From 34bdfc35c404eb7cc7121b74f85c580fac5598ea Mon Sep 17 00:00:00 2001
From: Daniel Gonzalez <dgonzale@pasteur.fr>
Date: Tue, 11 Aug 2020 16:16:41 +0200
Subject: [PATCH] Fix for sequence region batch: null pointer exception on
declare input
---
.../loop/SequenceRegionBatch.java | 46 +++++++++++--------
1 file changed, 28 insertions(+), 18 deletions(-)
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
index dd539a3..23bbe64 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
+++ b/src/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
@@ -4,6 +4,7 @@ import java.util.List;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROI;
import icy.sequence.Sequence;
import icy.sequence.SequenceUtil;
import plugins.adufour.blocks.lang.Batch;
@@ -25,35 +26,51 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
// important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
- protected final VarROIArray rois;
+ protected VarROIArray rois;
+ protected VarROIArray currentRoi;
public SequenceRegionBatch()
{
super();
+ }
- rois = new VarROIArray("ROI(s)");
+ @Override
+ public VarROIArray getBatchSource()
+ {
+ if (rois == null)
+ rois = new VarROIArray("ROI(s)");
+
+ return rois;
}
@Override
- public VarSequence getBatchSource()
+ public void declareInput(VarList inputMap)
{
- // initialize variable if needed
+ super.declareInput(inputMap);
if (inputSequence == null)
inputSequence = new VarSequence("Sequence", null);
- return inputSequence;
+ inputMap.add(inputSequence.getName(), inputSequence);
}
@Override
public VarSequence getBatchElement()
{
- // initialize element if needed
if (element == null)
element = new VarSequence("Channel Sequence", null);
return element;
}
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ super.declareOutput(outputMap);
+ if (currentRoi == null)
+ currentRoi = new VarROIArray("Current ROI");
+ outputMap.add(currentRoi.getName(), currentRoi);
+ }
+
@Override
public void initializeLoop()
{
@@ -70,8 +87,9 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
public void beforeIteration()
{
// set result in element
- element.setValue(SequenceUtil.getSubSequence(inputSequence.getValue(),
- rois.getValue()[getIterationCounter().getValue().intValue()]));
+ ROI roi = rois.getValue()[getIterationCounter().getValue().intValue()];
+ element.setValue(SequenceUtil.getSubSequence(inputSequence.getValue(), roi));
+ currentRoi.setValue(new ROI[] {roi});
}
@Override
@@ -80,20 +98,12 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
return getIterationCounter().getValue().intValue() >= rois.getValue().length;
}
- @Override
- public void declareInput(VarList inputMap)
- {
- super.declareInput(inputMap);
-
- inputMap.add("ROIs", rois);
- }
-
@Override
public void declareLoopVariables(List<Var<?>> loopVariables)
{
super.declareLoopVariables(loopVariables);
-
- loopVariables.add(rois);
+ loopVariables.add(inputSequence);
+ loopVariables.add(currentRoi);
}
@Override
--
GitLab