Java Code Examples for cern.colt.matrix.DoubleMatrix1D#toArray()

/**
 * Title:        Aero3D<p>
 * Description:  A Program to analyse aeroelestic evects in transonic wings<p>
 * Copyright:    Copyright (c) 1999 CERN - European Organization for Nuclear Research.
 * Company:      PIERSOL Engineering Inc.<p>
 * @author John R. Piersol
 * @version
 */
public static void doubleTest36() {
	double[] testSort = new double[5];
	testSort[0] = 5;
	testSort[1] = Double.NaN;
	testSort[2] = 2;
	testSort[3] = Double.NaN;
	testSort[4] = 1;
	DoubleMatrix1D doubleDense = new DenseDoubleMatrix1D(testSort);
	System.out.println("orig = "+doubleDense);
	doubleDense = doubleDense.viewSorted();
	doubleDense.toArray(testSort);
	System.out.println("sort = "+doubleDense);
	System.out.println("done\n");
}
 

/**
3-d OLAP cube operator; Fills all cells of the given vectors into the given histogram.
If you use hep.aida.ref.Converter.toString(histo) on the result, the OLAP cube of x-"column" vs. y-"column" vs. z-"column", summing the weights "column" will be printed.
For example, aggregate sales by product by region by time.
<p>
Computes the distinct values of x and y and z, yielding histogram axes that capture one distinct value per bin.
Then fills the histogram.
@return the histogram containing the cube.
@throws IllegalArgumentException if <tt>x.size() != y.size() || x.size() != z.size() || x.size() != weights.size()</tt>.
*/
public static hep.aida.IHistogram3D cube(DoubleMatrix1D x, DoubleMatrix1D y, DoubleMatrix1D z, DoubleMatrix1D weights) {
	if (x.size() != y.size() || x.size() != z.size() || x.size() != weights.size()) throw new IllegalArgumentException("vectors must have same size");
	
	double epsilon = 1.0E-9;
	cern.colt.list.DoubleArrayList distinct = new cern.colt.list.DoubleArrayList();
	double[] vals = new double[x.size()];
	cern.colt.list.DoubleArrayList sorted = new cern.colt.list.DoubleArrayList(vals);

	// compute distinct values of x
	x.toArray(vals); // copy x into vals
	sorted.sort();
	cern.jet.stat.Descriptive.frequencies(sorted, distinct, null);
	// since bins are right-open [from,to) we need an additional dummy bin so that the last distinct value does not fall into the overflow bin
	if (distinct.size()>0) distinct.add(distinct.get(distinct.size()-1) + epsilon);
	distinct.trimToSize();
	hep.aida.IAxis xaxis = new hep.aida.ref.VariableAxis(distinct.elements());

	// compute distinct values of y
	y.toArray(vals);
	sorted.sort();
	cern.jet.stat.Descriptive.frequencies(sorted, distinct, null);
	// since bins are right-open [from,to) we need an additional dummy bin so that the last distinct value does not fall into the overflow bin
	if (distinct.size()>0) distinct.add(distinct.get(distinct.size()-1) + epsilon);
	distinct.trimToSize();
	hep.aida.IAxis yaxis = new hep.aida.ref.VariableAxis(distinct.elements());

	// compute distinct values of z
	z.toArray(vals);
	sorted.sort();
	cern.jet.stat.Descriptive.frequencies(sorted, distinct, null);
	// since bins are right-open [from,to) we need an additional dummy bin so that the last distinct value does not fall into the overflow bin
	if (distinct.size()>0) distinct.add(distinct.get(distinct.size()-1) + epsilon);
	distinct.trimToSize();
	hep.aida.IAxis zaxis = new hep.aida.ref.VariableAxis(distinct.elements());

	hep.aida.IHistogram3D histo = new hep.aida.ref.Histogram3D("Cube",xaxis,yaxis,zaxis);
	return histogram(histo,x,y,z,weights);
}
 

