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Refactored visualizer to support vdescriptor

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This commit is contained in:
ebner
2014-04-16 08:34:24 +02:00
parent 21f86d7d69
commit 576d7eb048
6 changed files with 128 additions and 324 deletions
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2
ch.psi.fda/pom.xml
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@@ -10,7 +10,7 @@
<dependency>
<groupId>ch.psi</groupId>
<artifactId>ch.psi.fda.core</artifactId>
<version>0.0.1-SNAPSHOT</version>
<version>0.0.2</version>
</dependency>
<dependency>

30
ch.psi.fda/src/main/java/ch/psi/fda/AcquisitionMain.java
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@@ -56,13 +56,11 @@ import com.google.inject.Injector;
import sun.misc.Signal;
import sun.misc.SignalHandler;
import ch.psi.fda.aq.VisualizationMapper;
import ch.psi.fda.aq.XScanDescriptor;
import ch.psi.fda.edescriptor.EDescriptor;
import ch.psi.fda.gui.ProgressPanel;
import ch.psi.fda.gui.ScrollableFlowPanel;
import ch.psi.fda.install.ApplicationConfigurator;
import ch.psi.fda.model.v1.Configuration;
import ch.psi.fda.vdescriptor.VDescriptor;
import ch.psi.fda.visualizer.Visualizer;
import ch.psi.jcae.ChannelService;
import ch.psi.jcae.impl.DefaultChannelService;
@@ -189,15 +187,17 @@ public class AcquisitionMain {
EDescriptor edescriptor = null;
VDescriptor vdescriptor = null;
ServiceLoader<DescriptorProvider> providers = ServiceLoader.load(DescriptorProvider.class);
for (DescriptorProvider provider : providers) {
try{
provider.load(file);
edescriptor = provider.getEDescriptor();
vdescriptor = provider.getVDescriptor();
break;
}
catch(Exception e){
logger.log(Level.FINEST, provider.getClass().getName()+ " is not able to read provided descriptor files", e);
logger.log(Level.INFO, provider.getClass().getName()+ " is not able to read provided descriptor files", e);
}
}
@@ -218,25 +218,11 @@ public class AcquisitionMain {
Visualizer visualizer = null;
if(edescriptor instanceof XScanDescriptor){
XScanDescriptor d = (XScanDescriptor) edescriptor;
Configuration c = d.getConfiguration();
// Only register data visualization task/processor if there are visualizations
if(c.getVisualization().size()>0 && !nogui){
visualizer = new Visualizer(VisualizationMapper.mapVisualizations(c.getVisualization()));
b.register(visualizer);
// TODO eventually set update on delimiter/dim boundary here
// If there is a continous dimension only update plot at the end of a line
if(c.getScan() != null && c.getScan().getCdimension()!=null){
visualizer.setUpdateAtStreamElement(false);
visualizer.setUpdateAtStreamDelimiter(true);
visualizer.setUpdateAtEndOfStream(true);
}
}
// Only register data visualization task/processor if there are visualizations
if(vdescriptor.getPlots().size()>0 && !nogui){
visualizer = new Visualizer(vdescriptor);
b.register(visualizer);
}

273
ch.psi.fda/src/main/java/ch/psi/fda/aq/VisualizationMapper.java
View File

@@ -1,273 +0,0 @@
/**
*
* Copyright 2013 Paul Scherrer Institute. All rights reserved.
*
* This code is free software: you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* This code is distributed in the hope that it will be useful, but without any
* warranty; without even the implied warranty of merchantability or fitness for
* a particular purpose. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this code. If not, see <http://www.gnu.org/licenses/>.
