Merge branch 'development-fuw' into 'development'

#13 Development fuw

See merge request brain/svarog2!207

Author: Marian Dovgialo

svarog/src/main/java/org/signalml/app/config/ApplicationConfiguration.java

@@ -95,6 +95,7 @@ public class ApplicationConfiguration extends AbstractXMLConfiguration implement
 
 	private String openbciIPAddress;
 	private int openbciPort;
+	private boolean scrollingMode;
 	private String sentryDsn;
 	private String sentrySite;
 	private boolean sendSentryTelemetry;
@@ -601,6 +602,14 @@ public void setOpenbciPort(int openbciPort) {
 		this.openbciPort = openbciPort;
 	}
 
+	public boolean isScrollingMode() {
+		return scrollingMode;
+	}
+
+	public void setScrollingMode(boolean scrollingMode) {
+		this.scrollingMode = scrollingMode;
+	}
+
 	public String getSentryDsn() {
 		return sentryDsn;
 	}

svarog/src/main/java/org/signalml/app/config/ConfigurationDefaults.java

@@ -138,6 +138,7 @@ public static void setApplicationConfigurationDefaults(ApplicationConfiguration
 		config.setMonitorPageSize(getFloat("monitor.pageSize"));
 		config.setOpenbciIPAddress(getString("monitor.openbciIPAddress"));
 		config.setOpenbciPort(getInt("monitor.openbciPort"));
+		config.setScrollingMode(getBoolean("monitor.scrollingMode"));
 	}
 
 	public static void setZoomSignalSettingsDefaults(ZoomSignalSettings settings) {

svarog/src/main/java/org/signalml/app/document/MonitorSignalDocument.java

@@ -177,8 +177,7 @@ public void openDocument() throws SignalMLException, IOException {
 		}
 
 		logger.info("Start initializing monitor data.");
-		tagSet = new StyledMonitorTagSet(descriptor.getSignalParameters().getPageSize(), 5,
-			descriptor.getSignalParameters().getSamplingFrequency());
+		tagSet = new StyledMonitorTagSet(descriptor.getSignalParameters().getPageSize(), 5);
 		if (descriptor.getTagStyles() != null) {
 			tagSet.copyStylesFrom(descriptor.getTagStyles());
 		}

svarog/src/main/java/org/signalml/app/document/signal/AsciiSignalSampleSource.java

@@ -45,7 +45,7 @@ protected BaseSignalSampleSource duplicateInternal() throws IOException {
 	}
 
 	@Override
-	public synchronized void getSamples(int channel, double[] target, int signalOffset, int count, int arrayOffset) {
+	public synchronized long getSamples(int channel, double[] target, int signalOffset, int count, int arrayOffset) {
 		int channelCount = getChannelCount();
 		if (channel < 0 || channel >= channelCount) {
 			throw new IndexOutOfBoundsException("Bad channel number [" + channel + "]");
@@ -86,6 +86,7 @@ public synchronized void getSamples(int channel, double[] target, int signalOffs
 			parsingErrorDialogShown = true;
 			Dialogs.showError(_("CSV file is badly formatted. Some data may not be displayed properly."));
 		}
+		return 0;
 	}
 
 }

svarog/src/main/java/org/signalml/app/view/preferences/MonitorConfigPanel.java

@@ -5,6 +5,7 @@
 import javax.swing.BoxLayout;
 import javax.swing.GroupLayout;
 import javax.swing.GroupLayout.Alignment;
+import javax.swing.JCheckBox;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JSpinner.NumberEditor;
@@ -28,6 +29,7 @@ public class MonitorConfigPanel extends AbstractPanel {
 	 */
 	private JTextField openbciIpAddressTextField;
 	private IntegerSpinner openbciPortSpinner;
+	private JCheckBox scrollingModeCheckBox;
 
 	/**
 	 * Default constructor.
@@ -61,7 +63,7 @@ protected JPanel createOpenbciAddressPanel() {
 
 		hGroup.addGroup(layout.createParallelGroup().addComponent(openbciIpAddressLabel).addComponent(openbciPortLabel));
 
-		hGroup.addGroup(layout.createParallelGroup().addComponent(getOpenbciIpAddressTextField()).addComponent(getOpenbciPortSpinner()));
+		hGroup.addGroup(layout.createParallelGroup().addComponent(getOpenbciIpAddressTextField()).addComponent(getOpenbciPortSpinner()).addComponent(getScrollingModeCheckBox()));
 
 		layout.setHorizontalGroup(hGroup);
 
