diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
index 7c71c49e460b92be682cbc3760b10e92fd58f6ee..aaa28abc6d7b1b214f29337da55a73329f49ba2c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
@@ -222,8 +222,6 @@ abstract class AbstractTabularDataGraph<T extends TabularDataGraphConfiguration>
chart.setBackgroundPaint(Color.WHITE);
XYPlot plot = (XYPlot) chart.getPlot();
- // setAxisLabelFontSize(plot.getDomainAxis());
- // setAxisLabelFontSize(plot.getRangeAxis());
plot.setBackgroundPaint(Color.WHITE);
plot.setDomainGridlinesVisible(false);
plot.setRangeGridlinesVisible(true);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/HeatmapDataset.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/HeatmapDataset.java
new file mode 100644
index 0000000000000000000000000000000000000000..52af2ea9b112f1f898c85f4d1c5b7a8847fbd925
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/HeatmapDataset.java
@@ -0,0 +1,154 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.server.graph;
+
+import java.util.List;
+
+import org.jfree.data.DomainOrder;
+import org.jfree.data.Range;
+import org.jfree.data.general.DatasetChangeListener;
+import org.jfree.data.general.DatasetGroup;
+import org.jfree.data.xy.DefaultXYZDataset;
+import org.jfree.data.xy.XYZDataset;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class HeatmapDataset implements XYZDataset
+{
+ DefaultXYZDataset wrappedDataset;
+
+ Range range;
+
+ List<String> yLabels;
+
+ public HeatmapDataset(DefaultXYZDataset dataset)
+ {
+ wrappedDataset = dataset;
+ }
+
+ /**
+ * The range of the z values
+ */
+ public Range getRange()
+ {
+ return range;
+ }
+
+ /**
+ * Set the range of the z-values
+ */
+ public void setRange(Range range)
+ {
+ this.range = range;
+ }
+
+ /**
+ * The labels for the y axis.
+ */
+ public List<String> yLabels()
+ {
+ return yLabels;
+ }
+
+ /**
+ * Set the labels for the y axis.
+ */
+ public void setYLabels(List<String> yLabels)
+ {
+ this.yLabels = yLabels;
+ }
+
+ // XYZDataset
+ public Number getZ(int series, int item)
+ {
+ return wrappedDataset.getZ(series, item);
+ }
+
+ public double getZValue(int series, int item)
+ {
+ return wrappedDataset.getZValue(series, item);
+ }
+
+ public DomainOrder getDomainOrder()
+ {
+ return wrappedDataset.getDomainOrder();
+ }
+
+ public int getItemCount(int series)
+ {
+ return wrappedDataset.getItemCount(series);
+ }
+
+ public Number getX(int series, int item)
+ {
+ return wrappedDataset.getX(series, item);
+ }
+
+ public double getXValue(int series, int item)
+ {
+ return wrappedDataset.getXValue(series, item);
+ }
+
+ public Number getY(int series, int item)
+ {
+ return wrappedDataset.getY(series, item);
+ }
+
+ public double getYValue(int series, int item)
+ {
+ return wrappedDataset.getYValue(series, item);
+ }
+
+ public int getSeriesCount()
+ {
+ return wrappedDataset.getSeriesCount();
+ }
+
+ // The JFreeChart interface does not use generics
+ @SuppressWarnings("unchecked")
+ public Comparable getSeriesKey(int series)
+ {
+ return wrappedDataset.getSeriesKey(series);
+ }
+
+ @SuppressWarnings("unchecked")
+ public int indexOf(Comparable seriesKey)
+ {
+ return wrappedDataset.indexOf(seriesKey);
+ }
+
+ public void addChangeListener(DatasetChangeListener arg0)
+ {
+ wrappedDataset.addChangeListener(arg0);
+ }
+
+ public DatasetGroup getGroup()
+ {
+ return wrappedDataset.getGroup();
+ }
+
+ public void removeChangeListener(DatasetChangeListener arg0)
+ {
+ wrappedDataset.removeChangeListener(arg0);
+ }
+
+ public void setGroup(DatasetGroup arg0)
+ {
+ wrappedDataset.setGroup(arg0);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
index 364e0f3185aed980b944ac6fe299e9a8451e15f9..a25ea9023ad3b8eb40935e62ad7ef5651d4b81ab 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
