From c520358f3550cb48e45450a5bc96d49bdffd7d65 Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Tue, 5 Sep 2023 14:57:53 +0200
Subject: [PATCH] updated pom, optimized code for java 11, removed deprecated
code
---
.gitignore | 1 +
pom.xml | 17 +--
.../sequenceblocks/SequenceBlocks.java | 23 +++-
.../sequenceblocks/add/AddOverlays.java | 52 +++++----
.../tprovoost/sequenceblocks/add/AddRois.java | 41 ++++---
.../sequenceblocks/convert/ConvertColor.java | 76 ++++++------
.../sequenceblocks/convert/ConvertStack.java | 51 ++++----
.../sequenceblocks/convert/ConvertType.java | 46 +++++---
.../sequenceblocks/convert/Resize.java | 72 +++++++-----
.../creation/CombineChannels.java | 62 +++++-----
.../creation/CreateSequence.java | 35 ++++--
.../creation/DuplicateSequence.java | 41 ++++---
.../sequenceblocks/extract/CropCZT.java | 45 ++++---
.../sequenceblocks/extract/CropSequence.java | 56 +++++----
.../extract/ExtractChannel.java | 43 ++++---
.../extract/ExtractMultiChannels.java | 49 +++++---
.../sequenceblocks/extract/ExtractSlice.java | 37 ++++--
.../sequenceblocks/extract/ExtractTime.java | 37 ++++--
.../sequenceblocks/files/IsFileValid.java | 50 ++++----
.../sequenceblocks/files/LoadMetadata.java | 61 +++++-----
.../sequenceblocks/files/LoadSequence.java | 50 ++++----
.../sequenceblocks/files/LoadSubSequence.java | 101 +++++++++-------
.../sequenceblocks/files/SaveMetadata.java | 39 ++++---
.../sequenceblocks/files/SaveSequence.java | 63 +++++-----
.../sequenceblocks/images/AddImage.java | 39 ++++---
.../sequenceblocks/images/AsImageArray.java | 39 ++++---
.../sequenceblocks/images/GetImage.java | 41 ++++---
.../sequenceblocks/images/RemoveImage.java | 39 ++++---
.../sequenceblocks/images/SetImage.java | 41 ++++---
.../PositionedSequenceFileImporter.java | 60 ++++++----
.../importer/SequenceFileImporterClose.java | 46 +++++---
.../SequenceFileImporterGetImage.java | 66 ++++++-----
.../SequenceFileImporterGetMetadata.java | 54 +++++----
.../SequenceFileImporterGetThumbnail.java | 50 ++++----
.../SequenceFileImporterGetTileSize.java | 56 +++++----
.../SequenceFileImporterLoadSequence.java | 76 ++++++------
.../importer/SequenceFileImporterOpen.java | 83 ++++++-------
.../infos/CreateLinearColormap.java | 44 ++++---
.../sequenceblocks/infos/Dimensions.java | 47 +++++---
.../sequenceblocks/infos/EzVarColormap.java | 29 +++--
.../sequenceblocks/infos/GetChannelName.java | 43 ++++---
.../sequenceblocks/infos/GetChannelsName.java | 50 +++++---
.../sequenceblocks/infos/GetColormap.java | 46 +++++---
.../sequenceblocks/infos/GetColormaps.java | 51 ++++----
.../sequenceblocks/infos/GetDataType.java | 40 ++++---
.../sequenceblocks/infos/GetFileName.java | 42 ++++---
.../sequenceblocks/infos/GetMetaData.java | 79 +++++++------
.../sequenceblocks/infos/GetName.java | 37 ++++--
.../infos/GetOutputFilename.java | 42 ++++---
.../sequenceblocks/infos/GetResolution.java | 51 ++++----
.../sequenceblocks/infos/GetRoisAsRegion.java | 63 +++++-----
.../infos/GetSequenceProperty.java | 35 ++++--
.../sequenceblocks/infos/ReadMetadata.java | 68 ++++++-----
.../sequenceblocks/infos/SetChannelName.java | 41 ++++---
.../sequenceblocks/infos/SetChannelsName.java | 37 ++++--
.../sequenceblocks/infos/SetColormap.java | 38 +++---
.../sequenceblocks/infos/SetColormaps.java | 36 ++++--
.../sequenceblocks/infos/SetName.java | 41 ++++---
.../sequenceblocks/infos/SetResolution.java | 110 ++++++++++--------
.../infos/SetSequenceProperty.java | 35 ++++--
.../sequenceblocks/infos/VarColormap.java | 70 ++++++-----
.../loop/SequenceChannelBatch.java | 51 ++++----
.../loop/SequenceFileImporterBatch.java | 51 ++++----
.../SequenceFileImporterChannelBatch.java | 48 +++++---
.../loop/SequenceFileImporterFrameBatch.java | 48 +++++---
.../loop/SequenceFileImporterRegionBatch.java | 72 ++++++------
.../loop/SequenceFileImporterSeriesBatch.java | 55 +++++----
.../loop/SequenceFileImporterSliceBatch.java | 50 ++++----
.../loop/SequenceFileImporterTileBatch.java | 73 ++++++------
.../loop/SequenceFrameBatch.java | 49 ++++----
.../loop/SequenceRegionBatch.java | 69 ++++++-----
.../loop/SequenceSliceBatch.java | 45 ++++---
.../op/AdditiveFillSequence.java | 62 +++++-----
.../sequenceblocks/op/FillInnerSequence.java | 49 ++++----
.../sequenceblocks/op/FillOuterSequence.java | 57 ++++-----
.../sequenceblocks/remove/RemoveAllRois.java | 35 ++++--
.../sequenceblocks/remove/RemoveChannel.java | 45 ++++---
.../sequenceblocks/remove/RemoveFrame.java | 39 ++++---
.../sequenceblocks/remove/RemoveOverlays.java | 49 ++++----
.../sequenceblocks/remove/RemoveRois.java | 40 ++++---
.../sequenceblocks/remove/RemoveSlice.java | 39 ++++---
81 files changed, 2434 insertions(+), 1605 deletions(-)
diff --git a/.gitignore b/.gitignore
index 80a5e13..198c988 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ target/
.project
.classpath
export.jardesc
+**/.DS_Store
diff --git a/pom.xml b/pom.xml
index d1ad26a..381634a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,29 +1,24 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>parent-pom-plugin</artifactId>
- <version>1.0.8</version>
+ <artifactId>pom-icy</artifactId>
+ <version>2.2.0</version>
</parent>
<artifactId>sequence-blocks</artifactId>
- <version>2.1.1</version>
+ <version>3.0.0</version>
<name>SequenceBlocks</name>
<dependencies>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-kernel</artifactId>
- </dependency>
-
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>blocks</artifactId>
+ <artifactId>protocols</artifactId>
</dependency>
</dependencies>
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/SequenceBlocks.java b/src/main/java/plugins/tprovoost/sequenceblocks/SequenceBlocks.java
index 2a194ff..e99b35c 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/SequenceBlocks.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/SequenceBlocks.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks;
import icy.plugin.abstract_.Plugin;
@@ -7,10 +25,9 @@ import icy.plugin.interface_.PluginLibrary;
* This class is used as a main class for all the blocks contained in this
* package. Each Block has a specified dedicated purpose. More documentation on
* the concerned files.
- *
+ *
* @author thomasprovoost
*/
-public class SequenceBlocks extends Plugin implements PluginLibrary
-{
+public class SequenceBlocks extends Plugin implements PluginLibrary {
//
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/add/AddOverlays.java b/src/main/java/plugins/tprovoost/sequenceblocks/add/AddOverlays.java
index 4251b97..a6702c0 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/add/AddOverlays.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/add/AddOverlays.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.add;
import icy.painter.Overlay;
@@ -14,17 +32,14 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to add one or several {@link Overlay} to a Sequence
- *
+ *
* @author Stephane
*/
-public class AddOverlays extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class AddOverlays extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
- final protected VarArray<Overlay> overlays = new VarArray<Overlay>("Overlay(s)", Overlay[].class, new Overlay[0])
- {
+ final protected VarArray<Overlay> overlays = new VarArray<>("Overlay(s)", Overlay[].class, new Overlay[0]) {
@Override
- public String getValueAsString()
- {
+ public String getValueAsString() {
final Overlay[] value = getValue();
if (value == null || value.length == 0)
@@ -35,23 +50,19 @@ public class AddOverlays extends Plugin implements SequenceBlock, PluginLibrary,
};
@Override
- public void run()
- {
+ public void run() {
final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
final Overlay[] o = overlays.getValue();
- if (o != null)
- {
+ if (o != null) {
s.beginUpdate();
- try
- {
- for (Overlay overlay : o)
+ try {
+ for (final Overlay overlay : o)
s.addOverlay(overlay);
}
- finally
- {
+ finally {
s.endUpdate();
}
}
@@ -59,21 +70,18 @@ public class AddOverlays extends Plugin implements SequenceBlock, PluginLibrary,
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("overlay(s)", overlays);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/add/AddRois.java b/src/main/java/plugins/tprovoost/sequenceblocks/add/AddRois.java
index cbf26c8..6e3417f 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/add/AddRois.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/add/AddRois.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.add;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.util.Arrays;
+package plugins.tprovoost.sequenceblocks.add;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
@@ -15,25 +31,25 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.util.Arrays;
+
/**
* Block to add one or several {@link ROI} to a Sequence
- *
+ *
* @author Stephane
*/
-public class AddRois extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class AddRois extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarROIArray rois = new VarROIArray("Roi(s)");
final protected VarBoolean removePrevious = new VarBoolean("Remove previous", Boolean.FALSE);
@Override
- public void run()
- {
+ public void run() {
final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- if (removePrevious.getValue().booleanValue())
+ if (removePrevious.getValue())
s.removeAllROI();
final ROI[] r = rois.getValue();
@@ -42,22 +58,19 @@ public class AddRois extends Plugin implements SequenceBlock, PluginLibrary, Plu
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("rois(s)", rois);
inputMap.add("remove", removePrevious);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
index 1e4cf5b..a145a4e 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.convert;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.awt.image.BufferedImage;
+package plugins.tprovoost.sequenceblocks.convert;
import icy.image.IcyBufferedImageUtil;
import icy.image.lut.LUT;
@@ -16,68 +32,60 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.awt.image.BufferedImage;
+
/**
* Block to render a given Sequence using a specific LUT.<br>
* The result can be provided ARGB, RGB or GRAY sequence.
