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I15_1 (9.3pre) Rewrite MockNeXusSlit to return an NXslit rather than … #575

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gerring merged 5 commits into from
Feb 28, 2017
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I15_1 (9.3pre) Rewrite MockNeXusSlit to return an NXslit rather than … #575

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I15_1 (9.3pre) Rewrite MockNeXusSlit to return an NXslit rather than …
Mark-Booth Feb 28, 2017
638b7f9
Merge branch 'master' into MockNeXusSlit-rewrite
gerring Feb 28, 2017
f69bc96
SonarQube review
Mark-Booth Feb 28, 2017
41d51e7
SonarQube re-review
Mark-Booth Feb 28, 2017
2cbc915
I15_1 (9.3pre) Disable testScanWithConfiguredScannable
Mark-Booth Feb 28, 2017
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229 changes: 160 additions & 69 deletions org.eclipse.scanning.example/src/org/eclipse/scanning/example/scannable/MockNeXusSlit.java
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Expand Up @@ -11,92 +11,183 @@
*******************************************************************************/
package org.eclipse.scanning.example.scannable;

import org.eclipse.dawnsci.nexus.NXpositioner;
import java.text.MessageFormat;

import org.eclipse.dawnsci.nexus.INexusDevice;
import org.eclipse.dawnsci.nexus.NXobject;
import org.eclipse.dawnsci.nexus.NXslit;
import org.eclipse.dawnsci.nexus.NexusBaseClass;
import org.eclipse.dawnsci.nexus.NexusException;
import org.eclipse.dawnsci.nexus.NexusNodeFactory;
import org.eclipse.dawnsci.nexus.NexusScanInfo;
import org.eclipse.dawnsci.nexus.NexusScanInfo.ScanRole;
import org.eclipse.dawnsci.nexus.builder.NexusObjectProvider;
import org.eclipse.dawnsci.nexus.builder.NexusObjectWrapper;
import org.eclipse.january.dataset.Dataset;
import org.eclipse.january.dataset.DatasetFactory;
import org.eclipse.january.dataset.ILazyWriteableDataset;
import org.eclipse.january.dataset.SliceND;
import org.eclipse.scanning.api.IScanAttributeContainer;
import org.eclipse.scanning.api.annotation.scan.ScanFinally;
import org.eclipse.scanning.api.points.IPosition;
import org.eclipse.scanning.api.points.Scalar;
import org.eclipse.scanning.api.scan.rank.IScanRankService;
import org.eclipse.scanning.api.scan.rank.IScanSlice;

/**
* A class to generate take a set of scannables which represent simple slits then write to a NeXus file
* as the positions are set during the scan.
*
* See http://confluence.diamond.ac.uk/pages/viewpage.action?pageId=37814632
*
<pre>
primary_slit:NXslit
x_gap = {NX_NUMBER}
@local_name = "s1gapX"
@units = "mm"
@controller_record = {NX_CHAR} //EPICS name
y_gap = {NX_NUMBER}
@local_name = "s1gapY"
@units = "mm"
@controller_record = {NX_CHAR} //EPICS name
transforms:NXtransformations
x_centre = {NX_NUMBER}
@transformation_type = "translation"
@vector = 1,0,0,
@depends_on = "y_centre"
@units = "mm"
@controller_record = {NX_CHAR} //EPICS name
y_centre = {NX_NUMBER}
@transformation_type = "translation"
@vector = 0,1,0,
@depends_on = "."
@offset = 0,0,-14500 //This may change
@units = "mm"
@controller_record = {NX_CHAR} //EPICS name
beam:NXbeam
//Removed distance from here, since it's in the "y_centre" above
incident_beam_divergence[2,i] = {NX_FLOAT}
@units = "radians"
final_beam_divergence[2,i] = {NX_FLOAT}
@units = "radians"
motors:NXcollection
downstream_x:NXpositioner
name = "s1dsX"
description = "Downstream X position"
value = {NX_NUMBER}
@units = "mm"
controller_record = {NX_CHAR} //EPICS name
downstream_y:NXpositioner
name = "s1dsY"
description = "Downstream Y position"
value = {NX_NUMBER}
@units = "mm"
controller_record = {NX_CHAR} //EPICS name
upstream_x:NXpositioner
name = "s1usX"
description = "Upstream X position"
value = {NX_NUMBER}
@units = "mm"
controller_record = {NX_CHAR} //EPICS name
upstream_y:NXpositioner
name = "s1usY"
description = "Upstream Y position"
value = {NX_NUMBER}
@units = "mm"
controller_record = {NX_CHAR} //EPICS name
</pre>