@@ -20,8 +20,6 @@ import java.awt.Color;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.JFreeChart;
@@ -29,10 +27,11 @@ import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.axis.NumberTickUnit;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
-import org.jfree.chart.renderer.GrayPaintScale;
+import org.jfree.chart.renderer.LookupPaintScale;
import org.jfree.chart.renderer.PaintScale;
import org.jfree.chart.renderer.xy.XYBlockRenderer;
import org.jfree.chart.title.PaintScaleLegend;
+import org.jfree.data.Range;
import org.jfree.data.general.Dataset;
import org.jfree.data.xy.DefaultXYZDataset;
import org.jfree.data.xy.XYZDataset;
@@ -40,6 +39,7 @@ import org.jfree.ui.RectangleAnchor;
import org.jfree.ui.RectangleEdge;
import org.jfree.ui.RectangleInsets;
+import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
/**
@@ -48,8 +48,6 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLine
public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeatmapConfiguration>
{
- private final Pattern xySplitterPattern;
-
/**
* @param configuration
*/
@@ -57,7 +55,6 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
DatasetFileLines fileLines, OutputStream out)
{
super(configuration, fileLines, out);
- xySplitterPattern = Pattern.compile("([A-Z])([0-9]*)");
}
@Override
@@ -77,8 +74,10 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
HeatmapData data = parseData(xColumn, yColumn, zColumn);
double[][] dataArray = convertHeatmapDataToArray(data);
- DefaultXYZDataset dataset = new DefaultXYZDataset();
- dataset.addSeries(getTitle(), dataArray);
+ DefaultXYZDataset simpleDataset = new DefaultXYZDataset();
+ simpleDataset.addSeries(getTitle(), dataArray);
+ HeatmapDataset dataset = new HeatmapDataset(simpleDataset);
+ dataset.setRange(new Range(data.minZ, data.maxZ));
return dataset;
}
@@ -88,7 +87,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
JFreeChart chart = createHeatmap(getTitle(), // title
configuration.getXAxisColumn(), // x-axis label
configuration.getYAxisColumn(), // y-axis label
- (XYZDataset) dataset, // data
+ (HeatmapDataset) dataset, // data
PlotOrientation.HORIZONTAL, // plot orientation
false, // create legend?
false, // generate tooltips?
@@ -99,7 +98,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
}
private static JFreeChart createHeatmap(String title, String xAxisLabel, String yAxisLabel,
- XYZDataset dataset, PlotOrientation orientation, boolean legend, boolean tooltips,
+ HeatmapDataset dataset, PlotOrientation orientation, boolean legend, boolean tooltips,
boolean urls)
{
if (orientation == null)
@@ -114,7 +113,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
XYBlockRenderer renderer = new XYBlockRenderer();
renderer.setBlockAnchor(RectangleAnchor.BOTTOM_LEFT);
- PaintScale paintScale = new GrayPaintScale();
+ PaintScale paintScale = getPaintScale(dataset);
renderer.setPaintScale(paintScale);
XYPlot plot = new XYPlot(dataset, xAxis, yAxis, null);
@@ -122,13 +121,14 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
plot.setForegroundAlpha(0.5f);
plot.setRenderer(renderer);
plot.setBackgroundPaint(Color.WHITE);
- plot.setRangeGridlinePaint(Color.LIGHT_GRAY);
+ plot.setRangeGridlinePaint(Color.BLACK);
plot.setAxisOffset(new RectangleInsets(5, 5, 5, 5));
JFreeChart chart = new JFreeChart(title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
ChartFactory.getChartTheme().apply(chart);
NumberAxis scaleAxis = new NumberAxis("Scale");
+ scaleAxis.setRange(dataset.getRange());
PaintScaleLegend psl = new PaintScaleLegend(paintScale, scaleAxis);
psl.setMargin(new RectangleInsets(5, 5, 5, 5));
psl.setPosition(RectangleEdge.RIGHT);
@@ -137,6 +137,54 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
return chart;
}
+ /**
+ * Create a LookupPaintScale based on the <a href="http://colorbrewer.org/">Color Brewer</a>
+ * RdBu color scheme.
