Fixed calculation range handling

- Fixed calculation limit not updating on increase of calculation range
- Fixed data event handling related to changes in the range. Removed the
TRUNCATED type.
- Fixed copy constructor of NumericProperty not making exact copies of
the property, e.g. discrete state was ignored
- Allowed optimizers to select a larger gradient step for properties
marked discrete
- The gradient step is now relative, rather than absolute

src/main/java/pulse/input/ExperimentalData.java

@@ -2,7 +2,6 @@
 
 import static java.lang.Double.valueOf;
 import static java.util.Collections.max;
-import static pulse.input.listeners.DataEventType.TRUNCATED;
 import static pulse.properties.NumericProperties.derive;
 import static pulse.properties.NumericPropertyKeyword.NUMPOINTS;
 import static pulse.properties.NumericPropertyKeyword.PULSE_WIDTH;
@@ -18,6 +17,7 @@
 import pulse.AbstractData;
 import pulse.baseline.FlatBaseline;
 import pulse.input.listeners.DataEvent;
+import pulse.input.listeners.DataEventType;
 import pulse.input.listeners.DataListener;
 import pulse.properties.NumericProperty;
 import pulse.ui.Messages;
@@ -301,10 +301,7 @@ public void truncate() {
 		final double halfMaximum = halfRiseTime();
 		final double cutoff = CUTOFF_FACTOR * halfMaximum;
 
-		this.range.setUpperBound(derive(UPPER_BOUND, cutoff));
-		this.indexRange.set(getTimeSequence(), range);
-
-		fireDataChanged(new DataEvent(TRUNCATED, this));
+		this.range.setUpperBound(derive(UPPER_BOUND, cutoff));;
 	}
 
 	/**
@@ -407,8 +404,10 @@ private void doSetRange() {
 		indexRange.set(time, range);
 
 		addHierarchyListener(l -> {
-			if (l.getSource() == range)
+			if (l.getSource() == range) {
 				indexRange.set(time, range);
+				this.fireDataChanged(new DataEvent(DataEventType.RANGE_CHANGED, this));
+			}
 		});
 
 		if (metadata != null)

src/main/java/pulse/input/Range.java

@@ -11,6 +11,7 @@
 
 import pulse.math.ParameterVector;
 import pulse.math.Segment;
+import pulse.problem.schemes.solvers.SolverException;
 import pulse.properties.Flag;
 import pulse.properties.NumericProperty;
 import pulse.properties.NumericPropertyKeyword;
@@ -170,8 +171,8 @@ public void set(NumericPropertyKeyword type, NumericProperty property) {
 	@Override
 	public void optimisationVector(ParameterVector output, List<Flag> flags) {
 
-		double len = segment.length();
-		var bounds = new Segment(-0.25 * len, 0.25 * len);
+		var curve	 = (ExperimentalData)this.getParent();
+		Segment bounds;
 
 		for (int i = 0, size = output.dimension(); i < size; i++) {
 
@@ -180,9 +181,12 @@ public void optimisationVector(ParameterVector output, List<Flag> flags) {
 			switch (key) {
 			case UPPER_BOUND:
 				output.set(i, segment.getMaximum());
+				var seq = curve.getTimeSequence();
+				bounds = new Segment( 1.1 * curve.maxAdjustedSignal().getX(), seq.get(seq.size() - 1) );
 				break;
 			case LOWER_BOUND:
 				output.set(i, segment.getMinimum());
+				bounds = new Segment( 0.0, 0.35 * curve.halfRiseTime() );
 				break;
 			default:
 				continue;			
@@ -198,11 +202,14 @@ public void optimisationVector(ParameterVector output, List<Flag> flags) {
 	 * Tries to assign the upper and lower bound based on {@code params}.
 	 * 
 	 * @param params an {@code IndexedVector} which may contain the bounds.
+	 * @throws SolverException 
 	 */
 
