diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesGrid.java
index f902d8c3dbd71bca1b4bc08348f34c449cee3fff..b45ec835a01766951192757621ce162868a06cf2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesGrid.java
@@ -17,25 +17,28 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Collections;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageChannelsReference;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStack;
-
import com.extjs.gxt.ui.client.event.Events;
import com.extjs.gxt.ui.client.event.Listener;
import com.extjs.gxt.ui.client.event.SliderEvent;
import com.extjs.gxt.ui.client.widget.Label;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.extjs.gxt.ui.client.widget.Slider;
+import com.extjs.gxt.ui.client.widget.layout.HBoxLayout;
import com.extjs.gxt.ui.client.widget.layout.TableLayout;
import com.google.gwt.user.client.ui.Widget;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageChannelsReference;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStack;
+
/**
* Allows to view logical image which has series (e.g. timepoints).
*
@@ -48,42 +51,92 @@ class LogicalImageSeriesGrid
LogicalImageChannelsReference channelReferences, int imageWidth, int imageHeight)
{
LogicalImageSeriesViewerModel model = new LogicalImageSeriesViewerModel(channelStackImages);
+ List<List<ImageChannelStack>> sortedChannelStackSeriesPoints = model.getSortedChannelStackSeriesPoints();
List<LayoutContainer> frames =
- createSeriesFrames(model.getSortedChannelStackSeriesPoints(), channelReferences,
+ createSeriesFrames(sortedChannelStackSeriesPoints, channelReferences,
sessionId, imageWidth, imageHeight);
-
- return createMoviePlayer(frames, model.getSortedPoints());
+ if (model.isMatrixViewPossible())
+ {
+ return createTimeAndDepthViewer(frames, model);
+ }
+ return createMoviePlayer(frames, model);
}
-
- private static List<ImageSeriesPoint> sortPoints(Set<ImageSeriesPoint> points)
+
+ private static LayoutContainer createTimeAndDepthViewer(final List<LayoutContainer> frames,
+ final LogicalImageSeriesViewerModel model)
+ {
+ final LayoutContainer mainContainer = new LayoutContainer();
+ LayoutContainer sliderContainer = new LayoutContainer(new HBoxLayout());
+ mainContainer.add(sliderContainer);
+ LayoutContainer timeSliderContainer = new LayoutContainer();
+ sliderContainer.add(timeSliderContainer);
+ final int numberOfTimepoints = model.getNumberOfTimepoints();
+ final Label timeSliderLabel = new Label();
+ timeSliderContainer.add(timeSliderLabel);
+ final Slider timeSlider = createSlider(numberOfTimepoints);
+ timeSliderContainer.add(timeSlider);
+ Label spacer = new Label();
+ spacer.setWidth(80);
+ sliderContainer.add(spacer);
+ LayoutContainer depthSliderContainer = new LayoutContainer();
+ sliderContainer.add(depthSliderContainer);
+ final int numberOfDepthLevels = model.getNumberOfDepthLevels();
+ final Label depthSliderLabel = new Label();
+ depthSliderContainer.add(depthSliderLabel);
+ final Slider depthSlider = createSlider(numberOfDepthLevels);
+ depthSliderContainer.add(depthSlider);
+ Listener<SliderEvent> listener = new AbstractSliderListener(mainContainer, frames)
+ {
+ private int currentFrameIndex;
+
+ @Override
+ public void handleEvent(SliderEvent be)
+ {
+ super.handleEvent(be);
+ frames.get(currentFrameIndex).hide();
+ currentFrameIndex =
+ (timeSlider.getValue() - 1) * numberOfDepthLevels
+ + (depthSlider.getValue() - 1);
+ frames.get(currentFrameIndex).show();
+ int timeSliderValue = timeSlider.getValue();
+ int depthSliderValue = depthSlider.getValue();
+ setSliderLabels(model, timeSliderLabel, timeSliderValue, depthSliderLabel, depthSliderValue);
