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GemaCoreLib
The GeMA Core library
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GemaCoreLib
The GeMA Core library
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A class for wrapping up a sparse matrix either using CSR or CSC format. Can also differ on the type used for storing line and column indices. More...
#include <gmSparseMatrix.h>
Public Member Functions | |
| GmSparseMatrix (int n, const GmSparseMatrix< IndexType, T > *sharedLayout, GmSparseMatrixOptions options, bool arma) | |
| Constructor for a sparse square matrix stored either in CSR or CSC format. If sharedLayout is different from NULL, this matrix layout will be given by it. When the arma flag is set to true, the layout and data vector includes extra positions for storing sentinell values needed by the Armadillo CSC format. More... | |
| virtual | ~GmSparseMatrix () |
| Destructor. | |
| virtual bool | supportsBatchInsert () const |
| Does this matrix supports batch inserts? See comments on the class documentation. | |
| virtual bool | supportsSparseLayouts () const |
| Does this matrix supports sparse layouts? See comments on the class documentation. | |
| virtual bool | supportsRandomSet () const |
| Does this matrix supports setting a value on a random position outside the matrix initialization process (either by a batch insert or a layout builder)? | |
| virtual ParallelAddMode | supportedParallelAddMode () const |
| Returns the supported mode for calling add. | |
| virtual bool | beginBatchInsert (size_t expectedEntries=0) |
| Begins a batch insert process. Important: see comments on the class documentation. More... | |
| virtual bool | endBatchInsert (bool discardData=false) |
| Ends a batch insert process. Important: see comments on the class documentation. More... | |
| virtual GmSparseMatrixLayoutBuilder * | layoutBuilder () const |
| If the matrix supports sparse layouts, returns a builder object that can be used to initialize the matrix layout. Otherwise returns NULL. If the layout is being shared by several matrices, only the main matrix, owning the layout should return it. | |
| virtual bool | emptyLayout () const |
| If the matrix supports sparse layouts and the layout is currently empty, returns true. Otherwise, returns false. | |
| virtual bool | symmetric () const |
| Returns true if the matrix was marked as symmetric by setSymmetric() (it does not check for matrix symmetry itself) More... | |
| virtual void | setSymmetric (bool sym) |
| Marks the matrix as symmetric or not. More... | |
| virtual int | nlin () const |
| Returns the number of lines in the matrix. IMPORTANT: This function implementation MUST be thread safe. | |
| virtual int | ncol () const |
| Returns the number of columns in the matrix. IMPORTANT: This function implementation MUST be thread safe. | |
| virtual int | layoutSize () const |
| Returns the size of the sparse matrix layout. More... | |
| virtual double | at (int lin, int col) const |
| Returns the value in the position Mat[lin][col]. | |
| virtual bool | inLayout (int lin, int col) const |
| Returns true if the given position belongs to the matrix sparse layout. More... | |
| virtual void | set (int lin, int col, double value) |
| Sets the value in the position Mat[lin][col] to the specified value. More... | |
| virtual void | add (int lin, int col, double value) |
| Adds the given value to the value in the position Mat[lin][col]. More... | |
| virtual void | set (GmSolverMatrix *A, GmSolverMatrix *B, double c, bool sameStructure) |
| Sets the values of the whole matrix to the result of the expresion A + c * B, where A and B are matrices with the same size as this one and c is a constant. More... | |
| virtual void | clear (bool keepSparseLayout) |
| Clears the matrix, filling it with zeros. The keepSparseLayout flag is a hint that the matrix layout (non zero positions) will remain the same when the matrix is re-filled with data, and so, if the matrix supports sparse layouts, they should not be removed. This function marks the matrix as unsymmetric. | |
| virtual void | clearLineAndColumnSet (const QList< int > &indexList, bool setDiagonal, bool keepSparseLayout) |
| Clears a set of lines and columns from the matrix, filling them with zeroes, optionally puting a 1.0 at the diagonal. More... | |
