# HG changeset patch
# User Sascha L. Teichmann <teichmann@intevation.de>
# Date 1375978478 -7200
# Node ID 51eb6491c537b9be0f3a2ebeb1065433ff9f160f
# Parent  70b440dc53170d804e8f892be43f8ef45421b8d9
S/Q: Excel compat completed: Now the data is linearized before fitting. This can be prevented by setting the system property S/Q: Excel compat completed: Now the data is linearized before fitting. This can be prevented by setting the system property "minfo.sq.calcution.non.linear.fitting" to true.

diff -r 70b440dc5317 -r 51eb6491c537 artifacts/src/main/java/org/dive4elements/river/artifacts/model/sq/Fitting.java
--- a/artifacts/src/main/java/org/dive4elements/river/artifacts/model/sq/Fitting.java	Thu Aug 08 16:19:59 2013 +0200
+++ b/artifacts/src/main/java/org/dive4elements/river/artifacts/model/sq/Fitting.java	Thu Aug 08 18:14:38 2013 +0200
@@ -8,6 +8,7 @@
 
 package org.dive4elements.river.artifacts.model.sq;
 
+import org.dive4elements.artifacts.common.utils.StringUtils;
 import org.dive4elements.river.artifacts.math.fitting.Function;
 
 import java.util.ArrayList;
@@ -83,7 +84,7 @@
     public void initialize(List<SQ> sqs) throws MathException {
 
         if (USE_NON_LINEAR_FITTING
-        || function.getInitialGuess().length != 2) {
+        || function.getParameterNames().length != 2) {
             nonLinearFitting(sqs);
         }
         else {
@@ -92,43 +93,48 @@
     }
 
     protected void linearFitting(List<SQ> sqs) {
-
-        coeffs = linearRegression(sqs);
-
+        coeffs   = linearRegression(sqs);
         instance = function.instantiate(coeffs);
     }
 
     protected double [] linearRegression(List<SQ> sqs) {
 
+        String [] pns = function.getParameterNames();
+        double [] result = new double[pns.length];
+
+        if (sqs.size() < 2) {
+            log.debug("not enough points");
+            return result;
+        }
+
         SimpleRegression reg = new SimpleRegression();
 
-        int invalidPoints = 0;
         for (SQ sq: sqs) {
-            double s = sq.getS();
-            double q = sq.getQ();
-            if (s <= 0d || q <= 0d) {
-                ++invalidPoints;
-                continue;
-            }
-            reg.addData(Math.log(q), Math.log(s));
+            double s = sqView.getS(sq);
+            double q = sqView.getQ(sq);
+            reg.addData(q, s);
         }
 
-        if (sqs.size() - invalidPoints < 2) {
-            log.debug("not enough points");
-            return new double [] { 0, 0 };
-        }
-
-        double a = Math.exp(reg.getIntercept());
+        double m = reg.getIntercept();
         double b = reg.getSlope();
 
         if (log.isDebugEnabled()) {
-            log.debug("invalid points: " +
-                invalidPoints + " (" + sqs.size() + ")");
-            log.debug("a: " + a + " (" + Math.log(a) + ")");
+            log.debug("m: " + m);
             log.debug("b: " + b);
         }
 
-        return new double [] { a, b };
+        int mIdx = StringUtils.indexOf("m", pns);
+        int bIdx = StringUtils.indexOf("b", pns);
+
+        if (mIdx == -1 || bIdx == -1) {
+            log.error("index not found: " + mIdx + " " + bIdx);
+            return result;
+        }
+
+        result[bIdx] = m;
+        result[mIdx] = b;
+
+        return result;
     }
 
 
@@ -140,7 +146,7 @@
         CurveFitter cf = new CurveFitter(optimizer);
 
         for (SQ sq: sqs) {
-            cf.addObservedPoint(sq.getS(), sq.getQ());
+            cf.addObservedPoint(sqView.getQ(sq), sqView.getS(sq));
         }
 
         coeffs = cf.fit(
@@ -179,7 +185,7 @@
             chiSqr);
     }
 
-    public boolean fit(List<SQ> sqs, String   method, Callback callback) {
+    public boolean fit(List<SQ> sqs, String  method, Callback callback) {
 
         if (sqs.size() < 2) {
             log.warn("Too less points for fitting.");
diff -r 70b440dc5317 -r 51eb6491c537 artifacts/src/main/java/org/dive4elements/river/artifacts/model/sq/SQRelationCalculation.java
--- a/artifacts/src/main/java/org/dive4elements/river/artifacts/model/sq/SQRelationCalculation.java	Thu Aug 08 16:19:59 2013 +0200
+++ b/artifacts/src/main/java/org/dive4elements/river/artifacts/model/sq/SQRelationCalculation.java	Thu Aug 08 18:14:38 2013 +0200
@@ -8,6 +8,7 @@
 
 package org.dive4elements.river.artifacts.model.sq;
 