+ mainContainer.layout();
+ }
+ };
+ timeSlider.addListener(Events.Change, listener);
+ depthSlider.addListener(Events.Change, listener);
+ setSliderLabels(model, timeSliderLabel, 1, depthSliderLabel, 1);
+
+ // add only first frame to avoid loading images before the slider is touched
+ mainContainer.add(frames.get(0));
+ return mainContainer;
+ }
+
+ private static void setSliderLabels(LogicalImageSeriesViewerModel model, Label timeSliderLabel,
+ int timeSliderValue, Label depthSliderLabel, int depthSliderValue)
{
- ArrayList<ImageSeriesPoint> pointsList = new ArrayList<ImageSeriesPoint>(points);
- Collections.sort(pointsList);
- return pointsList;
+ int numberOfTimepoints = model.getNumberOfTimepoints();
+ int numberOfDepthLevels = model.getNumberOfDepthLevels();
+ ImageSeriesPoint imageSeriesPoint = model.get(timeSliderValue - 1, depthSliderValue - 1);
+ Float time = imageSeriesPoint.getTimePointOrNull();
+ timeSliderLabel.setText("Time: " + time + " sec (" + timeSliderValue + "/" + numberOfTimepoints + ")");
+ Float depth = imageSeriesPoint.getDepthOrNull();
+ depthSliderLabel.setText("Depth: " + depth + " (" + depthSliderValue + "/"
+ + numberOfDepthLevels + ")");
}
private static LayoutContainer createMoviePlayer(final List<LayoutContainer> frames,
- final List<ImageSeriesPoint> sortedPoints)
+ LogicalImageSeriesViewerModel model)
{
+ final List<ImageSeriesPoint> sortedPoints = model.getSortedPoints();
final LayoutContainer mainContainer = new LayoutContainer();
-
- final Slider slider = createSeriesSlider(frames.size(), new Listener<SliderEvent>()
+ Listener<SliderEvent> listener = new AbstractSliderListener(mainContainer, frames)
{
- private boolean isFirstMove = true;
-
+ @Override
public void handleEvent(SliderEvent e)
{
- if (isFirstMove)
- {
- // The first slider move has been made, so we add all hidden frames to the
- // DOM. The browser will start fetching images referenced in URLs in the
- // background.
- for (int i = 1; i < frames.size(); i++)
- {
- mainContainer.add(frames.get(i));
- }
- isFirstMove = false;
- }
+ super.handleEvent(e);
int oldValue = e.getOldValue();
int newValue = e.getNewValue();
if (oldValue > 0)
@@ -96,7 +149,9 @@ class LogicalImageSeriesGrid
mainContainer.layout();
}
- });
+ };
+ final Slider slider = createSlider(frames.size());
+ slider.addListener(Events.Change, listener);
// slider.setValue(1);
mainContainer.add(createSeriesPointLabel(sortedPoints, 1));
@@ -193,17 +248,16 @@ class LogicalImageSeriesGrid
return new Label(labelText);
}
- private static final Slider createSeriesSlider(int maxValue, Listener<SliderEvent> listener)
+ private static Slider createSlider(int maxValue)
{
final Slider slider = new Slider();
// we do not want the slider to be long when there are just few points
- slider.setWidth(Math.min(230, maxValue * 10));
+ slider.setWidth(Math.min(230, Math.max(100, maxValue * 10)));
slider.setIncrement(1);
slider.setMinValue(1);
slider.setMaxValue(maxValue);
slider.setClickToChange(true);
slider.setUseTip(false);
- slider.addListener(Events.Change, listener);
return slider;
}
@@ -227,11 +281,11 @@ class LogicalImageSeriesGrid
this.zOrNull = zOrNull;
this.seriesNumberOrNull = seriesNumberOrNull;
}
-
+
public String getLabel()
{
String desc = "";
- if (tOrNull != null)
+ if (isTimePointPresent())
{
if (desc.length() > 0)
{
@@ -239,7 +293,7 @@ class LogicalImageSeriesGrid
}
desc += "Time: " + tOrNull + " sec";
}
- if (zOrNull != null)
+ if (isDepthPresent())
{
if (desc.length() > 0)
{
@@ -247,7 +301,7 @@ class LogicalImageSeriesGrid
}
desc += "Depth: " + zOrNull;
}
- if (seriesNumberOrNull != null)
+ if (isSeriesNumberPresent())
{