| virtual void | ensureDiagonal () |
| Updates any zero diagonal value to 1.0. If diagonal values do not belong to the layout, the matrix must NOT be shared! | |
| virtual void | matAdd (const GmVector &a, const GmVector &b, double zeroTol=0.0) |
| Adds to the current matrix ('X') the (dense) matrix resulting from multiplying the column vector 'a' by the transpose of the column vector 'b' (X = X + a * b.t()). More... | |
| virtual void | mul (const GmVector &a, GmVector &b) const |
| Multiplies the matrix ('X') by a vector 'a' storing the result in 'b' (b = X * a). More... | |
| virtual void | mulAdd (const GmVector &a, GmVector &b) const |
| Multiplies the matrix ('X') by a vector 'a' adding the result to 'b' (b = b + X * a). More... | |
| virtual void | mulSub (const GmVector &a, GmVector &b) const |
| Multiplies the matrix ('X') by a vector 'a' subtracting the result from 'b' (b = b - X * a). More... | |
| virtual void | columnMulAdd (int col, GmVector &f, double v, const bool *skipRows=NULL) const |
| Updates the given vector adding to it a matrix column multiplied by a scalar value. More... | |
| virtual size_t | usedMemory () const |
| Returns an estimative of the memory used by the matrix in bytes. More... | |
 Public Member Functions inherited from QObject | |
| virtual const QMetaObject * | metaObject () const const |
| virtual void * | qt_metacast (const char *) |
| virtual int | qt_metacall (QMetaObject::Call, int, void **) |
| QObject (QObject *parent) | |
| virtual bool | event (QEvent *e) |
| virtual bool | eventFilter (QObject *watched, QEvent *event) |
| QString | objectName () const const |
| void | setObjectName (const QString &name) |
| bool | isWidgetType () const const |
| bool | isWindowType () const const |
| bool | signalsBlocked () const const |
| bool | blockSignals (bool block) |
| QThread * | thread () const const |
| void | moveToThread (QThread *targetThread) |
| int | startTimer (int interval, Qt::TimerType timerType) |
| int | startTimer (std::chrono::milliseconds time, Qt::TimerType timerType) |
| void | killTimer (int id) |
| T | findChild (const QString &name, Qt::FindChildOptions options) const const |
| QList< T > | findChildren (const QString &name, Qt::FindChildOptions options) const const |
| QList< T > | findChildren (const QRegExp ®Exp, Qt::FindChildOptions options) const const |
| QList< T > | findChildren (const QRegularExpression &re, Qt::FindChildOptions options) const const |
| const QObjectList & | children () const const |
| void | setParent (QObject *parent) |
| void | installEventFilter (QObject *filterObj) |
| void | removeEventFilter (QObject *obj) |
| QMetaObject::Connection | connect (const QObject *sender, const char *signal, const char *method, Qt::ConnectionType type) const const |
| bool | disconnect (const char *signal, const QObject *receiver, const char *method) const const |
| bool | disconnect (const QObject *receiver, const char *method) const const |
| void | dumpObjectTree () |
| void | dumpObjectInfo () |
| void | dumpObjectTree () const const |
| void | dumpObjectInfo () const const |
| bool | setProperty (const char *name, const QVariant &value) |
| QVariant | property (const char *name) const const |
| QList< QByteArray > | dynamicPropertyNames () const const |
| void | destroyed (QObject *obj) |
| void | objectNameChanged (const QString &objectName) |
| QObject * | parent () const const |
| bool | inherits (const char *className) const const |
| void | deleteLater () |
| Public Member Functions inherited from GmSolverMatrix | |
| virtual | ~GmSolverMatrix () |
| Virtual destructor. | |
| double | operator() (int lin, int col) const |
| Returns the value in the position Mat[lin][col]. More... | |
| bool | isSymmetric (double relTol=GM_DOUBLECMP_RELTOL, double absTol=GM_DOUBLECMP_ABSTOL) const |
| Returns true if the matrix is symmetric, false otherwise. More... | |
| void | print (const GmLogCategory &logger, GmLogLevel level, int fieldWidth=0, char format='g', int precision=-1) |
| Prints the matrix using the specified logger, level and precision fields. | |
Protected Member Functions | |
| virtual void | matrixLayoutReady () |
| Allocates space for matrix values when notified that the layout is ready. | |
| void | addBatch (int lin, int col, double value) |
