From a4a7954218e0af7b1a62b27eceaf3291d938ea75 Mon Sep 17 00:00:00 2001
From: Stephane Dallongeville <stephane.dallongeville@pasteur.fr>
Date: Fri, 25 Nov 2022 10:52:43 +0100
Subject: [PATCH] Updated to last kernel
---
pom.xml | 2 +-
.../sequenceblocks/convert/ConvertColor.java | 11 +++++--
.../sequenceblocks/convert/ConvertStack.java | 22 ++++++++-----
.../sequenceblocks/convert/ConvertType.java | 9 +++++-
.../creation/DuplicateSequence.java | 10 +++++-
.../sequenceblocks/extract/CropSequence.java | 11 +++++--
.../extract/ExtractChannel.java | 13 ++++++--
.../extract/ExtractMultiChannels.java | 14 +++++++--
.../PositionedSequenceFileImporter.java | 2 +-
.../loop/SequenceChannelBatch.java | 12 +++++--
.../loop/SequenceRegionBatch.java | 15 ++++++---
.../op/AdditiveFillSequence.java | 19 ++++++++----
.../sequenceblocks/op/FillInnerSequence.java | 17 +++++++---
.../sequenceblocks/op/FillOuterSequence.java | 31 ++++++++++++-------
.../sequenceblocks/remove/RemoveChannel.java | 9 +++++-
15 files changed, 145 insertions(+), 52 deletions(-)
diff --git a/pom.xml b/pom.xml
index d077427..d1ad26a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,7 +11,7 @@
</parent>
<artifactId>sequence-blocks</artifactId>
- <version>2.1.0</version>
+ <version>2.1.1</version>
<name>SequenceBlocks</name>
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
index 3347c03..1e4cf5b 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
@@ -44,7 +44,14 @@ public class ConvertColor extends Plugin implements SequenceBlock, PluginBundled
if (s == null)
throw new VarException(EZseq, "Input sequence is null.");
- varOut.setValue(convertColor(s, getImageType(EZtype.getValue()), EZlut.getValue()));
+ try
+ {
+ varOut.setValue(convertColor(s, getImageType(EZtype.getValue()), EZlut.getValue()));
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
@@ -83,7 +90,7 @@ public class ConvertColor extends Plugin implements SequenceBlock, PluginBundled
}
}
- public static Sequence convertColor(Sequence source, int imageType, LUT lut)
+ public static Sequence convertColor(Sequence source, int imageType, LUT lut) throws IllegalArgumentException, InterruptedException
{
final Sequence result = new Sequence(OMEUtil.createOMEXMLMetadata(source.getOMEXMLMetadata()));
// image receiver
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
index e7dbfdc..7eae544 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
@@ -5,6 +5,7 @@ import icy.plugin.interface_.PluginBundled;
import icy.sequence.Sequence;
import icy.sequence.SequenceUtil;
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
+import plugins.adufour.blocks.util.BlocksException;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarEnum;
import plugins.adufour.vars.lang.VarSequence;
@@ -32,13 +33,20 @@ public class ConvertStack extends Plugin implements SequenceBlock, PluginBundled
if (in == null)
throw new VarException(inputSequence, "Input sequence is null.");
- // create a copy as we don't want to modify input
- Sequence out = SequenceUtil.getCopy(in);
- if (type.getValue() == TypeConversion.TIME)
- SequenceUtil.convertToTime(out);
- else
- SequenceUtil.convertToStack(out);
- outputSequence.setValue(out);
+ try
+ {
+ // create a copy as we don't want to modify input
+ Sequence out = SequenceUtil.getCopy(in);
+ if (type.getValue() == TypeConversion.TIME)
+ SequenceUtil.convertToTime(out);
+ else
+ SequenceUtil.convertToStack(out);
+ outputSequence.setValue(out);
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
index 0ec910c..48a11a4 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
@@ -31,7 +31,14 @@ public class ConvertType extends Plugin implements SequenceBlock, PluginLibrary,
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- outputSequence.setValue(SequenceUtil.convertToType(s, type.getValue(), rescale.getValue().booleanValue()));
+ try
+ {
+ outputSequence.setValue(SequenceUtil.convertToType(s, type.getValue(), rescale.getValue().booleanValue()));
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
