001 package util.sdss;
002
003 import java.text.DecimalFormat;
004 import org.eso.fits.*;
005 import java.util.*;
006
007 /**
008 * A data container to hold the emission line instances and hold a reference
009 * to the source star.
010 */
011 public class Line implements Comparable<Line> {
012
013 static DecimalFormat formatter = new DecimalFormat("0.00");
014
015 Star source;
016
017 public double wavelength; // Line center
018 public double wavelengthErr; // Error in line center
019 public double sigma; // Sigma of fitted Gaussian
020 public double sigmaErr; // Error in sigma
021 public double height; // Height of gaussian (10^-17 ergs/s/cm^2/Å)
022 public double heightErr; // Error in height
023 public double equivalentWitdth; // Equivalent width
024 public double equivalentWitdthErr;// Error in equivalent width
025 public double continuum; // Value of continuum at line center (10^-17 ergs/s/cm^2/Å)
026 public double index; // Spectral index
027 public double significance; // Significance of line in number of sigma
028
029 //double redshift;
030
031 public Line(Star aSource, double aWavelength,
032 double aWavelengthErr,
033 double aSigma,
034 double aSigmaErr,
035 double aHeight,
036 double aHeightErr,
037 double anEquivalentWitdth,
038 double anEquivalentWitdthErr,
039 double aContinuum,
040 double anIndex,
041 double aSignificance) {
042 source = aSource;
043 wavelength = aWavelength;
044 wavelengthErr = aWavelengthErr;
045 sigma = aSigma;
046 sigmaErr = aSigmaErr;
047 height = aHeight;
048 heightErr = aHeightErr;
049 equivalentWitdth = anEquivalentWitdth;
050 equivalentWitdthErr = anEquivalentWitdthErr;
051 continuum = aContinuum;
052 index = anIndex;
053 significance = aSignificance;
054 }
055
056 public Line(Star aSource, double aWavelength) {
057 source = aSource;
058 wavelength = aWavelength;
059 }
060
061 public Star getSource() {
062 return source;
063 }
064
065 /** Get the emission line wavelength as centroid of the fitted gaussian line profile */
066 public double getWavelength() {
067 return wavelength;
068 }
069
070 static double gaussianFactor = Math.sqrt(2.0*Math.PI);
071
072 /** Get the emission strength as area under the fitted gaussian line profile */
073 public double getStrength() {
074 return height * sigma * gaussianFactor;
075 }
076
077 public static List<Line> getLines(Star aSource, FitsTable table) {
078 List<Line> lines = new ArrayList<Line>();
079 for (int i = 0; i < table.getNoRows(); i++) {
080 Line line = new Line(aSource,
081 table.getColumn(0).getReal(i),
082 table.getColumn(1).getReal(i),
083 table.getColumn(4).getReal(i),
084 table.getColumn(5).getReal(i),
085 table.getColumn(8).getReal(i),
086 table.getColumn(9).getReal(i),
087 table.getColumn(11).getReal(i),
088 table.getColumn(12).getReal(i),
089 table.getColumn(10).getReal(i),
090 table.getColumn(14).getReal(i),
091 table.getColumn(15).getReal(i));
092 lines.add(line);
093 }
094 return lines;
095 }
096
097 /** Show emission lines, for testing purposes only */
098 public static void showLines(FitsTable dm) {
099 int nrow = dm.getNoRows();
100 int ncol = dm.getNoColumns();
101 FitsColumn col[] = new FitsColumn[ncol];
102 System.out.println(" Columns: " + ncol + ", Rows: " + nrow);
103 for (int n = 0; n < ncol; n++) {
104 col[n] = dm.getColumn(n);
105 System.out.print(" " + n + " >" + col[n].getLabel() + "<, ");
106 System.out.print(col[n].getRepeat() + " ");
107 System.out.print(col[n].getDataType() + ", >");