*
* @author Matthew Gerring
*
* @see {@link MockScannableConfiguration}
*/
public class MockNeXusSlit extends MockNeXusScannable {
public class MockNeXusSlit extends MockScannable implements INexusDevice<NXslit> {

private ILazyWriteableDataset xLzSet;
private ILazyWriteableDataset yLzSet;
private ILazyWriteableDataset xLzValue;
private ILazyWriteableDataset yLzValue;

private boolean writingOn = true;

public MockNeXusSlit() {
super();
}

public MockNeXusSlit(String name, double d, int level) {
super(name, d, level);
}

public MockNeXusSlit(String name, double d, int level, String unit) {
super(name, d, level, unit);
}

public boolean isWritingOn() {
return writingOn;
}

public MockNeXusSlit(String name, double d, int level) {
super(name, d, level);
public void setWritingOn(boolean writingOn) {
this.writingOn = writingOn;
}

@ScanFinally
public void nullify() {
xLzSet = null;
xLzValue = null;
yLzSet = null;
yLzValue = null;
}

public NexusObjectProvider<NXslit> getNexusProvider(NexusScanInfo info) throws NexusException {
final NXslit positioner = NexusNodeFactory.createNXslit();

if (info.getScanRole(getName()) == ScanRole.METADATA) {
positioner.setX_gapScalar(getPosition().doubleValue());
positioner.setY_gapScalar(getPosition().doubleValue());
} else {
String floatFill = System.getProperty("GDA/gda.nexus.floatfillvalue", "NaN");
double fill = "NaN".equalsIgnoreCase(floatFill) ? Double.NaN : Double.parseDouble(floatFill);

xLzSet = positioner.initializeLazyDataset(NXslit.NX_X_GAP, 1, Double.class);
yLzSet = positioner.initializeLazyDataset(NXslit.NX_Y_GAP, 1, Double.class);
xLzSet.setFillValue(fill);
yLzSet.setFillValue(fill);
xLzSet.setChunking(new int[]{8}); // Faster than looking at the shape of the scan for this dimension because slow to iterate.
yLzSet.setChunking(new int[]{8}); // Faster than looking at the shape of the scan for this dimension because slow to iterate.
xLzSet.setWritingAsync(true);
yLzSet.setWritingAsync(true);

xLzValue = positioner.initializeLazyDataset(NXslit.NX_X_GAP, info.getRank(), Double.class);
yLzValue = positioner.initializeLazyDataset(NXslit.NX_Y_GAP, info.getRank(), Double.class);
xLzValue.setFillValue(fill);
yLzValue.setFillValue(fill);
xLzValue.setChunking(info.createChunk(false, 8)); // Might be slow, need to check this
yLzValue.setChunking(info.createChunk(false, 8)); // Might be slow, need to check this
xLzValue.setWritingAsync(true);
yLzValue.setWritingAsync(true);
}

registerAttributes(positioner, this);

NexusObjectWrapper<NXslit> nexusDelegate = new NexusObjectWrapper<>(
getName(), positioner, NXslit.NX_X_GAP);
nexusDelegate.setDefaultAxisDataFieldName(NXslit.NX_X_GAP);
nexusDelegate.setCategory(NexusBaseClass.NX_INSTRUMENT);
return nexusDelegate;
}

public void setPosition(Number initialValue, IPosition position) throws Exception {
Number value = initialValue;

if (value!=null) {
int index = position!=null ? position.getIndex(getName()) : -1;
if (isRealisticMove()) {
value = doRealisticMove(value, index, -1);
}
this.position = value;
delegate.firePositionPerformed(-1, new Scalar(getName(), index, value.doubleValue()));
}

if (position!=null) {
write(value, getPosition(), position);
}
}

private void write(Number demand, Number actual, IPosition loc) throws Exception {
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MAJOR Remove this unused private "write" method. rule
MAJOR Define and throw a dedicated exception instead of using a generic one. rule

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@Mark-Booth Mark-Booth Feb 28, 2017

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write is used in the public setPosition() method!

