From c621eaad3849fb93731c4288e0ef8059b65ba41b Mon Sep 17 00:00:00 2001
From: Stephane Dallongeville <stephane@outlook.com>
Date: Mon, 14 Sep 2020 17:36:07 +0200
Subject: [PATCH] Fixed merging from mavenization (restored all lost changes
hopefully) + minors changes.
---
.classpath | 38 ------------
export.jardesc | 2 +-
.../SequenceFileImporterGetImage.java | 20 ++++---
.../SequenceFileImporterLoadSequence.java | 12 ++--
.../sequenceblocks/infos/GetFileName.java | 2 +-
.../loop/SequenceChannelBatch.java | 7 +--
.../loop/SequenceFileImporterBatch.java | 43 ++++++++++++-
.../SequenceFileImporterChannelBatch.java | 3 +-
.../loop/SequenceFileImporterFrameBatch.java | 3 +-
.../loop/SequenceFileImporterRegionBatch.java | 8 ++-
.../loop/SequenceFileImporterSeriesBatch.java | 41 +++++++++++--
.../loop/SequenceFileImporterSliceBatch.java | 5 +-
.../loop/SequenceFileImporterTileBatch.java | 51 ++++++++++++----
.../loop/SequenceFrameBatch.java | 2 +-
.../loop/SequenceRegionBatch.java | 60 ++++++++++++-------
.../loop/SequenceSliceBatch.java | 4 +-
16 files changed, 190 insertions(+), 111 deletions(-)
diff --git a/.classpath b/.classpath
index f31c84e..396fa4f 100644
--- a/.classpath
+++ b/.classpath
@@ -2,47 +2,9 @@
<classpath>
<classpathentry kind="src" path="src/main/java"/>
<classpathentry kind="src" path="src/main/resources"/>
- <classpathentry kind="src" path="src/test/java"/>
<classpathentry kind="lib" path="/Icy-App/plugins/adufour/ezplug/EzPlug.jar"/>
<classpathentry kind="lib" path="/Icy-App/plugins/adufour/blocks/Blocks.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
<classpathentry kind="var" path="ICY_JAR"/>
- <classpathentry kind="lib" path="F:/SDKs/Java/jdk1.8.0_241/lib/tools.jar"/>
- <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
- <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
- <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
- <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
- <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-kernel:2.1.0"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.sf.ehcache:ehcache:2.10.6"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.slf4j:slf4j-api:1.7.25"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-bioformats:6.3.1"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-insubstantial:7.3.7"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-vtk:6.3.0.1"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.imagej:ij:1.52q"/>
- <classpathentry kind="lib" path="D:/SDKs/Java/jdk1.8.0_241/lib/tools.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: javax.media:jai-core:1.1.3"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: javax.media:jai-codec:1.1.3"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all:2.1.5-01"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-linux-amd64:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-linux-i586:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-macosx-universal:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-windows-amd64:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-windows-i586:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt:2.1.5-01"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-linux-amd64:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-linux-i586:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-macosx-universal:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-windows-amd64:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-windows-i586:2.1.5"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.javassist:javassist:3.22.0-GA"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.sourceforge.jexcelapi:jxl:2.6.12"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: log4j:log4j:1.2.14"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.swinglabs.swingx:swingx-all:1.6.5-1"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-blocks:1.0.1"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-protocols:3.0.9"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-javadocparser:1.0.0"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: com.nativelibs4java:ochafik-util:0.12"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-ezplug:3.15.13"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