108 System.out.print(col[n].getDisplay() + "<, >");
109 System.out.println(col[n].getUnit() + "<");
110 if (col[n].getDataType() == 'F' || col[n].getDataType() == 'E' || col[n].getDataType() == 'D') {
111 int npix = 0;
112 double mean, rms, val;
113 mean = rms = 0.0;
114 for (int nr=0; nr<nrow; nr++) {
115 val = col[n].getReal(nr);
116 if ("wave".equals(col[n].getLabel())) System.out.println(val);
117 if (Double.isNaN(val)) continue;
118 npix++;
119 mean += val;
120 rms += val*val;
121 }
122 mean = mean/npix;
123 rms = rms/npix - mean*mean;
124 rms = ((0.0<rms) ? Math.sqrt(rms) : 0.0);
125 System.out.println(" no,mean,rms: " + npix + ", " + (float)mean + ", " + (float)rms);
126 } else if (col[n].getDataType() == 'I' || col[n].getDataType() == 'J' || col[n].getDataType() == 'B') {
127 int npix = 0;
128 double mean, rms, val;
129 mean = rms = 0.0;
130 for (int nr=0; nr<nrow; nr++) {
131 val = col[n].getInt(nr);
132 if (val == Long.MIN_VALUE) continue;
133 npix++;
134 mean += val;
135 rms += val*val;
136 }
137 mean = mean/npix;
138 rms = rms/npix - mean*mean;
139 rms = ((0.0<rms) ? Math.sqrt(rms) : 0.0);
140 System.out.println(" no,mean,rms: " + npix + ", " + (float)mean + ", " + (float)rms);
141 }
142 }
143 }
144
145 /** default comparator is based on line wavelength */
146 public int compareTo(Line aLine) {
147 return WAVELENGTH_COMPARATOR.compare(this, aLine);
148 }
149
150 /** Comparator based on line wavelength. */
151 public static final Comparator<Line> WAVELENGTH_COMPARATOR = new Comparator<Line>() {
152 public int compare(Line line1, Line line2) {
153 if (line1 == null || line2 == null) throw(new NullPointerException("Compare to null Line instance"));
154 return (int)(line2.getWavelength() - line1.getWavelength());
155 }
156 public boolean equals(Object obj) {
157 return this == obj;
158 }
159 };
160
161 /** Comparator based on line width. */
162 public static final Comparator<Line> WIDTH_COMPARATOR = new Comparator<Line>() {
163 public int compare(Line line1, Line line2) {
164 if (line1 == null || line2 == null) throw(new NullPointerException("Compare to null Line instance"));
165 return (int)(line2.sigma - line1.sigma);
166 }
167 public boolean equals(Object obj) {
168 return this == obj;
169 }
170 };
171
172 /** Comparator based on line strength. Useful only for lines in the same star. */
173 public static final Comparator<Line> STRENGTH_COMPARATOR = new Comparator<Line>() {
174 public int compare(Line line1, Line line2) {
175 if (line1 == null || line2 == null) throw(new NullPointerException("Compare to null Line instance"));
176 return (int)(line2.getStrength() - line1.getStrength());
177 }
178 public boolean equals(Object obj) {
179 return this == obj;
180 }
181 };
182
183 /** Comparator based on line height. Useful only for lines in the same star. */
184 public static final Comparator<Line> HEIGHT_COMPARATOR = new Comparator<Line>() {
185 public int compare(Line line1, Line line2) {
186 if (line1 == null || line2 == null) throw(new NullPointerException("Compare to null Line instance"));
187 return (int)(line2.height - line1.height);
188 }
189 public boolean equals(Object obj) {
190 return this == obj;
191 }
192 };
193
194 //TODO: make this more flexible
195 public String toString() {
196 String wavelengthString = formatter.format(getWavelength());
197 if (wavelengthString.length() == 7) wavelengthString = " " + wavelengthString;
198 return wavelengthString;
199 }
200 }