if (desc.length() > 0)
{
@@ -258,6 +312,36 @@ class LogicalImageSeriesGrid
return desc;
}
+ private boolean isDepthPresent()
+ {
+ return zOrNull != null;
+ }
+
+ Float getDepthOrNull()
+ {
+ return zOrNull;
+ }
+
+ private boolean isTimePointPresent()
+ {
+ return tOrNull != null;
+ }
+
+ Float getTimePointOrNull()
+ {
+ return tOrNull;
+ }
+
+ private boolean isSeriesNumberPresent()
+ {
+ return seriesNumberOrNull != null;
+ }
+
+ Integer getSeriesNumberOrNull()
+ {
+ return seriesNumberOrNull;
+ }
+
public int compareTo(ImageSeriesPoint o)
{
int cmp;
@@ -288,9 +372,9 @@ class LogicalImageSeriesGrid
int result = 1;
result =
prime * result
- + ((seriesNumberOrNull == null) ? 0 : seriesNumberOrNull.hashCode());
- result = prime * result + ((tOrNull == null) ? 0 : tOrNull.hashCode());
- result = prime * result + ((zOrNull == null) ? 0 : zOrNull.hashCode());
+ + (isSeriesNumberPresent() ? seriesNumberOrNull.hashCode() : 0);
+ result = prime * result + (isTimePointPresent() ? tOrNull.hashCode() : 0);
+ result = prime * result + (isDepthPresent() ? zOrNull.hashCode() : 0);
return result;
}
@@ -298,30 +382,48 @@ class LogicalImageSeriesGrid
public boolean equals(Object obj)
{
if (this == obj)
+ {
return true;
+ }
if (obj == null)
+ {
return false;
+ }
if (getClass() != obj.getClass())
+ {
return false;
+ }
ImageSeriesPoint other = (ImageSeriesPoint) obj;
- if (seriesNumberOrNull == null)
+ if (isSeriesNumberPresent() == false)
{
- if (other.seriesNumberOrNull != null)
+ if (other.isSeriesNumberPresent())
+ {
return false;
- } else if (!seriesNumberOrNull.equals(other.seriesNumberOrNull))
+ }
+ } else if (seriesNumberOrNull.equals(other.seriesNumberOrNull) == false)
+ {
return false;
- if (tOrNull == null)
+ }
+ if (isTimePointPresent() == false)
{
- if (other.tOrNull != null)
+ if (other.isTimePointPresent())
+ {
return false;
- } else if (!tOrNull.equals(other.tOrNull))
+ }
+ } else if (tOrNull.equals(other.tOrNull) == false)
+ {
return false;
- if (zOrNull == null)
+ }
+ if (isDepthPresent() == false)
{
- if (other.zOrNull != null)
+ if (other.isDepthPresent())
+ {
return false;
- } else if (!zOrNull.equals(other.zOrNull))
+ }
+ } else if (zOrNull.equals(other.zOrNull) == false)
+ {
return false;
+ }
return true;
}
}
@@ -329,41 +431,101 @@ class LogicalImageSeriesGrid
// private
static class LogicalImageSeriesViewerModel
{
+ private final Map<ImageSeriesPoint, List<ImageChannelStack>> channelStackImagesBySeries;
+
private final List<ImageSeriesPoint> sortedPoints;
+
+ private final int numberOfTimepoints;
+
+ private final int numberOfDepthLevels;
+
+ private final boolean matrixViewPossible;
- private final List<List<ImageChannelStack>> sortedChannelStackSeriesPoints;
+ private List<List<ImageSeriesPoint>> matrix;
public LogicalImageSeriesViewerModel(List<ImageChannelStack> channelStackImages)
{
- Map<ImageSeriesPoint, List<ImageChannelStack>> channelStackImagesBySeries =
- groupImagesBySeries(channelStackImages);
- this.sortedPoints = sortPoints(channelStackImagesBySeries.keySet());
- this.sortedChannelStackSeriesPoints =
- getSortedSeries(channelStackImagesBySeries, sortedPoints);
- }
-
- private static Map<ImageSeriesPoint, List<ImageChannelStack>> groupImagesBySeries(
- List<ImageChannelStack> channelStackImages)
- {
- Map<ImageSeriesPoint, List<ImageChannelStack>> result =
- new TreeMap<ImageSeriesPoint, List<ImageChannelStack>>();
+ channelStackImagesBySeries = new TreeMap<ImageSeriesPoint, List<ImageChannelStack>>();
+ TreeMap<Float/* TimePoint */, Map<Float/* Depth */, ImageSeriesPoint>> timePointDepthMatrix =
+ new TreeMap<Float/* TimePoint */, Map<Float/* Depth */, ImageSeriesPoint>>();
