Fixes for filters, SpectrumNormalizationFilter no longer crashes tryi…

…ng to normalize a fitting with no energy calibration
nsherry4 · Jan 6, 2024 · 4c90ccf · 4c90ccf
1 parent 2f968b1
commit 4c90ccf
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Showing 5 changed files with 41 additions and 24 deletions.
diff --git a/...rc/main/java/org/peakaboo/framework/autodialog/model/style/layouts/FramedLayoutStyle.java b/...rc/main/java/org/peakaboo/framework/autodialog/model/style/layouts/FramedLayoutStyle.java
@@ -2,20 +2,26 @@
 
 public class FramedLayoutStyle extends SimpleLayoutStyle {
 
-	private boolean hiddenOnDisable;
+	private boolean hiddenOnDisable = false, showBorder = true;
 
 	public FramedLayoutStyle() {
 		super("layout-frames");
 	}
 
-	public FramedLayoutStyle(boolean hideWhenDisabled) {
+	public FramedLayoutStyle(boolean hideWhenDisabled, boolean showBorder) {
 		this();
 		this.hiddenOnDisable = hideWhenDisabled;
+		this.showBorder = showBorder;
 	}
 
 	public boolean isHiddenOnDisable() {
 		return hiddenOnDisable;
 	}
+
+	public boolean isShowBorder() {
+		return showBorder;
+	}
+
 
 
 

diff --git a/...src/main/java/org/peakaboo/framework/autodialog/view/swing/layouts/FramesSwingLayout.java b/...src/main/java/org/peakaboo/framework/autodialog/view/swing/layouts/FramesSwingLayout.java
@@ -7,16 +7,23 @@
 import javax.swing.border.TitledBorder;
 
 import org.peakaboo.framework.autodialog.model.style.layouts.FramedLayoutStyle;
+import org.peakaboo.framework.stratus.api.Spacing;
 
 public class FramesSwingLayout extends SimpleSwingLayout {
 
 	@Override
 	public JComponent getComponent() {
+		FramedLayoutStyle style = (FramedLayoutStyle) group.getStyle();
+
 		JPanel panel = new JPanel(new BorderLayout());
 		panel.add(root, BorderLayout.CENTER);
-		panel.setBorder(new TitledBorder(group.getName()));
+		var border = new TitledBorder(group.getName());
+		if (!style.isShowBorder()) { 
+			border.setBorder(Spacing.bNone());
+		}
+		panel.setBorder(border);
+
 
-		FramedLayoutStyle style = (FramedLayoutStyle) group.getStyle();
 		if (style.isHiddenOnDisable()) {
 			panel.setVisible(group.isEnabled());
 			group.getEnabledHook().addListener(e -> {

diff --git a/LibPeakaboo/src/main/java/org/peakaboo/curvefit/curve/fitting/FittingParameters.java b/LibPeakaboo/src/main/java/org/peakaboo/curvefit/curve/fitting/FittingParameters.java
@@ -30,7 +30,7 @@ public FittingParameters(FittingParametersView params, FittingSet fits) {
 
 	/**
 	 * Constructs a new "dead" or "unwired" FittingParameters object without a
-	 * reference to a parent {@link FittingSet} since a readonly params does not
+	 * reference to a parent {@link FittingSet} since a params view does not
 	 * provide access to that.
 	 */
 	public FittingParameters(FittingParametersView params) {

diff --git a/...kaboo/src/main/java/org/peakaboo/filter/plugins/advanced/SpectrumNormalizationFilter.java b/...kaboo/src/main/java/org/peakaboo/filter/plugins/advanced/SpectrumNormalizationFilter.java
@@ -19,8 +19,8 @@
 import org.peakaboo.framework.autodialog.model.style.editors.RealStyle;
 import org.peakaboo.framework.autodialog.model.style.layouts.FramedLayoutStyle;
 import org.peakaboo.framework.cyclops.spectrum.ArraySpectrum;
-import org.peakaboo.framework.cyclops.spectrum.SpectrumView;
 import org.peakaboo.framework.cyclops.spectrum.SpectrumCalculations;
+import org.peakaboo.framework.cyclops.spectrum.SpectrumView;
 
 
 public class SpectrumNormalizationFilter extends AbstractFilter {
@@ -45,7 +45,7 @@ public enum SmoothingIntensity {
 	private static final String MODE_RANGE = "Channel Range";
 	private static final String MODE_MAX = "Strongest Channel";
 	private static final String MODE_SUM = "All Channels";
-	private static final String MODE_FIT = "Element";
+	private static final String MODE_FIT = "Element Fitting";
 
 	@Override
 	public String pluginVersion() {
@@ -55,32 +55,32 @@ public String pluginVersion() {
 	@Override
 	public void initialize() {
 
-		pMode = new SelectionParameter<>("Mode", new ListStyle<String>(), MODE_FIT, this::validate);
+		pMode = new SelectionParameter<>("Mode", new ListStyle<String>(), MODE_SUM, this::validate);
 		pMode.setPossibleValues(MODE_FIT, MODE_RANGE, MODE_MAX, MODE_SUM);
 		addParameter(pMode);
 
-		pHeight = new Parameter<>("Normalized Intensity", new RealStyle(), 10f, this::validate);
+		pHeight = new Parameter<>("Target Intensity", new RealStyle(), 10f, this::validate);
 		addParameter(pHeight);
 