/**
 * Title:        Aero3D<p>
 * Description:  A Program to analyse aeroelestic evects in transonic wings<p>
 * Copyright:    Copyright (c) 1998<p>
 * Company:      PIERSOL Engineering Inc.<p>
 * @author John R. Piersol
 * @version
 */
public static void doubleTest36() {
	double[] testSort = new double[5];
	testSort[0] = 5;
	testSort[1] = Double.NaN;
	testSort[2] = 2;
	testSort[3] = Double.NaN;
	testSort[4] = 1;
	DoubleMatrix1D doubleDense = new DenseDoubleMatrix1D(testSort);
	System.out.println("orig = "+doubleDense);
	doubleDense = doubleDense.viewSorted();
	doubleDense.toArray(testSort);
	System.out.println("sort = "+doubleDense);
	System.out.println("done\n");
}
 

/**
Modifies the given vector <tt>A</tt> such that it is permuted as specified; Useful for pivoting.
Cell <tt>A[i]</tt> will go into cell <tt>A[indexes[i]]</tt>.
<p>
<b>Example:</b>
<pre>
Reordering
[A,B,C,D,E] with indexes [0,4,2,3,1] yields 
[A,E,C,D,B]
In other words A[0]<--A[0], A[1]<--A[4], A[2]<--A[2], A[3]<--A[3], A[4]<--A[1].

Reordering
[A,B,C,D,E] with indexes [0,4,1,2,3] yields 
[A,E,B,C,D]
In other words A[0]<--A[0], A[1]<--A[4], A[2]<--A[1], A[3]<--A[2], A[4]<--A[3].
</pre>

@param   A   the vector to permute.
@param   indexes the permutation indexes, must satisfy <tt>indexes.length==A.size() && indexes[i] >= 0 && indexes[i] < A.size()</tt>;
@param   work the working storage, must satisfy <tt>work.length >= A.size()</tt>; set <tt>work==null</tt> if you don't care about performance.
@return the modified <tt>A</tt> (for convenience only).
@throws	IndexOutOfBoundsException if <tt>indexes.length != A.size()</tt>.
*/
public DoubleMatrix1D permute(DoubleMatrix1D A, int[] indexes, double[] work) {
	// check validity
	int size = A.size();
	if (indexes.length != size) throw new IndexOutOfBoundsException("invalid permutation");

	/*
	int i=size;
	int a;
	while (--i >= 0 && (a=indexes[i])==i) if (a < 0 || a >= size) throw new IndexOutOfBoundsException("invalid permutation");
	if (i<0) return; // nothing to permute
	*/

	if (work==null || size > work.length) {
		work = A.toArray();
	}
	else {
		A.toArray(work);
	}
	for (int i=size; --i >= 0; ) A.setQuick(i, work[indexes[i]]);
	return A;
}
 

public void setDOFs(DoubleMatrix1D x){
    //x: free DOFs (relative to center, so can eval polys directly)
    
    int numRes = residues.size();
    
    int numDOFsFull = fullDOFPolys.length;
    double fullDOFVals[] = new double[fullDOFPolys.length];
    
    for(int fullDOF=0; fullDOF<numDOFsFull; fullDOF++)
        fullDOFVals[fullDOF] = SeriesFitter.evalSeries(fullDOFPolys[fullDOF], x, x.size(), true, polyOrder);
                
    //record current information needed for placement of sidechain
    double genChi1[] = new double[numRes];
    double SCTranslations[][] = new double[numRes][3];
    
    //now set each residue in the right place
    
    //start with the CA's and N's
    for(int resNum=0; resNum<numRes; resNum++){
        
        Residue curRes = residues.get(resNum);
        
        //the sidechain will be translated based on CA motion
        if(resNum>0 && resNum<numRes-1){//CA moves, so translate sidechain with it
            double curCACoords[] = curRes.getCoordsByAtomName("CA");
            for(int dim=0; dim<3; dim++)
                SCTranslations[resNum][dim] = fullDOFVals[6*(resNum-1)+3+dim] - curCACoords[dim];
        }
        
        genChi1[resNum] = GenChi1Calc.getGenChi1(curRes);
        