+import org.dive4elements.artifacts.common.utils.StringUtils;
 import org.dive4elements.river.artifacts.access.SQRelationAccess;
 
 import org.dive4elements.river.artifacts.math.fitting.Function;
@@ -21,6 +22,7 @@
 import org.dive4elements.river.backend.SedDBSessionHolder;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.apache.log4j.Logger;
@@ -30,7 +32,11 @@
     private static final Logger log =
         Logger.getLogger(SQRelationCalculation.class);
 
-    public static final String SQ_FUNCTION_NAME = "sq-pow";
+    public static final boolean NON_LINEAR_FITTING =
+        Boolean.getBoolean("minfo.sq.calcution.non.linear.fitting");
+
+    public static final String SQ_POW_FUNCTION_NAME = "sq-pow";
+    public static final String SQ_LIN_FUNCTION_NAME = "linear";
 
     protected String    river;
     protected double    location;
@@ -49,8 +55,6 @@
         Double    outliers = access.getOutliers();
         String    method   = access.getOutlierMethod();
 
-        //river = "Rhein";
-
         if (river == null) {
             // TODO: i18n
             addProblem("sq.missing.river");
@@ -102,20 +106,76 @@
         }
     }
 
+    public interface TransformCoeffs {
+        double [] transform(double [] coeffs);
+    }
+
+    public static final TransformCoeffs IDENTITY_TRANS =
+        new TransformCoeffs() {
+            @Override
+            public double [] transform(double [] coeffs) {
+                return coeffs;
+            }
+        };
+
+    public static final TransformCoeffs LINEAR_TRANS =
+        new TransformCoeffs() {
+            @Override
+            public double [] transform(double [] coeffs) {
+                log.debug("before transform: " + Arrays.toString(coeffs));
+                if (coeffs.length == 2) {
+                    coeffs = new double [] { Math.exp(coeffs[1]), coeffs[0] };
+                }
+                log.debug("after transform: " + Arrays.toString(coeffs));
+                return coeffs;
+            }
+        };
+
     protected CalculationResult internalCalculate() {
 
-        Function function = FunctionFactory
+        Function powFunction = FunctionFactory
             .getInstance()
-            .getFunction(SQ_FUNCTION_NAME);
+            .getFunction(SQ_POW_FUNCTION_NAME);
 
-        if (function == null) {
-            log.error("No '" + SQ_FUNCTION_NAME + "' function found.");
+        if (powFunction == null) {
+            log.error("No '" + SQ_POW_FUNCTION_NAME + "' function found.");
             // TODO: i18n
             addProblem("sq.missing.sq.function");
+            return new CalculationResult(new SQResult[0], this);
         }
 
-        SQ.View    sqView    = SQ.SQ_VIEW;
-        SQ.Factory sqFactory = SQ.SQ_FACTORY;
+        Function         function;
+        SQ.View          sqView;
+        SQ.Factory       sqFactory;
+        ParameterCreator pc;
+
+
+        if (NON_LINEAR_FITTING) {
+            log.debug("Use non linear fitting.");
+            sqView    = SQ.SQ_VIEW;
+            sqFactory = SQ.SQ_FACTORY;
+            function  = powFunction;
+            pc = new ParameterCreator(
+                powFunction.getParameterNames(),
+                powFunction.getParameterNames());
+        }
+        else {
+            log.debug("Use linear fitting.");
+            sqView    = LogSQ.LOG_SQ_VIEW;
+            sqFactory = LogSQ.LOG_SQ_FACTORY;
+            function  = FunctionFactory
+                .getInstance()
+                .getFunction(SQ_LIN_FUNCTION_NAME);
+            if (function == null) {
+                log.error("No '" + SQ_LIN_FUNCTION_NAME + "' function found.");
+                // TODO: i18n
+                addProblem("sq.missing.sq.function");
+                return new CalculationResult(new SQResult[0], this);
+            }
+            pc = new LinearParameterCreator(
+                powFunction.getParameterNames(),
+                function.getParameterNames());
+        }
 