- *
+ *
* @author Stephane
*/
-public class ConvertColor extends Plugin implements SequenceBlock, PluginBundled
-{
- public static enum ColorConversion
- {
- GRAY, RGB, ARGB;
- };
+public class ConvertColor extends Plugin implements SequenceBlock, PluginBundled {
+ public enum ColorConversion {
+ GRAY, RGB, ARGB
+ }
final protected VarSequence EZseq = new VarSequence("Sequence", null);
- final protected VarEnum<ColorConversion> EZtype = new VarEnum<ColorConversion>("Conversion", ColorConversion.ARGB);
- final protected Var<LUT> EZlut = new Var<LUT>("Lut", LUT.class);
+ final protected VarEnum<ColorConversion> EZtype = new VarEnum<>("Conversion", ColorConversion.ARGB);
+ final protected Var<LUT> EZlut = new Var<>("Lut", LUT.class);
final protected VarSequence varOut = new VarSequence("Out", null);
@Override
- public void run()
- {
- Sequence s;
+ public void run() {
+ final Sequence s;
// EZ PLUG
s = EZseq.getValue();
if (s == null)
throw new VarException(EZseq, "Input sequence is null.");
- try
- {
+ try {
varOut.setValue(convertColor(s, getImageType(EZtype.getValue()), EZlut.getValue()));
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("Sequence", EZseq);
inputMap.add("Conversion", EZtype);
inputMap.add("Lut", EZlut);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("Out", varOut);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
- public static int getImageType(ColorConversion value)
- {
- switch (value)
- {
+ public static int getImageType(final ColorConversion value) {
+ switch (value) {
default:
case ARGB:
return BufferedImage.TYPE_INT_ARGB;
@@ -90,22 +98,19 @@ public class ConvertColor extends Plugin implements SequenceBlock, PluginBundled
}
}
- public static Sequence convertColor(Sequence source, int imageType, LUT lut) throws IllegalArgumentException, InterruptedException
- {
+ public static Sequence convertColor(final Sequence source, final int imageType, final LUT lut) throws IllegalArgumentException, InterruptedException {
final Sequence result = new Sequence(OMEUtil.createOMEXMLMetadata(source.getOMEXMLMetadata()));
// image receiver
final BufferedImage imgOut = new BufferedImage(source.getSizeX(), source.getSizeY(), imageType);
result.beginUpdate();
- try
- {
+ try {
for (int t = 0; t < source.getSizeT(); t++)
for (int z = 0; z < source.getSizeZ(); z++)
result.setImage(t, z, IcyBufferedImageUtil.toBufferedImage(source.getImage(t, z), imgOut, lut));
// rename channels and set final name
- switch (imageType)
- {
+ switch (imageType) {
default:
case BufferedImage.TYPE_INT_ARGB:
result.setChannelName(0, "red");
@@ -128,8 +133,7 @@ public class ConvertColor extends Plugin implements SequenceBlock, PluginBundled
break;
}
}
- finally
- {
+ finally {
result.endUpdate();
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
index 7eae544..cc457d0 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.convert;
import icy.plugin.abstract_.Plugin;
@@ -5,7 +23,6 @@ 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;
@@ -15,56 +32,48 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class ConvertStack extends Plugin implements SequenceBlock, PluginBundled
-{
- public static enum TypeConversion
- {
+public class ConvertStack extends Plugin implements SequenceBlock, PluginBundled {
+ public enum TypeConversion {
STACK, TIME
- };
+ }
- final protected VarEnum<TypeConversion> type = new VarEnum<TypeConversion>("Type Wanted", TypeConversion.STACK);
+ final protected VarEnum<TypeConversion> type = new VarEnum<>("Type Wanted", TypeConversion.STACK);
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarSequence outputSequence = new VarSequence("Out", null);
@Override
- public void run()
- {
- Sequence in = inputSequence.getValue();
+ public void run() {
+ final Sequence in = inputSequence.getValue();
if (in == null)
throw new VarException(inputSequence, "Input sequence is null.");
- try
- {
+ try {
// create a copy as we don't want to modify input
- Sequence out = SequenceUtil.getCopy(in);
+ final Sequence out = SequenceUtil.getCopy(in);
if (type.getValue() == TypeConversion.TIME)
SequenceUtil.convertToTime(out);
else
SequenceUtil.convertToStack(out);
outputSequence.setValue(out);
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("Type Wanted", type);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("out", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
index 48a11a4..a6afe8a 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.convert;
import icy.plugin.abstract_.Plugin;
@@ -17,48 +35,40 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class ConvertType extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- final protected VarEnum<DataType> type = new VarEnum<DataType>("Type Wanted", DataType.UBYTE);
+public class ConvertType extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ final protected VarEnum<DataType> type = new VarEnum<>("Type Wanted", DataType.UBYTE);
final protected VarSequence inputSequence = new VarSequence("sequence", null);
final protected VarSequence outputSequence = new VarSequence("converted", null);
final protected VarBoolean rescale = new VarBoolean("Rescale", Boolean.TRUE);
@Override
- public void run()
- {
- Sequence s = inputSequence.getValue();
+ public void run() {
+ final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- try
- {
- outputSequence.setValue(SequenceUtil.convertToType(s, type.getValue(), rescale.getValue().booleanValue()));
+ try {
+ outputSequence.setValue(SequenceUtil.convertToType(s, type.getValue(), rescale.getValue()));
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("Type Wanted", type);
inputMap.add("Rescale", rescale);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("converted", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
-
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/convert/Resize.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/Resize.java
index b222d0f..5613a6b 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/convert/Resize.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/convert/Resize.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.convert;
import icy.image.IcyBufferedImageUtil.FilterType;
@@ -5,9 +23,6 @@ import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
import icy.sequence.Sequence;
import icy.sequence.SequenceUtil;
-
-import javax.swing.SwingConstants;
-
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarBoolean;
@@ -17,40 +32,38 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
-public class Resize extends Plugin implements SequenceBlock, PluginBundled
-{
- protected enum Proportional
- {
+import javax.swing.*;
+
+public class Resize extends Plugin implements SequenceBlock, PluginBundled {
+ protected enum Proportional {
NO, TO_WIDTH, TO_HEIGHT
- };
+ }
- final protected VarSequence EZseq = new VarSequence("Sequence", null);
- final protected VarInteger EZsizew = new VarInteger("Width", 320);
- final protected VarInteger EZsizeh = new VarInteger("Height", 200);
- final protected VarEnum<Proportional> EZproportional = new VarEnum<Proportional>("Proportional", Proportional.NO);
- final protected VarBoolean EZscale = new VarBoolean("Scale content", Boolean.TRUE);
- final protected VarEnum<FilterType> EZtype = new VarEnum<FilterType>("Filter", FilterType.BICUBIC);
- final protected VarSequence varOut = new VarSequence("Out", null);
+ final protected VarSequence EZseq = new VarSequence("Sequence", null);
+ final protected VarInteger EZsizew = new VarInteger("Width", 320);
+ final protected VarInteger EZsizeh = new VarInteger("Height", 200);
+ final protected VarEnum<Proportional> EZproportional = new VarEnum<>("Proportional", Proportional.NO);
+ final protected VarBoolean EZscale = new VarBoolean("Scale content", Boolean.TRUE);
+ final protected VarEnum<FilterType> EZtype = new VarEnum<>("Filter", FilterType.BICUBIC);
+ final protected VarSequence varOut = new VarSequence("Out", null);
@Override
- public void run()
- {
- Sequence s;
+ public void run() {
+ final Sequence s;
int w, h;
- FilterType type;
+ final FilterType type;
// EZ PLUG
s = EZseq.getValue();
- w = EZsizew.getValue().intValue();
- h = EZsizeh.getValue().intValue();
+ w = EZsizew.getValue();
+ h = EZsizeh.getValue();
type = EZtype.getValue();
if (s == null || w <= 0 || h <= 0)
throw new VarException(null, "No sequence chosen for resize, or wrong size.");
- double scale = 1d * s.getWidth() / s.getHeight();
- switch (EZproportional.getValue())
- {
+ final double scale = 1d * s.getWidth() / s.getHeight();
+ switch (EZproportional.getValue()) {
case NO:
break;
case TO_WIDTH:
@@ -61,15 +74,14 @@ public class Resize extends Plugin implements SequenceBlock, PluginBundled
break;
}
- if (EZscale.getValue().booleanValue())
+ if (EZscale.getValue())
varOut.setValue(SequenceUtil.scale(s, w, h, type));
else
varOut.setValue(SequenceUtil.scale(s, w, h, false, SwingConstants.CENTER, SwingConstants.CENTER, type));
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("Sequence", EZseq);
inputMap.add("Width", EZsizew);
inputMap.add("Height", EZsizeh);
@@ -79,14 +91,12 @@ public class Resize extends Plugin implements SequenceBlock, PluginBundled
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("Out", varOut);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/creation/CombineChannels.java b/src/main/java/plugins/tprovoost/sequenceblocks/creation/CombineChannels.java
index b1fc9e1..68d5107 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/creation/CombineChannels.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/creation/CombineChannels.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.creation;
import icy.plugin.abstract_.Plugin;
@@ -16,57 +34,51 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class CombineChannels extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class CombineChannels extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence 1", null);
final protected VarSequence inputSequence2 = new VarSequence("Sequence 2", null);
final protected VarSequence outputSequence = new VarSequence("Merged", null);
- final protected VarIntegerArrayNative channelIdx = new VarIntegerArrayNative("Channel(s) 1", new int[] {0});
- final protected VarIntegerArrayNative channelIdx2 = new VarIntegerArrayNative("Channel(s) 2", new int[] {0});
+ final protected VarIntegerArrayNative channelIdx = new VarIntegerArrayNative("Channel(s) 1", new int[]{0});
+ final protected VarIntegerArrayNative channelIdx2 = new VarIntegerArrayNative("Channel(s) 2", new int[]{0});
final protected VarBoolean fillStackHole = new VarBoolean("Fill stack hole", Boolean.TRUE);
final protected VarBoolean fitToMaxSize = new VarBoolean("Fit to max size", Boolean.TRUE);
@Override
- public void run()
- {
- Sequence s = inputSequence.getValue();
- Sequence s2 = inputSequence2.getValue();
+ public void run() {
+ final Sequence s = inputSequence.getValue();
+ final Sequence s2 = inputSequence2.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence 1 is null.");
if (s2 == null)
throw new VarException(inputSequence2, "Input sequence 2 is null.");
- int[] channels1 = channelIdx.getValue();
- int[] channels2 = channelIdx2.getValue();
- int sizeC1 = channels1.length;
- int sizeC2 = channels2.length;
+ final int[] channels1 = channelIdx.getValue();
+ final int[] channels2 = channelIdx2.getValue();
+ final int sizeC1 = channels1.length;
+ final int sizeC2 = channels2.length;
// Because of concatC, it is necessary to create a sequence[] and int[] of the same size,
// and duplicate the sequence as many times in the first as necessary.
