resulting direction. For speed-up: we calculate the decomposition of the projected Phi_s before this function. So the argument for this function is U_B instead of Phi_s.
[in] | p_matProj_G | The projected Lead Field combination. This is a m x 6 matrix composed of the Lead Field combination of two Points for all m channels and 3 orthogonal components (x y z). |
[in] | p_matU_B | The matrix U is the subspace projection of the orthogonal projected Phi_s |
[out] | p_vec_phi_k_1 | Returns the orientation for a correlated dipole pair. (phi_x1, phi_y1, phi_z1, phi_x2, phi_y2, phi_z2) |
Definition at line 679 of file rapmusic.cpp.
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inlinestaticprotected |
lt. Mosher 1998 -> Only Retain those Components of U_A and U_B that correspond to nonzero singular values for U_A and U_B the number of columns corresponds to their ranks
[in] | p_Mat | The Matrix which should be reduced to its rank. |
[in] | p_matSigma_src | The singular values of the matrix |
[out] | p_matFull_Rank | The corresponding full rank matrix. |
[in] | type | Whether p_Mat is transposed, than rows and columns are changed. |
Definition at line 394 of file rapmusic.h.
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Wether the algorithm is initialized.
Definition at line 331 of file rapmusic.h.
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Threshold which defines the minimal correlation. Is the correlation of the found dipole pair smaller as this threshold than the RAP MUSIC calculation is stopped.
Definition at line 319 of file rapmusic.h.
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The Forward operator which should be scanned through
Definition at line 316 of file rapmusic.h.
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Percentage of localization window overlap
Definition at line 335 of file rapmusic.h.
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Number of available CPU threads.
Definition at line 329 of file rapmusic.h.
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Number of Sources to find
Definition at line 318 of file rapmusic.h.
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Number of channels
Definition at line 324 of file rapmusic.h.
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Number of Grid points.
Definition at line 323 of file rapmusic.h.
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Number of Lead Filed combinations (grid points + 1 over 2)
Definition at line 325 of file rapmusic.h.
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Number of samples per localization window
Definition at line 334 of file rapmusic.h.
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Index combination vector with grid pair indices.
Definition at line 327 of file rapmusic.h.