*
*/
package ch.psi.fda.aq;
import java.util.ArrayList;
import java.util.List;
import ch.psi.fda.model.v1.ArrayDetector;
import ch.psi.fda.model.v1.ContinuousPositioner;
import ch.psi.fda.model.v1.Detector;
import ch.psi.fda.model.v1.LinearPositioner;
import ch.psi.fda.model.v1.Positioner;
import ch.psi.fda.model.v1.PseudoPositioner;
import ch.psi.fda.model.v1.Visualization;
import ch.psi.fda.visualizer.SeriesDataFilter;
import ch.psi.fda.visualizer.XYSeriesArrayDataFilter;
import ch.psi.fda.visualizer.XYSeriesDataFilter;
import ch.psi.fda.visualizer.XYZSeriesArrayDataFilter;
import ch.psi.fda.visualizer.XYZSeriesDataFilter;
import ch.psi.plot.xyz.MatrixPlot;
import ch.psi.plot.xyz.MatrixPlotData;
public class VisualizationMapper {
/**
* Retrieve id string of the passed object
* @param object
* @return Id string of object
*/
private static String getId(Object object){
String id;
if(object instanceof Positioner){
id = ((Positioner)object).getId();
}
else if (object instanceof Detector){
id = ((Detector)object).getId();
}
else if (object instanceof ch.psi.fda.model.v1.Manipulation){
id = ((ch.psi.fda.model.v1.Manipulation)object).getId();
}
// For testing purposes
else if(object instanceof String){
id = (String) object;
}
else{
throw new RuntimeException("Unable to identify id of object reference "+object);
}
return id;
}
/**
* Converts a list of visualizations into a list of data filters which can be applied to the data stream
*
* @param vl
* @return
*/
public static List<SeriesDataFilter> mapVisualizations(List<Visualization> vl){
List<SeriesDataFilter> filters = new ArrayList<SeriesDataFilter>();
for(Visualization v: vl){
if(v instanceof ch.psi.fda.model.v1.LinePlot){
ch.psi.fda.model.v1.LinePlot lp = (ch.psi.fda.model.v1.LinePlot) v;
// Create plot for visualization
ch.psi.plot.xy.LinePlot plot = new ch.psi.plot.xy.LinePlot(lp.getTitle());
// Create data filter for visualization
String idX = getId(lp.getX());
List<Object> l = lp.getY();
for(Object o: l){
String idY = getId(o);
XYSeriesDataFilter filter = new XYSeriesDataFilter(idX, idY, plot);
filter.setSeriesName(idY);
filters.add(filter);
}
}
else if(v instanceof ch.psi.fda.model.v1.LinePlotArray){
// Array visualization
ch.psi.fda.model.v1.LinePlotArray lp = (ch.psi.fda.model.v1.LinePlotArray) v;
// Create plot for visualization
ch.psi.plot.xy.LinePlot plot = new ch.psi.plot.xy.LinePlot(lp.getTitle());
// Create data filter for visualization
List<Object> l = lp.getY();
for(Object o: l){
String idY = getId(o);
XYSeriesArrayDataFilter filter = new XYSeriesArrayDataFilter(idY, plot);
filter.setMaxSeries(lp.getMaxSeries()*lp.getY().size()); // Workaround - keep for each array max series
filter.setOffset(lp.getOffset());
filter.setSize(lp.getSize());
filter.setSeriesName(idY);
filters.add(filter);
}
}
else if(v instanceof ch.psi.fda.model.v1.MatrixPlot){
// MatrixPlot does currently not support RegionPositioners because of the
// plotting problems this would cause. If regions of the positioner have different
// step sizes it is not easily possible (without (specialized) rasterization) to plot the data.