@@ -71,6 +73,8 @@ protected JPanel createOpenbciAddressPanel() {
 
 		vGroup.addGroup(layout.createParallelGroup(Alignment.BASELINE).addComponent(openbciPortLabel).addComponent(getOpenbciPortSpinner()));
 
+		vGroup.addGroup(layout.createParallelGroup(Alignment.BASELINE).addComponent(getScrollingModeCheckBox()));
+
 		layout.setVerticalGroup(vGroup);
 
 		return openbciAddressPanel;
@@ -92,6 +96,13 @@ protected IntegerSpinner getOpenbciPortSpinner() {
 		return openbciPortSpinner;
 	}
 
+	protected JCheckBox getScrollingModeCheckBox() {
+		if (scrollingModeCheckBox == null) {
+			scrollingModeCheckBox = new JCheckBox("View in scrolling mode (change will not affect any currently open signals)");
+		}
+		return scrollingModeCheckBox;
+	}
+
 	/**
 	 * Fills all the fields of this panel from the given
 	 * {@link ApplicationConfiguration configuration} of Svarog.
@@ -102,6 +113,7 @@ protected IntegerSpinner getOpenbciPortSpinner() {
 	public void fillPanelFromModel(ApplicationConfiguration applicationConfig) {
 		getOpenbciIpAddressTextField().setText(applicationConfig.getOpenbciIPAddress());
 		getOpenbciPortSpinner().setValue(applicationConfig.getOpenbciPort());
+		getScrollingModeCheckBox().setSelected(applicationConfig.isScrollingMode());
 	}
 
 	/**
@@ -113,7 +125,8 @@ public void fillPanelFromModel(ApplicationConfiguration applicationConfig) {
 	 */
 	public void fillModelFromPanel(ApplicationConfiguration applicationConfig) {
 		applicationConfig.setOpenbciIPAddress(getOpenbciIpAddressTextField().getText());
-		applicationConfig.setOpenbciPort(openbciPortSpinner.getValue());
+		applicationConfig.setOpenbciPort(getOpenbciPortSpinner().getValue());
+		applicationConfig.setScrollingMode(getScrollingModeCheckBox().isSelected());
 	}
 
 	/**

svarog/src/main/java/org/signalml/app/view/signal/InitialTagTiming.java

@@ -0,0 +1,18 @@
+package org.signalml.app.view.signal;
+
+/**
+ * Simple data structure with tag's position (start) and
+ * a number of epoch in which it has been created.
+ * Used internally in StaticRenderingHelper.
+ */
+class InitialTagTiming {
+
+	public final double position;
+
+	public final long cycleNumber;
+
+	InitialTagTiming(double position, long cycleNumber) {
+		this.position = position;
+		this.cycleNumber = cycleNumber;
+	}
+}

svarog/src/main/java/org/signalml/app/view/signal/SignalPlot.java

@@ -58,6 +58,7 @@
 import org.signalml.domain.signal.raw.RawSignalSampleSource;
 import org.signalml.domain.signal.samplesource.MultichannelSampleSource;
 import org.signalml.domain.signal.samplesource.OriginalMultichannelSampleSource;
+import org.signalml.domain.tag.MonitorTag;
 import org.signalml.domain.tag.StyledTagSet;
 import org.signalml.domain.tag.TagDifference;
 import org.signalml.domain.tag.TagDifferenceSet;
@@ -179,6 +180,9 @@ public class SignalPlot extends JComponent implements PropertyChangeListener, Ch
 	private int horizontalPixelLead;
 	private int verticalPixelLead;
 
+	/** used for static (non-scrolling) rendering of on-line signal tags */
+	private final StaticRenderingHelper staticRendering;
+
 	private boolean compensationEnabled = true;
 	private boolean ignoreSliderEvents = false;
 
@@ -214,8 +218,9 @@ public SignalPlot(SignalDocument document, SignalView view, SignalPlot masterPlo
 		setBackground(Color.WHITE);
 		setFocusable(true);
 
-		if (document.getSampleSource() instanceof RawSignalSampleSource) {
-			double timestamp = ((RawSignalSampleSource) document.getSampleSource()).getFirstSampleTimestamp();
+		OriginalMultichannelSampleSource sampleSource = document.getSampleSource();
+		if (sampleSource instanceof RawSignalSampleSource) {
+			double timestamp = ((RawSignalSampleSource) sampleSource).getFirstSampleTimestamp();
 			firstSampleTimestamp = Math.round(timestamp);
 		} else {
 			firstSampleTimestamp = 0;
@@ -328,8 +333,15 @@ private void maybeShowPopupMenu(MouseEvent e) {
 