-		pSmooth = new SelectionParameter<>("Noise Reduction", new ListStyle<>(), SmoothingIntensity.Low, new EnumClassInfo<>(SmoothingIntensity.class), this::validate);
+		pSmooth = new SelectionParameter<>("Denoise", new ListStyle<>(), SmoothingIntensity.Low, new EnumClassInfo<>(SmoothingIntensity.class), this::validate);
 		pSmooth.setPossibleValues(SmoothingIntensity.values());
 		addParameter(pSmooth);
 
 		pStartChannel = new Parameter<>("Start Channel", new IntegerStyle(), 1, this::validate);
 		pEndChannel = new Parameter<>("End Channel", new IntegerStyle(), 10, this::validate);
-		gChannelRange = new Group("Channel Range", new FramedLayoutStyle(true), pStartChannel, pEndChannel);
+		gChannelRange = new Group("Channel Range", new FramedLayoutStyle(true, false), pStartChannel, pEndChannel);
 		addParameter(gChannelRange);
 
 
-		pElement = new SelectionParameter<>("Fiting Element", new ListStyle<>(), Element.Ar, new EnumClassInfo<>(Element.class), this::validate);
+		pElement = new SelectionParameter<>("Element", new ListStyle<>(), Element.Ar, new EnumClassInfo<>(Element.class), this::validate);
 		pElement.setPossibleValues(Element.values());
 		pElement.setEnabled(false);
 
-		pShell = new SelectionParameter<>("Fitting Shell", new ListStyle<>(), TransitionShell.K, new EnumClassInfo<>(TransitionShell.class), this::validate);
+		pShell = new SelectionParameter<>("Shell", new ListStyle<>(), TransitionShell.K, new EnumClassInfo<>(TransitionShell.class), this::validate);
 		pShell.setPossibleValues(TransitionShell.K, TransitionShell.L, TransitionShell.M);
 		pShell.setEnabled(false);
 
-		gElement = new Group("Element Selection", new FramedLayoutStyle(true), pElement, pShell);
+		gElement = new Group("Fitting Selection", new FramedLayoutStyle(true, false), pElement, pShell);
 		addParameter(gElement);
 
 		validate(null);
@@ -127,14 +127,18 @@ protected SpectrumView filterApplyTo(SpectrumView data, Optional<FilterContext>
 			ITransitionSeries ts = PeakTable.SYSTEM.get(pElement.getValue(), pShell.getValue());
 			FilterContext context = requireContext(ctx);
 
-
-			float energy = ts.getStrongestTransition().energyValue;
-			int channel = context.fittings().getFittingParameters().getCalibration().channelFromEnergy(energy);
-			startChannel = Math.max(channel-5, 0);
-			endChannel = Math.min(channel+5, data.size()-1);
-			int frange = (endChannel - startChannel) + 1;
-			currentIntensity = filteredData.subSpectrum(startChannel, endChannel).sum() / frange;
-
+			var calibration = context.fittings().getFittingParameters().getCalibration();
+			if (calibration.isZero()) {
+				//Can't filter, return original data
+				return data;
+			} else {
+				float energy = ts.getStrongestTransition().energyValue;
+				int channel = context.fittings().getFittingParameters().getCalibration().channelFromEnergy(energy);
+				startChannel = Math.max(channel-5, 0);
+				endChannel = Math.min(channel+5, data.size()-1);
+				int frange = (endChannel - startChannel) + 1;
+				currentIntensity = filteredData.subSpectrum(startChannel, endChannel).sum() / frange;
+			}
 		}
 
 		float ratio = currentIntensity / desiredIntensity;

diff --git a/LibPeakaboo/src/main/java/org/peakaboo/filter/plugins/noise/SavitskyGolayNoiseFilter.java b/LibPeakaboo/src/main/java/org/peakaboo/filter/plugins/noise/SavitskyGolayNoiseFilter.java
@@ -14,8 +14,8 @@
 import org.peakaboo.framework.autodialog.model.style.editors.RealStyle;
 import org.peakaboo.framework.autodialog.model.style.editors.SeparatorStyle;
 import org.peakaboo.framework.cyclops.spectrum.ArraySpectrum;
-import org.peakaboo.framework.cyclops.spectrum.SpectrumView;
 import org.peakaboo.framework.cyclops.spectrum.Spectrum;
+import org.peakaboo.framework.cyclops.spectrum.SpectrumView;
 
 //From Handbook of X-Ray Spectrometry
 public class SavitskyGolayNoiseFilter extends AbstractFilter {
@@ -51,7 +51,7 @@ public void initialize() {
 
 		reach = new Parameter<>("Half-Window Size", new IntegerStyle(), 4, this::validate);
 		order = new Parameter<>("Polynomial Order", new IntegerStyle(), 3, this::validate);
-		Parameter<?> sep = new Parameter<>(null, new SeparatorStyle(), 0);
+		Parameter<?> sep = new Parameter<>("separator", new SeparatorStyle(), 0);
 		ignore = new Parameter<>("Only Smooth Weak Signal", new BooleanStyle(), false, this::validate);
 		max = new Parameter<>("Smoothing Cutoff: (counts)", new RealStyle(), 4.0f, this::validate);
 		max.setEnabled(false);