ch.psi.fda.model.v1.MatrixPlot mp = (ch.psi.fda.model.v1.MatrixPlot) v;
double minX, maxX;
int nX;
double minY, maxY;
int nY;
String idX, idY, idZ;
// X Axis
if(mp.getX() instanceof LinearPositioner){
LinearPositioner linp = ((LinearPositioner)mp.getX());
idX = linp.getId();
minX = (Math.min(linp.getStart(), linp.getEnd()));
maxX = (Math.max(linp.getStart(), linp.getEnd()));
nX = ((int) Math.floor((Math.abs(maxX-minX))/linp.getStepSize()) + 1);
}
else if(mp.getX() instanceof PseudoPositioner){
PseudoPositioner pp = ((PseudoPositioner)mp.getX());
idX = pp.getId();
minX = (1); // Count starts at 1
maxX = (pp.getCounts());
nX = (pp.getCounts());
}
else if(mp.getX() instanceof ContinuousPositioner){
ContinuousPositioner conp = ((ContinuousPositioner)mp.getX());
idX = conp.getId();
minX = (Math.min(conp.getStart(), conp.getEnd()));
maxX = (Math.max(conp.getStart(), conp.getEnd()));
nX = ((int) Math.floor((Math.abs(maxX-minX))/conp.getStepSize()) + 1);
}
else{
// Fail as we cannot determine the min, max and number of steps
throw new RuntimeException(mp.getX().getClass().getName()+" is not supported as x-axis of a MatrixPlot");
}
// Y Axis
if(mp.getY() instanceof LinearPositioner){
LinearPositioner linp = ((LinearPositioner)mp.getY());
idY = linp.getId();
minY = (Math.min(linp.getStart(), linp.getEnd()));
maxY = (Math.max(linp.getStart(), linp.getEnd()));
nY = ((int) Math.floor((Math.abs(maxY-minY))/linp.getStepSize()) + 1);
}
else if(mp.getY() instanceof PseudoPositioner){
PseudoPositioner pp = ((PseudoPositioner)mp.getY());
idY = pp.getId();
minY = (1); // Count starts at 1
maxY = (pp.getCounts());
nY = (pp.getCounts());
}
else{
// Fail as we cannot determine the min, max and number of steps
throw new RuntimeException(mp.getY().getClass().getName()+" is not supported as y-axis of a MatrixPlot");
}
// Z Dimension
idZ = getId(mp.getZ());
// Create plot for visualization
MatrixPlotData data = new MatrixPlotData(minX, maxX, nX, minY, maxY, nY);
MatrixPlot plot = new MatrixPlot(mp.getTitle(), data);
XYZSeriesDataFilter filter = new XYZSeriesDataFilter(idX, idY, idZ, plot);
filters.add(filter);
}
else if(v instanceof ch.psi.fda.model.v1.MatrixPlotArray){
// Support for 2D waveform plots
ch.psi.fda.model.v1.MatrixPlotArray mp = (ch.psi.fda.model.v1.MatrixPlotArray) v;
// Get size of the array detector
int arraySize = 0;
Object o = mp.getZ();
if(o instanceof ArrayDetector){
ArrayDetector ad = (ArrayDetector) o;
arraySize = ad.getArraySize();
}
else{
// Workaround
arraySize = mp.getSize(); // of array is from a manipulation the size is not known. Then the size will indicate the size of the array to display
}
int offset = mp.getOffset();
// Determine size for array
int size = mp.getSize();
if(size>0 && offset+size<arraySize){
size = mp.getSize();
}
else{
size=arraySize-offset;
}
double minY, maxY;
int nY;
double minX = offset;
double maxX = offset+size-1;
int nX = size;
String idY, idZ;
// Y Axis
if(mp.getY() instanceof LinearPositioner){
LinearPositioner linp = ((LinearPositioner)mp.getY());
idY = linp.getId();
minY = (Math.min(linp.getStart(), linp.getEnd()));
maxY = (Math.max(linp.getStart(), linp.getEnd()));