 		});
 		if (document instanceof MonitorSignalDocument) {
+			if (!config.isScrollingMode()) {
+				staticRendering = new StaticRenderingHelper(sampleSource.getChannelCount(), sampleSource.getSampleCount(0), sampleSource.getSamplingFrequency());
+			} else {
+				staticRendering = null;
+			}
 			//for online signals renderrer should know that it's online
 			renderer.setOnline(true);
+		} else {
+			staticRendering = null;
 		}
 
 	}
@@ -832,6 +844,16 @@ protected void paintComponent(Graphics gOrig) {
 		int clipEndX = clip.x + clip.width - 1;
 		int clipEndY = clip.y + clip.height - 1;
 
+		if (staticRendering != null) try {
+			// pre-fetching data and updating rendering state
+			// to avoid mismatch between signal and tags
+			staticRendering.fetchSamples(signalChain);
+		} catch (RuntimeException ex) {
+			logger.error("failed to read samples in static rendering mode", ex);
+			setVisible(false);
+			throw ex;
+		}
+
 		prepareToPaintTags();
 
 		PositionedTag tagSelection = view.getTagSelection(this);
@@ -918,10 +940,8 @@ protected void paintComponent(Graphics gOrig) {
 		}
 
 		visibleCount = 0;
-		channel = startChannel;
-		while (visibleCount < maxNumberOfChannels && channel < channelCount) {
+		for (channel=startChannel; visibleCount < maxNumberOfChannels && channel < channelCount; ++channel) {
 			if (!isChannelVisible(channel)) {
-				channel++;
 				continue;
 			}
 			visibleCount++;
@@ -938,8 +958,12 @@ protected void paintComponent(Graphics gOrig) {
 			}
 
 			try {
-
-				signalChain.getSamples(channel, samples, firstSample, length, 0);
+				if (staticRendering != null) {
+					int samplesMargin = (int) (10 / timeZoomFactor); // 10 pixels
+					staticRendering.getSamples(samplesMargin, channel, samples, firstSample, length);
+				} else {
+					signalChain.getSamples(channel, samples, firstSample, length, 0);
+				}
 			} catch (RuntimeException ex) {
 				logger.error(format("failed to read %d samples starting at %d, till %d, channel %d",
 						length, firstSample, lastSample, sampleCount[channel]));
@@ -954,8 +978,6 @@ protected void paintComponent(Graphics gOrig) {
 					channelLevel[channel], timeZoomFactor, pixelPerValueForChannel,
 					clamped ? clampLimit : null, dcOffsetRemoved
 			);
-
-			channel++;
 		}
 
 		if (signalXOR) {
@@ -1472,14 +1494,23 @@ public int toChannelSpace(Point p) {
 		return channel + numberOfInvisibleChannels;
 	}
 
+	TagTiming computeTagTiming(SignalSelection tag) {
+		if (staticRendering != null && (tag instanceof MonitorTag)) {
+			return staticRendering.computeTagTiming((MonitorTag) tag);
+		} else {
+			return new TagTiming(tag.getPosition(), tag.getLength());
+		}
+	}
+
 	public Rectangle getPixelSelectionBounds(SignalSelection selection, Rectangle useRect) {
 
-		double position = selection.getPosition();
-		double length = selection.getLength();
+		TagTiming timing = computeTagTiming(selection);
+		final double position = timing.position;
+		final double length = timing.length;
 		SignalSelectionType type = selection.getType();
 
-		int selLeft = (int) Math.floor(selection.getPosition() * pixelPerSecond);
-		int selRight = (int) Math.ceil(selection.getLength() * pixelPerSecond);
+		int selLeft = (int) Math.floor(position * pixelPerSecond);
+		int selRight = (int) Math.ceil((position + length) * pixelPerSecond);
 		int selTop;
 		int selBottom;
 
@@ -1528,7 +1559,7 @@ public Rectangle getPixelBlockTagBounds(SignalSelection tag, boolean marker, int
 		Rectangle rect = getTagSelectionRectangle(tag, marker, tagCnt, useRect);
 
 		if (rect.x > 0 && blockLinesVisible && pixelPerBlock > 4) {
-			int linePosition = (int) ((int) ((tag.getPosition() / blockSize)) * pixelPerBlock);
+			int linePosition = (int) ((int) ((computeTagTiming(tag).position / blockSize)) * pixelPerBlock);
 			if (linePosition == rect.x) {
 				rect.x++; // block tags are drawn only inside the block
 			}
@@ -1577,6 +1608,9 @@ public Rectangle getTagSelectionRectangle(SignalSelection tag, boolean marker, i
 			rect = useRect;
 		}
 