+ boolean seriesNumberPresent = false;
+ boolean timepointOrDepthNotPresent = false;
for (ImageChannelStack ref : channelStackImages)
{
ImageSeriesPoint point = new ImageSeriesPoint(ref);
- List<ImageChannelStack> imageReferences = result.get(point);
+ List<ImageChannelStack> imageReferences = channelStackImagesBySeries.get(point);
if (imageReferences == null)
{
imageReferences = new ArrayList<ImageChannelStack>();
- result.put(point, imageReferences);
+ channelStackImagesBySeries.put(point, imageReferences);
}
imageReferences.add(ref);
+ Integer seriesNumberOrNull = ref.tryGetSeriesNumber();
+ if (seriesNumberOrNull != null)
+ {
+ seriesNumberPresent = true;
+ }
+ Float timepoint = ref.tryGetTimepoint();
+ Float depth = ref.tryGetDepth();
+ if (timepoint == null || depth == null)
+ {
+ timepointOrDepthNotPresent = true;
+ } else
+ {
+ Map<Float, ImageSeriesPoint> depthMap = timePointDepthMatrix.get(timepoint);
+ if (depthMap == null)
+ {
+ depthMap = new TreeMap<Float, LogicalImageSeriesGrid.ImageSeriesPoint>();
+ timePointDepthMatrix.put(timepoint, depthMap);
+ }
+ depthMap.put(depth, point);
+ }
}
- return result;
+ sortedPoints = new ArrayList<ImageSeriesPoint>(channelStackImagesBySeries.keySet());
+ Collections.sort(sortedPoints);
+ numberOfTimepoints = timePointDepthMatrix.size();
+ Collection<Map<Float, ImageSeriesPoint>> values = timePointDepthMatrix.values();
+ matrix = new ArrayList<List<ImageSeriesPoint>>();
+
+ Set<Integer> depthMapSizes = new HashSet<Integer>();
+ for (Map<Float, ImageSeriesPoint> depthMap : values)
+ {
+ matrix.add(new ArrayList<ImageSeriesPoint>(depthMap.values()));
+ depthMapSizes.add(depthMap.size());
+ }
+ int depthMapSizesSize = depthMapSizes.size();
+ numberOfDepthLevels = depthMapSizesSize == 0 ? 0 : depthMapSizes.iterator().next();
+ matrixViewPossible =
+ seriesNumberPresent == false && timepointOrDepthNotPresent == false
+ && depthMapSizesSize == 1;
+ }
+
+ public ImageSeriesPoint get(int timeIndex, int depthIndex)
+ {
+ return matrix.get(timeIndex).get(depthIndex);
+ }
+
+ public final int getNumberOfTimepoints()
+ {
+ return numberOfTimepoints;
+ }
+
+ public final int getNumberOfDepthLevels()
+ {
+ return numberOfDepthLevels;
+ }
+
+ public final boolean isMatrixViewPossible()
+ {
+ return matrixViewPossible;
+ }
+
+ public List<ImageSeriesPoint> getSortedPoints()
+ {
+ return sortedPoints;
}
- private static List<List<ImageChannelStack>> getSortedSeries(
- Map<ImageSeriesPoint, List<ImageChannelStack>> channelStackImagesBySeries,
- List<ImageSeriesPoint> sortedPoints)
+ public List<List<ImageChannelStack>> getSortedChannelStackSeriesPoints()
{
List<List<ImageChannelStack>> sortedSeries = new ArrayList<List<ImageChannelStack>>();
for (ImageSeriesPoint point : sortedPoints)
@@ -373,15 +535,35 @@ class LogicalImageSeriesGrid
}
return sortedSeries;
}
+ }
- public List<ImageSeriesPoint> getSortedPoints()
+ private abstract static class AbstractSliderListener implements Listener<SliderEvent>
+ {
+ private boolean isFirstMove = true;
+
+ private final LayoutContainer mainContainer;
+
+ private final List<LayoutContainer> frames;
+
+ AbstractSliderListener(LayoutContainer mainContainer, List<LayoutContainer> frames)
{
- return sortedPoints;
+ this.mainContainer = mainContainer;
+ this.frames = frames;
}
- public List<List<ImageChannelStack>> getSortedChannelStackSeriesPoints()
+ public void handleEvent(SliderEvent be)
{
- return sortedChannelStackSeriesPoints;
+ if (isFirstMove)
+ {
+ // The first slider move has been made, so we add all hidden frames to the
+ // DOM. The browser will start fetching images referenced in URLs in the
+ // background.