        //OK now place the backbone...
        if(resNum>0){//N or CA moves
            int CAIndex = curRes.getAtomIndexByName("CA");
            int NIndex = curRes.getAtomIndexByName("N");

            for(int dim=0; dim<3; dim++){
                if(resNum<numRes-1)//CA moves
                    curRes.coords[3*CAIndex+dim] = fullDOFVals[6*(resNum-1)+3+dim];
                
                curRes.coords[3*NIndex+dim] = fullDOFVals[6*(resNum-1)+dim];
            }
        }
    }
    
    //OK now that the CA's and N's are in place, we can finish each peptide plane
    for(int pepPlaneNum=0; pepPlaneNum<numRes-1; pepPlaneNum++){
        //set each atom based on CA and N (linear relationship)
        Residue res1 = residues.get(pepPlaneNum);//residue at start of peptide plane...
        Residue res2 = residues.get(pepPlaneNum+1);//...and at end
        
        double CA1[] = res1.getCoordsByAtomName("CA");
        double N[] = res2.getCoordsByAtomName("N");
        double CA2[] = res2.getCoordsByAtomName("CA");
                    
        res1.setCoordsByAtomName("C", pepPlanes[pepPlaneNum].calcCCoords(CA1,N,CA2,false));
        res1.setCoordsByAtomName("O", pepPlanes[pepPlaneNum].calcOCoords(CA1,N,CA2));
        res2.setCoordsByAtomName("H", pepPlanes[pepPlaneNum].calcHCoords(CA1,N,CA2));
    }
        
    
    
    //OK and now that the backbone atoms are in place, we can handle the sidechains and HA's
    for(int resNum=0; resNum<numRes; resNum++){
        //first translate into place...
        RigidBodyMotion motion = new RigidBodyMotion(new double[3], RotationMatrix.identity(), SCTranslations[resNum]);
        SidechainIdealizer.moveSidechain(residues.get(resNum), motion);
        //...now idealize
        SidechainIdealizer.idealizeSidechain(EnvironmentVars.resTemplates, residues.get(resNum));
        //and get gen chi1 to where it was before, so this BB motion commutes w/ sidechain dihedral changes
        GenChi1Calc.setGenChi1(residues.get(resNum), genChi1[resNum]);
    }
    
    curFreeDOFVals = x.toArray();
}
 

/**
Modifies the given vector <tt>A</tt> such that it is permuted as specified; Useful for pivoting.
Cell <tt>A[i]</tt> will go into cell <tt>A[indexes[i]]</tt>.
<p>
<b>Example:</b>
<pre>
Reordering
[A,B,C,D,E] with indexes [0,4,2,3,1] yields 
[A,E,C,D,B]
In other words A[0]<--A[0], A[1]<--A[4], A[2]<--A[2], A[3]<--A[3], A[4]<--A[1].

Reordering
[A,B,C,D,E] with indexes [0,4,1,2,3] yields 
[A,E,B,C,D]
In other words A[0]<--A[0], A[1]<--A[4], A[2]<--A[1], A[3]<--A[2], A[4]<--A[3].
</pre>

@param   A   the vector to permute.
@param   indexes the permutation indexes, must satisfy <tt>indexes.length==A.size() && indexes[i] >= 0 && indexes[i] < A.size()</tt>;
@param   work the working storage, must satisfy <tt>work.length >= A.size()</tt>; set <tt>work==null</tt> if you don't care about performance.
@return the modified <tt>A</tt> (for convenience only).
@throws	IndexOutOfBoundsException if <tt>indexes.length != A.size()</tt>.
*/
public DoubleMatrix1D permute(DoubleMatrix1D A, int[] indexes, double[] work) {
	// check validity
	int size = A.size();
	if (indexes.length != size) throw new IndexOutOfBoundsException("invalid permutation");