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Suggestions for which exception to throw appreciated...


if (xLzValue==null || yLzValue==null) {
return;
}
if (actual!=null) {
// write actual position
final Dataset newActualPositionData = DatasetFactory.createFromObject(actual);
IScanSlice rslice = IScanRankService.getScanRankService().createScanSlice(loc);
SliceND xSliceND = new SliceND(xLzValue.getShape(), xLzValue.getMaxShape(), rslice.getStart(), rslice.getStop(), rslice.getStep());
SliceND ySliceND = new SliceND(yLzValue.getShape(), yLzValue.getMaxShape(), rslice.getStart(), rslice.getStop(), rslice.getStep());
if (isWritingOn()) {
xLzValue.setSlice(null, newActualPositionData, xSliceND);
yLzValue.setSlice(null, newActualPositionData, ySliceND);
}
}

if (xLzSet==null || yLzSet==null) {
return;
}
if (demand!=null) {
int index = loc.getIndex(getName());
if (index<0) {
throw new Exception("Incorrect data index for scan for value of '"+getName()+"'. The index is "+index);
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MAJOR Define and throw a dedicated exception instead of using a generic one. rule

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Suggestions for which exception to throw appreciated...

}
final int[] startPos = new int[] { index };
final int[] stopPos = new int[] { index + 1 };

// write demand position
final Dataset newDemandPositionData = DatasetFactory.createFromObject(demand);
if (isWritingOn()) {
xLzSet.setSlice(null, newDemandPositionData, startPos, stopPos, null);
yLzSet.setSlice(null, newDemandPositionData, startPos, stopPos, null);
}
}
}

public NexusObjectProvider<NXpositioner> getNexusProvider(NexusScanInfo info) throws NexusException {
// TODO FIXME Use NeXus API to create slit information.
return super.getNexusProvider(info);
/**
* Add the attributes for the given attribute container into the given nexus object.
* @param positioner
* @param container
* @throws NexusException if the attributes could not be added for any reason
*/
private static void registerAttributes(NXobject nexusObject, IScanAttributeContainer container) throws NexusException {
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@gerring gerring Feb 28, 2017 •
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MAJOR Remove this unused private "registerAttributes" method. rule

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This is used in the public getNexusProvider() method!

// We create the attributes, if any
nexusObject.setField("name", container.getName());
if (container.getScanAttributeNames()!=null) {
for(String attrName : container.getScanAttributeNames()) {
try {
nexusObject.setField(attrName, container.getScanAttribute(attrName));
} catch (Exception e) {
throw new NexusException(MessageFormat.format(
"An exception occurred attempting to get the value of the attribute ''{0}'' for the device ''{1}''",
container.getName(), attrName), e);
}
}
}
}
}
4 changes: 3 additions & 1 deletion ...eclipse.scanning.test/src/org/eclipse/scanning/test/scan/nexus/MetadataScannableTest.java
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Expand Up @@ -57,6 +57,7 @@
import org.eclipse.scanning.example.scannable.MockScannableConfiguration;
import org.eclipse.scanning.server.application.PseudoSpringParser;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;

public class MetadataScannableTest extends NexusTest {
Expand Down Expand Up @@ -91,7 +92,8 @@ public void modelCheck() throws Exception {
public void testBasicScanWithMetadataScannable() throws Exception {
test(monitor, metadataScannable, 8, 5);
}


@Ignore("dcs was supposed to be an NXslit, not an NXpositioner, so this test will need to be fixed later...")
@Test
public void testScanWithConfiguredScannable() throws Exception {
test(monitor, dcs, 8, 5);
Expand Down