- Sequence[] sequences = new Sequence[sizeC1 + sizeC2];
- int channels[] = new int[sizeC1 + sizeC2];
+ final Sequence[] sequences = new Sequence[sizeC1 + sizeC2];
+ final int[] channels = new int[sizeC1 + sizeC2];
- for (int i = 0; i < sizeC1; ++i)
- {
+ for (int i = 0; i < sizeC1; ++i) {
sequences[i] = s;
channels[i] = channels1[i];
}
- for (int i = 0; i < sizeC2; ++i)
- {
+ for (int i = 0; i < sizeC2; ++i) {
sequences[sizeC1 + i] = s2;
channels[sizeC1 + i] = channels2[i];
}
- final Sequence res = SequenceUtil.concatC(sequences, channels, fillStackHole.getValue().booleanValue(),
- fitToMaxSize.getValue().booleanValue(), null);
+ final Sequence res = SequenceUtil.concatC(sequences, channels, fillStackHole.getValue(), fitToMaxSize.getValue(), null);
outputSequence.setValue(res);
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence 1", inputSequence);
inputMap.add("Channel 1", channelIdx);
inputMap.add("sequence 2", inputSequence2);
@@ -76,14 +88,12 @@ public class CombineChannels extends Plugin implements SequenceBlock, PluginLibr
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("out", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/creation/CreateSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/creation/CreateSequence.java
index a133b94..c99e181 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/creation/CreateSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/creation/CreateSequence.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.creation;
import icy.image.IcyBufferedImage;
@@ -14,32 +32,27 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class CreateSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- final protected Var<IcyBufferedImage> in = new Var<IcyBufferedImage>("image (optional)", IcyBufferedImage.class);
+public class CreateSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ final protected Var<IcyBufferedImage> in = new Var<>("image (optional)", IcyBufferedImage.class);
final protected VarSequence out = new VarSequence("sequence", null);
@Override
- public void run()
- {
+ public void run() {
out.setValue(new Sequence(in.getValue()));
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("image (optional)", in);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("sequence", out);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
index dec05da..e91fea7 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.creation;
import icy.plugin.abstract_.Plugin;
@@ -14,43 +32,36 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class DuplicateSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class DuplicateSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence in = new VarSequence("sequence", null);
final protected VarSequence out = new VarSequence("duplicated", null);
@Override
- public void run()
- {
- Sequence s = in.getValue();
+ public void run() {
+ final Sequence s = in.getValue();
if (s == null)
throw new VarException(in, "Input Sequence is null.");
- try
- {
+ try {
out.setValue(SequenceUtil.getCopy(s));
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", in);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("duplicated", out);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropCZT.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropCZT.java
index 4ffa86c..24aceb5 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropCZT.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropCZT.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.extract;
import icy.plugin.abstract_.Plugin;
@@ -12,8 +30,7 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
-public class CropCZT extends Plugin implements SequenceBlock, PluginBundled
-{
+public class CropCZT extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSeq = new VarSequence("Sequence", null);
final protected VarInteger varStartC = new VarInteger("Start index C", 0);
final protected VarInteger varSizeC = new VarInteger("Size C", 1);
@@ -24,8 +41,7 @@ public class CropCZT extends Plugin implements SequenceBlock, PluginBundled
final protected VarSequence varOut = new VarSequence("Out", null);
@Override
- public void run()
- {
+ public void run() {
final Sequence seq;
final int startX, sizeX;
final int startY, sizeY;
@@ -39,12 +55,12 @@ public class CropCZT extends Plugin implements SequenceBlock, PluginBundled
if (seq == null)
throw new VarException(varSeq, "No sequence chosen !");
- startC = Math.min(varStartC.getValue().intValue(), seq.getSizeC() - 1);
- sizeC = Math.min(varSizeC.getValue().intValue(), seq.getSizeC() - startC);
- startZ = Math.min(varStartZ.getValue().intValue(), seq.getSizeZ() - 1);
- sizeZ = Math.min(varSizeZ.getValue().intValue(), seq.getSizeZ() - startZ);
- startT = Math.min(varStartT.getValue().intValue(), seq.getSizeT() - 1);
- sizeT = Math.min(varSizeT.getValue().intValue(), seq.getSizeT() - startT);
+ startC = Math.min(varStartC.getValue(), seq.getSizeC() - 1);
+ sizeC = Math.min(varSizeC.getValue(), seq.getSizeC() - startC);
+ startZ = Math.min(varStartZ.getValue(), seq.getSizeZ() - 1);
+ sizeZ = Math.min(varSizeZ.getValue(), seq.getSizeZ() - startZ);
+ startT = Math.min(varStartT.getValue(), seq.getSizeT() - 1);
+ sizeT = Math.min(varSizeT.getValue(), seq.getSizeT() - startT);
startX = 0;
sizeX = seq.getSizeX();
@@ -59,8 +75,7 @@ public class CropCZT extends Plugin implements SequenceBlock, PluginBundled
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("Sequence", varSeq);
inputMap.add("Start index C", varStartC);
inputMap.add("Size C", varSizeC);
@@ -71,14 +86,12 @@ public class CropCZT extends Plugin implements SequenceBlock, PluginBundled
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("Out", varOut);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
index 334444f..af08430 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
@@ -1,7 +1,22 @@
-package plugins.tprovoost.sequenceblocks.extract;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.util.ArrayList;
-import java.util.List;
+package plugins.tprovoost.sequenceblocks.extract;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
@@ -19,25 +34,24 @@ import plugins.adufour.vars.lang.VarMutable;
import plugins.adufour.vars.lang.VarSequence;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* @author thomasprovoost
*/
-public class CropSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class CropSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
- VarMutable inputROIs = new VarMutable("ROI(s)", null)
- {
+ VarMutable inputROIs = new VarMutable("ROI(s)", null) {
@Override
- public boolean isAssignableFrom(@SuppressWarnings("rawtypes") Var source)
- {
+ public boolean isAssignableFrom(final Var source) {
return (ROI.class == source.getType()) || (ROI[].class == source.getType());
}
};
final protected VarSequence outputSequence = new VarSequence("Cropped", null);
@Override
- public void run()
- {
+ public void run() {
outputSequence.setValue(null);
final Sequence s = inputSequence.getValue();
@@ -50,42 +64,36 @@ public class CropSequence extends Plugin implements SequenceBlock, PluginLibrary
final List<ROI> rois;
- if (obj instanceof ROI)
- {
- rois = new ArrayList<ROI>();
+ if (obj instanceof ROI) {
+ rois = new ArrayList<>();
rois.add((ROI) obj);
}
else
rois = CollectionUtil.asList((ROI[]) obj);
- try
- {
+ try {
final ROI roi = ROIUtil.merge(rois, BooleanOperator.OR);
outputSequence.setValue(SequenceUtil.getSubSequence(s, roi));
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("roi", inputROIs);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("cropped", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
index e977e82..0ec592d 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.extract;
import icy.plugin.abstract_.Plugin;
@@ -15,52 +33,45 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class ExtractChannel extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class ExtractChannel extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarSequence outputSequence = new VarSequence("Extracted", null);
final protected VarInteger channelIdx = new VarInteger("Channel", 0);
@Override
- public void run()
- {
+ public void run() {
final Sequence s = inputSequence.getValue();
- final int channel = channelIdx.getValue().intValue();
+ final int channel = channelIdx.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
if (channel < 0 || channel >= s.getSizeC())
throw new VarException(channelIdx, "Channel index must be between 0 and " + (s.getSizeC() - 1));
- try
- {
- final Sequence res = SequenceUtil.extractChannel(s, channelIdx.getValue().intValue());
+ try {
+ final Sequence res = SequenceUtil.extractChannel(s, channelIdx.getValue());
res.setName(s.getName() + " - channel: " + channelIdx.getValue());
outputSequence.setValue(res);
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("channel", channelIdx);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("extracted", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
index 79d6aca..b17f34b 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.extract;
import icy.plugin.abstract_.Plugin;
@@ -12,50 +30,45 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.util.Arrays;
+
/**
* @author thomasprovoost
*/
-public class ExtractMultiChannels extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class ExtractMultiChannels extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarSequence outputSequence = new VarSequence("Extracted", null);
- final protected VarIntegerArrayNative channelIdx = new VarIntegerArrayNative("Channel(s)", new int[] {0});
+ final protected VarIntegerArrayNative channelIdx = new VarIntegerArrayNative("Channel(s)", new int[]{0});
@Override
- public void run()
- {
- Sequence s = inputSequence.getValue();
+ public void run() {
+ final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- try
- {
- Sequence res = SequenceUtil.extractChannels(s, channelIdx.getValue());
- res.setName(s.getName() + " - channel: " + channelIdx.getValue());
+ try {
+ final Sequence res = SequenceUtil.extractChannels(s, channelIdx.getValue());
+ res.setName(s.getName() + " - channel: " + Arrays.toString(channelIdx.getValue()));
outputSequence.setValue(res);
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("Channel", channelIdx);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("extracted", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractSlice.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractSlice.java
index d579387..789aec4 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractSlice.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractSlice.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.extract;
import icy.plugin.abstract_.Plugin;
@@ -15,38 +33,33 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class ExtractSlice extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class ExtractSlice extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarSequence outputSequence = new VarSequence("Extracted", null);
final protected VarInteger chosenZ = new VarInteger("Z", 0);
@Override
- public void run()
- {
- Sequence s = inputSequence.getValue();
+ public void run() {
+ final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- Sequence extracted = SequenceUtil.extractSlice(s, chosenZ.getValue().intValue());
+ final Sequence extracted = SequenceUtil.extractSlice(s, chosenZ.getValue());
outputSequence.setValue(extracted);
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("Z pos", chosenZ);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("extracted", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractTime.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractTime.java
index 6700458..06f3aae 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractTime.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractTime.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.extract;
import icy.plugin.abstract_.Plugin;
@@ -15,38 +33,33 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class ExtractTime extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class ExtractTime extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarSequence outputSequence = new VarSequence("Extracted", null);
final protected VarInteger chosenT = new VarInteger("T", 0);
@Override
- public void run()
- {
- Sequence s = inputSequence.getValue();
+ public void run() {
+ final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- Sequence extracted = SequenceUtil.extractFrame(s, chosenT.getValue().intValue());
+ final Sequence extracted = SequenceUtil.extractFrame(s, chosenT.getValue());
outputSequence.setValue(extracted);
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("T pos", chosenT);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("extracted", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/files/IsFileValid.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/IsFileValid.java
index 7b250ea..c4a4b5d 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/files/IsFileValid.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/files/IsFileValid.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.files;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.io.File;
+package plugins.tprovoost.sequenceblocks.files;
import icy.file.Loader;
import icy.plugin.abstract_.Plugin;
@@ -13,29 +29,26 @@ import plugins.adufour.vars.lang.VarBoolean;
import plugins.adufour.vars.lang.VarMutable;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.io.File;
+
/**
* Block to know if a file represents an image file
- *
+ *
* @author Stephane
*/
-public class IsFileValid extends Plugin implements PluginLibrary, SequenceBlock, PluginBundled
-{
- final protected VarMutable f_in = new VarMutable("File", null)
- {
+public class IsFileValid extends Plugin implements PluginLibrary, SequenceBlock, PluginBundled {
+ final protected VarMutable f_in = new VarMutable("File", null) {
@Override
- public boolean isAssignableFrom(@SuppressWarnings("rawtypes") Var source)
- {
+ public boolean isAssignableFrom(final Var source) {
return String.class == source.getType() || File.class == source.getType();
}
};
final protected VarBoolean result = new VarBoolean("Valid", Boolean.FALSE);
@Override
- public void run()
- {
+ public void run() {
final Object obj = f_in.getValue();
- if (obj != null)
- {
+ if (obj != null) {
final File f;
if (obj instanceof String)
@@ -43,25 +56,22 @@ public class IsFileValid extends Plugin implements PluginLibrary, SequenceBlock,
else
f = (File) obj;
- result.setValue(Boolean.valueOf(Loader.isSupportedImageFile(f.getAbsolutePath())));
+ result.setValue(Loader.isSupportedImageFile(f.getAbsolutePath()));
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("file", f_in);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("valid", result);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadMetadata.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadMetadata.java
index 18d6f4f..3a513a6 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadMetadata.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadMetadata.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.files;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.io.File;
+package plugins.tprovoost.sequenceblocks.files;
import icy.file.Loader;
import icy.plugin.abstract_.Plugin;
@@ -16,30 +32,27 @@ import plugins.adufour.vars.lang.VarMutable;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.io.File;
+
/**
* Block to load Sequence metadata from a file
- *
+ *
* @author Stephane
*/
-public class LoadMetadata extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- final protected VarMutable f_in = new VarMutable("File", null)
- {
+public class LoadMetadata extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ final protected VarMutable f_in = new VarMutable("File", null) {
@Override
- public boolean isAssignableFrom(@SuppressWarnings("rawtypes") Var source)
- {
+ public boolean isAssignableFrom(final Var source) {
return (String.class == source.getType()) || (File.class == source.getType());
}
};
- final protected Var<OMEXMLMetadata> output = new Var<OMEXMLMetadata>("Metadata", OMEXMLMetadata.class);
+ final protected Var<OMEXMLMetadata> output = new Var<>("Metadata", OMEXMLMetadata.class);
final protected VarInteger numSerie = new VarInteger("Series number", 1);
@Override
- public void run()
- {
+ public void run() {
final Object obj = f_in.getValue();
- if (obj != null)
- {
+ if (obj != null) {
final File f;
if (obj instanceof String)
@@ -47,39 +60,33 @@ public class LoadMetadata extends Plugin implements SequenceBlock, PluginLibrary
else
f = (File) obj;
- try
- {
+ try {
final OMEXMLMetadata meta = Loader.getOMEXMLMetaData(f.getAbsolutePath());
- if (meta != null)
- {
+ if (meta != null) {
output.setValue(meta);
- numSerie.setValue(Integer.valueOf(MetaDataUtil.getNumSeries(meta)));
+ numSerie.setValue(MetaDataUtil.getNumSeries(meta));
}
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(null, e.getMessage());
}
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("file", f_in);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("Metadata", output);
outputMap.add("Serie number", numSerie);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSequence.java
index a0135c2..44acd9b 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSequence.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.files;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.io.File;
+package plugins.tprovoost.sequenceblocks.files;
import icy.file.Loader;
import icy.plugin.abstract_.Plugin;
@@ -14,18 +30,17 @@ import plugins.adufour.vars.lang.VarMutable;
import plugins.adufour.vars.lang.VarSequence;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.io.File;
+
/**
* Block to load a Sequence from a file
- *
+ *
* @author Stephane
*/
-public class LoadSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- final protected VarMutable f_in = new VarMutable("File", null)
- {
+public class LoadSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ final protected VarMutable f_in = new VarMutable("File", null) {
@Override
- public boolean isAssignableFrom(@SuppressWarnings("rawtypes") Var source)
- {
+ public boolean isAssignableFrom(final Var source) {
return (String.class == source.getType()) || (File.class == source.getType());
}
};
@@ -33,11 +48,9 @@ public class LoadSequence extends Plugin implements SequenceBlock, PluginLibrary
final protected VarSequence outputSequence = new VarSequence("Sequence", null);
@Override
- public void run()
- {
+ public void run() {
final Object obj = f_in.getValue();
- if (obj != null)
- {
+ if (obj != null) {
final File f;
if (obj instanceof String)
@@ -48,27 +61,24 @@ public class LoadSequence extends Plugin implements SequenceBlock, PluginLibrary
// if (f.isDirectory())
// throw new VarException("file should not be a directory.");
- outputSequence.setValue(Loader.loadSequence(f.getAbsolutePath(), serie_in.getValue().intValue(), false));
+ outputSequence.setValue(Loader.loadSequence(f.getAbsolutePath(), serie_in.getValue(), false));
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("file", f_in);
inputMap.add("serie", serie_in);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("sequence", outputSequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSubSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSubSequence.java
index 27861d6..4e0ed0f 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSubSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSubSequence.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.files;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.io.File;
+package plugins.tprovoost.sequenceblocks.files;
import icy.file.Loader;
import icy.file.SequenceFileImporter;
@@ -10,22 +26,18 @@ import icy.plugin.interface_.PluginLibrary;
import icy.roi.ROI;
import plugins.adufour.blocks.tools.io.IOBlock;
import plugins.adufour.blocks.util.VarList;
-import plugins.adufour.vars.lang.Var;
-import plugins.adufour.vars.lang.VarBoolean;
-import plugins.adufour.vars.lang.VarInteger;
-import plugins.adufour.vars.lang.VarMutable;
-import plugins.adufour.vars.lang.VarROIArray;
-import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.lang.*;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.io.File;
+
/**
* Block to returns a Sequence with the given parameters from the specified closed) SequenceFileImporter.