| Worker function for adding an entry to the matrix while inside a beginBatchInsert() / endBatchInsert() block. | |
| void | addToPtrIndexFromThread (int tid, int ptr, int index, double value) |
| Worker function for adding an entry to the matrix while inside a beginBatchInsert() / endBatchInsert() block, from the given thread and with line and column defined by the matrix layot ptr and index values. | |
| virtual GmSparseMatrix< IndexType, T > * | detachAndClear () |
| Creates a new matrix that inherits the layout and matrix data from this matrix and clears this matrix. More... | |
| GmSparseMatrixLayoutBuilder * | createLayoutBuilder (GmSparseMatrixLayoutMode mode, GmCSxSparseMatrixLayout< IndexType, T > *layout) |
| Creates a new layout builder from the given layout mode and layout. | |
| Protected Member Functions inherited from QObject | |
| QObject * | sender () const const |
| int | senderSignalIndex () const const |
| int | receivers (const char *signal) const const |
| bool | isSignalConnected (const QMetaMethod &signal) const const |
| virtual void | timerEvent (QTimerEvent *event) |
| virtual void | childEvent (QChildEvent *event) |
| virtual void | customEvent (QEvent *event) |
| virtual void | connectNotify (const QMetaMethod &signal) |
| virtual void | disconnectNotify (const QMetaMethod &signal) |
Protected Attributes | |
| GmSparseMatrixOptions | _opt |
| The matrix options, including the mode used to build the matrix. | |
| bool | _batch |
| Flag to signal that the matrix is inside a batch op (for _opt.mode() == TRIPLET_LIST/STRIPLET_LIST) | |
| int | _n |
| The number of lines and columns in the matrix. | |
| QAtomicInt | _sym |
| Flag marking the matrix as symmetric or not. | |
| double * | _values |
| The vector with matrix values. | |
| const GmCSxSparseMatrixLayout< IndexType, T > * | _layout |
| The read-only matrix layout data. Can be shared from other matrices. | |
| GmCSxSparseMatrixLayout< IndexType, T > * | _masterLayout |
| The master layout data (equal to _layout) if this matrix is the layout owner, NULL for matrices sharing a layout. | |
| GmSparseMatrixLayoutBuilder * | _layoutBuilder |
| The layout builder if _masterLayout is not NULL. | |
| GmSparseMatrixTripletBuffer< T > * | _batchData |
| Intermediate structure while building the matrix with a triplet list. | |
Private Member Functions | |
| Q_DISABLE_COPY (GmSparseMatrix) | |
Additional Inherited Members | |
| Public Types inherited from GmSolverMatrix | |
| enum | ParallelAddMode { NO_SUPPORT, THREAD_SAFE_SUPPORT, REENTRANT_SUPPORT } |
| Supported modes for calling add from multiple threads in parallel. More... | |
| Static Public Member Functions inherited from QObject | |
| QString | tr (const char *sourceText, const char *disambiguation, int n) |
| QString | trUtf8 (const char *sourceText, const char *disambiguation, int n) |
| QMetaObject::Connection | connect (const QObject *sender, const char *signal, const QObject *receiver, const char *method, Qt::ConnectionType type) |
| QMetaObject::Connection | connect (const QObject *sender, const QMetaMethod &signal, const QObject *receiver, const QMetaMethod &method, Qt::ConnectionType type) |
| QMetaObject::Connection | connect (const QObject *sender, PointerToMemberFunction signal, const QObject *receiver, PointerToMemberFunction method, Qt::ConnectionType type) |
| QMetaObject::Connection | connect (const QObject *sender, PointerToMemberFunction signal, Functor functor) |
| QMetaObject::Connection | connect (const QObject *sender, PointerToMemberFunction signal, const QObject *context, Functor functor, Qt::ConnectionType type) |
| bool | disconnect (const QObject *sender, const char *signal, const QObject *receiver, const char *method) |
| bool | disconnect (const QObject *sender, const QMetaMethod &signal, const QObject *receiver, const QMetaMethod &method) |
| bool | disconnect (const QMetaObject::Connection &connection) |
| bool | disconnect (const QObject *sender, PointerToMemberFunction signal, const QObject *receiver, PointerToMemberFunction method) |
| Protected Slots inherited from GmSparseMatrixBase | |
| Properties inherited from QObject | |
| objectName | |
A class for wrapping up a sparse matrix either using CSR or CSC format. Can also differ on the type used for storing line and column indices.