nY = ((int) Math.floor((Math.abs(maxY-minY))/linp.getStepSize()) + 1);
}
else if(mp.getY() instanceof PseudoPositioner){
PseudoPositioner pp = ((PseudoPositioner)mp.getY());
idY = pp.getId();
minY = (1); // Count starts at 1
maxY = (pp.getCounts());
nY = (pp.getCounts());
}
else if(mp.getY() instanceof ContinuousPositioner){
ContinuousPositioner conp = ((ContinuousPositioner)mp.getY());
idY = conp.getId();
minY = (Math.min(conp.getStart(), conp.getEnd()));
maxY = (Math.max(conp.getStart(), conp.getEnd()));
nY = ((int) Math.floor((Math.abs(maxY-minY))/conp.getStepSize()) + 1);
}
else{
// Fail as we cannot determine the min, max and number of steps
throw new RuntimeException(mp.getY().getClass().getName()+" is not supported as x-axis of a MatrixPlot");
}
// Z Dimension
idZ = getId(mp.getZ());
// Create plot for visualization
MatrixPlotData data = new MatrixPlotData(minX, maxX, nX, minY, maxY, nY);
MatrixPlot plot = new MatrixPlot(mp.getTitle(), data);
XYZSeriesArrayDataFilter filter = new XYZSeriesArrayDataFilter(idY, idZ, offset, size, plot);
filters.add(filter);
}
else{
// Visualization type (currently) not supported
throw new RuntimeException(v.getClass().getName()+" is not supported as visualization type");
}
}
return filters;
}
}

16
ch.psi.fda/src/main/java/ch/psi/fda/aq/XScanDescriptorProvider.java
View File

@@ -33,7 +33,6 @@ public class XScanDescriptorProvider implements DescriptorProvider {
@Override
public void load(File... files) {
if(files.length<1 || files[0]==null){
throw new IllegalArgumentException("There need to be at lease one file specified");
}
@@ -78,11 +77,16 @@ public class XScanDescriptorProvider implements DescriptorProvider {
c.setNumberOfExecution(1);
}
edescriptor = new XScanDescriptor(c);
vdescriptor = mapVisualizations(c.getVisualization());
this.edescriptor = new XScanDescriptor(c);
this.vdescriptor = mapVisualizations(c.getVisualization());
}
/**
* Create a vdescriptor out of the scan description
* @param vl
* @return
*/
private VDescriptor mapVisualizations(List<Visualization> vl){
VDescriptor vd = new VDescriptor();
@@ -113,8 +117,8 @@ public class XScanDescriptorProvider implements DescriptorProvider {
String idY = getId(o);
// TODO Need to actually check if minX of
lineplot.setMinX(lp.getOffset());
lineplot.setMaxX(lp.getOffset()+lp.getSize());
lineplot.setMinX(new Double(lp.getOffset()));
lineplot.setMaxX(new Double(lp.getOffset()+lp.getSize()));
lineplot.getData().add(new YSeries(idY));
}
}
@@ -320,7 +324,7 @@ public class XScanDescriptorProvider implements DescriptorProvider {
@Override
public VDescriptor getVDescriptor() {
return null;
return vdescriptor;
}
}

70
ch.psi.fda/src/main/java/ch/psi/fda/visualizer/Visualizer.java
View File

@@ -32,6 +32,12 @@ import com.google.common.eventbus.Subscribe;
import ch.psi.fda.messages.DataMessage;
import ch.psi.fda.messages.EndOfStreamMessage;
import ch.psi.fda.messages.StreamDelimiterMessage;
import ch.psi.fda.vdescriptor.Series;
import ch.psi.fda.vdescriptor.VDescriptor;
import ch.psi.fda.vdescriptor.XYSeries;
import ch.psi.fda.vdescriptor.XYZSeries;
import ch.psi.fda.vdescriptor.YSeries;