         Measurements measurements =
             MeasurementFactory.getMeasurements(
@@ -124,13 +184,14 @@
         SQFractionResult [] fractionResults =
             new SQFractionResult[SQResult.NUMBER_FRACTIONS];
 
+
         for (int i = 0; i < fractionResults.length; ++i) {
             List<SQ> sqs = measurements.getSQs(i);
 
             SQFractionResult fractionResult;
 
             List<SQFractionResult.Iteration> iterations =
-                doFitting(function, sqs, sqView);
+                doFitting(function, sqs, sqView, pc);
 
             if (iterations == null) {
                 // TODO: i18n
@@ -152,9 +213,10 @@
     }
 
     protected List<SQFractionResult.Iteration> doFitting(
-        final Function function,
-        List<SQ>       sqs,
-        SQ.View        sqView
+        final Function         function,
+        List<SQ>               sqs,
+        SQ.View                sqView,
+        final ParameterCreator pc
     ) {
         final List<SQFractionResult.Iteration> iterations =
             new ArrayList<SQFractionResult.Iteration>();
@@ -171,8 +233,7 @@
                     double    standardDeviation,
                     double    chiSqr
                 ) {
-                    Parameters parameters = createParameters(
-                        function.getParameterNames(),
+                    Parameters parameters = pc.createParameters(
                         coeffs,
                         standardDeviation,
                         chiSqr);
@@ -186,22 +247,75 @@
         return success ? iterations : null;
     }
 
-    public static final Parameters createParameters(
-        String [] names,
-        double [] values,
-        double    standardDeviation,
-        double    chiSqr
-    ) {
-        String [] columns = new String[names.length + 2];
-        columns[0] = "chi_sqr";
-        columns[1] = "std_dev";
-        System.arraycopy(names, 0, columns, 2, names.length);
-        Parameters parameters = new Parameters(columns);
-        int row = parameters.newRow();
-        parameters.set(row, names, values);
-        parameters.set(row, "chi_sqr", chiSqr);
-        parameters.set(row, "std_dev", standardDeviation);
-        return parameters;
+    public static class ParameterCreator {
+
+        protected String [] origNames;
+        protected String [] proxyNames;
+
+        public ParameterCreator(String [] origNames, String [] proxyNames) {
+            this.origNames  = origNames;
+            this.proxyNames = proxyNames;
+        }
+
+        protected double [] transformCoeffs(double [] coeffs) {
+            return coeffs;
+        }
+
+        public Parameters createParameters(
+            double [] coeffs,
+            double    standardDeviation,
+            double    chiSqr
+        ) {
+            String [] columns = new String[origNames.length + 2];
+            columns[0] = "chi_sqr";
+            columns[1] = "std_dev";
+            System.arraycopy(origNames, 0, columns, 2, origNames.length);
+            Parameters parameters = new Parameters(columns);
+            int row = parameters.newRow();
+            parameters.set(row, origNames, transformCoeffs(coeffs));
+            parameters.set(row, "chi_sqr", chiSqr);
+            parameters.set(row, "std_dev", standardDeviation);
+            return parameters;
+        }
+    }
+
+    /** We need to transform the coeffs back to the original function. */
+    public static class LinearParameterCreator extends ParameterCreator {
+
+        public LinearParameterCreator(
+            String [] origNames,
+            String [] proxyNames
+        ) {
+            super(origNames, proxyNames);
+        }
+
+        @Override
+        protected double [] transformCoeffs(double [] coeffs) {
+
+            int bP = StringUtils.indexOf("m", proxyNames);
+            int mP = StringUtils.indexOf("b", proxyNames);
+
+            int aO = StringUtils.indexOf("a", origNames);
+            int bO = StringUtils.indexOf("b", origNames);
+
+            if (bP == -1 || mP == -1 || aO == -1 || bO == -1) {
+                log.error("index not found: "
+                    + bP + " " + mP + " " 
+                    + aO + " " + bO);
+                return coeffs;
+            }
+
+            double [] ncoeffs = (double [])coeffs.clone();
+            ncoeffs[aO] = Math.exp(coeffs[mP]);
+            ncoeffs[bO] = coeffs[bP];
+
+            if (log.isDebugEnabled()) {
+                log.debug("before transform: " + Arrays.toString(coeffs));
+                log.debug("after transform: " + Arrays.toString(ncoeffs));
+            }
+
+            return ncoeffs;
+        }
     }
 }
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