index 3379d9d..dec05da 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
@@ -25,7 +25,15 @@ public class DuplicateSequence extends Plugin implements SequenceBlock, PluginLi
Sequence s = in.getValue();
if (s == null)
throw new VarException(in, "Input Sequence is null.");
- out.setValue(SequenceUtil.getCopy(s));
+
+ try
+ {
+ out.setValue(SequenceUtil.getCopy(s));
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
index 8379e58..334444f 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
@@ -58,9 +58,16 @@ public class CropSequence extends Plugin implements SequenceBlock, PluginLibrary
else
rois = CollectionUtil.asList((ROI[]) obj);
- final ROI roi = ROIUtil.merge(rois, BooleanOperator.OR);
+ try
+ {
+ final ROI roi = ROIUtil.merge(rois, BooleanOperator.OR);
- outputSequence.setValue(SequenceUtil.getSubSequence(s, roi));
+ outputSequence.setValue(SequenceUtil.getSubSequence(s, roi));
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
index 4ed5c38..e977e82 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
@@ -32,10 +32,17 @@ public class ExtractChannel extends Plugin implements SequenceBlock, PluginLibra
if (channel < 0 || channel >= s.getSizeC())
throw new VarException(channelIdx, "Channel index must be between 0 and " + (s.getSizeC() - 1));
- final Sequence res = SequenceUtil.extractChannel(s, channelIdx.getValue().intValue());
- res.setName(s.getName() + " - channel: " + channelIdx.getValue());
+ try
+ {
+ final Sequence res = SequenceUtil.extractChannel(s, channelIdx.getValue().intValue());
+ res.setName(s.getName() + " - channel: " + channelIdx.getValue());
- outputSequence.setValue(res);
+ outputSequence.setValue(res);
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
index 56f892e..79d6aca 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
@@ -27,9 +27,17 @@ public class ExtractMultiChannels extends Plugin implements SequenceBlock, Plugi
Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- Sequence res = SequenceUtil.extractChannels(s, channelIdx.getValue());
- res.setName(s.getName() + " - channel: " + channelIdx.getValue());
- outputSequence.setValue(res);
+
+ try
+ {
+ Sequence res = SequenceUtil.extractChannels(s, channelIdx.getValue());
+ res.setName(s.getName() + " - channel: " + channelIdx.getValue());
+ outputSequence.setValue(res);
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
index 75a25a7..946af74 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
@@ -52,7 +52,7 @@ public class PositionedSequenceFileImporter
positionedImporter.z, positionedImporter.c, positionedImporter.xyRegion);
}
- public OMEXMLMetadata getMetadata() throws UnsupportedFormatException, IOException
+ public OMEXMLMetadata getMetadata() throws UnsupportedFormatException, IOException, InterruptedException
{
// not yet defined --> take it from importer if possible
if ((metadata == null) && (importer.getOpened() != null))
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
index 763ccaa..ed0dbe8 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
@@ -53,9 +53,15 @@ public class SequenceChannelBatch extends Batch implements SequenceBlock, Plugin
@Override
public void beforeIteration()
{
- // set result in element
- element.setValue(
- SequenceUtil.extractChannel(inputSequence.getValue(), getIterationCounter().getValue().intValue()));
+ try
+ {
+ // set result in element
+ element.setValue(SequenceUtil.extractChannel(inputSequence.getValue(), getIterationCounter().getValue().intValue()));
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
index 8da2ca7..99fc20a 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
@@ -23,7 +23,7 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
*/
public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
- // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
+ // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
protected VarROIArray rois;
@@ -91,9 +91,16 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
{
// set result in element
final ROI roi = rois.getValue()[getIterationCounter().getValue().intValue()];
-
