public boolean ok(String out, String reference) {
// log.fine("out1: " + a);
// log.fine("out2: " + b);
Scanner sa = new Scanner(out);
Scanner sb = new Scanner(reference);
while (sa.hasNext() && sb.hasNext()) {
if (sa.hasNextDouble() || sb.hasNextDouble()) {
if (!sa.hasNextDouble() || !sb.hasNextDouble()) return true;
double da = sa.nextDouble();
double db = sb.nextDouble();
double d_abs = Math.abs(da - db);
double d_rel = d_abs / Math.abs(db);
if (!(d_abs < EPS || d_rel < EPS)) {
log.fine("NOK, " + da + " too far from " + db);
return false;
}
} else {
String xa = sa.next();
String xb = sb.next();
if (!xa.equals(xb)) {
log.fine("NOK, " + xa + " != " + xb);
return false;
}
}
}
if (sa.hasNext() || sb.hasNext()) {
log.fine("NOK: different number of tokens.");
return false;
}
return true;
}
/**
* Loads into a double[][] a plain text file of numbers, with newlines dividing the numbers into
* rows and tabs or spaces delimiting columns. The Y dimension is not flipped.
*/
public static double[][] loadTextFile(InputStream stream) throws IOException {
Scanner scan = new Scanner(stream);
ArrayList rows = new ArrayList();
int width = -1;
while (scan.hasNextLine()) {
String srow = scan.nextLine().trim();
if (srow.length() > 0) {
int w = 0;
if (width == -1) // first time compute width
{
ArrayList firstRow = new ArrayList();
Scanner rowScan = new Scanner(new StringReader(srow));
while (rowScan.hasNextDouble()) {
firstRow.add(new Double(rowScan.nextDouble())); // ugh, boxed
w++;
}
width = w;
double[] row = new double[width];
for (int i = 0; i < width; i++) row[i] = ((Double) (firstRow.get(i))).doubleValue();
rows.add(row);
} else {
double[] row = new double[width];
Scanner rowScan = new Scanner(new StringReader(srow));
while (rowScan.hasNextDouble()) {
if (w == width) // uh oh
throw new IOException("Row lengths do not match in text file");
row[w] = rowScan.nextDouble();
w++;
}
if (w < width) // uh oh
throw new IOException("Row lengths do not match in text file");
rows.add(row);
}
}
}
if (width == -1) // got nothing
return new double[0][0];
double[][] fieldTransposed = new double[rows.size()][];
for (int i = 0; i < rows.size(); i++) fieldTransposed[i] = ((double[]) (rows.get(i)));
// now transpose because we have width first
double[][] field = new double[width][fieldTransposed.length];
for (int i = 0; i < field.length; i++)
for (int j = 0; j < field[i].length; j++) field[i][j] = fieldTransposed[j][i];
return field;
}
public static void main(String[] args) {
while (scan.hasNextDouble()) {
double t1 = scan.nextDouble();
double t2 = scan.nextDouble();
int i1, i2;
for (i1 = 0; i1 < s1.length; i1++) {
if (t1 < s1[i1]) break;
}
for (i2 = 0; i2 < s2.length; i2++) {
if (t2 < s2[i2]) break;
}
System.out.println(r[Math.max(i1, i2)]);
}
}
protected static ArrayList<Position> readReferencePositions(String filePath)
throws FileNotFoundException {
ArrayList<Position> positions = new ArrayList<Position>();
Scanner scanner = new Scanner(new File(filePath));
while (scanner.hasNextDouble()) {
double lat = scanner.nextDouble();
double lon = scanner.nextDouble();
double elevation = scanner.nextDouble();
positions.add(Position.fromDegrees(lat, lon, elevation));
}
return positions;
}
public static void main(String[] args) throws IOException {
Scanner s = new Scanner(new File("number.txt")).useDelimiter(";");
int noo1 = 0, noo2 = 0, noo3 = 0, noo4 = 0, noo5 = 0;
String line;
while (s.hasNextDouble()) {
double val = s.nextDouble();
if ((val > 0) && (val < 20)) noo1++;
else if ((val > 20) && (val < 40)) noo2++;
else if ((val > 40) && (val < 60)) noo3++;
else if ((val > 60) && (val < 80)) noo4++;
else if ((val > 80) && (val < 100)) noo5++;
}
s.close();
System.out.println("Range 0 to 20: " + noo1);
System.out.println("Range 20 to 40: " + noo2);
System.out.println("Range 40 to 60: " + noo3);
System.out.println("Range 60 to 80: " + noo4);
System.out.println("Range 80 to 100: " + noo5);
}
private static String countFile(String filename)
{
String result = "";
int row = 0;
int rowCheck = 0;
int col = 0;
Scanner fileScanner = new Scanner(File filename));
while(fileScanner.hasNextLine())
{
Scanner lineScanner = new Scanner(fileScanner.nextLine());
while(lineScanner.hasNextDouble())
{
row++;
lineScanner.next();
}
col++;
if(row = 0)
{
rowCheck = row;
}
else if(row != rowCheck)
{
System.out.println("Number of rows in the file is inconsistent.");
}
lineScanner.close();
}
fileScanner.close();