import ch.psi.fda.vdescriptor.YZSeries;
import ch.psi.plot.Plot;
import ch.psi.plot.xy.LinePlot;
import ch.psi.plot.xy.XYSeriesCollectionP;
@@ -56,8 +62,61 @@ public class Visualizer {
private boolean first = true;
public Visualizer(List<SeriesDataFilter> filters){
this.filters = filters;
public Visualizer(VDescriptor vdescriptor){
filters = new ArrayList<SeriesDataFilter>();
for(ch.psi.fda.vdescriptor.Plot vplot: vdescriptor.getPlots()){
if(vplot instanceof ch.psi.fda.vdescriptor.LinePlot){
ch.psi.fda.vdescriptor.LinePlot lp = (ch.psi.fda.vdescriptor.LinePlot) vplot;
// Create plot for visualization
ch.psi.plot.xy.LinePlot plot = new ch.psi.plot.xy.LinePlot(lp.getTitle());
for(Series s: lp.getData()){
if(s instanceof XYSeries){
XYSeries sxy = (XYSeries)s;
XYSeriesDataFilter filter = new XYSeriesDataFilter(sxy.getX(), sxy.getY(), plot);
filter.setSeriesName(sxy.getY());
filters.add(filter);
}
else if(s instanceof YSeries){
YSeries sy = (YSeries)s;
XYSeriesArrayDataFilter filter = new XYSeriesArrayDataFilter(sy.getY(), plot);
// filter.setMaxSeries(lp.getMaxSeries()*lp.getY().size()); // Workaround - keep for each array max series
// filter.setOffset(lp.getOffset());
// filter.setSize(lp.getSize());
filter.setSeriesName(sy.getY());
filters.add(filter);
}
}
}
else if(vplot instanceof ch.psi.fda.vdescriptor.MatrixPlot){
// MatrixPlot does currently not support RegionPositioners because of the
// plotting problems this would cause. If regions of the positioner have different
// step sizes it is not easily possible (without (specialized) rasterization) to plot the data.
ch.psi.fda.vdescriptor.MatrixPlot lp = (ch.psi.fda.vdescriptor.MatrixPlot) vplot;
MatrixPlotData data = new MatrixPlotData(lp.getMinX(), lp.getMaxX(), lp.getnX(), lp.getMinY(), lp.getMaxY(), lp.getnY());
MatrixPlot plot = new MatrixPlot(lp.getTitle(), data);
for(Series s: lp.getData()){
if(s instanceof XYZSeries){
XYZSeries sxyz = (XYZSeries) s;
filters.add(new XYZSeriesDataFilter(sxyz.getX(), sxyz.getY(), sxyz.getZ(), plot));
}
else if(s instanceof YZSeries){
YZSeries syz = (YZSeries) s;
XYZSeriesArrayDataFilter filter = new XYZSeriesArrayDataFilter(syz.getY(), syz.getZ(), 0, 0, plot);
filters.add(filter);
}
}
}
}
}
@@ -164,9 +223,10 @@ public class Visualizer {
try{
double[] data = (double[]) message.getData(xyzfilter.getIdZ());
double y = (Double) message.getData(xyzfilter.getIdY());
int offset = xyzfilter.getOffset();
int size = xyzfilter.getSize();
for(int i=offset;i<offset+size; i++){
// int offset = xyzfilter.getOffset();
// int size = xyzfilter.getSize();
// for(int i=offset;i<offset+size; i++){
for(int i=0;i<data.length; i++){
((MatrixPlot)xyzfilter.getPlot()).getData().addData(i, y, data[i]);
}
// Update data if update by point is enabled

61
ch.psi.fda/src/test/java/ch/psi/fda/visualizer/DataVisualizerTest.java
View File

@@ -37,8 +37,10 @@ import ch.psi.fda.messages.DataMessage;
import ch.psi.fda.messages.EndOfStreamMessage;
import ch.psi.fda.messages.Metadata;
import ch.psi.fda.messages.StreamDelimiterMessage;
import ch.psi.plot.xy.LinePlot;
import ch.psi.plot.xyz.MatrixPlotData;