diff --git a/export.jardesc b/export.jardesc
index 718e9ce..690764f 100644
--- a/export.jardesc
+++ b/export.jardesc
@@ -11,6 +11,6 @@
</sealing>
</manifest>
<selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
- <javaElement handleIdentifier="=SequenceBlocks/src"/>
+ <javaElement handleIdentifier="=SequenceBlocks/src\/main\/java"/>
</selectedElements>
</jardesc>
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
index 3720a15..20f07dc 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
@@ -38,11 +38,11 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
super();
importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
- series = new VarInteger("Series", 0);
+ series = new VarInteger("Series", -1);
resolution = new VarInteger("Resolution (0=full, 1=1/2, ..)", 0);
region = new VarROIArray("XY region (ROI)", null);
- zIndex = new VarInteger("Z (slice) index", 0);
- tIndex = new VarInteger("T (frame) index", 0);
+ zIndex = new VarInteger("Z (slice) index", -1);
+ tIndex = new VarInteger("T (frame) index", -1);
cIndex = new VarInteger("C (channel) index", -1);
image = new Var<IcyBufferedImage>("Image", IcyBufferedImage.class);
@@ -71,17 +71,21 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds()
: null;
- // default values ? use internal position if any defined
- if ((s == 0) && (pi.s != -1))
+ // undefined values ? use internal position if any defined
+ if ((s == -1) && (pi.s != -1))
s = pi.s;
- if ((z == 0) && (pi.z != -1))
+ if ((z == -1) && (pi.z != -1))
z = pi.z;
- if ((t == 0) && (pi.t != -1))
+ if ((t == -1) && (pi.t != -1))
t = pi.t;
- if ((c == 0) && (pi.c != -1))
+ if ((c == -1) && (pi.c != -1))
c = pi.c;
if ((rect == null) && (pi.xyRegion != null))
rect = pi.xyRegion;
+
+ // still undefined ? --> set default value for series
+ if (s == -1)
+ s = 0;
try
{
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
index 34c8ba2..666f65c 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
@@ -43,7 +43,7 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
- series = new VarInteger("Series", 0);
+ series = new VarInteger("Series", -1);
resolution = new VarInteger("Resolution (0=full, 1=1/2, ..)", 0);
region = new VarROIArray("XY region (ROI)", null);
minZIndex = new VarInteger("Z min (slice)", -1);
@@ -80,8 +80,8 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds()
: null;
- // default values ? use internal position if any defined
- if ((s == 0) && (pi.s != -1))
+ // undefined values ? use internal position if any defined
+ if ((s == -1) && (pi.s != -1))
s = pi.s;
if ((minZ == -1) && (maxZ == -1) && (pi.z != -1))
{
@@ -93,10 +93,14 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
minT = pi.t;
maxT = pi.t;
}
- if ((c == 0) && (pi.c != -1))
+ if ((c == -1) && (pi.c != -1))
c = pi.c;
if ((rect == null) && (pi.xyRegion != null))
rect = pi.xyRegion;
+
+ // still undefined ? --> set default value for series
+ if (s == -1)
+ s = 0;
try
{
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
index 477a915..2bf3699 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
@@ -42,7 +42,7 @@ public class GetFileName extends Plugin implements SequenceBlock, PluginBundled
result = FileUtil.getFileName(result);
// remove extension ?
