Java Code Examples for cern.colt.matrix.DoubleMatrix1D#toArray()
The following examples show how to use
cern.colt.matrix.DoubleMatrix1D#toArray() .
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Example 1
| Source File: TestMatrix2D.java From database with GNU General Public License v2.0 | 5 votes |
|
/**
* 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");
}
Example 2
| Source File: Statistic.java From jAudioGIT with GNU Lesser General Public License v2.1 | 5 votes |
|
/**
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);
}
Example 3
| Source File: TestMatrix2D.java From jAudioGIT with GNU Lesser General Public License v2.1 | 5 votes |
|
/**
* 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");
}
Example 4
| Source File: Algebra.java From database with GNU General Public License v2.0 | 4 votes |
|
/**
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;
}
Example 5
| Source File: BBFreeBlock.java From OSPREY3 with GNU General Public License v2.0 | 4 votes |
|
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();
}
Example 6
| Source File: Algebra.java From jAudioGIT with GNU Lesser General Public License v2.1 | 4 votes |
|
/**
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;
}
Example 7
| Source File: Statistic.java From jAudioGIT with GNU Lesser General Public License v2.1 | 3 votes |
|
/**
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:
Entries=5000, ExtraEntries=0
MeanX=4.9838, RmsX=NaN
MeanY=2.5304, RmsY=NaN
xAxis: Min=0, Max=10, Bins=11
yAxis: Min=0, Max=5, Bins=6
Heights:
| X
| 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
4 | 43 106 112 96 92 94 107 98 98 110 47 | 1003
3 | 39 134 87 93 102 103 110 90 114 98 51 | 1021
2 | 44 81 113 96 101 86 109 83 111 93 42 | 959
1 | 54 94 103 99 115 92 98 97 103 90 44 | 989
0 | 24 54 52 44 42 56 46 47 56 53 20 | 494
----------------------------------------------------------
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);
}