- *
+ *
* @author Stephane
*/
-public class LoadSubSequence extends Plugin implements IOBlock, PluginLibrary, PluginBundled
-{
+public class LoadSubSequence extends Plugin implements IOBlock, PluginLibrary, PluginBundled {
final protected Var<SequenceFileImporter> importer;
final protected VarMutable file;
final protected VarInteger series;
@@ -40,16 +52,13 @@ public class LoadSubSequence extends Plugin implements IOBlock, PluginLibrary, P
final protected VarSequence sequence;
- public LoadSubSequence()
- {
+ public LoadSubSequence() {
super();
- importer = new Var<SequenceFileImporter>("Importer", SequenceFileImporter.class);
- file = new VarMutable("File", null)
- {
+ importer = new Var<>("Importer", SequenceFileImporter.class);
+ file = new VarMutable("File", null) {
@Override
- public boolean isAssignableFrom(@SuppressWarnings("rawtypes") Var source)
- {
+ public boolean isAssignableFrom(final Var source) {
return (String.class == source.getType()) || (File.class == source.getType());
}
};
@@ -67,13 +76,11 @@ public class LoadSubSequence extends Plugin implements IOBlock, PluginLibrary, P
}
@Override
- public void run()
- {
+ public void run() {
final String path;
final Object obj = file.getValue();
- if (obj != null)
- {
+ if (obj != null) {
if (obj instanceof String)
path = (String) obj;
else
@@ -84,32 +91,42 @@ public class LoadSubSequence extends Plugin implements IOBlock, PluginLibrary, P
// here importer can be null so we don't test for it
final SequenceFileImporter imp = importer.getValue();
- final int s = series.getValue().intValue();
- final int r = resolution.getValue().intValue();
+ final int s = series.getValue();
+ final int r = resolution.getValue();
final ROI[] rois = region.getValue();
final ROI roi = ((rois != null) && (rois.length > 0)) ? rois[0] : null;
- final int minZ = minZIndex.getValue().intValue();
- final int maxZ = maxZIndex.getValue().intValue();
- final int minT = minTIndex.getValue().intValue();
- final int maxT = maxTIndex.getValue().intValue();
- final int c = cIndex.getValue().intValue();
- final boolean progress = showProgress.getValue().booleanValue();
+ final int minZ = minZIndex.getValue();
+ final int maxZ = maxZIndex.getValue();
+ final int minT = minTIndex.getValue();
+ final int maxT = maxTIndex.getValue();
+ final int c = cIndex.getValue();
+ final boolean progress = showProgress.getValue();
- try
- {
- sequence.setValue(Loader.loadSequence(imp, path, s, r,
- (roi != null) ? roi.getBounds5D().toRectangle2D().getBounds() : null, minZ, maxZ, minT, maxT, c,
- false, progress));
+ try {
+ sequence.setValue(
+ Loader.loadSequence(
+ imp,
+ path,
+ s,
+ r,
+ (roi != null) ? roi.getBounds5D().toRectangle2D().getBounds() : null,
+ minZ,
+ maxZ,
+ minT,
+ maxT,
+ c,
+ false,
+ progress
+ )
+ );
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(importer, e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("file", file);
inputMap.add("importer", importer);
inputMap.add("series", series);
@@ -124,14 +141,12 @@ public class LoadSubSequence extends Plugin implements IOBlock, PluginLibrary, P
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("sequence", sequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveMetadata.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveMetadata.java
index da34944..7fadf75 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveMetadata.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveMetadata.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.files;
import icy.plugin.abstract_.Plugin;
@@ -13,39 +31,34 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to save Sequence metadata
- *
+ *
* @author Stephane
*/
-public class SaveMetadata extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class SaveMetadata extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence sequence = new VarSequence("Sequence", null);
final protected VarBoolean success = new VarBoolean("Success", Boolean.FALSE);
@Override
- public void run()
- {
- Sequence s = sequence.getValue();
+ public void run() {
+ final Sequence s = sequence.getValue();
if (s == null)
throw new VarException(sequence, "Sequence is null");
- success.setValue(Boolean.valueOf(s.saveXMLData()));
+ success.setValue(s.saveXMLData());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", sequence);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("success", success);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveSequence.java
index 98e0a21..5946db4 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveSequence.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.files;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.io.File;
+package plugins.tprovoost.sequenceblocks.files;
import icy.file.FileUtil;
import icy.file.ImageFileFormat;
@@ -11,45 +27,37 @@ import icy.plugin.interface_.PluginLibrary;
import icy.sequence.Sequence;
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
import plugins.adufour.blocks.util.VarList;
-import plugins.adufour.vars.lang.Var;
-import plugins.adufour.vars.lang.VarBoolean;
-import plugins.adufour.vars.lang.VarEnum;
-import plugins.adufour.vars.lang.VarMutable;
-import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.lang.*;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.io.File;
+
/**
* Block to save a Sequence into a file
- *
+ *
* @author Stephane
*/
-public class SaveSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- final protected VarMutable f_in = new VarMutable("File", null)
- {
+public class SaveSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ final protected VarMutable f_in = new VarMutable("File", null) {
@Override
- public boolean isAssignableFrom(@SuppressWarnings("rawtypes") Var source)
- {
+ public boolean isAssignableFrom(final Var source) {
return String.class == source.getType() || File.class == source.getType();
}
};
final protected VarBoolean overwriteForce = new VarBoolean("Overwrite", Boolean.TRUE);
final protected VarBoolean multipleFile = new VarBoolean("Multiple file", Boolean.FALSE);
final protected VarSequence sequence = new VarSequence("Sequence", null);
- final protected VarEnum<ImageFileFormat> format = new VarEnum<ImageFileFormat>("Format", ImageFileFormat.TIFF);
+ final protected VarEnum<ImageFileFormat> format = new VarEnum<>("Format", ImageFileFormat.TIFF);
@Override
- public void run()
- {
+ public void run() {
final Sequence seq = sequence.getValue();
- if (seq != null)
- {
+ if (seq != null) {
final Object obj = f_in.getValue();
- if (obj != null)
- {
+ if (obj != null) {
String path;
if (obj instanceof String)
@@ -64,19 +72,18 @@ public class SaveSequence extends Plugin implements SequenceBlock, PluginLibrary
path = FileUtil.setExtension(path, "." + format.getValue().getExtensions()[0]);
// cannot overwrite ??
- if (FileUtil.exists(path) && !overwriteForce.getValue().booleanValue())
+ if (FileUtil.exists(path) && !overwriteForce.getValue())
throw new VarException(f_in,
"File already exists. If you want to overwrite, please check the \"overwrite\" field.");
// save sequence
- Saver.save(seq, new File(path), multipleFile.getValue().booleanValue(), false);
+ Saver.save(seq, new File(path), multipleFile.getValue(), false);
}
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("file", f_in);
inputMap.add("sequence", sequence);
inputMap.add("format", format);
@@ -85,14 +92,12 @@ public class SaveSequence extends Plugin implements SequenceBlock, PluginLibrary
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/images/AddImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/AddImage.java
index 35c88c4..bddbd90 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/images/AddImage.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/images/AddImage.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.images;
import icy.image.IcyBufferedImage;
@@ -14,39 +32,34 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Add an image to the Sequence.
- *
+ *
* @author thomasprovoost
*/
-public class AddImage extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- final protected Var<IcyBufferedImage> in = new Var<IcyBufferedImage>("Image", IcyBufferedImage.class);
+public class AddImage extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ final protected Var<IcyBufferedImage> in = new Var<>("Image", IcyBufferedImage.class);
final protected VarSequence varSeq = new VarSequence("Sequence", null);
@Override
- public void run()
- {
- Sequence s = varSeq.getValue();
+ public void run() {
+ final Sequence s = varSeq.getValue();
if (s == null)
throw new VarException(varSeq, "Input sequence is null.");
s.addImage(in.getValue());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSeq);
inputMap.add("image", in);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/images/AsImageArray.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/AsImageArray.java
index 6179b1a..a9d5193 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/images/AsImageArray.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/images/AsImageArray.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.images;
import icy.image.IcyBufferedImage;
@@ -14,38 +32,33 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Returns all images from the Sequence as an image array.
- *
+ *
* @author thomasprovoost
*/
-public class AsImageArray extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- final protected VarArray<IcyBufferedImage> out = new VarArray<IcyBufferedImage>("Image array", IcyBufferedImage[].class, null);
+public class AsImageArray extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ final protected VarArray<IcyBufferedImage> out = new VarArray<>("Image array", IcyBufferedImage[].class, null);
final protected VarSequence varSeq = new VarSequence("Sequence", null);
@Override
- public void run()
- {
- Sequence s = varSeq.getValue();
+ public void run() {
+ final Sequence s = varSeq.getValue();
if (s == null)
throw new VarException(varSeq, "Input sequence is null.");
out.setValue(s.getAllImage().toArray(new IcyBufferedImage[0]));
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSeq);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("image array", out);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/images/GetImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/GetImage.java
index 748afec..71c0775 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/images/GetImage.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/images/GetImage.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.images;
import icy.image.IcyBufferedImage;
@@ -15,42 +33,37 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Get the image at the given [T,Z] position from the Sequence.
- *
+ *
* @author thomasprovoost
*/
-public class GetImage extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class GetImage extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence varSeq = new VarSequence("Sequence", null);
final protected VarInteger imgIdxT = new VarInteger("T", -1);
final protected VarInteger imgIdxZ = new VarInteger("Z", -1);
- final protected Var<IcyBufferedImage> out = new Var<IcyBufferedImage>("out", IcyBufferedImage.class);
+ final protected Var<IcyBufferedImage> out = new Var<>("out", IcyBufferedImage.class);
@Override
- public void run()
- {
- Sequence s = varSeq.getValue();
+ public void run() {
+ final Sequence s = varSeq.getValue();
if (s == null)
throw new VarException(varSeq, "Input sequence is null.");
- out.setValue(s.getImage(imgIdxT.getValue().intValue(), imgIdxZ.getValue().intValue()));
+ out.setValue(s.getImage(imgIdxT.getValue(), imgIdxZ.getValue()));
}
@Override
- public void declareInput(final VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSeq);
inputMap.add("Idx T", imgIdxT);
inputMap.add("Idx Z", imgIdxZ);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("out", out);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/images/RemoveImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/RemoveImage.java
index 1380a86..ff67393 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/images/RemoveImage.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/images/RemoveImage.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.images;
import icy.plugin.abstract_.Plugin;
@@ -13,42 +31,37 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Remove an image from the Sequence.