| GmSparseMatrix< IndexType, T >::GmSparseMatrix | ( | int | n, |
| const GmSparseMatrix< IndexType, T > * | sharedLayout, | ||
| GmSparseMatrixOptions | options, | ||
| bool | arma | ||
| ) |
Constructor for a sparse square matrix stored either in CSR or CSC format. If sharedLayout is different from NULL, this matrix layout will be given by it. When the arma flag is set to true, the layout and data vector includes extra positions for storing sentinell values needed by the Armadillo CSC format.
IMPORTANT: When sharing a layout with another matrix, this matrix will become invalid if the matrix owning the layout is destroyed.
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inlinevirtual |
Adds the given value to the value in the position Mat[lin][col].
In general this function can be used only to change values over positions that belong to the matrix sparse layout (its set of non zero positions) or inside a beginBatchInsert() / endBatchInsert() region. It can only be used to set values on random positions if supportsRandomSet() returns true.
See the class description for comments about calling this function from multiple threads in parallel.
Implements GmSolverMatrix.
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virtual |
Begins a batch insert process. Important: see comments on the class documentation.
The expectedEntries parameters is an estimative of the number of times that add() will be called for this beginBatchInsert() / endBatchInsert() block.
Uses a 64 bits value for the size since this list can grow quite quickly and a 32 bits limit can be achieved. An hex27 element with 5 dofs per node generates a 135 x 135 local matrix, translating into 135 * 135 = 18.225 calls to append() per mesh element. That will overflow a standard int with less than 120.000 elements.
Implements GmSolverMatrix.
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virtual |
Clears a set of lines and columns from the matrix, filling them with zeroes, optionally puting a 1.0 at the diagonal.
This function is semantically equivalent to the code below, but potentially quicker for sparse matrices. It should be used only for square matrices.
If keepSparseLayout is set to true, matrix values will be changed without updating the internal matrix sparse layout. This can be important for performance if the matrix is later reused to host another set of values with the same layout as the one before removing the set of lines and columns.
IMPORTANT: When enabling both keepSparseLayout and setDiagonal, it is NECESSARY that the diagonal items of the selected rows belong to the current sparse layout. In most cases this is true anyway. Failing to do so will result in undefined behaviour.
If keepSpraseLayout is set to false, the matrix layout can NOT be shared with other matrices since this operation would change the layout.
Implements GmSolverMatrix.
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virtual |
Updates the given vector adding to it a matrix column multiplied by a scalar value.
Given the matrix column 'col', for each row 'i' in the matrix makes f[i] += Mat[i][col] * v. If the boolean vector skipRows is not NULL, the above operation will be executed only if skipRows[i] is not true.
This function is semantically equivalent to the code below, but potentially quicker for sparse matrices.
Implements GmSolverMatrix.
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protectedvirtual |
Creates a new matrix that inherits the layout and matrix data from this matrix and clears this matrix.
Since the internal layout will be changed, it should not be shared...
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virtual |
Ends a batch insert process. Important: see comments on the class documentation.
The discardData parameter is a flag that when set to true informs that the matrix building process was interrupted and so the current matrix data is invalid and should be discarded.
