Changeset 7810 for trunk

Timestamp:

11/18/11 19:55:02 (8 years ago)

Author:

aivar

Message:

Got rid of the idea of creating an ICurveFitter for each fit type (i.e. RLD, LMA, RLD_LMA).

Location:

trunk/projects/curve-fitter/src/main/java/loci/curvefitter

Files:

• AbstractCurveFitter.java (modified) (1 diff)
• CurveFitData.java (modified) (2 diffs)
• GrayCurveFitter.java (modified) (2 diffs)
• GrayNRCurveFitter.java (modified) (2 diffs)
• ICurveFitData.java (modified) (1 diff)
• ICurveFitter.java (modified) (3 diffs)
• SLIMCurveFitter.java (modified) (7 diffs)

trunk/projects/curve-fitter/src/main/java/loci/curvefitter/AbstractCurveFitter.java

@@ -41 +41 @@
  */
 public abstract class AbstractCurveFitter implements ICurveFitter {
+    FitAlgorithm m_fitAlgorithm;
     FitFunction m_fitFunction;
     double m_xInc = ICurveFitter.DEFAULT_X_INC;
     boolean[] m_free;
     double[] m_instrumentResponse;
+    
+    @Override
+    public FitAlgorithm getFitAlgorithm() {
+        return m_fitAlgorithm;
+    }
+    
+    @Override
+    public void setFitAlgorithm(FitAlgorithm algorithm) {
+        m_fitAlgorithm = algorithm;
+    }
     
     @Override

trunk/projects/curve-fitter/src/main/java/loci/curvefitter/CurveFitData.java

@@ -53 +53 @@
     double[] m_sig;
     double[] m_yFitted;
+    double m_chiSquareTarget;
     double m_chiSquare;
     Object m_userData;
@@ -136 +137 @@
     }
 
+    @Override
+    public double getChiSquareTarget() {
+        return m_chiSquareTarget;
+    }
+
+    @Override
+    public void setChiSquareTarget(double chiSquareTarget) {
+        m_chiSquareTarget = chiSquareTarget;
+    }
+    
+    @Override
     public double getChiSquare() {
         return m_chiSquare;
     }
 
+    @Override
     public void setChiSquare(double chiSquare) {
         m_chiSquare = chiSquare;

trunk/projects/curve-fitter/src/main/java/loci/curvefitter/GrayCurveFitter.java

@@ -81 +81 @@
     }
 
-    public GrayCurveFitter(int algType) {
-        m_algType = algType;
-    }
-
-    public GrayCurveFitter() {
-        m_algType = 0;
-    }
-
     @Override
     public int fitData(ICurveFitData[] dataArray, int start, int stop) {
@@ -98 +90 @@
         //TODO ARG August use initial X of 0.
 
-        if (0 == m_algType) {
+        if (FitAlgorithm.RLD.equals(m_fitAlgorithm)) {
             float xincr = (float) m_xInc;
             int fitStart = start;

trunk/projects/curve-fitter/src/main/java/loci/curvefitter/GrayNRCurveFitter.java

@@ -120 +120 @@
     }
 
-    public GrayNRCurveFitter(int algType) {
-        m_algType = algType;
-    }
-
-    public GrayNRCurveFitter() {
-        m_algType = 0;
-    }
-
 
     @Override
@@ -160 +152 @@
         }
 
-        if (0 == m_algType) { //TODO crude; use enums
+        if (FitAlgorithm.RLD.equals(m_fitAlgorithm)) {
             // RLD or triple integral fit
             DoubleByReference z = new DoubleByReference();

trunk/projects/curve-fitter/src/main/java/loci/curvefitter/ICurveFitData.java

@@ -158 +158 @@
      */
     public void setYFitted(double yFit[]);
+
+    /**
+     * Gets chi square target.
+     * 
+     * @return targetted chisquare
+     */
+    public double getChiSquareTarget();
+    
+    /**
+     * Sets chi square target
+     * 
+     * @param chiSquare targetted chi square
+     */
+    public void setChiSquareTarget(double chiSquareTarget);
+    
+
+    /**
+     * Gets fitted chi square.
+     * 
+     * @return fitted chisquare
+     */
+    public double getChiSquare();
+    
+    /**
+     * Sets fitted chi square
+     * 
+     * @param chiSquare fitted chi square
+     */
+    public void setChiSquare(double chiSquare);
 }

