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Various bugfixes for the combined image view, especially when synchro…
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…nizing images with different dimensions.
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@AndreasBurger
AndreasBurger committed Jul 6, 2016
1 parent 858a546 commit fc481bf
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Showing 6 changed files with 121 additions and 22 deletions.
36 changes: 29 additions & 7 deletions org.knime.knip.base/src/org/knime/knip/base/nodes/view/CombinedCellViewFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@
import org.knime.knip.cellviewer.interfaces.CellViewFactory;
import org.knime.knip.core.awt.ColorLabelingRenderer;
import org.knime.knip.core.awt.Real2GreyRenderer;
import org.knime.knip.core.data.img.DefaultImgMetadata;
import org.knime.knip.core.ui.imgviewer.CombinedImgViewer;
import org.knime.knip.core.ui.imgviewer.events.ImgWithMetadataChgEvent;
import org.knime.knip.core.ui.imgviewer.events.LabelingWithMetadataChgEvent;
Expand All @@ -71,7 +72,11 @@
import org.knime.knip.core.ui.imgviewer.panels.providers.LabelingRU;
import org.knime.knip.core.util.waitingindicator.WaitingIndicatorUtils;

import net.imagej.ImgPlusMetadata;
import net.imglib2.img.Img;
import net.imglib2.img.ImgView;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;

/**
* TODO Auto-generated
Expand Down Expand Up @@ -111,6 +116,7 @@ public void onReset() {
// Nothing to do here
}

@SuppressWarnings("unchecked")
@Override
public void updateComponent(final List<DataValue> valueToView) {
WaitingIndicatorUtils.setWaiting(m_view, true);
Expand All @@ -120,12 +126,28 @@ public void updateComponent(final List<DataValue> valueToView) {
for (DataValue v : valueToView) {
if (v instanceof ImgPlusValue) {
final ImgPlusValue imgPlusValue = (ImgPlusValue)v;
ImageRU ru = new ImageRU(((RealType)imgPlusValue.getImgPlus().firstElement()).getMinValue());
m_view.addRU(ru);
m_view.publishToPrev(new RendererSelectionChgEvent(new Real2GreyRenderer(
((RealType)imgPlusValue.getImgPlus().firstElement()).getMinValue())));
m_view.publishToPrev(new ImgWithMetadataChgEvent<>(imgPlusValue.getImgPlus(),
imgPlusValue.getMetadata()));

if (imgPlusValue.getMetadata().numDimensions() <= 1) {
Img img2d = imgPlusValue.getImgPlus().getImg();
ImgPlusMetadata meta = imgPlusValue.getMetadata();

img2d = ImgView.wrap(Views.addDimension(img2d, 0, 0), img2d.factory());
meta = new DefaultImgMetadata(2);
ImageRU ru = new ImageRU(((RealType)img2d.firstElement()).getMinValue());
m_view.addRU(ru);
m_view.publishToPrev(new RendererSelectionChgEvent(
new Real2GreyRenderer(((RealType)img2d.firstElement()).getMinValue())));
m_view.publishToPrev(new ImgWithMetadataChgEvent<>(img2d, meta));

} else {
ImageRU ru =
new ImageRU(((RealType)imgPlusValue.getImgPlus().firstElement()).getMinValue());
m_view.addRU(ru);
m_view.publishToPrev(new RendererSelectionChgEvent(new Real2GreyRenderer(
((RealType)imgPlusValue.getImgPlus().firstElement()).getMinValue())));
m_view.publishToPrev(new ImgWithMetadataChgEvent<>(imgPlusValue.getImgPlus(),
imgPlusValue.getMetadata()));
}

} else if (v instanceof LabelingValue) {
final LabelingValue labValue = (LabelingValue)v;
Expand Down Expand Up @@ -189,7 +211,7 @@ public String getCellViewDescription() {
}

@Override
public int getPriority(){
public int getPriority() {
return Integer.MAX_VALUE;
}

