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A fast and easy to use dense and sparse matrix linear algebra library written in Java.
/*
* Copyright (c) 2009-2017, Peter Abeles. All Rights Reserved.
*
* This file is part of Efficient Java Matrix Library (EJML).
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ejml.data;
import org.ejml.ops.SortCoupledArray_F64;
import java.util.Arrays;
/**
* Compressed Column (CC) sparse matrix format. Only non-zero elements are stored.
*
* Format:
* Row indexes for column j are stored in rol_idx[col_idx[j]] to rol_idx[col_idx[j+1]-1]. The values
* for the corresponding elements are stored at data[col_idx[j]] to data[col_idx[j+1]-1].
*
* Row indexes must be specified in chronological order.
*
*
*
* TODO fully describe
*
* @author Peter Abeles
*/
public class DMatrixSparseCSC implements DMatrixSparse {
/**
* Storage for non-zero values. Only valid up to length-1.
*/
public double nz_values[];
/**
* Length of data. Number of non-zero values in the matrix
*/
public int nz_length;
/**
* Specifies which row a specific non-zero value corresponds to. If they are sorted or not with in each column
* is specified by the {@link #indicesSorted} flag.
*/
public int nz_rows[];
/**
* Stores the range of indexes in the non-zero lists that belong to each column. Column 'i' corresponds to
* indexes col_idx[i] to col_idx[i+1]-1, inclusive.
*/
public int col_idx[];
/**
* Number of rows in the matrix
*/
public int numRows;
/**
* Number of columns in the matrix
*/
public int numCols;
/**
* Flag that's used to indicate of the row indices are sorted or not.
*/
public boolean indicesSorted=false;
/**
* Constructor with a default arrayLength of zero.
*
* @param numRows Number of rows
* @param numCols Number of columns
*/
public DMatrixSparseCSC(int numRows , int numCols ) {
this(numRows,numCols,0);
}
/**
* Specifies shape and number of non-zero elements that can be stored.
*
* @param numRows Number of rows
* @param numCols Number of columns
* @param arrayLength Initial maximum number of non-zero elements that can be in the matrix
*/
public DMatrixSparseCSC(int numRows , int numCols , int arrayLength) {
arrayLength = Math.min(numCols*numRows, arrayLength);
this.numRows = numRows;
this.numCols = numCols;
this.nz_length = 0;
nz_values = new double[ arrayLength ];
col_idx = new int[ numCols+1 ];
nz_rows = new int[ arrayLength ];
}
public DMatrixSparseCSC(DMatrixSparseCSC original ) {
this(original.numRows, original.numCols, original.nz_length);
set(original);
}
@Override
public int getNumRows() {
return numRows;
}
@Override
public int getNumCols() {
return numCols;
}
@Override
public DMatrixSparseCSC copy() {
return new DMatrixSparseCSC(this);
}
@Override
public DMatrixSparseCSC createLike() {
return new DMatrixSparseCSC(numRows,numCols);
}
@Override
public void set(Matrix original) {
DMatrixSparseCSC o = (DMatrixSparseCSC)original;
reshape(o.numRows, o.numCols, o.nz_length);
this.nz_length = o.nz_length;
System.arraycopy(o.nz_values, 0, nz_values, 0, nz_length);
System.arraycopy(o.nz_rows, 0, nz_rows, 0, nz_length);
System.arraycopy(o.col_idx, 0, col_idx, 0, numCols+1);
this.indicesSorted = o.indicesSorted;
}
@Override
public void print() {
System.out.println(getClass().getSimpleName()+"\nnumRows = "+numRows+" , numCols = "+numCols
+" , nz_length = "+ nz_length);
for (int row = 0; row < numRows; row++) {
for (int col = 0; col < numCols; col++) {
int index = nz_index(row,col);
if( index >= 0 )
System.out.printf("%6.3f",get(row,col));
else
System.out.print(" * ");
if( col != numCols-1 )
System.out.print(" ");
}
System.out.println();
}
}
@Override
public void printNonZero() {
System.out.println(getClass().getSimpleName()+"\nnumRows = "+numRows+" , numCols = "+numCols
+" , nz_length = "+ nz_length);
for (int col = 0; col < numCols; col++) {
int idx0 = col_idx[col];
int idx1 = col_idx[col+1];
for (int i = idx0; i < idx1; i++) {
int row = nz_rows[i];
double value = nz_values[i];
System.out.printf("%d %d %f\n",row,col,value);
}
}
}
@Override
public boolean isAssigned(int row, int col) {
return nz_index(row,col) >= 0;
}
@Override
public double get(int row, int col) {
if( row < 0 || row >= numRows || col < 0 || col >= numCols )
throw new IllegalArgumentException("Outside of matrix bounds");
return unsafe_get(row,col);
}
@Override
public double unsafe_get(int row, int col) {
int index = nz_index(row,col);
if( index >= 0 )
return nz_values[index];
return 0;
}
/**
* Returns the index in nz_rows for the element at (row,col) if it already exists in the matrix. If not then -1
* is returned.