import ch.psi.fda.vdescriptor.VDescriptor;
import ch.psi.fda.vdescriptor.XYSeries;
import ch.psi.fda.vdescriptor.XYZSeries;
import ch.psi.fda.vdescriptor.YSeries;
/**
* All test cases in this test class are meant to be executed manually Remove @Ignore
@@ -66,12 +68,22 @@ public class DataVisualizerTest {
EventBus bus = new EventBus();
List<SeriesDataFilter> list = new ArrayList<>();
list.add(new XYSeriesDataFilter("id1", "id2", new LinePlot("One")));
list.add(new XYSeriesDataFilter("id1", "id3", new LinePlot("Two")));
// List<SeriesDataFilter> list = new ArrayList<>();
// list.add(new XYSeriesDataFilter(, new LinePlot("One")));
// list.add(new XYSeriesDataFilter("id1", "id3", new LinePlot("Two")));
VDescriptor vdescriptor = new VDescriptor();
ch.psi.fda.vdescriptor.LinePlot plot = new ch.psi.fda.vdescriptor.LinePlot("One");
plot.getData().add(new XYSeries("id1", "id2"));
vdescriptor.getPlots().add(plot);
plot = new ch.psi.fda.vdescriptor.LinePlot("Two");
plot.getData().add(new XYSeries("id1", "id3"));
vdescriptor.getPlots().add(plot);
// Create visualizer
Visualizer visualizer = new Visualizer(list);
Visualizer visualizer = new Visualizer(vdescriptor);
bus.register(visualizer);
JFrame f = new JFrame();
@@ -112,11 +124,14 @@ public class DataVisualizerTest {
EventBus bus = new EventBus();
List<SeriesDataFilter> list = new ArrayList<>();
list.add(new XYSeriesArrayDataFilter("id1", new LinePlot("One")));
VDescriptor vdescriptor = new VDescriptor();
ch.psi.fda.vdescriptor.LinePlot plot = new ch.psi.fda.vdescriptor.LinePlot("One");
plot.getData().add(new YSeries("id1"));
vdescriptor.getPlots().add(plot);
// Create visualizer
Visualizer visualizer = new Visualizer(list);
Visualizer visualizer = new Visualizer(vdescriptor);
bus.register(visualizer);
JFrame f = new JFrame();
@@ -154,8 +169,8 @@ public class DataVisualizerTest {
@Test
public void testRun2D() throws InterruptedException {
int nx = 1000;
int ny = 1000;
double nx = 1000;
double ny = 1000;
List<Metadata> metadata = new ArrayList<>();
metadata.add(new Metadata("id1"));
@@ -165,12 +180,24 @@ public class DataVisualizerTest {
// EventBus bus = new AsyncEventBus(Executors.newFixedThreadPool(1));
EventBus bus = new EventBus();
List<SeriesDataFilter> list = new ArrayList<>();
list.add(new XYSeriesDataFilter("id2", "id3", new LinePlot("Line")));
list.add(new XYZSeriesDataFilter("id1", "id2", "id3", new ch.psi.plot.xyz.MatrixPlot("Matrix", new MatrixPlotData(1, nx, nx, 1, ny, ny))));
VDescriptor vdescriptor = new VDescriptor();
ch.psi.fda.vdescriptor.LinePlot lplot = new ch.psi.fda.vdescriptor.LinePlot("One");
lplot.getData().add(new XYSeries("id2", "id3"));
vdescriptor.getPlots().add(lplot);
ch.psi.fda.vdescriptor.MatrixPlot mplot = new ch.psi.fda.vdescriptor.MatrixPlot("One");
mplot.setMinX(1.0);
mplot.setMaxX(nx);
mplot.setnX((int)nx);
mplot.setMinY(1.0);
mplot.setMaxY(ny);
mplot.setnY((int)ny);
mplot.getData().add(new XYZSeries("id1", "id2", "id3"));
vdescriptor.getPlots().add(mplot);
// Create visualizer
Visualizer visualizer = new Visualizer(list);
Visualizer visualizer = new Visualizer(vdescriptor);
bus.register(visualizer);
JFrame f = new JFrame();