Expand Down
3 changes: 3 additions & 0 deletions org.knime.knip.core/src/org/knime/knip/core/ui/imgviewer/CombinedImgViewer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -195,6 +195,7 @@ public void addRU(final RenderUnit ru) {
broadcast(new CombinedRUSynchEventClone(false));
m_ru.setStackedRendering(true);
m_controlPanel.resetCheckboxes();
m_tabbedMenu.setSelectedIndex(0);
}

public void clear() {
Expand Down Expand Up @@ -250,6 +251,8 @@ public void onCombinedRUSynchChange(final CombinedRUSynchEvent e) {
broadcast(new CombinedRUSynchEventClone(e));
if (!m_sync) {
broadcast(new RebroadcastSelectionEvent());
} else {
m_eventServices.get(m_tabbedMenu.getSelectedIndex()).publish(new RebroadcastSelectionEvent());
}
}

Expand Down
4 changes: 3 additions & 1 deletion ...nip.core/src/org/knime/knip/core/ui/imgviewer/events/NormalizationParametersChgEvent.java
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Original file line number Diff line number Diff line change
Expand Up @@ -159,10 +159,12 @@ public <T extends RealType<T>> double[] getNormalizationParameters(final RandomA
final ValuePair<T, T> oldMinMax =
Operations.compute(new MinMaxWithSaturation<T>(m_saturation, element), Views
.iterable(Views.offsetInterval(Views.zeroMin(src), sel.getInterval(Views.zeroMin(src)))));
return new double[]{

double[] retVal = new double[]{
Normalize.normalizationFactor(oldMinMax.a.getRealDouble(), oldMinMax.b.getRealDouble(),
element.getMinValue(), element.getMaxValue()),
oldMinMax.a.getRealDouble()};
return retVal;
}

}
Expand Down
27 changes: 25 additions & 2 deletions org.knime.knip.core/src/org/knime/knip/core/ui/imgviewer/panels/providers/CombinedRU.java
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,9 @@
import org.knime.knip.core.ui.event.EventService;
import org.knime.knip.core.ui.imgviewer.events.TransparencyPanelValueChgEvent;
import org.knime.knip.core.ui.imgviewer.panels.CombinedRUSynchEvent;
import org.knime.knip.core.util.MiscViews;

import net.imglib2.FinalInterval;
import net.imglib2.Interval;

/**
Expand Down Expand Up @@ -150,10 +152,12 @@ public Image createImage() {
int first = i;
int w = 0, h = 0;
Interval target = null;

if (m_sync) {
target = m_renderUnits.get(i).getInterval();
target = calculateHull();
m_renderUnits.get(i).limitTo(target);
}

Image img = m_renderUnits.get(i).createImage();
w += img.getWidth(null);
h = Math.max(h, img.getHeight(null));
Expand Down Expand Up @@ -190,10 +194,12 @@ public Image createImage() {
//at least one active image

Interval target = null;

if (m_sync) {
target = m_renderUnits.get(i).getInterval();
target = calculateHull();
m_renderUnits.get(i).limitTo(target);
}

Image img = m_renderUnits.get(i).createImage();
joinedImg = m_graphicsConfig.createCompatibleImage(img.getWidth(null), img.getHeight(null),
java.awt.Transparency.TRANSLUCENT);
Expand All @@ -206,9 +212,11 @@ public Image createImage() {
//blend in the other active images
while (i < m_renderUnits.size()) {
if (m_renderUnits.get(i).isActive()) {

if (m_sync) {
m_renderUnits.get(i).limitTo(target);
}

g.drawImage(Transparency.makeColorTransparent(m_renderUnits.get(i).createImage(), Color.WHITE,
m_transparency),
0, 0, null);
Expand All @@ -232,6 +240,21 @@ public Image createImage() {

}

private Interval calculateHull() {
Interval result = new FinalInterval();
for (RenderUnit ru : m_renderUnits) {
if (ru.isActive()) {
Interval target = ru.getInterval();
if (result.numDimensions() > target.numDimensions()) {
result = MiscViews.synchronizeDimensionality(target, result);
} else {
result = MiscViews.synchronizeDimensionality(result, target);
}
}
}
return result;
}