result = row + " " col;
return result;
}
public static void main(String[] args) {
//////////////////////////
// The values in following 4 lines should be user input
int startPos = 200;
int endPos = 1000;
int totalNumPixel = 1044;
double threshhold = 0.0001;
/////////////////////////
int numPixel = endPos - startPos;
double wavelength[] = new double[totalNumPixel];
double photonCount[] = new double[totalNumPixel];
double SpecNoBk[] = new double[numPixel];
double ThisSpectrum[] = new double[numPixel];
double ThisXaxis[] = new double[numPixel];
double Po[] = new double[numPixel];
double Re[] = new double[numPixel];
double P[] = new double[6];
double Re2[] = new double[numPixel - 1];
double mySUM[] = new double[numPixel];
int ind[];
double DEV;
double prevDEV;
Connection connection = null;
Statement stmt = null;
String pattern = "##.##";
try {
Scanner in = new Scanner(new FileReader(args[0]));
int i = 0;
while (in.hasNextDouble()) {
wavelength[i] = in.nextDouble();
photonCount[i] = in.nextDouble();
++i;
}
} catch (FileNotFoundException e) {
e.printStackTrace();
}
ThisSpectrum = Arrays.copyOfRange(photonCount, startPos, endPos);
ThisXaxis = Arrays.copyOfRange(wavelength, startPos, endPos);
final WeightedObservedPoints obs = new WeightedObservedPoints();
for (int i = 0; i < numPixel; i++) {
obs.add(ThisXaxis[i], ThisSpectrum[i]);
}
final PolynomialCurveFitter fitter = PolynomialCurveFitter.create(5);
P = fitter.fit(obs.toList());
Polyval pVal = new Polyval(P, ThisXaxis, numPixel);
Po = pVal.evl();
for (int i = 0; i < numPixel; i++) {
Re[i] = ThisSpectrum[i] - Po[i];
}
for (int i = 0; i < numPixel - 1; i++) {
Re2[i] = Re[i + 1] - Re[i];
}
DEV = Math.sqrt(StatUtils.populationVariance(Re2, 0, Re2.length));
for (int i = 0; i < numPixel; i++) {
mySUM[i] = Po[i] + DEV;
}
int jj = 0; // jj is the length of points to be removed
for (int i = 0; i < numPixel; i++) {
if (ThisSpectrum[i] > mySUM[i]) {
jj++;
;
}
}
ind = new int[jj];
int jjj = 0;
for (int i = 0; i < numPixel; i++) {
if (ThisSpectrum[i] > mySUM[i]) {
ind[jjj] = i;
jjj++;
}
}
int indKeepLength = numPixel - ind.length;
int indKeep[] = new int[indKeepLength];
int k = 0;
for (int i = 0; i < numPixel; i++) {
if (!ArrayUtils.contains(ind, i)) {
indKeep[k] = i;
k++;
}
}
double ThisSpectrumKeep[] = new double[indKeepLength];
double ThisXaxisKeep[] = new double[indKeepLength];
double PoKeep[] = new double[indKeepLength];
double ReKeep[] = new double[indKeepLength];
double Re2Keep[] = new double[indKeepLength - 1];
double mySUMKeep[] = new double[indKeepLength];
for (int i = 0; i < indKeepLength; i++) {
ThisSpectrumKeep[i] = ThisSpectrum[indKeep[i]];
ThisXaxisKeep[i] = ThisXaxis[indKeep[i]];
}
prevDEV = DEV;
// at the point, ThisSpectrum and ThisXaxis should have reduced size
final WeightedObservedPoints obs1 = new WeightedObservedPoints();
for (int i = 0; i < indKeepLength; i++) {
obs1.add(ThisXaxisKeep[i], ThisSpectrumKeep[i]);
}
while (true) {
final PolynomialCurveFitter fitter1 = PolynomialCurveFitter.create(5);
P = fitter1.fit(obs1.toList());
Polyval pVal1 = new Polyval(P, ThisXaxisKeep, indKeepLength);
PoKeep = pVal1.evl();
for (int i = 0; i < indKeepLength; i++) {
ReKeep[i] = ThisSpectrumKeep[i] - PoKeep[i];
}
for (int i = 0; i < indKeepLength - 1; i++) {
Re2Keep[i] = ReKeep[i + 1] - ReKeep[i];
}
DEV = Math.sqrt(StatUtils.populationVariance(Re2Keep, 0, Re2Keep.length));
for (int i = 0; i < indKeepLength; i++) {
mySUMKeep[i] = PoKeep[i] + DEV;
}
for (int i = 0; i < indKeepLength; i++) {
if (ThisSpectrumKeep[i] > mySUMKeep[i]) ThisSpectrumKeep[i] = mySUMKeep[i];
}
if ((Math.abs(DEV - prevDEV) / DEV) < threshhold) break;
prevDEV = DEV;
obs1.clear();
for (int i = 0; i < indKeepLength; i++) {
obs1.add(ThisXaxisKeep[i], ThisSpectrumKeep[i]);
}
}
Polyval pVal2 = new Polyval(P, ThisXaxis, numPixel);
double FLbk[] = pVal2.evl();
for (int i = 0; i < ThisXaxis.length; i++) {
SpecNoBk[i] = ThisSpectrum[i] - FLbk[i];
}
// the write-to-file part is only for testing purpose, ThisXaxis and SpecNoBk are two outputs
try {
FileWriter fr = new FileWriter(args[1]);
BufferedWriter br = new BufferedWriter(fr);
PrintWriter out = new PrintWriter(br);
DecimalFormat df = new DecimalFormat(pattern);
for (int j = 0; j < ThisXaxis.length; j++) {
if (Double.toString(wavelength[j]) != null) out.write(ThisXaxis[j] + "\t" + SpecNoBk[j]);
out.write("\r\n");
}
out.close();
} catch (IOException e) {
System.out.println(e);
}
}