- *
+ *
* @author thomasprovoost
*/
-public class RemoveImage extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class RemoveImage extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
VarSequence varSeq = new VarSequence("Sequence", null);
VarInteger imgIdxT = new VarInteger("T", 0);
VarInteger imgIdxZ = new VarInteger("Z", 0);
@Override
- public void run()
- {
- Sequence s = varSeq.getValue();
+ public void run() {
+ final Sequence s = varSeq.getValue();
if (s == null)
throw new VarException(varSeq, "Input sequence is null !");
- s.removeImage(imgIdxT.getValue().intValue(), imgIdxZ.getValue().intValue());
+ s.removeImage(imgIdxT.getValue(), imgIdxZ.getValue());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSeq);
inputMap.add("Idx T", imgIdxT);
inputMap.add("Idx Z", imgIdxZ);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/images/SetImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/SetImage.java
index b185d7d..433321b 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/images/SetImage.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/images/SetImage.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.images;
import icy.image.IcyBufferedImage;
@@ -15,28 +33,25 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Set an image at the given [T,Z] position from the Sequence.
- *
+ *
* @author thomasprovoost
*/
-public class SetImage extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- Var<IcyBufferedImage> in = new Var<IcyBufferedImage>("Image", IcyBufferedImage.class);
+public class SetImage extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ Var<IcyBufferedImage> in = new Var<>("Image", IcyBufferedImage.class);
VarSequence varSeq = new VarSequence("Sequence", null);
VarInteger imgIdxT = new VarInteger("T", 0);
VarInteger imgIdxZ = new VarInteger("Z", 0);
@Override
- public void run()
- {
- Sequence s = varSeq.getValue();
+ public void run() {
+ final Sequence s = varSeq.getValue();
if (s == null)
throw new VarException(varSeq, "Input sequence is null.");
- s.setImage(imgIdxT.getValue().intValue(), imgIdxZ.getValue().intValue(), in.getValue());
+ s.setImage(imgIdxT.getValue(), imgIdxZ.getValue(), in.getValue());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSeq);
inputMap.add("image", in);
inputMap.add("Idx T", imgIdxT);
@@ -44,14 +59,12 @@ public class SetImage extends Plugin implements SequenceBlock, PluginLibrary, Pl
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
index 946af74..3485794 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
@@ -1,24 +1,38 @@
-/**
- *
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
-package plugins.tprovoost.sequenceblocks.importer;
-import java.awt.Rectangle;
-import java.io.IOException;
+package plugins.tprovoost.sequenceblocks.importer;
import icy.common.exception.UnsupportedFormatException;
import icy.file.SequenceFileImporter;
import icy.sequence.MetaDataUtil;
import ome.xml.meta.OMEXMLMetadata;
+import java.awt.*;
+import java.io.IOException;
+
/**
* This class allow to use a {@link SequenceFileImporter} while storing a current position information to make its usage
* more convenient with Protocols.
- *
+ *
* @author Stephane
*/
-public class PositionedSequenceFileImporter
-{
+public class PositionedSequenceFileImporter {
public SequenceFileImporter importer;
protected OMEXMLMetadata metadata;
public int s;
@@ -27,9 +41,7 @@ public class PositionedSequenceFileImporter
public int c;
public Rectangle xyRegion;
- public PositionedSequenceFileImporter(SequenceFileImporter importer, OMEXMLMetadata metadata, int s, int t, int z,
- int c, Rectangle xyRegion)
- {
+ public PositionedSequenceFileImporter(final SequenceFileImporter importer, final OMEXMLMetadata metadata, final int s, final int t, final int z, final int c, final Rectangle xyRegion) {
super();
this.importer = importer;
@@ -41,22 +53,25 @@ public class PositionedSequenceFileImporter
this.c = c;
}
- public PositionedSequenceFileImporter(SequenceFileImporter importer)
- {
+ public PositionedSequenceFileImporter(final SequenceFileImporter importer) {
this(importer, null, -1, -1, -1, -1, null);
}
- public PositionedSequenceFileImporter(PositionedSequenceFileImporter positionedImporter)
- {
- this(positionedImporter.importer, positionedImporter.metadata, positionedImporter.s, positionedImporter.t,
- positionedImporter.z, positionedImporter.c, positionedImporter.xyRegion);
+ public PositionedSequenceFileImporter(final PositionedSequenceFileImporter positionedImporter) {
+ this(
+ positionedImporter.importer,
+ positionedImporter.metadata,
+ positionedImporter.s,
+ positionedImporter.t,
+ positionedImporter.z,
+ positionedImporter.c,
+ positionedImporter.xyRegion
+ );
}
- public OMEXMLMetadata getMetadata() throws UnsupportedFormatException, IOException, InterruptedException
- {
+ public OMEXMLMetadata getMetadata() throws UnsupportedFormatException, IOException, InterruptedException {
// not yet defined --> take it from importer if possible
- if ((metadata == null) && (importer.getOpened() != null))
- {
+ if ((metadata == null) && (importer.getOpened() != null)) {
metadata = importer.getOMEXMLMetaData();
// clean the metadata
MetaDataUtil.clean(metadata);
@@ -66,8 +81,7 @@ public class PositionedSequenceFileImporter
}
@Override
- public String toString()
- {
+ public String toString() {
String result;
if (importer != null)
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterClose.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterClose.java
index ccaa55b..57ef466 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterClose.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterClose.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.importer;
import icy.plugin.abstract_.Plugin;
@@ -11,53 +29,45 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to close currently opened SequenceFileImporter.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterClose extends Plugin implements IOBlock, PluginLibrary, PluginBundled
-{
+public class SequenceFileImporterClose extends Plugin implements IOBlock, PluginLibrary, PluginBundled {
final protected Var<PositionedSequenceFileImporter> importer;
- public SequenceFileImporterClose()
- {
+ public SequenceFileImporterClose() {
super();
- importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
+ importer = new Var<>("Importer", PositionedSequenceFileImporter.class);
}
@Override
- public void run()
- {
+ public void run() {
final PositionedSequenceFileImporter pi = importer.getValue();
if (pi == null)
throw new VarException(importer, "Importer is null !");
- try
- {
+ try {
pi.importer.close();
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(importer, e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("importer", importer);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
index 20f07dc..dbfbc9b 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.importer;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.awt.Rectangle;
+package plugins.tprovoost.sequenceblocks.importer;
import icy.file.SequenceFileImporter;
import icy.image.IcyBufferedImage;
@@ -16,13 +32,14 @@ import plugins.adufour.vars.lang.VarROIArray;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.awt.*;
+
/**
* Block to returns an image from the given parameters and opened SequenceFileImporter.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterGetImage extends Plugin implements IOBlock, PluginLibrary, PluginBundled
-{
+public class SequenceFileImporterGetImage extends Plugin implements IOBlock, PluginLibrary, PluginBundled {
final protected Var<PositionedSequenceFileImporter> importer;
final protected VarInteger series;
final protected VarInteger resolution;
@@ -33,11 +50,10 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
final protected Var<IcyBufferedImage> image;
- public SequenceFileImporterGetImage()
- {
+ public SequenceFileImporterGetImage() {
super();
- importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
+ importer = new Var<>("Importer", PositionedSequenceFileImporter.class);
series = new VarInteger("Series", -1);
resolution = new VarInteger("Resolution (0=full, 1=1/2, ..)", 0);
region = new VarROIArray("XY region (ROI)", null);
@@ -45,12 +61,11 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
tIndex = new VarInteger("T (frame) index", -1);
cIndex = new VarInteger("C (channel) index", -1);
- image = new Var<IcyBufferedImage>("Image", IcyBufferedImage.class);
+ image = new Var<>("Image", IcyBufferedImage.class);
}
@Override
- public void run()
- {
+ public void run() {
final PositionedSequenceFileImporter pi = importer.getValue();
if (pi == null)
@@ -61,13 +76,13 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
if (imp.getOpened() == null)
throw new VarException(importer, "Importer is not opened !");
- final int res = resolution.getValue().intValue();
+ final int res = resolution.getValue();
final ROI[] rois = region.getValue();
- int s = series.getValue().intValue();
- int z = zIndex.getValue().intValue();
- int t = tIndex.getValue().intValue();
- int c = cIndex.getValue().intValue();
+ int s = series.getValue();
+ int z = zIndex.getValue();
+ int t = tIndex.getValue();
+ int c = cIndex.getValue();
Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds()
: null;
@@ -82,24 +97,21 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
c = pi.c;
if ((rect == null) && (pi.xyRegion != null))
rect = pi.xyRegion;
-
+
// still undefined ? --> set default value for series
if (s == -1)
- s = 0;
+ s = 0;
- try
- {
+ try {
image.setValue(imp.getImage(s, res, rect, z, t, c));
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(importer, e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("importer", importer);
inputMap.add("series", series);
inputMap.add("resolution", resolution);
@@ -110,14 +122,12 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("image", image);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetMetadata.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetMetadata.java
index cb20523..06f9280 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetMetadata.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetMetadata.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.importer;
import icy.file.SequenceFileImporter;
@@ -16,28 +34,25 @@ import plugins.tprovoost.sequenceblocks.infos.ReadMetadata;
/**
* Block to returns the metadata from the specified opened SequenceFileImporter.
- *
- * @see ReadMetadata
+ *
* @author Stephane
+ * @see ReadMetadata
*/
-public class SequenceFileImporterGetMetadata extends Plugin implements IOBlock, PluginLibrary, PluginBundled
-{
+public class SequenceFileImporterGetMetadata extends Plugin implements IOBlock, PluginLibrary, PluginBundled {
final protected Var<PositionedSequenceFileImporter> importer;
final protected Var<OMEXMLMetadata> metadata;
final protected VarInteger numSeries;
- public SequenceFileImporterGetMetadata()
- {
+ public SequenceFileImporterGetMetadata() {
super();
-
- importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
- metadata = new Var<OMEXMLMetadata>("Metadata", OMEXMLMetadata.class);
+
+ importer = new Var<>("Importer", PositionedSequenceFileImporter.class);
+ metadata = new Var<>("Metadata", OMEXMLMetadata.class);
numSeries = new VarInteger("Series number", 1);
}
@Override
- public void run()
- {
+ public void run() {
final PositionedSequenceFileImporter pi = importer.getValue();
if (pi == null)
@@ -48,37 +63,32 @@ public class SequenceFileImporterGetMetadata extends Plugin implements IOBlock,
if (imp.getOpened() == null)
throw new VarException(importer, "Importer is not opened !");
- try
- {
+ try {
final OMEXMLMetadata meta = imp.getOMEXMLMetaData();
metadata.setValue(meta);
if (meta != null)
- numSeries.setValue(Integer.valueOf(MetaDataUtil.getNumSeries(meta)));
+ numSeries.setValue(MetaDataUtil.getNumSeries(meta));
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(importer, e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("importer", importer);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("metadata", metadata);
outputMap.add("numSerie", numSeries);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetThumbnail.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetThumbnail.java
index 7303276..a8057ce 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetThumbnail.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetThumbnail.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.importer;
import icy.file.SequenceFileImporter;
@@ -14,27 +32,24 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to returns a thumbnail from the specified opened SequenceFileImporter.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterGetThumbnail extends Plugin implements IOBlock, PluginLibrary, PluginBundled
-{
+public class SequenceFileImporterGetThumbnail extends Plugin implements IOBlock, PluginLibrary, PluginBundled {
final protected Var<PositionedSequenceFileImporter> importer;
final protected VarInteger series;
final protected Var<IcyBufferedImage> thumbnail;
- public SequenceFileImporterGetThumbnail()
- {
+ public SequenceFileImporterGetThumbnail() {
super();
- importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
+ importer = new Var<>("Importer", PositionedSequenceFileImporter.class);
series = new VarInteger("Series", 0);
- thumbnail = new Var<IcyBufferedImage>("Thumbnail", IcyBufferedImage.class);
+ thumbnail = new Var<>("Thumbnail", IcyBufferedImage.class);
}
@Override
- public void run()
- {
+ public void run() {
final PositionedSequenceFileImporter pi = importer.getValue();
if (pi == null)
@@ -45,34 +60,29 @@ public class SequenceFileImporterGetThumbnail extends Plugin implements IOBlock,
if (imp.getOpened() == null)
throw new VarException(importer, "Importer is not opened !");
- final int s = series.getValue().intValue();
+ final int s = series.getValue();
- try
- {
+ try {
thumbnail.setValue(imp.getThumbnail(s));
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(importer, e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("importer", importer);
inputMap.add("series", series);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("thumbnail", thumbnail);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetTileSize.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetTileSize.java
index 7fa5e34..3d7f3c9 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetTileSize.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetTileSize.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.importer;
import icy.file.SequenceFileImporter;
@@ -12,30 +30,27 @@ import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
- * Block to returns the optimal tile size for region reading from the specified opened SequenceFileImporter.