/**
* @return combined HashCode of all {@link RenderUnit}s. By contract that allows to identify images generated by
* {@link #createImage()} including all parameters that have influence on the creation.
Expand Down
56 changes: 47 additions & 9 deletions org.knime.knip.core/src/org/knime/knip/core/ui/imgviewer/panels/providers/ImageRU.java
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Original file line number Diff line number Diff line change
Expand Up @@ -63,12 +63,16 @@
import org.knime.knip.core.ui.imgviewer.events.ImgAndLabelingChgEvent;
import org.knime.knip.core.ui.imgviewer.events.ImgWithMetadataChgEvent;
import org.knime.knip.core.ui.imgviewer.events.NormalizationParametersChgEvent;
import org.knime.knip.core.ui.imgviewer.events.PlaneSelectionEvent;
import org.knime.knip.core.ui.imgviewer.events.ViewClosedEvent;
import org.knime.knip.core.ui.imgviewer.panels.transfunc.LookupTableChgEvent;
import org.knime.knip.core.util.MiscViews;

import net.imglib2.Interval;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.display.ColorTable;
import net.imglib2.display.screenimage.awt.AWTScreenImage;
import net.imglib2.outofbounds.OutOfBoundsConstantValueFactory;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;
Expand Down Expand Up @@ -125,6 +129,9 @@ public int hashCode() {

// event members

/** Caches the current restriction interval */
private Interval m_interval;

private LookupTable<T, ARGBType> m_lookupTable = new SimpleTable();

private NormalizationParametersChgEvent m_normalizationParameters = new NormalizationParametersChgEvent(0, false);
Expand All @@ -133,11 +140,13 @@ public int hashCode() {

private RandomAccessibleInterval<T> m_src;

private RandomAccessibleInterval<T> m_unmodSrc;

/** default constructor that creates a renderer selection dependent image {@link RenderUnit}. */
public ImageRU(final double min) {
this(false);

this.m_greyRenderer = new Real2GreyRenderer<T>(0.0);

}

/**
Expand All @@ -148,6 +157,7 @@ public ImageRU(final double min) {
*/
public ImageRU(final boolean enforceGreyScale) {
m_enforceGreyScale = enforceGreyScale;
this.m_greyRenderer = new Real2GreyRenderer<T>(0.0);
}

@SuppressWarnings("unchecked")
Expand All @@ -156,13 +166,14 @@ public Image createImage() {
if (m_lastImage != null && m_hashOfLastRendering == generateHashCode()) {
return m_lastImage;
}

PlaneSelectionEvent pSel = m_planeSelection;
if(m_interval != null && m_planeSelection.numDimensions() != m_interval.numDimensions()) {
pSel = MiscViews.adjustPlaneSelection(m_planeSelection, m_interval);
}
//+ allows normalization - breaks type safety
@SuppressWarnings("rawtypes")
RandomAccessibleInterval convertedSrc = AWTImageProvider.convertIfDouble(m_src);
final double[] normParams =
m_normalizationParameters.getNormalizationParameters(convertedSrc, m_planeSelection);

final double[] normParams = m_normalizationParameters.getNormalizationParameters(convertedSrc, pSel);
//set parameters of the renderer
if (m_renderer instanceof RendererWithNormalization) {
((RendererWithNormalization)m_renderer).setNormalizationParameters(normParams[0], normParams[1]);
Expand All @@ -178,12 +189,12 @@ public Image createImage() {

final AWTScreenImage ret;
if (!m_enforceGreyScale) {
ret = m_renderer.render(Views.zeroMin(convertedSrc), m_planeSelection.getPlaneDimIndex1(),
m_planeSelection.getPlaneDimIndex2(), m_planeSelection.getPlanePos());
ret = m_renderer.render(Views.zeroMin(convertedSrc), pSel.getPlaneDimIndex1(),
pSel.getPlaneDimIndex2(), pSel.getPlanePos());
} else {
m_greyRenderer.setNormalizationParameters(normParams[0], normParams[1]);
ret = m_greyRenderer.render(Views.zeroMin(convertedSrc), m_planeSelection.getPlaneDimIndex1(),
m_planeSelection.getPlaneDimIndex2(), m_planeSelection.getPlanePos());
ret = m_greyRenderer.render(Views.zeroMin(convertedSrc), pSel.getPlaneDimIndex1(),
pSel.getPlaneDimIndex2(), pSel.getPlanePos());
}

m_lastImage = ret.image();
Expand Down Expand Up @@ -213,6 +224,31 @@ public boolean isActive() {
return (m_src != null);
}