+ for (int i = 1; i < frames.size(); i++)
+ {
+ mainContainer.add(frames.get(i));
+ }
+ isFirstMove = false;
+ }
}
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewerModelTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewerModelTest.java
index 55249b6bebeea04a5e6d9732bba62c1bf4563c3f..ff04cc6b804b596a8fbe1e6031b4fe32bfabc3f3 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewerModelTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewerModelTest.java
@@ -45,6 +45,10 @@ public class LogicalImageSeriesViewerModelTest extends AssertJUnit
{ 1, 2, 3, null };
LogicalImageSeriesViewerModel model = createModel(times, depths, series);
+
+ assertEquals(false, model.isMatrixViewPossible());
+ assertEquals(3, model.getNumberOfDepthLevels());
+ assertEquals(3, model.getNumberOfTimepoints());
List<ImageSeriesPoint> sortedPoints = model.getSortedPoints();
ImageSeriesPoint firstPoint = new ImageSeriesPoint(null, null, null);
@@ -59,6 +63,83 @@ public class LogicalImageSeriesViewerModelTest extends AssertJUnit
List<ImageChannelStack> lastList = stackSeriesPoints.get(stackSeriesPoints.size() - 1);
assertEquals(lastPoint, new ImageSeriesPoint(lastList.get(0)));
}
+
+ @Test
+ public void testMatrixViewIsPossible()
+ {
+ Float times[] = new Float[]
+ { 1.5f, 3f, 4.5f };
+ Float depths[] = new Float[]
+ { 2.5f, 5f };
+ Integer series[] = new Integer[]
+ { null };
+
+ LogicalImageSeriesViewerModel model = createModel(times, depths, series);
+
+ assertEquals(true, model.isMatrixViewPossible());
+ assertEquals(3, model.getNumberOfTimepoints());
+ assertEquals(2, model.getNumberOfDepthLevels());
+ }
+
+ @Test
+ public void testMatrixViewIsNotPossibleBecauseOfSeriesNumbers()
+ {
+ Float times[] = new Float[]
+ { 1.5f, 3f, 4.5f };
+ Float depths[] = new Float[]
+ { 2.5f, 5f };
+ Integer series[] = new Integer[]
+ { 1 };
+
+ LogicalImageSeriesViewerModel model = createModel(times, depths, series);
+
+ assertEquals(false, model.isMatrixViewPossible());
+ assertEquals(3, model.getNumberOfTimepoints());
+ assertEquals(2, model.getNumberOfDepthLevels());
+ }
+
+ @Test
+ public void testMatrixViewIsNotPossibleBecauseOfMissingTimePoint()
+ {
+ List<ImageChannelStack> stacks = new ArrayList<ImageChannelStack>();
+ stacks.add(stack(1, 1, null, 2.5f, null));
+ stacks.add(stack(1, 1, 1f, 2.5f, null));
+
+ LogicalImageSeriesViewerModel model = new LogicalImageSeriesViewerModel(stacks);
+
+ assertEquals(false, model.isMatrixViewPossible());
+ assertEquals(1, model.getNumberOfTimepoints());
+ assertEquals(1, model.getNumberOfDepthLevels());
+ }
+
+ @Test
+ public void testMatrixViewIsNotPossibleBecauseOfMissingDepth()
+ {
+ List<ImageChannelStack> stacks = new ArrayList<ImageChannelStack>();
+ stacks.add(stack(1, 1, 1f, null, null));
+ stacks.add(stack(1, 1, 1f, 2.5f, null));
+
+ LogicalImageSeriesViewerModel model = new LogicalImageSeriesViewerModel(stacks);
+
+ assertEquals(false, model.isMatrixViewPossible());
+ assertEquals(1, model.getNumberOfTimepoints());
+ assertEquals(1, model.getNumberOfDepthLevels());
+ }
+
+ @Test
+ public void testMatrixViewIsNotPossibleBecauseOfSparseMatrix()
+ {
+ List<ImageChannelStack> stacks = new ArrayList<ImageChannelStack>();
+ stacks.add(stack(1, 1, 1f, 1f, null));
+ stacks.add(stack(1, 1, 1f, 2f, null));
+ stacks.add(stack(1, 1, 2f, 2f, null));
+
+ LogicalImageSeriesViewerModel model = new LogicalImageSeriesViewerModel(stacks);
+
+ assertEquals(false, model.isMatrixViewPossible());
+ assertEquals(2, model.getNumberOfTimepoints());
+ assertEquals(2, model.getNumberOfDepthLevels());
+ }
private LogicalImageSeriesViewerModel createModel(Float[] times, Float[] depths,
Integer[] series)
@@ -70,15 +151,15 @@ public class LogicalImageSeriesViewerModelTest extends AssertJUnit
{
for (int seriesNum = 0; seriesNum < series.length; seriesNum++)
{
- stacks.add(mkStack(1, 1, times[time], depths[depth], series[seriesNum]));
- stacks.add(mkStack(2, 2, times[time], depths[depth], series[seriesNum]));
+ stacks.add(stack(1, 1, times[time], depths[depth], series[seriesNum]));
+ stacks.add(stack(2, 2, times[time], depths[depth], series[seriesNum]));
}
}
}
return new LogicalImageSeriesViewerModel(stacks);
}
- private static ImageChannelStack mkStack(int row, int col, Float tOrNull, Float zOrNull,
+ private static ImageChannelStack stack(int row, int col, Float tOrNull, Float zOrNull,
Integer seriesNumberOrNull)
{
return new ImageChannelStack(0, row, col, tOrNull, zOrNull, seriesNumberOrNull);