 	@Override
-	public void assign(ParameterVector params) {
-
+	public void assign(ParameterVector params) throws SolverException {
+		if(!params.validate())
+			throw new SolverException("Parameter values not sensible");
+
 		NumericProperty p = null;
 
 		for (int i = 0, size = params.dimension(); i < size; i++) {
@@ -219,7 +226,7 @@ public void assign(ParameterVector params) {
 			default:
 				continue;
 			}
-
+			
 		}
 
 	}

src/main/java/pulse/input/listeners/DataEventType.java

@@ -8,13 +8,13 @@
 public enum DataEventType {
 	/**
 	 * <p>
-	 * The {@code TRUNCATED} {@code DataEventType} indicates the range of the
-	 * {@code ExperimentalData} has been truncated. Note this means that only the
+	 * The {@code RANGE_CHANGED} {@code DataEventType} indicates the range of the
+	 * {@code ExperimentalData} has either been truncated or extended. Note this means that only the
 	 * range is affected and not the data itself.
 	 * 
 	 * @see pulse.input.ExperimentalData.truncate()
 	 */
 
-	TRUNCATED
+	RANGE_CHANGED
 
 }

src/main/java/pulse/io/export/XMLConverter.java

@@ -177,8 +177,8 @@ public static List<NumericProperty> readXML(InputStream inputStream)
 				Element eElement = (Element) nNode;
 				NumericPropertyKeyword keyword = NumericPropertyKeyword.valueOf(eElement.getAttribute("keyword"));
 				boolean autoAdjustable = Boolean.valueOf(eElement.getAttribute("auto-adjustable"));
-				boolean discreet = Boolean.valueOf(eElement.getAttribute("discreet"));
-				String descriptor = eElement.getAttribute("descriptor");
+				boolean discrete	= Boolean.valueOf(eElement.getAttribute("discreet"));
+				String descriptor	= eElement.getAttribute("descriptor");
 				String abbreviation = eElement.getAttribute("abbreviation");
 				boolean defSearch = Boolean.valueOf(eElement.getAttribute("default-search-variable"));
 
@@ -200,7 +200,7 @@ public static List<NumericProperty> readXML(InputStream inputStream)
 				np.setDescriptor(descriptor);
 				np.setAbbreviation(abbreviation);
 				np.setAutoAdjustable(autoAdjustable);
-				np.setDiscreet(discreet);
+				np.setDiscrete(discrete);
 				np.setDefaultSearchVariable(defSearch);
 				properties.add(np);
 			}

src/main/java/pulse/problem/statements/Problem.java

@@ -281,12 +281,7 @@ protected void setHeatLossParameter(ParameterVector output, int i, double Bi) {
 	 */
 
 	@Override
-	public void assign(ParameterVector params) throws SolverException {
-
-		if(!params.validate()) {
-			throw new SolverException("Parameter values not sensible");
-		}
-
+	public void assign(ParameterVector params) throws SolverException {	
 		baseline.assign(params);
 		for (int i = 0, size = params.dimension(); i < size; i++) {
 

src/main/java/pulse/properties/NumericProperty.java

@@ -38,7 +38,7 @@ public class NumericProperty implements Property, Comparable<NumericProperty> {
 	private NumericPropertyKeyword type;
 
 	private boolean autoAdjustable;
-	private boolean discreet;
+	private boolean discrete;
 	private boolean defaultSearchVariable;
 
 	/**
@@ -82,14 +82,17 @@ public NumericProperty(NumericPropertyKeyword type, Number... params) {
 	 */
 
 	public NumericProperty(NumericProperty num) {
-		this.value = num.value;
-		this.descriptor = num.descriptor;
-		this.abbreviation = num.abbreviation;
-		this.minimum = num.minimum;
-		this.maximum = num.maximum;
-		this.type = num.type;
+		this.value			= num.value;
+		this.descriptor		= num.descriptor;
+		this.abbreviation	= num.abbreviation;
+		this.minimum		= num.minimum;
+		this.maximum		= num.maximum;
+		this.type 			= num.type;
+		this.discrete		= num.discrete;
 		this.dimensionFactor = num.dimensionFactor;
-		this.autoAdjustable = num.autoAdjustable;
+		this.autoAdjustable  = num.autoAdjustable;
+		this.error			 = num.error;
+		this.defaultSearchVariable = num.defaultSearchVariable;
 	}
 