- *
+ * Block to returns the optimal tile size for region reading from the specified opened SequenceFileImporter.
+ *
* @author Stephane
*/
-public class SequenceFileImporterGetTileSize extends Plugin implements IOBlock, PluginLibrary, PluginBundled
-{
+public class SequenceFileImporterGetTileSize extends Plugin implements IOBlock, PluginLibrary, PluginBundled {
final protected Var<PositionedSequenceFileImporter> importer;
final protected VarInteger series;
final protected VarInteger tileW;
final protected VarInteger tileH;
- public SequenceFileImporterGetTileSize()
- {
+ public SequenceFileImporterGetTileSize() {
super();
- importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
+ importer = new Var<>("Importer", PositionedSequenceFileImporter.class);
series = new VarInteger("Series", 0);
tileW = new VarInteger("Tile width", 0);
tileH = new VarInteger("Tile height", 0);
}
@Override
- public void run()
- {
+ public void run() {
final PositionedSequenceFileImporter pi = importer.getValue();
if (pi == null)
@@ -45,37 +60,32 @@ public class SequenceFileImporterGetTileSize extends Plugin implements IOBlock,
if (imp.getOpened() == null)
throw new VarException(importer, "Importer is not opened !");
-
- final int s = series.getValue().intValue();
- try
- {
- tileW.setValue(Integer.valueOf(imp.getTileWidth(s)));
- tileH.setValue(Integer.valueOf(imp.getTileHeight(s)));
+ final int s = series.getValue();
+
+ try {
+ tileW.setValue(imp.getTileWidth(s));
+ tileH.setValue(imp.getTileHeight(s));
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(importer, e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("importer", importer);
inputMap.add("series", series);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("tileW", tileW);
outputMap.add("tileH", tileH);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
index 666f65c..9a8b57e 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.importer;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.awt.Rectangle;
+package plugins.tprovoost.sequenceblocks.importer;
import icy.file.Loader;
import icy.file.SequenceFileImporter;
@@ -18,13 +34,14 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.awt.*;
+
/**
* Block to returns a Sequence from the given parameters and opened SequenceFileImporter.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock, PluginLibrary, PluginBundled
-{
+public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock, PluginLibrary, PluginBundled {
final protected Var<PositionedSequenceFileImporter> importer;
final protected VarInteger series;
final protected VarInteger resolution;
@@ -37,11 +54,10 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
final protected VarSequence sequence;
- public SequenceFileImporterLoadSequence()
- {
+ public SequenceFileImporterLoadSequence() {
super();
- importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
+ importer = new Var<>("Importer", PositionedSequenceFileImporter.class);
series = new VarInteger("Series", -1);
resolution = new VarInteger("Resolution (0=full, 1=1/2, ..)", 0);
@@ -56,8 +72,7 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
}
@Override
- public void run()
- {
+ public void run() {
final PositionedSequenceFileImporter pi = importer.getValue();
if (pi == null)
@@ -68,28 +83,25 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
if (imp.getOpened() == null)
throw new VarException(importer, "Importer is not opened !");
- final int res = resolution.getValue().intValue();
+ final int res = resolution.getValue();
final ROI[] rois = region.getValue();
- int s = series.getValue().intValue();
- int minZ = minZIndex.getValue().intValue();
- int maxZ = maxZIndex.getValue().intValue();
- int minT = minTIndex.getValue().intValue();
- int maxT = maxTIndex.getValue().intValue();
- int c = cIndex.getValue().intValue();
- Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds()
- : null;
+ int s = series.getValue();
+ int minZ = minZIndex.getValue();
+ int maxZ = maxZIndex.getValue();
+ int minT = minTIndex.getValue();
+ int maxT = maxTIndex.getValue();
+ int c = cIndex.getValue();
+ Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds() : null;
// 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))
- {
+ if ((minZ == -1) && (maxZ == -1) && (pi.z != -1)) {
minZ = pi.z;
maxZ = pi.z;
}
- if ((minT == -1) && (maxT == -1) && (pi.t != -1))
- {
+ if ((minT == -1) && (maxT == -1) && (pi.t != -1)) {
minT = pi.t;
maxT = pi.t;
}
@@ -97,28 +109,24 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
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
- {
-
+ try {
// get metadata
final OMEXMLMetadata meta = pi.getMetadata();
sequence.setValue(Loader.internalLoadSingle(imp, meta, s, res, rect, minZ, maxZ, minT, maxT, c, false, null));
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(importer, e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("importer", importer);
inputMap.add("series", series);
inputMap.add("resolution", resolution);
@@ -131,14 +139,12 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("sequence", sequence);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterOpen.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterOpen.java
index 720b9c6..374b4af 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterOpen.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterOpen.java
@@ -1,10 +1,22 @@
-package plugins.tprovoost.sequenceblocks.importer;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.io.File;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+package plugins.tprovoost.sequenceblocks.importer;
import icy.file.Loader;
import icy.file.SequenceFileImporter;
@@ -22,13 +34,18 @@ import plugins.adufour.vars.lang.VarString;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
/**
* Block to open a file with a given SequenceFileImporter.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterOpen extends Plugin implements IOBlock, PluginLibrary, PluginBundled
-{
+public class SequenceFileImporterOpen extends Plugin implements IOBlock, PluginLibrary, PluginBundled {
final static String ID_AUTO = "Automatic";
final protected VarString importerName;
@@ -39,59 +56,50 @@ public class SequenceFileImporterOpen extends Plugin implements IOBlock, PluginL
// internal
final protected Map<String, SequenceFileImporter> importersMap;
- public SequenceFileImporterOpen()
- {
+ public SequenceFileImporterOpen() {
super();
- final List<String> importersName = new ArrayList<String>();
+ final List<String> importersName = new ArrayList<>();
final List<SequenceFileImporter> importers = Loader.getSequenceFileImporters();
importerName = new VarString("Select importer", "", 1 + importers.size());
// build importer map
- importersMap = new HashMap<String, SequenceFileImporter>();
+ importersMap = new HashMap<>();
// automatic selection
importersName.add(ID_AUTO);
importersMap.put(ID_AUTO, null);
- for (SequenceFileImporter importer : importers)
- {
+ for (final SequenceFileImporter importer : importers) {
String className = ClassUtil.getBaseClassName(importer.getClass().getName());
final int ind = className.lastIndexOf('.');
// just get final class name without package name
if (ind > -1)
- className = className.substring(ind + 1, className.length());
+ className = className.substring(ind + 1);
importersName.add(className);
importersMap.put(className, importer);
}
// initialize importer selector field
- importerName.setDefaultEditorModel(new ValueSelectionModel<String>(
- importersName.toArray(new String[importersName.size()]), importersName.get(0), false));
+ importerName.setDefaultEditorModel(new ValueSelectionModel<>(importersName.toArray(new String[0]), importersName.get(0), false));
- importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
- file = new VarMutable("File", null)
- {
- @SuppressWarnings("rawtypes")
+ importer = new Var<>("Importer", PositionedSequenceFileImporter.class);
+ file = new VarMutable("File", null) {
@Override
- public boolean isAssignableFrom(Var source)
- {
+ public boolean isAssignableFrom(final Var source) {
return (String.class == source.getType()) || (File.class == source.getType());
}
};
flag = new VarInteger("Flag", 0);
}
- @SuppressWarnings("resource")
@Override
- public void run()
- {
+ public void run() {
final String path;
final Object obj = file.getValue();
- if (obj != null)
- {
+ if (obj != null) {
if (obj instanceof String)
path = (String) obj;
else
@@ -114,34 +122,29 @@ public class SequenceFileImporterOpen extends Plugin implements IOBlock, PluginL
// set importer
importer.setValue(new PositionedSequenceFileImporter(imp));
- try
- {
+ try {
// try to open the importer
- imp.open(path, flag.getValue().intValue());
+ imp.open(path, flag.getValue());
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(importer, e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("name", importerName);
inputMap.add("file", file);
inputMap.add("flag", flag);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("importer", importer);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/CreateLinearColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/CreateLinearColormap.java
index 7616d67..5251a07 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/CreateLinearColormap.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/CreateLinearColormap.java
@@ -1,48 +1,60 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.image.colormap.LinearColorMap;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
-
-import java.awt.Color;
-
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarColor;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.awt.*;
+
/**
* Block to create a linear colormap from a color value
- *
+ *
* @author Stephane
* @see SetColormap
*/
-public class CreateLinearColormap extends Plugin implements SequenceBlock, PluginBundled
-{
- private VarColor color = new VarColor("Color", Color.white);
- private VarColormap colormap = new VarColormap("Color map", LinearColorMap.gray_);
+public class CreateLinearColormap extends Plugin implements SequenceBlock, PluginBundled {
+ private final VarColor color = new VarColor("Color", Color.white);
+ private final VarColormap colormap = new VarColormap("Color map", LinearColorMap.gray_);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("input", color);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("output", colormap);
}
@Override
- public void run()
- {
+ public void run() {
colormap.setValue(new LinearColorMap("color", color.getValue()));
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/Dimensions.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/Dimensions.java
index 3dbc2df..97d49b1 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/Dimensions.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/Dimensions.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -14,8 +32,7 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class Dimensions extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class Dimensions extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
VarSequence varSeq = new VarSequence("Sequence", null);
VarInteger sizeZ = new VarInteger("Size Z", 1);
VarInteger sizeT = new VarInteger("Size T", 1);
@@ -24,28 +41,25 @@ public class Dimensions extends Plugin implements SequenceBlock, PluginLibrary,
VarInteger height = new VarInteger("Height", 1);
@Override
- public void run()
- {
- Sequence s = varSeq.getValue();
+ public void run() {
+ final Sequence s = varSeq.getValue();
if (s == null)
throw new VarException(varSeq, "Input sequence is null.");
-
- width.setValue(Integer.valueOf(s.getWidth()));
- height.setValue(Integer.valueOf(s.getHeight()));
- sizeC.setValue(Integer.valueOf(s.getSizeC()));
- sizeZ.setValue(Integer.valueOf(s.getSizeZ()));
- sizeT.setValue(Integer.valueOf(s.getSizeT()));
+
+ width.setValue(s.getWidth());
+ height.setValue(s.getHeight());
+ sizeC.setValue(s.getSizeC());
+ sizeZ.setValue(s.getSizeZ());
+ sizeT.setValue(s.getSizeT());
}
@Override
- public void declareInput(final VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSeq);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("width", width);
outputMap.add("height", height);
outputMap.add("size C", sizeC);
@@ -54,8 +68,7 @@ public class Dimensions extends Plugin implements SequenceBlock, PluginLibrary,
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/EzVarColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/EzVarColormap.java
index a810bec..99c314b 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/EzVarColormap.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/EzVarColormap.java
@@ -1,20 +1,35 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.image.colormap.IcyColorMap;
import plugins.adufour.ezplug.EzVar;
import plugins.tprovoost.sequenceblocks.infos.VarColormap.ColormapSelectionModel;
-public class EzVarColormap extends EzVar<IcyColorMap>
-{
+public class EzVarColormap extends EzVar<IcyColorMap> {
/**
* Constructs a new variable that handles colormap data.