trunk/projects/curve-fitter/src/main/java/loci/curvefitter/ICurveFitter.java

@@ -41 +41 @@
  */
 public interface ICurveFitter {
-
+    
+    /**
+     * Specifies fitting algorithm.
+     */
+    public enum FitAlgorithm {
+        RLD, LMA, RLD_LMA
+    }
+    
     /**
      * Specifies curves that this fits.
@@ -53 +60 @@
      */
     public double DEFAULT_X_INC = 1.0f;
+    
+    /**
+     * Get fitting algorithm.
+     * 
+     * @return fitting algorithm
+     */
+    public FitAlgorithm getFitAlgorithm();
+    
+    /**
+     * Set fitting algorithm.
+     * 
+     * @param fitting algorithm
+     */
+    public void setFitAlgorithm(FitAlgorithm algorithm);
 
     /**
@@ -132 +153 @@
      * @return status code
      */
-    public int fitData(ICurveFitData[] data, int start, int stop);
+    public int fitData(ICurveFitData[] data, int start, int stop); 
 }

trunk/projects/curve-fitter/src/main/java/loci/curvefitter/SLIMCurveFitter.java

@@ -55 +55 @@
  */
 public class SLIMCurveFitter extends AbstractCurveFitter {
-    public enum AlgorithmType { RLD, LMA, RLD_LMA };
-
     private static boolean s_libraryLoaded = false;
     private static boolean s_libraryOnPath = false;
     private static CLibrary s_library;
-
-    private AlgorithmType m_algorithmType;
 
     /**
@@ -182 +178 @@
                            );
 
-    /**
-     * Create a curve fitter for a given algorithm type.
-     *
-     * @param algorithmType
-     */
-    public SLIMCurveFitter(AlgorithmType algorithmType) {
-        m_algorithmType = algorithmType;
-    }
-
-    /**
-     * Create the default curve fitter, which uses RLD.
-     *
-     */
-    public SLIMCurveFitter() {
-        m_algorithmType = AlgorithmType.RLD;
-    }
-
-
     @Override
     public int fitData(ICurveFitData[] dataArray, int start, int stop) {
@@ -239 +217 @@
 
         boolean[] free = m_free.clone();
-        if (AlgorithmType.RLD.equals(m_algorithmType)) {
+        if (FitAlgorithm.RLD.equals(m_fitAlgorithm)) {
             // pure RLD (versus RLD followed by LMA) has no way to fix
             // parameters
@@ -251 +229 @@
             DoubleByReference chiSquare = new DoubleByReference();
             double chiSquareTarget = 1.0; //TODO s/b specified incoming
-
-            if (AlgorithmType.RLD.equals(m_algorithmType) || AlgorithmType.RLD_LMA.equals(m_algorithmType)) {
+            
+            if (FitAlgorithm.RLD.equals(m_fitAlgorithm) || FitAlgorithm.RLD_LMA.equals(m_fitAlgorithm)) {
                 // RLD or triple integral fit
                 DoubleByReference z = new DoubleByReference();
@@ -299 +277 @@
                 }
             }
-
-            if (AlgorithmType.LMA.equals(m_algorithmType) || AlgorithmType.RLD_LMA.equals(m_algorithmType)) {
+            
+            if (FitAlgorithm.LMA.equals(m_fitAlgorithm) || FitAlgorithm.RLD_LMA.equals(m_fitAlgorithm)) {
                 // LMA fit
                 for (ICurveFitData data: dataArray) {
@@ -331 +309 @@
             double[] chiSquare = new double[1];
             double chiSquareTarget = 1.0; //TODO s/b specified incoming
-
-            if (AlgorithmType.RLD.equals(m_algorithmType) || AlgorithmType.RLD_LMA.equals(m_algorithmType)) {
+            
+            if (FitAlgorithm.RLD.equals(m_fitAlgorithm) || FitAlgorithm.RLD_LMA.equals(m_fitAlgorithm)) {
                 // RLD or triple integral fit
 
@@ -382 +360 @@
             }
 
-            if (AlgorithmType.LMA.equals(m_algorithmType) || AlgorithmType.RLD_LMA.equals(m_algorithmType)) {
+            if (FitAlgorithm.LMA.equals(m_fitAlgorithm) || FitAlgorithm.RLD_LMA.equals(m_fitAlgorithm)) {
                 // LMA fit
                 for (ICurveFitData data: dataArray) {