 	public NumericPropertyKeyword getType() {
@@ -270,11 +273,11 @@ public int compareTo(NumericProperty arg0) {
 	}
 
 	public boolean isDiscrete() {
-		return discreet;
+		return discrete;
 	}
 
-	public void setDiscreet(boolean discreet) {
-		this.discreet = discreet;
+	public void setDiscrete(boolean discrete) {
+		this.discrete = discrete;
 	}
 
 	@Override

src/main/java/pulse/search/direction/GradientBasedOptimiser.java

@@ -11,6 +11,7 @@
 import pulse.math.ParameterVector;
 import pulse.math.linear.Vector;
 import pulse.problem.schemes.solvers.SolverException;
+import pulse.properties.NumericProperties;
 import pulse.properties.NumericProperty;
 import pulse.properties.NumericPropertyKeyword;
 import pulse.properties.Property;
@@ -78,11 +79,14 @@ public Vector gradient(SearchTask task) throws SolverException {
 		final var params = task.searchVector();
 		var grad = new Vector(params.dimension());
 
-		boolean discreteGradient = params.getIndices().stream().anyMatch(index -> isDiscrete(index));
-		final double dxGrid = task.getCurrentCalculation().getScheme().getGrid().getXStep();
-		final double dx = discreteGradient ? dxGrid : gradientResolution;
 
+		final double resolutionHigh = (double) getGradientResolution().getValue();
+		final double resolutionLow  = 5E-2; //TODO 
+
 		for (int i = 0; i < params.dimension(); i++) {
+			boolean discrete = NumericProperties.def(params.getIndex(i)).isDiscrete();
+			double dx		 = (discrete ? resolutionLow : resolutionHigh) * params.get(i);			
+
 			final var shift = new Vector(params.dimension());
 			shift.set(i, 0.5 * dx);
 

src/main/java/pulse/search/direction/LMOptimiser.java

@@ -15,6 +15,7 @@
 import pulse.math.linear.SquareMatrix;
 import pulse.math.linear.Vector;
 import pulse.problem.schemes.solvers.SolverException;
+import pulse.properties.NumericProperties;
 import pulse.properties.NumericProperty;
 import pulse.properties.NumericPropertyKeyword;
 import pulse.properties.Property;
@@ -174,10 +175,14 @@ public RectangularMatrix jacobian(SearchTask task) throws SolverException {
 
 		var jacobian = new double[numPoints][numParams];
 
-		final double dx = super.getGradientStep();
+		final double resolutionHigh = super.getGradientStep();
+		final double resolutionLow  = 1E-2; //TODO 
 
 		for (int i = 0; i < numParams; i++) {
 
+			boolean discrete = NumericProperties.def(params.getIndex(i)).isDiscrete();
+			double dx		 = (discrete ? resolutionLow : resolutionHigh) * params.get(i);
+
 			final var shift = new Vector(numParams);
 			shift.set(i, 0.5 * dx);
 
@@ -191,7 +196,7 @@ public RectangularMatrix jacobian(SearchTask task) throws SolverException {
 			task.solveProblemAndCalculateCost();
 			var r2 = residualVector(residualCalculator);
 
-			for (int j = 0; j < numPoints; j++) {
+			for (int j = 0, realNumPoints = Math.min(numPoints, r2.length); j < realNumPoints; j++) {
 
 				jacobian[j][i] = (r1[j] - r2[j]) / dx;
 