- element.setValue(SequenceUtil.getSubSequence(inputSequence.getValue(), roi));
- currentRoi.setValue(new ROI[] {roi});
+
+ try
+ {
+ element.setValue(SequenceUtil.getSubSequence(inputSequence.getValue(), roi));
+ currentRoi.setValue(new ROI[] {roi});
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
index ec957c7..2ed300e 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
@@ -36,21 +36,28 @@ public class AdditiveFillSequence extends Plugin implements SequenceBlock, Plugi
if (sequence == null)
throw new VarException(inputSequence, "Input sequence is null.");
- if (rois.getValue() != null)
+ try
{
- for (ROI roi : rois.getValue())
- doAdditiveFill(sequence, roi, 1d);
+ if (rois.getValue() != null)
+ {
+ for (ROI roi : rois.getValue())
+ doAdditiveFill(sequence, roi, 1d);
- sequence.dataChanged();
+ sequence.dataChanged();
+ }
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
}
}
- public static void doAdditiveFill(Sequence sequence, ROI roi, double value)
+ public static void doAdditiveFill(Sequence sequence, ROI roi, double value) throws InterruptedException
{
doAdditiveFill(new SequenceDataIterator(sequence, roi), value);
}
- public static void doAdditiveFill(DataIterator it, double value)
+ public static void doAdditiveFill(DataIterator it, double value) throws InterruptedException
{
it.reset();
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
index 39c7c63..7dc0f45 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
@@ -36,14 +36,21 @@ public class FillInnerSequence extends Plugin implements SequenceBlock, PluginLi
if (sequence == null)
throw new VarException(inputSequence, "Input sequence is null.");
- if (rois.getValue() != null)
+ try
{
- final double value = fillValue.getValue().doubleValue();
+ if (rois.getValue() != null)
+ {
+ final double value = fillValue.getValue().doubleValue();
- for (ROI roi : rois.getValue())
- DataIteratorUtil.set(new SequenceDataIterator(sequence, roi), value);
+ for (ROI roi : rois.getValue())
+ DataIteratorUtil.set(new SequenceDataIterator(sequence, roi), value);
- sequence.dataChanged();
+ sequence.dataChanged();
+ }
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
index 7e3faea..89d47ed 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
@@ -40,25 +40,32 @@ public class FillOuterSequence extends Plugin implements SequenceBlock, PluginLi
if (sequence == null)
throw new VarException(inputSequence, "Input sequence is null.");
- if (rois.getValue() != null)
+ try
{
- try
+ if (rois.getValue() != null)
{
- final ROI roiUnion = ROIUtil.merge(CollectionUtil.asList(rois.getValue()), BooleanOperator.OR);
- final ROI roiSeq = new ROI5DStackRectangle(sequence.getBounds5D());
- final ROI roi = roiSeq.getSubtraction(roiUnion);
+ try
+ {
+ final ROI roiUnion = ROIUtil.merge(CollectionUtil.asList(rois.getValue()), BooleanOperator.OR);
+ final ROI roiSeq = new ROI5DStackRectangle(sequence.getBounds5D());
+ final ROI roi = roiSeq.getSubtraction(roiUnion);
- final double value = fillValue.getValue().doubleValue();
+ final double value = fillValue.getValue().doubleValue();
- DataIteratorUtil.set(new SequenceDataIterator(sequence, roi), value);
+ DataIteratorUtil.set(new SequenceDataIterator(sequence, roi), value);
- sequence.dataChanged();
- }
- catch (UnsupportedOperationException e)
- {
- throw new VarException(rois, e.getMessage());
+ sequence.dataChanged();
+ }
+ catch (UnsupportedOperationException e)
+ {
+ throw new VarException(rois, e.getMessage());
+ }
}
}
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
index 946b5cb..2fb63bf 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
@@ -35,7 +35,14 @@ public class RemoveChannel extends Plugin implements SequenceBlock, PluginLibrar
if (channel < 0 || channel >= s.getSizeC())
throw new VarException(channelIdx, "Channel index must be between 0 and " + (s.getSizeC() - 1));
- SequenceUtil.removeChannel(s, channel);
+ try
+ {
+ SequenceUtil.removeChannel(s, channel);
+ }
+ catch (InterruptedException e)
+ {
+ // nothing to do
+ }
}
@Override
--
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