if (!withExtension.getValue().booleanValue())
- FileUtil.setExtension(result, "");
+ result = FileUtil.setExtension(result, "");
filename.setValue(result);
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
index f227dcd..763ccaa 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
@@ -17,15 +17,10 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
*/
public class SequenceChannelBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
- // important to not initialize 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;
- public SequenceChannelBatch()
- {
- super();
- }
-
@Override
public VarSequence getBatchSource()
{
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
index 782c76c..d487731 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
@@ -1,11 +1,15 @@
package plugins.tprovoost.sequenceblocks.loop;
+import java.util.List;
+
import icy.file.SequenceFileImporter;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
import plugins.adufour.blocks.lang.Batch;
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
+import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarInteger;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
@@ -20,6 +24,7 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
// important to not initialize and create them in getBatchSource() and getBatchElement()
protected Var<PositionedSequenceFileImporter> positionedImporter;
protected Var<PositionedSequenceFileImporter> element;
+ protected VarInteger series;
// internal
protected int limit;
@@ -58,8 +63,42 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
if (imp.getOpened() == null)
throw new VarException(positionedImporter, "Importer is not opened !");
- // init element with a copy of current positioned importer
- element.setValue(new PositionedSequenceFileImporter(value));
+ // create new positioned importer for element initialization
+ final PositionedSequenceFileImporter pi = new PositionedSequenceFileImporter(value);
+
+ final int s = series.getValue().intValue();
+
+ // defined series ? --> set series position
+ if (s != -1)
+ pi.s = s;
+
+ // init element with a copy of current positioned importer (and eventually set serie position)
+ element.setValue(pi);
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ // lazy creation
+ if (series == null)
+ series = new VarInteger("Series", -1);
+
+ inputMap.add("series", series);
+ }
+
+ @Override
+ public void declareLoopVariables(List<Var<?>> loopVariables)
+ {
+ // need to be called after
+ super.declareLoopVariables(loopVariables);
+
+ // lazy creation
+ if (series == null)
+ series = new VarInteger("Series", -1);
+
+ loopVariables.add(series);
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
index 46640c5..afc3b04 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
@@ -17,7 +17,8 @@ public class SequenceFileImporterChannelBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
try
{
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
index e91d5f4..ba8bf10 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
@@ -17,7 +17,8 @@ public class SequenceFileImporterFrameBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
try
{
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
index 0bbd8bb..05f0518 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
@@ -24,6 +24,7 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
*/
public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
{
+ // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
protected VarROIArray rois;
protected VarInteger inputRoisResolution;
protected VarInteger inputRoisMargin;
@@ -34,7 +35,8 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
// can iterate over XY dimension ?
if ((pi.xyRegion == null) && (rois.getValue() != null))
@@ -114,6 +116,8 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
@Override
public void declareLoopVariables(List<Var<?>> loopVariables)
{
+ super.declareLoopVariables(loopVariables);
+
// lazy creation
if (rois == null)
rois = new VarROIArray("XY regions (ROIs)");
@@ -125,8 +129,6 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
loopVariables.add(rois);
loopVariables.add(inputRoisResolution);
loopVariables.add(inputRoisMargin);
-
- super.declareLoopVariables(loopVariables);
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
index 255c14c..ffb8e57 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
@@ -1,7 +1,11 @@
package plugins.tprovoost.sequenceblocks.loop;
+import java.util.List;
+
import icy.file.SequenceFileImporter;
import icy.sequence.MetaDataUtil;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
@@ -17,12 +21,16 @@ public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
try
{
- // force series iteration as by default series is set to 0
- limit = MetaDataUtil.getNumSeries(pi.getMetadata());
+ // can iterate over S dimension ?
+ if (pi.s == -1)
+ limit = MetaDataUtil.getNumSeries(pi.getMetadata());
+ else
+ limit = 1;
}
catch (Exception e)
{
@@ -31,13 +39,34 @@ public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
}
}
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ // we don't want it here
+ inputMap.remove(series);
+ }
+
+ @Override
+ public void declareLoopVariables(List<Var<?>> loopVariables)
+ {
+ super.declareLoopVariables(loopVariables);
+
+ // we don't want it here
+ loopVariables.remove(series);
+ }
+
@Override
public void beforeIteration()
{
// set current position S
- element.getValue().s = getIterationCounter().getValue().intValue();
- // force element changed event so loop get correctly executed
- element.valueChanged(element, element.getValue(), element.getValue());
+ if (positionedImporter.getValue().s == -1)
+ {
+ element.getValue().s = getIterationCounter().getValue().intValue();
+ // force element changed event so loop get correctly executed
+ element.valueChanged(element, element.getValue(), element.getValue());
+ }
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
index 061b76d..16f1dad 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
@@ -17,8 +17,9 @@ public class SequenceFileImporterSliceBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
-
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
+
try
{
// can iterate over Z dimension ?