@@ -217,8 +222,8 @@ public GradientGuidedPath initState(SearchTask t) {
 	}
 
 	private Vector halfGradient(LMPath path) {
-		var jacobian = path.getJacobian();
-		var residuals = path.getResidualVector();
+		var jacobian	= path.getJacobian();
+		var residuals	= path.getResidualVector();
 		return jacobian.transpose().multiply(new Vector(residuals));
 	}
 

src/main/java/pulse/search/statistics/ResidualStatistic.java

@@ -71,11 +71,11 @@ public void calculateResiduals(SearchTask task) {
 
 		var s = estimate.getSplineInterpolation();
 
-		int startIndex = max(closestLeft(estimate.timeAt(0), time), indexRange.getLowerBound());
-		int endIndex = min(closestRight(estimate.timeLimit(), time), indexRange.getUpperBound());
-
-		double interpolated;
+		int startIndex	= max(closestLeft(estimate.timeAt(0), time), indexRange.getLowerBound());
+		int endIndex	= min(closestRight(estimate.timeLimit(), time), indexRange.getUpperBound());
 
+		double interpolated;
+
 		for (int i = startIndex; i <= endIndex; i++) {
 			/*
 			 * find the point on the calculated heating curve which has the closest time

src/main/java/pulse/tasks/SearchTask.java

@@ -220,13 +220,13 @@ public ParameterVector searchVector() {
 	public void assign(ParameterVector searchParameters) {
 		try {
 			current.getProblem().assign(searchParameters);
+			curve.getRange().assign(searchParameters);
 		} catch (SolverException e) {
 			var status = FAILED;
 			status.setDetails(Details.PARAMETER_VALUES_NOT_SENSIBLE);
 			setStatus(status);
 			e.printStackTrace();
 		}
-		curve.getRange().assign(searchParameters);
 	}
 
 	/**

src/main/java/pulse/ui/components/panels/ChartToolbar.java

@@ -12,6 +12,9 @@
 import static javax.swing.JOptionPane.showConfirmDialog;
 import static javax.swing.JOptionPane.showOptionDialog;
 import static javax.swing.SwingUtilities.getWindowAncestor;
+import static pulse.properties.NumericProperties.derive;
+import static pulse.properties.NumericPropertyKeyword.LOWER_BOUND;
+import static pulse.properties.NumericPropertyKeyword.UPPER_BOUND;
 import static pulse.tasks.listeners.TaskRepositoryEvent.State.TASK_FINISHED;
 import static pulse.ui.Messages.getString;
 import static pulse.ui.frames.MainGraphFrame.getChart;
@@ -234,18 +237,24 @@ private void validateRange(double a, double b) {
 		sb.append(getString("RangeSelectionFrame.ConfirmationMessage1"));
 		sb.append("</p><br>");
 		sb.append(getString("RangeSelectionFrame.ConfirmationMessage2"));
-		sb.append(expCurve.getEffectiveStartTime());
+		sb.append(format("%3.6f", expCurve.getEffectiveStartTime()));
 		sb.append(" to ");
-		sb.append(expCurve.getEffectiveEndTime());
+		sb.append(format("%3.6f", expCurve.getEffectiveEndTime()));
 		sb.append("<br><br>");
 		sb.append(getString("RangeSelectionFrame.ConfirmationMessage3"));
-		sb.append(format("%3.4f", a) + " to " + format("%3.4f", b));
+		sb.append(format("%3.6f", a) + " to " + format("%3.6f", b));
 		sb.append("</html>");
 
 		var dialogResult = showConfirmDialog(getWindowAncestor(this), sb.toString(), "Confirm chocie", YES_NO_OPTION);
 
-		if (dialogResult == YES_OPTION)
-			expCurve.setRange(new Range(a, b));
+		if (dialogResult == YES_OPTION) {
+			if(expCurve.getRange() == null)
+				expCurve.setRange(new Range(a, b));
+			else {
+				expCurve.getRange().setLowerBound(derive(LOWER_BOUND, a));
+				expCurve.getRange().setUpperBound(derive(UPPER_BOUND, b));
+			}
+		}
 