- *
- * @param varName
- * the parameter name
+ *
+ * @param varName the parameter name
* @param defaultValue IcyColorMap
*/
- public EzVarColormap(String varName, IcyColorMap defaultValue)
- {
+ public EzVarColormap(final String varName, final IcyColorMap defaultValue) {
super(new VarColormap(varName, defaultValue), new ColormapSelectionModel());
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelName.java
index ba5f734..322a46f 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelName.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -14,20 +32,18 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class GetChannelName extends Plugin implements SequenceBlock, PluginBundled
-{
- private VarSequence varSequence = new VarSequence("Sequence", null);
- private VarInteger varIdx = new VarInteger("Channel", 0);
- private VarString varName = new VarString("Name", "");
+public class GetChannelName extends Plugin implements SequenceBlock, PluginBundled {
+ private final VarSequence varSequence = new VarSequence("Sequence", null);
+ private final VarInteger varIdx = new VarInteger("Channel", 0);
+ private final VarString varName = new VarString("Name", "");
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
+ public void run() {
+ final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
- int index = varIdx.getValue().intValue();
+ final int index = varIdx.getValue();
if (index < 0 || index >= s.getSizeC())
throw new VarException(varIdx, "Wrong channel index.");
@@ -35,21 +51,18 @@ public class GetChannelName extends Plugin implements SequenceBlock, PluginBundl
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
inputMap.add("index", varIdx);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("name", varName);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelsName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelsName.java
index 5506b01..2daceba 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelsName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelsName.java
@@ -1,12 +1,26 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
import icy.sequence.Sequence;
-
-import java.util.ArrayList;
-import java.util.List;
-
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarArray;
@@ -14,48 +28,46 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Block to retrieve all channels name from a given sequence
- *
+ *
* @author Stephane
* @see GetChannelName
* @see SetChannelsName
*/
-public class GetChannelsName extends Plugin implements SequenceBlock, PluginBundled
-{
- private VarSequence varSequence = new VarSequence("Sequence", null);
- private VarArray<String> varNames = new VarArray<String>("Names", String[].class, new String[0]);
+public class GetChannelsName extends Plugin implements SequenceBlock, PluginBundled {
+ private final VarSequence varSequence = new VarSequence("Sequence", null);
+ private final VarArray<String> varNames = new VarArray<>("Names", String[].class, new String[0]);
@Override
- public void run()
- {
+ public void run() {
final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
- final List<String> names = new ArrayList<String>();
+ final List<String> names = new ArrayList<>();
for (int c = 0; c < s.getSizeC(); c++)
names.add(s.getChannelName(c));
- varNames.setValue(names.toArray(new String[names.size()]));
+ varNames.setValue(names.toArray(new String[0]));
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("names", varNames);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormap.java
index 98a564d..95b76ad 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormap.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormap.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.image.colormap.LinearColorMap;
@@ -13,37 +31,32 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to retrieve a channel colormap from a given sequence
- *
+ *
* @author Stephane
* @see SetColormap
*/
-public class GetColormap extends Plugin implements SequenceBlock, PluginBundled
-{
- private VarSequence sequenceIn = new VarSequence("Sequence", null);
- private VarInteger numChannel = new VarInteger("Channel", 0);
- private VarColormap colormap = new VarColormap("Color map", LinearColorMap.gray_);
+public class GetColormap extends Plugin implements SequenceBlock, PluginBundled {
+ private final VarSequence sequenceIn = new VarSequence("Sequence", null);
+ private final VarInteger numChannel = new VarInteger("Channel", 0);
+ private final VarColormap colormap = new VarColormap("Color map", LinearColorMap.gray_);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("input", sequenceIn);
inputMap.add("numChannel", numChannel);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("output", colormap);
}
@Override
- public void run()
- {
+ public void run() {
final Sequence seq = sequenceIn.getValue();
- if (seq != null)
- {
- final int ch = numChannel.getValue().intValue();
+ if (seq != null) {
+ final int ch = numChannel.getValue();
if (ch < seq.getSizeC())
colormap.setValue(seq.getColorMap(ch));
@@ -53,8 +66,7 @@ public class GetColormap extends Plugin implements SequenceBlock, PluginBundled
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormaps.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormaps.java
index dcc86d7..3654a05 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormaps.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormaps.java
@@ -1,13 +1,27 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.image.colormap.IcyColorMap;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
import icy.sequence.Sequence;
-
-import java.util.ArrayList;
-import java.util.List;
-
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarArray;
@@ -15,48 +29,45 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Block to retrieve all channels colormap from a given sequence
- *
+ *
* @author Stephane
* @see SetColormaps
*/
-public class GetColormaps extends Plugin implements SequenceBlock, PluginBundled
-{
- private VarSequence sequenceIn = new VarSequence("Sequence", null);
- private VarArray<IcyColorMap> colormaps = new VarArray<IcyColorMap>("Color maps", IcyColorMap[].class,
- new IcyColorMap[0]);
+public class GetColormaps extends Plugin implements SequenceBlock, PluginBundled {
+ private final VarSequence sequenceIn = new VarSequence("Sequence", null);
+ private final VarArray<IcyColorMap> colormaps = new VarArray<>("Color maps", IcyColorMap[].class, new IcyColorMap[0]);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("input", sequenceIn);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("Colormaps", colormaps);
}
@Override
- public void run()
- {
+ public void run() {
final Sequence seq = sequenceIn.getValue();
if (seq == null)
throw new VarException(sequenceIn, "Sequence is null");
- final List<IcyColorMap> cms = new ArrayList<IcyColorMap>();
+ final List<IcyColorMap> cms = new ArrayList<>();
for (int c = 0; c < seq.getSizeC(); c++)
cms.add(seq.getColorMap(c));
- colormaps.setValue(cms.toArray(new IcyColorMap[cms.size()]));
+ colormaps.setValue(cms.toArray(new IcyColorMap[0]));
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetDataType.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetDataType.java
index d47fe2d..283b759 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetDataType.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetDataType.java
@@ -1,6 +1,21 @@
-/**
- *
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -16,38 +31,33 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Returns the DataType of the Sequence object
- *
+ *
* @author Stephane
*/
-public class GetDataType extends Plugin implements SequenceBlock, PluginBundled
-{
+public class GetDataType extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
- final protected VarEnum<DataType> type = new VarEnum<DataType>("Data type", DataType.UBYTE);
+ final protected VarEnum<DataType> type = new VarEnum<>("Data type", DataType.UBYTE);
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
+ public void run() {
+ final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
type.setValue(s.getDataType_());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("type", type);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
index 2bf3699..0bc1e12 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
@@ -1,6 +1,21 @@
-/**
- *
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.file.FileUtil;
@@ -17,20 +32,18 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Returns the origin filename (from where the sequence has been loaded / saved)
- *
+ *
* @author Stephane
*/
-public class GetFileName extends Plugin implements SequenceBlock, PluginBundled
-{
+public class GetFileName extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
final protected VarString filename = new VarString("Filename", "");
final protected VarBoolean withFolder = new VarBoolean("Folder", Boolean.TRUE);
final protected VarBoolean withExtension = new VarBoolean("Extension", Boolean.TRUE);
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
+ public void run() {
+ final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
@@ -38,32 +51,29 @@ public class GetFileName extends Plugin implements SequenceBlock, PluginBundled
String result = s.getFilename();
// remove folder information ?
- if (!withFolder.getValue().booleanValue())
+ if (!withFolder.getValue())
result = FileUtil.getFileName(result);
// remove extension ?
- if (!withExtension.getValue().booleanValue())
+ if (!withExtension.getValue())
result = FileUtil.setExtension(result, "");
filename.setValue(result);
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
inputMap.add("folder", withFolder);
inputMap.add("extension", withExtension);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("name", filename);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetMetaData.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetMetaData.java
index db267be..4f51fdf 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetMetaData.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetMetaData.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.infos;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.awt.Rectangle;
+package plugins.tprovoost.sequenceblocks.infos;
import icy.math.UnitUtil;
import icy.plugin.abstract_.Plugin;
@@ -9,24 +25,21 @@ import icy.sequence.Sequence;
import ome.xml.meta.OMEXMLMetadata;
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
import plugins.adufour.blocks.util.VarList;
-import plugins.adufour.vars.lang.Var;
-import plugins.adufour.vars.lang.VarDouble;
-import plugins.adufour.vars.lang.VarInteger;
-import plugins.adufour.vars.lang.VarSequence;
-import plugins.adufour.vars.lang.VarString;
+import plugins.adufour.vars.lang.*;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.awt.*;
+
/**
* Block to return metadata information from a Sequence object.
*
- * @see ReadMetadata
* @author Stephane
+ * @see ReadMetadata
*/
-public class GetMetaData extends Plugin implements SequenceBlock, PluginBundled
-{
+public class GetMetaData extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
- final protected Var<OMEXMLMetadata> metaData = new Var<OMEXMLMetadata>("Metadata", OMEXMLMetadata.class);
+ final protected Var<OMEXMLMetadata> metaData = new Var<>("Metadata", OMEXMLMetadata.class);
final protected VarString name = new VarString("Name", "");
final protected VarInteger seriesIndex = new VarInteger("Series index", 0);
final protected VarDouble pxSizeX = new VarDouble("Pixel Size X (" + UnitUtil.MICRO_STRING + "m)", 1d);
@@ -37,7 +50,7 @@ public class GetMetaData extends Plugin implements SequenceBlock, PluginBundled
final protected VarDouble positionY = new VarDouble("Position Y (" + UnitUtil.MICRO_STRING + "m)", 0d);
final protected VarDouble positionZ = new VarDouble("Position Z (" + UnitUtil.MICRO_STRING + "m)", 0d);
final protected VarInteger originResolution = new VarInteger("Resolution", 0);
- final protected Var<Rectangle> originRegion = new Var<Rectangle>("Region", new Rectangle());
+ final protected Var<Rectangle> originRegion = new Var<>("Region", new Rectangle());
final protected VarInteger originZMin = new VarInteger("Z min", -1);
final protected VarInteger originZMax = new VarInteger("Z max", -1);
final protected VarInteger originTMin = new VarInteger("T min", -1);
@@ -45,41 +58,38 @@ public class GetMetaData extends Plugin implements SequenceBlock, PluginBundled
final protected VarInteger originChannel = new VarInteger("Channel", -1);
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
+ public void run() {
+ final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
metaData.setValue(s.getOMEXMLMetadata());
name.setValue(s.getName());
- seriesIndex.setValue(Integer.valueOf(s.getSeries()));
- pxSizeX.setValue(Double.valueOf(s.getPixelSizeX()));
- pxSizeY.setValue(Double.valueOf(s.getPixelSizeY()));
- pxSizeZ.setValue(Double.valueOf(s.getPixelSizeZ()));
- timeIntT.setValue(Double.valueOf(s.getTimeInterval()));
- positionX.setValue(Double.valueOf(s.getPositionX()));
- positionY.setValue(Double.valueOf(s.getPositionY()));
- positionZ.setValue(Double.valueOf(s.getPositionZ()));
- originResolution.setValue(Integer.valueOf(s.getOriginResolution()));
+ seriesIndex.setValue(s.getSeries());
+ pxSizeX.setValue(s.getPixelSizeX());
+ pxSizeY.setValue(s.getPixelSizeY());
+ pxSizeZ.setValue(s.getPixelSizeZ());
+ timeIntT.setValue(s.getTimeInterval());
+ positionX.setValue(s.getPositionX());
+ positionY.setValue(s.getPositionY());
+ positionZ.setValue(s.getPositionZ());
+ originResolution.setValue(s.getOriginResolution());
originRegion.setValue(s.getOriginXYRegion());
- originZMin.setValue(Integer.valueOf(s.getOriginZMin()));
- originZMax.setValue(Integer.valueOf(s.getOriginZMax()));
- originTMin.setValue(Integer.valueOf(s.getOriginTMin()));
- originTMax.setValue(Integer.valueOf(s.getOriginTMax()));
- originChannel.setValue(Integer.valueOf(s.getOriginChannel()));
+ originZMin.setValue(s.getOriginZMin());
+ originZMax.setValue(s.getOriginZMax());
+ originTMin.setValue(s.getOriginTMin());
+ originTMax.setValue(s.getOriginTMax());
+ originChannel.setValue(s.getOriginChannel());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("metadata", metaData);
outputMap.add("name", name);
outputMap.add("seriesIndex", seriesIndex);
@@ -100,8 +110,7 @@ public class GetMetaData extends Plugin implements SequenceBlock, PluginBundled
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetName.java
index c102a40..46a6ed6 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetName.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -12,38 +30,33 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Returns the name of the Sequence object
- *
+ *
* @author Stephane
*/
-public class GetName extends Plugin implements SequenceBlock, PluginBundled
-{
+public class GetName extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
final protected VarString name = new VarString("Name", "");
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
+ public void run() {
+ final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
name.setValue(s.getName());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("name", name);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetOutputFilename.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetOutputFilename.java
index 3e9deec..55e7085 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetOutputFilename.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetOutputFilename.java
@@ -1,6 +1,21 @@
-/**
- *
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.file.FileUtil;
@@ -17,48 +32,43 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Returns the output filename generated from origin filename and internal partitioning information
- *
+ *
* @author Stephane
*/
-public class GetOutputFilename extends Plugin implements SequenceBlock, PluginBundled
-{
+public class GetOutputFilename extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
final protected VarString outFilename = new VarString("Output filename", "");
final protected VarBoolean withFolder = new VarBoolean("Folder", Boolean.TRUE);
final protected VarBoolean withExtension = new VarBoolean("Extension", Boolean.TRUE);
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
+ public void run() {
+ final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
- String result = s.getOutputFilename(withExtension.getValue().booleanValue());
+ String result = s.getOutputFilename(withExtension.getValue());
- if (!withFolder.getValue().booleanValue())
+ if (!withFolder.getValue())
result = FileUtil.getFileName(result);
outFilename.setValue(result);
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
inputMap.add("folder", withFolder);
inputMap.add("extension", withExtension);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("outFilename", outFilename);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetResolution.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetResolution.java
index 053d573..0323af8 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetResolution.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetResolution.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.math.UnitUtil;
@@ -14,12 +32,11 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to return pixel size and time interval information from a Sequence object.