+ */
+ private static PaintScale getPaintScale(HeatmapDataset dataset)
+ {
+ LookupPaintScale paintScale = new LookupPaintScale();
+ // Use the Color Brewer RdBu color scheme with 11 steps
+ Range range = dataset.getRange();
+ double binMin = range.getLowerBound();
+ double binStep = range.getLength() / 11;
+ // 0
+ paintScale.add(0, new Color(255, 255, 255));
+ // 1
+ paintScale.add(binMin, new Color(5, 48, 97));
+ // 2
+ binMin += binStep;
+ paintScale.add(binMin, new Color(33, 102, 172));
+ // 3
+ binMin += binStep;
+ paintScale.add(binMin, new Color(67, 147, 195));
+ // 4
+ binMin += binStep;
+ paintScale.add(binMin, new Color(146, 197, 222));
+ // 5
+ binMin += binStep;
+ paintScale.add(binMin, new Color(209, 229, 240));
+ // 6
+ binMin += binStep;
+ paintScale.add(binMin, new Color(247, 247, 247));
+ // 7
+ binMin += binStep;
+ paintScale.add(binMin, new Color(253, 219, 199));
+ // 8
+ binMin += binStep;
+ paintScale.add(binMin, new Color(244, 165, 130));
+ // 9
+ binMin += binStep;
+ paintScale.add(binMin, new Color(214, 96, 77));
+ // 10
+ binMin += binStep;
+ paintScale.add(binMin, new Color(178, 24, 43));
+ // 11
+ binMin += binStep;
+ paintScale.add(binMin, new Color(103, 0, 31));
+ return paintScale;
+ }
+
private HeatmapData parseData(int xColumn, int yColumn, int zColumn)
{
HeatmapData heatmapData = new HeatmapData();
@@ -144,6 +192,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
// Note what the max x and max y values are, so we can convert to an array
heatmapData.maxX = 0;
heatmapData.maxY = 0;
+ boolean areZBoundsInitialized = false;
List<String[]> lines = fileLines.getDataLines();
for (String[] line : lines)
{
@@ -154,9 +203,18 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
element.y = Integer.parseInt(line[yColumn]);
} else
{
- splitColumnIntoXandY(line[xColumn], element);
+ Location loc = Location.tryCreateLocationFromMatrixCoordinate(line[xColumn]);
+ // transpose the x and y here
+ element.x = loc.getY();
+ element.y = loc.getX();
}
element.z = Double.parseDouble(line[zColumn]);
+ if (false == areZBoundsInitialized)
+ {
+ heatmapData.minZ = element.z;
+ heatmapData.maxZ = element.z;
+ areZBoundsInitialized = true;
+ }
heatmapData.elements.add(element);
if (element.x > heatmapData.maxX)
@@ -167,24 +225,19 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
{
heatmapData.maxY = element.y;
}
+ if (element.z < heatmapData.minZ)
+ {
+ heatmapData.minZ = element.z;
+ }
+ if (element.z > heatmapData.maxZ)
+ {
+ heatmapData.maxZ = element.z;
+ }
}
return heatmapData;
}
- private void splitColumnIntoXandY(String string, HeatmapElement element)
- {
- Pattern p = xySplitterPattern;
- Matcher m = p.matcher(string);
- if (m.matches())
- {
- String wellX = m.group(1);
- // The x index is the index of the letter minus the index of 'A'
- element.x = (wellX.charAt(0) - 'A') + 1;
- element.y = Integer.parseInt(m.group(2));
- }
- }
-
private double[][] convertHeatmapDataToArray(HeatmapData data)
{
double[][] dataArray = new double[3][];
@@ -220,6 +273,10 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
private int maxY;
+ private double minZ = 0;
+
+ private double maxZ = 0;
+
private final ArrayList<HeatmapElement> elements = new ArrayList<HeatmapElement>();
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
index 32cfaf119d6b111c4ac1e8843035fc42e031b9e8..afeadce9c611932dd2cbad17244ebd1fc3b74200 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
@@ -21,6 +21,10 @@ import java.io.OutputStream;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.StandardXYBarPainter;
+import org.jfree.chart.renderer.xy.XYBarRenderer;
+import org.jfree.chart.renderer.xy.XYItemRenderer;
import org.jfree.data.general.Dataset;
import org.jfree.data.statistics.HistogramDataset;
@@ -80,6 +84,14 @@ public class TabularDataHistogram extends
false // generate URLs?
);
+ XYItemRenderer r = ((XYPlot) chart.getPlot()).getRenderer();
+ if (r instanceof XYBarRenderer)
+ {
+ XYBarRenderer renderer = (XYBarRenderer) r;
+ renderer.setShadowVisible(false);
+ renderer.setBarPainter(new StandardXYBarPainter());
+ }
+
return chart;
}
}