 	}
 

src/main/resources/NumericProperty.xml

@@ -257,7 +257,7 @@
 	<NumericProperty keyword="ITERATION_LIMIT"
 		abbreviation="Iteration limit" auto-adjustable="true"
 		descriptor="Iteration limit" dimensionfactor="1" maximum="1000"
-		minimum="1" primitive-type="int" value="128" discreet="false">
+		minimum="1" primitive-type="int" value="256" discreet="false">
 	</NumericProperty>
 	<NumericProperty
 		abbreviation="&lt;i&gt;a&lt;/i&gt;&lt;sub&gt;c&lt;/sub&gt; (mm&lt;sup&gt;2&lt;/sup&gt;s&lt;sup&gt;-1&lt;/sup&gt;) "
@@ -409,7 +409,7 @@
 	<NumericProperty abbreviation="Resolution (total)"
 		auto-adjustable="false" descriptor="Resolution (total)"
 		dimensionfactor="1.0" keyword="ERROR_TOLERANCE" maximum="0.1"
-		minimum="1.0E-7" value="0.0001" primitive-type="double"
+		minimum="1.0E-7" value="0.00001" primitive-type="double"
 		discreet="false" default-search-variable="false" />
 	<NumericProperty abbreviation="FOV&lt;sub&gt;inner&lt;/sub&gt; (mm)"
 		auto-adjustable="true"
@@ -423,7 +423,7 @@
 		descriptor="Field of view (outer), FOV&lt;sub&gt;outer&lt;/sub&gt; (mm)"
 		dimensionfactor="1000.0" keyword="FOV_OUTER" maximum="0.1"
 		minimum="1.0E-6" value="0.01" primitive-type="double" discreet="true"
-		default-search-variable="true" />
+		default-search-variable="false" />
 	<NumericProperty abbreviation="Baseline (slope)"
 		auto-adjustable="true" descriptor="Baseline (slope)"
 		dimensionfactor="1.0" keyword="BASELINE_SLOPE" maximum="10.0"
@@ -439,7 +439,7 @@
 		descriptor="Heat loss (side surface), Bi&lt;sub&gt;s&lt;/sub&gt;"
 		dimensionfactor="1.0" keyword="HEAT_LOSS_SIDE" maximum="10.0"
 		minimum="0.0" value="0.2" primitive-type="double" discreet="false"
-		default-search-variable="true" />
+		default-search-variable="true" ></NumericProperty>
 	<NumericProperty keyword="HEAT_LOSS" abbreviation="Bi"
 		auto-adjustable="true" descriptor="Heat loss, Bi" dimensionfactor="1"
 		maximum="10" minimum="0.0" primitive-type="double" value="0.2"
@@ -496,15 +496,15 @@
 		abbreviation="&lt;i&gt;t&lt;/i&gt;&lt;sub&gt;min&lt;/sub&gt;"
 		auto-adjustable="false"
 		descriptor="Lower bound, &lt;i&gt;t&lt;/i&gt;&lt;sub&gt;min&lt;/sub&gt;"
-		dimensionfactor="1" discreet="false" keyword="LOWER_BOUND"
+		dimensionfactor="1" discreet="true" keyword="LOWER_BOUND"
 		maximum="100" minimum="-100" primitive-type="double" value="0.0"
 		default-search-variable="false">
 	</NumericProperty>
 	<NumericProperty
 		abbreviation="&lt;i&gt;t&lt;/i&gt;&lt;sub&gt;max&lt;/sub&gt;"
 		auto-adjustable="false"
 		descriptor="Upper bound, &lt;i&gt;t&lt;/i&gt;&lt;sub&gt;max&lt;/sub&gt;"
-		dimensionfactor="1" discreet="false" keyword="UPPER_BOUND"
+		dimensionfactor="1" discreet="true" keyword="UPPER_BOUND"
 		maximum="100" minimum="-100" primitive-type="double" value="1.0"
 		default-search-variable="false">
 	</NumericProperty>