Implements GmSolverMatrix.
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inlinevirtual |
Returns true if the given position belongs to the matrix sparse layout.
This is different from testing if the value is zero since it is possible for a zero value to belong to the layout in antecipation of a future set opertaion. If the matrix does not support the layout concept, it should just test that the value is non zero.
Implements GmSolverMatrix.
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inlinevirtual |
Returns the size of the sparse matrix layout.
The returned size is aproximatelly equal to the number of nonzero entries in the matrix. It will be different if the layout includes places for zero values that might change in the future. If the matriz does not have that information, returns -1.
Implements GmSolverMatrix.
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virtual |
Adds to the current matrix ('X') the (dense) matrix resulting from multiplying the column vector 'a' by the transpose of the column vector 'b' (X = X + a * b.t()).
In order to keep some kind of sparsisity of the matrix, if the resulting values is smaller than the given tolerance, it will not be stored (set to zero).
Implements GmSolverMatrix.
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virtual |
Multiplies the matrix ('X') by a vector 'a' storing the result in 'b' (b = X * a).
If X is a matrix with size equal to M x N, a should have size N and b will have size M.
Implements GmSolverMatrix.
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Multiplies the matrix ('X') by a vector 'a' adding the result to 'b' (b = b + X * a).
If X is a matrix with size equal to M x N, a should have size N and b will have size M.
Implements GmSolverMatrix.
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virtual |
Multiplies the matrix ('X') by a vector 'a' subtracting the result from 'b' (b = b - X * a).
If X is a matrix with size equal to M x N, a should have size N and b will have size M.
Implements GmSolverMatrix.
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inlinevirtual |
Sets the value in the position Mat[lin][col] to the specified value.
In general this function can be used only to set values over positions that belong to the matrix sparse layout (its set of non zero positions). It can only be used to set values on random positions if supportsRandomSet() returns true. (For performance reasons, no exception is made, even when setting a value of 0.0 over an already 0.0 value since that would probably add an if to the critical path).
This function can not be called at all while inside a beginBatchInsert() / endBatchInsert() region.
Implements GmSolverMatrix.
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virtual |
Sets the values of the whole matrix to the result of the expresion A + c * B, where A and B are matrices with the same size as this one and c is a constant.
Conceptually this operation is equivalent to calling set(i, j, A(i, j) + c * B(i, j)) for every line & column of the matrices, but when working with sparse matrices doing it in a batch can be much faster.
If sameStructure is set to true, this functions assumes that A, B and the current matrix object have all the SAME layout (same non-zero structure). When set to false, the matrix layout can not be shared with other matrices since it would change the layout.
Keep in mind that matrix A or matrix B CAN be equal to the current matrix (this).
If the current matrix is marked as symmetric and either A or B is not marked as symmetric, the current matrix will be marked as unsymmetric.
Implements GmSolverMatrix.
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inlinevirtual |
Marks the matrix as symmetric or not.
Marking a symmetric matrix as such might help the numeric solver. When constructed, the matrix is marked as NOT symmetric
Bear in mind that this method DOES NOT CHECK weather the matrix is really symmetric or not. You can do that by calling isSymmetric().
It is also a user responsability to call setSymmetric() again if a matrix operation turns the matrix as unsymmetric.
IMPORTANT: This function implementation MUST be thread safe
Implements GmSolverMatrix.
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inlinevirtual |
Returns true if the matrix was marked as symmetric by setSymmetric() (it does not check for matrix symmetry itself)
IMPORTANT: This function implementation MUST be thread safe
Implements GmSolverMatrix.
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virtual |
Returns an estimative of the memory used by the matrix in bytes.
It returns in general the variable memory that depends on the number of set entries but does not include constant overheads used by the class for control
In particular, this method might return different values before and after a call to endBatchInsert(). If the matrix shares a layout with another matrix, only the layout owner will account for its size.
Implements GmSolverMatrix.
1.8.15