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
index 5386fb6..4d6e434 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
@@ -6,6 +6,8 @@ import java.util.List;
import icy.file.SequenceFileImporter;
import icy.image.ImageUtil;
import icy.sequence.MetaDataUtil;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarInteger;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
@@ -17,25 +19,19 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
*/
public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
{
- protected final VarInteger tileW;
- protected final VarInteger tileH;
+ // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
+ protected VarInteger tileW;
+ protected VarInteger tileH;
protected List<Rectangle> tiles;
- public SequenceFileImporterTileBatch()
- {
- super();
-
- tileW = new VarInteger("Tile width (-1 = auto)", 0);
- tileH = new VarInteger("Tile height (-1 = auto)", 0);
- }
-
@Override
public void initializeLoop()
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
// can iterate over XY dimension ?
if (pi.xyRegion == null)
@@ -63,7 +59,7 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
}
catch (Exception e)
{
- throw new VarException(positionedImporter,
+ throw new VarException(element,
"Error while initializing SequenceFileImporter tile batch: " + e.getMessage());
}
@@ -89,6 +85,37 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
limit = 1;
}
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ // lazy creation
+ if (tileW == null)
+ tileW = new VarInteger("Tile width (-1 = auto)", -1);
+ if (tileH == null)
+ tileH = new VarInteger("Tile height (-1 = auto)", -1);
+
+ inputMap.add("tileWidht", tileW);
+ inputMap.add("tileHeight", tileH);
+ }
+
+ @Override
+ public void declareLoopVariables(List<Var<?>> loopVariables)
+ {
+ // need to be called after
+ super.declareLoopVariables(loopVariables);
+
+ // lazy creation
+ if (tileW == null)
+ tileW = new VarInteger("Tile width (-1 = auto)", -1);
+ if (tileH == null)
+ tileH = new VarInteger("Tile height (-1 = auto)", -1);
+
+ loopVariables.add(tileW);
+ loopVariables.add(tileH);
+ }
+
@Override
public void beforeIteration()
{
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
index d06b0a6..2a77e4f 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
@@ -40,7 +40,7 @@ public class SequenceFrameBatch extends Batch implements PluginLibrary, PluginBu
{
// initialize element if needed
if (element == null)
- element = new VarSequence("Channel Sequence", null);
+ element = new VarSequence("Frame Sequence", null);
return element;
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
index 548ba91..8da2ca7 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
+++ b/src/main/java/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;
@@ -22,38 +23,57 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
*/
public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
- // important to not initialize 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 final VarROIArray rois;
+ protected VarROIArray rois;
+ protected VarROIArray currentRoi;
public SequenceRegionBatch()
{
super();
-
- rois = new VarROIArray("ROI(s)");
}
@Override
- public VarSequence getBatchSource()
+ public VarROIArray getBatchSource()
{
- // initialize variable if needed
- if (inputSequence == null)
- inputSequence = new VarSequence("Sequence", null);
+ if (rois == null)
+ rois = new VarROIArray("ROI(s)");
- return inputSequence;
+ return rois;
}
@Override
public VarSequence getBatchElement()
{
- // initialize element if needed
if (element == null)
- element = new VarSequence("Channel Sequence", null);
+ element = new VarSequence("Region Sequence", null);
return element;
}
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ if (inputSequence == null)
+ inputSequence = new VarSequence("Sequence", null);
+
+ inputMap.add(inputSequence.getName(), inputSequence);
+ }
+
+ @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 +90,10 @@ 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()]));
+ final ROI roi = rois.getValue()[getIterationCounter().getValue().intValue()];
+
+ element.setValue(SequenceUtil.getSubSequence(inputSequence.getValue(), roi));
+ currentRoi.setValue(new ROI[] {roi});
}
@Override
@@ -80,20 +102,12 @@ 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
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
index d1bc689..e8c2003 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
@@ -17,7 +17,7 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
*/
public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
- // important to not initialize 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;
@@ -36,7 +36,7 @@ public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLi
{
// initialize element if needed
if (element == null)
- element = new VarSequence("Channel Sequence", null);
+ element = new VarSequence("Slice Sequence", null);
return element;
}
--
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