+		TagTiming timing = computeTagTiming(tag);
+		double position = timing.position;
+		double length = timing.length;
 		if (marker) {
 
 			int rWidth = pixelPerChannel / (3 * tagCnt); // 1/3 of the height for this tag
@@ -1585,12 +1619,12 @@ public Rectangle getTagSelectionRectangle(SignalSelection tag, boolean marker, i
 			} else if (rWidth < 5) {
 				rWidth = 5;
 			}
-			rect.x = (int) (tag.getPosition() * pixelPerSecond) - rWidth / 2;
+			rect.x = (int) (position * pixelPerSecond) - rWidth / 2;
 			rect.width = rWidth;
 
 		} else {
-			rect.x = (int) (tag.getPosition() * pixelPerSecond);
-			rect.width = (int) (tag.getLength() * pixelPerSecond);
+			rect.x = (int) (position * pixelPerSecond);
+			rect.width = (int) (length * pixelPerSecond);
 		}
 
 		return rect;
@@ -1797,7 +1831,7 @@ public SignalSelection getChannelSelection(float fromPosition, float toPosition,
 	 */
 	protected SignalSelection transformToMarkerSelection(SignalSelection selection) {
 
-		double startPosition = selection.getPosition();
+		double startPosition = computeTagTiming(selection).position;
 		int sampleAtPoint = (int) (startPosition * samplingFrequency);
 		float newStartPosition = sampleAtPoint / samplingFrequency;
 
@@ -2039,23 +2073,26 @@ public ArrayList<PositionedTag> getTagsAtPoint(Point point, ArrayList<Positioned
 					continue;
 				}
 
+				TagTiming timing = computeTagTiming(tag);
+				double position = timing.position;
+				double length = timing.length;
 				if (tag.getStyle().getType() == SignalSelectionType.BLOCK) {
-					if (time >= tag.getPosition() && time < (tag.getPosition() + tag.getLength())) {
+					if (time >= position && time < position + length) {
 						tagBounds = getPixelBlockTagBounds(tag, tag.isMarker(), tagCnt, cnt, viewportPoint, viewportSize, plotSize, comparing, tempBounds);
 						if (tagBounds.contains(point)) {
 							list.add(new PositionedTag(tag, tagIndex));
 						}
 					}
 				} else if (tag.getStyle().getType() == SignalSelectionType.CHANNEL) {
 					if (tag.getChannel() == channel) {
-						if (tag.isMarker() || (time >= tag.getPosition() && time < tag.getEndPosition())) {
+						if (tag.isMarker() || (time >= position && time < position + length)) {
 							tagBounds = getPixelChannelTagBoundsInChannel(tag, tag.isMarker(), tagCnt, cnt, viewChannel, comparing, tempBounds);
 							if (tagBounds.contains(point)) {
 								list.add(new PositionedTag(tag, tagIndex));
 							}
 						}
 					} else if (tag.getChannel() == Tag.CHANNEL_NULL) {
-						if (tag.isMarker() || (time >= tag.getPosition() && time < (tag.getPosition() + tag.getLength()))) {
+						if (tag.isMarker() || (time >= position && time < position + length)) {
 							tagBounds = getPixelBlockTagBounds(tag, tag.isMarker(), tagCnt, cnt, viewportPoint, viewportSize, plotSize, comparing, tempBounds);
 							if (tagBounds.contains(point)) {
 								list.add(new PositionedTag(tag, tagIndex));

svarog/src/main/java/org/signalml/app/view/signal/SignalView.java

@@ -1242,8 +1242,9 @@ public void showTag(Tag tag) {
 		JViewport viewport = scrollPane.getViewport();
 
 		Dimension viewportSize = viewport.getExtentSize();
-		int startX = plot.timeToPixel(tag.getPosition());
-		int endX = plot.timeToPixel(tag.getPosition() + tag.getLength());
+		TagTiming tagTiming = plot.computeTagTiming(tag);
+		int startX = plot.timeToPixel(tagTiming.position);
+		int endX = plot.timeToPixel(tagTiming.position + tagTiming.length);
 
 		int optimalX = startX - (viewportSize.width - (endX - startX)) / 2;