@Override
public void limitTo(final Interval interval) {
if (!interval.equals(m_interval)) {
T val = m_src.randomAccess().get().createVariable();
val.setReal(val.getMinValue());
OutOfBoundsConstantValueFactory<T, RandomAccessibleInterval<T>> fac =
new OutOfBoundsConstantValueFactory<>(val);
m_interval = interval;
m_src = Views.interval(MiscViews.synchronizeDimensionality(m_unmodSrc, interval, fac), interval);
m_hashOfLastRendering = -1;
}
}

@Override
public void resetLimit() {
m_interval = null;
m_src = m_unmodSrc;
m_hashOfLastRendering = -1;
}

@Override
public Interval getInterval() {
return m_src;
}

//event handling

/**
Expand Down Expand Up @@ -244,6 +280,7 @@ public void onLookupTableChgEvent(final LookupTableChgEvent<T, ARGBType> event)
@EventListener
public void onImageUpdated(final ImgWithMetadataChgEvent<T> e) {
m_src = e.getRandomAccessibleInterval();
m_unmodSrc = e.getRandomAccessibleInterval();

final int size = e.getImgMetaData().getColorTableCount();
m_colorTables = new ColorTable[size];
Expand All @@ -261,6 +298,7 @@ public void onImageUpdated(final ImgWithMetadataChgEvent<T> e) {
@EventListener
public void onImageUpdated(final ImgAndLabelingChgEvent<T, ?> e) {
m_src = e.getRandomAccessibleInterval();
m_unmodSrc = e.getRandomAccessibleInterval();
}

/**
Expand Down
17 changes: 14 additions & 3 deletions org.knime.knip.core/src/org/knime/knip/core/ui/imgviewer/panels/providers/LabelingRU.java
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Original file line number Diff line number Diff line change
Expand Up @@ -68,12 +68,15 @@
import org.knime.knip.core.ui.imgviewer.events.LabelPanelIsHiliteModeEvent;
import org.knime.knip.core.ui.imgviewer.events.LabelPanelVisibleLabelsChgEvent;
import org.knime.knip.core.ui.imgviewer.events.LabelingWithMetadataChgEvent;
import org.knime.knip.core.ui.imgviewer.events.PlaneSelectionEvent;
import org.knime.knip.core.ui.imgviewer.events.RulebasedLabelFilter.Operator;
import org.knime.knip.core.ui.imgviewer.events.ViewClosedEvent;
import org.knime.knip.core.util.MiscViews;

import net.imglib2.Interval;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.display.screenimage.awt.AWTScreenImage;
import net.imglib2.outofbounds.OutOfBoundsConstantValueFactory;
import net.imglib2.roi.labeling.LabelingType;
import net.imglib2.view.Views;

Expand Down Expand Up @@ -134,6 +137,11 @@ public Image createImage() {
return m_lastImage;
}

PlaneSelectionEvent pSel = m_planeSelection;
if(m_interval != null && m_planeSelection.numDimensions() != m_interval.numDimensions()) {
pSel = MiscViews.adjustPlaneSelection(m_planeSelection, m_interval);
}

if (m_renderer instanceof RendererWithLabels) {
@SuppressWarnings("unchecked")
final RendererWithLabels<L> r = (RendererWithLabels<L>)m_renderer;
Expand All @@ -155,8 +163,8 @@ public Image createImage() {
}

final AWTScreenImage ret =
m_renderer.render(m_src, m_planeSelection.getPlaneDimIndex1(), m_planeSelection.getPlaneDimIndex2(),
m_planeSelection.getPlanePos());
m_renderer.render(m_src, pSel.getPlaneDimIndex1(), pSel.getPlaneDimIndex2(),
pSel.getPlanePos());

m_hashOfLastRendering = generateHashCode();
m_lastImage = ret.image();
Expand All @@ -169,8 +177,11 @@ public void limitTo(final Interval interval) {
if (!interval.equals(m_interval)) {
LabelingType<L> val = m_src.randomAccess().get().createVariable();
val.clear();
OutOfBoundsConstantValueFactory<LabelingType<L>, RandomAccessibleInterval<LabelingType<L>>> fac =
new OutOfBoundsConstantValueFactory<>(val);
m_interval = interval;
m_src = Views.interval(Views.extendValue(m_unmodSrc, val), interval);
m_src = Views.interval(MiscViews.synchronizeDimensionality(m_unmodSrc, interval, fac), interval);
m_hashOfLastRendering = -1;
}
}

Expand Down

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