	/*
	int i=size;
	int a;
	while (--i >= 0 && (a=indexes[i])==i) if (a < 0 || a >= size) throw new IndexOutOfBoundsException("invalid permutation");
	if (i<0) return; // nothing to permute
	*/

	if (work==null || size > work.length) {
		work = A.toArray();
	}
	else {
		A.toArray(work);
	}
	for (int i=size; --i >= 0; ) A.setQuick(i, work[indexes[i]]);
	return A;
}
 

/**
2-d OLAP cube operator; Fills all cells of the given vectors into the given histogram.
If you use hep.aida.ref.Converter.toString(histo) on the result, the OLAP cube of x-"column" vs. y-"column" , summing the weights "column" will be printed.
For example, aggregate sales by product by region.
<p>
Computes the distinct values of x and y, yielding histogram axes that capture one distinct value per bin.
Then fills the histogram.
<p>
Example output:
<table>
<td class="PRE"> 
<pre>
Cube:
&nbsp;&nbsp;&nbsp;Entries=5000, ExtraEntries=0
&nbsp;&nbsp;&nbsp;MeanX=4.9838, RmsX=NaN
&nbsp;&nbsp;&nbsp;MeanY=2.5304, RmsY=NaN
&nbsp;&nbsp;&nbsp;xAxis: Min=0, Max=10, Bins=11
&nbsp;&nbsp;&nbsp;yAxis: Min=0, Max=5, Bins=6
Heights:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;| X
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;| 0   1   2   3   4   5   6   7   8   9   10  | Sum 
----------------------------------------------------------
Y 5   |  30  53  51  52  57  39  65  61  55  49  22 |  534
&nbsp;&nbsp;4   |  43 106 112  96  92  94 107  98  98 110  47 | 1003
&nbsp;&nbsp;3   |  39 134  87  93 102 103 110  90 114  98  51 | 1021
&nbsp;&nbsp;2   |  44  81 113  96 101  86 109  83 111  93  42 |  959
&nbsp;&nbsp;1   |  54  94 103  99 115  92  98  97 103  90  44 |  989
&nbsp;&nbsp;0   |  24  54  52  44  42  56  46  47  56  53  20 |  494
----------------------------------------------------------
&nbsp;&nbsp;Sum | 234 522 518 480 509 470 535 476 537 493 226 |     
</pre>
</td>
</table>
@return the histogram containing the cube.
@throws IllegalArgumentException if <tt>x.size() != y.size() || y.size() != weights.size()</tt>.
*/
public static hep.aida.IHistogram2D cube(DoubleMatrix1D x, DoubleMatrix1D y, DoubleMatrix1D weights) {
	if (x.size() != y.size() || y.size() != weights.size()) throw new IllegalArgumentException("vectors must have same size");
	
	double epsilon = 1.0E-9;
	cern.colt.list.DoubleArrayList distinct = new cern.colt.list.DoubleArrayList();
	double[] vals = new double[x.size()];
	cern.colt.list.DoubleArrayList sorted = new cern.colt.list.DoubleArrayList(vals);

	// compute distinct values of x
	x.toArray(vals); // copy x into vals
	sorted.sort();
	cern.jet.stat.Descriptive.frequencies(sorted, distinct, null);
	// since bins are right-open [from,to) we need an additional dummy bin so that the last distinct value does not fall into the overflow bin
	if (distinct.size()>0) distinct.add(distinct.get(distinct.size()-1) + epsilon);
	distinct.trimToSize();
	hep.aida.IAxis xaxis = new hep.aida.ref.VariableAxis(distinct.elements());

	// compute distinct values of y
	y.toArray(vals);
	sorted.sort();
	cern.jet.stat.Descriptive.frequencies(sorted, distinct, null);
	// since bins are right-open [from,to) we need an additional dummy bin so that the last distinct value does not fall into the overflow bin
	if (distinct.size()>0) distinct.add(distinct.get(distinct.size()-1) + epsilon);
	distinct.trimToSize();
	hep.aida.IAxis yaxis = new hep.aida.ref.VariableAxis(distinct.elements());

	hep.aida.IHistogram2D histo = new hep.aida.ref.Histogram2D("Cube",xaxis,yaxis);
	return histogram(histo,x,y,weights);
}