* @param row row coordinate
* @param col column coordinate
* @return nz_row index or -1 if the element does not exist
*/
public int nz_index( int row , int col ) {
int col0 = col_idx[col];
int col1 = col_idx[col+1];
for (int i = col0; i < col1; i++) {
if( nz_rows[i] == row ) {
return i;
}
}
return -1;
}
@Override
public void set(int row, int col, double val) {
if( row < 0 || row >= numRows || col < 0 || col >= numCols )
throw new IllegalArgumentException("Outside of matrix bounds");
unsafe_set(row,col,val);
}
@Override
public void unsafe_set(int row, int col, double val) {
int index = nz_index(row,col);
if( index >= 0 ) {
nz_values[index] = val;
} else {
int idx0 = col_idx[col];
int idx1 = col_idx[col+1];
// determine the index the new element should be inserted at. This is done to keep it sorted if
// it was already sorted
for( index = idx0; index < idx1; index++ ) {
if( row < nz_rows[index] ) {
break;
}
}
// shift all the col_idx after this point by 1
for (int i = col+1; i <= numCols; i++) {
col_idx[i]++;
}
// if it's already at the maximum array length grow the arrays
if( nz_length >= nz_values.length )
growMaxLength(nz_length*2+1, true);
// shift everything by one
for (int i = nz_length; i > index; i--) {
nz_rows[i] = nz_rows[i-1];
nz_values[i] = nz_values[i-1];
}
nz_rows[index] = row;
nz_values[index] = val;
nz_length++;
}
}
@Override
public void remove( int row , int col ) {
int index = nz_index(row,col);
if( index < 0 ) // it's not in the nz structure
return;
// shift all the col_idx after this point by -1
for (int i = col+1; i <= numCols; i++) {
col_idx[i]--;
}
nz_length--;
for (int i = index; i < nz_length; i++) {
nz_rows[i] = nz_rows[i+1];
nz_values[i] = nz_values[i+1];
}
}
@Override
public void zero() {
Arrays.fill(col_idx,0,numCols+1,0);
nz_length = 0;
indicesSorted = false; // see justification in reshape
}
@Override
public int getNumElements() {
return nz_length;
}
@Override
public void reshape( int numRows , int numCols , int arrayLength ) {
// OK so technically it is sorted, but forgetting to correctly set this flag is a common mistake so
// decided to be conservative and mark it as unsorted so that stuff doesn't blow up
this.indicesSorted = false;
this.numRows = numRows;
this.numCols = numCols;
growMaxLength( arrayLength , false);
this.nz_length = 0;
if( numCols+1 > col_idx.length ) {
col_idx = new int[ numCols+1 ];
} else {
Arrays.fill(col_idx,0,numCols+1,0);
}
}
@Override
public void shrinkArrays() {
if( nz_length < nz_values.length ) {
double tmp_values[] = new double[nz_length];
int tmp_rows[] = new int[nz_length];
System.arraycopy(this.nz_values,0,tmp_values,0,nz_length);
System.arraycopy(this.nz_rows,0,tmp_rows,0,nz_length);
this.nz_values = tmp_values;
this.nz_rows = tmp_rows;
}
}
/**
* Increases the maximum size of the data array so that it can store sparse data up to 'length'. The class
* parameter nz_length is not modified by this function call.
*
* @param arrayLength Desired maximum length of sparse data
* @param preserveValue If true the old values will be copied into the new arrays. If false that step will be skipped.
*/
public void growMaxLength( int arrayLength , boolean preserveValue ) {
// don't increase the size beyound the max possible matrix size
arrayLength = Math.min(numRows*numCols, arrayLength);
if( arrayLength > this.nz_values.length ) {
double[] data = new double[ arrayLength ];
int[] row_idx = new int[ arrayLength ];
if( preserveValue ) {
System.arraycopy(this.nz_values, 0, data, 0, this.nz_length);
System.arraycopy(this.nz_rows, 0, row_idx, 0, this.nz_length);
}
this.nz_values = data;
this.nz_rows = row_idx;
}
}
/**
* Increases the maximum number of columns in the matrix.
* @param desiredColumns Desired number of columns.
* @param preserveValue If the array needs to be expanded should it copy the previous values?
*/
public void growMaxColumns( int desiredColumns , boolean preserveValue ) {
if( col_idx.length < desiredColumns+1 ) {
int[] c = new int[ desiredColumns+1 ];
if( preserveValue )
System.arraycopy(col_idx,0,c,0,col_idx.length);
col_idx = c;
}
}
/**
* Given the histogram of columns compute the col_idx for the matrix. Then overwrite histogram with
* those values. nz_length is automatically set and nz_values will grow if needed.
* @param histogram histogram of column values in the sparse matrix. modified, see above.
*/
public void colsum(int histogram[] ) {
col_idx[0] = 0;
int index = 0;
for (int i = 1; i <= numCols; i++) {
col_idx[i] = index += histogram[i-1];
}
System.arraycopy(col_idx,0,histogram,0,numCols); // TODO move this outside?
nz_length = index;
growMaxLength( nz_length , false);
if( col_idx[numCols] != nz_length )
throw new RuntimeException("Egads");
}
/**
* Sorts the row indices in ascending order.
* @param sorter (Optional) Used to sort rows. If null a new instance will be declared internally.
*/
public void sortIndices(SortCoupledArray_F64 sorter ) {
if( sorter == null )
sorter = new SortCoupledArray_F64();
sorter.quick(col_idx,numCols+1,nz_rows,nz_values);
indicesSorted = true;
}
/**
* Copies the non-zero structure of orig into "this"
* @param orig Matrix who's structure is to be copied
*/
public void copyStructure( DMatrixSparseCSC orig ) {
reshape(orig.numRows, orig.numCols, orig.nz_length);
this.nz_length = orig.nz_length;
System.arraycopy(orig.col_idx,0,col_idx,0,orig.numCols+1);
System.arraycopy(orig.nz_rows,0,nz_rows,0,orig.nz_length);
}
/**
* If the indices has been sorted or not
* @return true if sorted or false if not sorted
*/
public boolean isIndicesSorted() {
return indicesSorted;
}
/**
* Returns true if number of non-zero elements is the maximum size
* @return true if no more non-zero elements can be added
*/
public boolean isFull() {
return nz_length == numRows*numCols;
}
@Override
public MatrixType getType() {
return MatrixType.DSCC;
}
}