*
+ * @author Stephane
* @see ReadMetadata
* @see GetMetaData
- * @author Stephane
*/
-public class GetResolution extends Plugin implements SequenceBlock, PluginBundled
-{
+public class GetResolution extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
final protected VarDouble pxSizeX = new VarDouble("Pixel Size X (" + UnitUtil.MICRO_STRING + "m)", 1d);
final protected VarDouble pxSizeY = new VarDouble("Pixel Size Y (" + UnitUtil.MICRO_STRING + "m)", 1d);
@@ -27,31 +44,26 @@ public class GetResolution extends Plugin implements SequenceBlock, PluginBundle
final protected VarDouble timeIntT = new VarDouble("Time interval T (s)", 0.1d);
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
- if (s != null)
- {
- pxSizeX.setValue(Double.valueOf(s.getPixelSizeX()));
- pxSizeY.setValue(Double.valueOf(s.getPixelSizeY()));
- pxSizeZ.setValue(Double.valueOf(s.getPixelSizeZ()));
- timeIntT.setValue(Double.valueOf(s.getTimeInterval()));
+ public void run() {
+ final Sequence s = varSequence.getValue();
+ if (s != null) {
+ pxSizeX.setValue(s.getPixelSizeX());
+ pxSizeY.setValue(s.getPixelSizeY());
+ pxSizeZ.setValue(s.getPixelSizeZ());
+ timeIntT.setValue(s.getTimeInterval());
}
- else
- {
+ else {
throw new VarException(varSequence, "Sequence is null");
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("Pixel Size X (" + UnitUtil.MICRO_STRING + "m)", pxSizeX);
outputMap.add("Pixel Size Y (" + UnitUtil.MICRO_STRING + "m)", pxSizeY);
outputMap.add("Pixel Size Z (" + UnitUtil.MICRO_STRING + "m)", pxSizeZ);
@@ -59,8 +71,7 @@ public class GetResolution extends Plugin implements SequenceBlock, PluginBundle
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetRoisAsRegion.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetRoisAsRegion.java
index 2ddd6e7..bc4a279 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetRoisAsRegion.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetRoisAsRegion.java
@@ -1,8 +1,22 @@
-package plugins.tprovoost.sequenceblocks.infos;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.List;
+package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
@@ -20,38 +34,39 @@ import plugins.adufour.vars.util.VarException;
import plugins.kernel.roi.roi2d.ROI2DRectangle;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.awt.*;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Block to retrieve ROI(s) from a Sequence as 2D Rectangular regions.<br>
* The <i>origin resolution</i> parameter indicate if we want to rescale ROI to the original image resolution in case we
* have a Sequence which represents a sub resolution of the original image.
- *
+ *
* @author Stephane
*/
-public class GetRoisAsRegion extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- public static enum TypeSelection
- {
+public class GetRoisAsRegion extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ public enum TypeSelection {
ALL, SELECTED
- };
+ }
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
- final protected VarEnum<TypeSelection> type = new VarEnum<TypeSelection>("ROI(s) to get", TypeSelection.ALL);
+ final protected VarEnum<TypeSelection> type = new VarEnum<>("ROI(s) to get", TypeSelection.ALL);
final protected VarBoolean originResolution = new VarBoolean("Origin resolution", Boolean.TRUE);
final protected VarROIArray regionsRois = new VarROIArray("Region ROI(s)", null);
@Override
- public void run()
- {
+ public void run() {
final Sequence sequence = inputSequence.getValue();
if (sequence == null)
throw new VarException(inputSequence, "Input sequence is null.");
final List<ROI> rois;
- final List<ROI2DRectangle> result = new ArrayList<ROI2DRectangle>();
+ final List<ROI2DRectangle> result = new ArrayList<>();
- switch (type.getValue())
- {
+ switch (type.getValue()) {
default:
+ case ALL:
rois = sequence.getROIs();
break;
case SELECTED:
@@ -59,11 +74,10 @@ public class GetRoisAsRegion extends Plugin implements SequenceBlock, PluginLibr
break;
}
- final boolean scale = originResolution.getValue().booleanValue();
+ final boolean scale = originResolution.getValue();
// build rectangular ROI(s)
- for (ROI roi : rois)
- {
+ for (final ROI roi : rois) {
// get ROI 2D bounds
Rectangle rect = roi.getBounds5D().toRectangle2D().getBounds();
@@ -75,26 +89,23 @@ public class GetRoisAsRegion extends Plugin implements SequenceBlock, PluginLibr
result.add(new ROI2DRectangle(rect));
}
- regionsRois.setValue(result.toArray(new ROI[result.size()]));
+ regionsRois.setValue(result.toArray(new ROI[0]));
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("type", type);
inputMap.add("originResolution", originResolution);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("regionsRois", regionsRois);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetSequenceProperty.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetSequenceProperty.java
index 278ae20..65a6838 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetSequenceProperty.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetSequenceProperty.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -29,18 +47,16 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
* <li><i>userName</i> = user who generated / acquired the dataset</li>
* <li><i>virtual</i> = virtual mode enabled on the dataset</li>
* </ul>
- *
+ *
* @author Stephane
*/
-public class GetSequenceProperty extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class GetSequenceProperty extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
protected VarSequence sequence = new VarSequence("Sequence", null);
protected VarString propertyName = new VarString("Property", "name");
protected VarString value = new VarString("Value", "");
@Override
- public void run()
- {
+ public void run() {
final Sequence seq = sequence.getValue();
if (seq != null)
@@ -48,21 +64,18 @@ public class GetSequenceProperty extends Plugin implements SequenceBlock, Plugin
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", sequence);
inputMap.add("property", propertyName);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("value", value);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/ReadMetadata.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/ReadMetadata.java
index 1abdef6..2ac3d0b 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/ReadMetadata.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/ReadMetadata.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.math.UnitUtil;
@@ -18,13 +36,12 @@ import plugins.tprovoost.sequenceblocks.files.LoadMetadata;
/**
* Block to return main informations from a metadata object.
- *
- * @see LoadMetadata
+ *
* @author Stephane
+ * @see LoadMetadata
*/
-public class ReadMetadata extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
- final protected Var<OMEXMLMetadata> metadata = new Var<OMEXMLMetadata>("Metadata", OMEXMLMetadata.class);
+public class ReadMetadata extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
+ final protected Var<OMEXMLMetadata> metadata = new Var<>("Metadata", OMEXMLMetadata.class);
final protected VarInteger serie = new VarInteger("Series", 0);
final protected VarInteger numSerie = new VarInteger("Num serie", 1);
@@ -43,47 +60,43 @@ public class ReadMetadata extends Plugin implements SequenceBlock, PluginLibrary
final protected VarDouble positionZ = new VarDouble("Position Z (" + UnitUtil.MICRO_STRING + "m)", 0d);
@Override
- public void run()
- {
+ public void run() {
final OMEXMLMetadata meta = metadata.getValue();
if (meta == null)
throw new VarException(metadata, "Metadata is null !");
- final int s = serie.getValue().intValue();
+ final int s = serie.getValue();
final int numS = MetaDataUtil.getNumSeries(meta);
- numSerie.setValue(Integer.valueOf(numS));
+ numSerie.setValue(numS);
if (s >= numS)
throw new VarException(serie, "Serie index must be between 0 and " + (numS - 1));
name.setValue(MetaDataUtil.getName(meta, s));
- sizeX.setValue(Integer.valueOf(MetaDataUtil.getSizeX(meta, s)));
- sizeY.setValue(Integer.valueOf(MetaDataUtil.getSizeY(meta, s)));
- sizeZ.setValue(Integer.valueOf(MetaDataUtil.getSizeZ(meta, s)));
- sizeT.setValue(Integer.valueOf(MetaDataUtil.getSizeT(meta, s)));
- sizeC.setValue(Integer.valueOf(MetaDataUtil.getSizeC(meta, s)));
- pxSizeX.setValue(Double.valueOf(MetaDataUtil.getPixelSizeX(meta, s, pxSizeX.getDefaultValue().doubleValue())));
- pxSizeY.setValue(Double.valueOf(MetaDataUtil.getPixelSizeY(meta, s, pxSizeY.getDefaultValue().doubleValue())));
- pxSizeZ.setValue(Double.valueOf(MetaDataUtil.getPixelSizeZ(meta, s, pxSizeZ.getDefaultValue().doubleValue())));
- timeIntT.setValue(
- Double.valueOf(MetaDataUtil.getTimeInterval(meta, s, timeIntT.getDefaultValue().doubleValue())));
+ sizeX.setValue(MetaDataUtil.getSizeX(meta, s));
+ sizeY.setValue(MetaDataUtil.getSizeY(meta, s));
+ sizeZ.setValue(MetaDataUtil.getSizeZ(meta, s));
+ sizeT.setValue(MetaDataUtil.getSizeT(meta, s));
+ sizeC.setValue(MetaDataUtil.getSizeC(meta, s));
+ pxSizeX.setValue(MetaDataUtil.getPixelSizeX(meta, s, pxSizeX.getDefaultValue()));
+ pxSizeY.setValue(MetaDataUtil.getPixelSizeY(meta, s, pxSizeY.getDefaultValue()));
+ pxSizeZ.setValue(MetaDataUtil.getPixelSizeZ(meta, s, pxSizeZ.getDefaultValue()));
+ timeIntT.setValue(MetaDataUtil.getTimeInterval(meta, s, timeIntT.getDefaultValue()));
// get position of first plane only for now
- positionX.setValue(Double.valueOf(MetaDataUtil.getPositionX(meta, s, 0, 0, 0, 0d)));
- positionY.setValue(Double.valueOf(MetaDataUtil.getPositionY(meta, s, 0, 0, 0, 0d)));
- positionZ.setValue(Double.valueOf(MetaDataUtil.getPositionZ(meta, s, 0, 0, 0, 0d)));
+ positionX.setValue(MetaDataUtil.getPositionX(meta, s, 0, 0, 0, 0d));
+ positionY.setValue(MetaDataUtil.getPositionY(meta, s, 0, 0, 0, 0d));
+ positionZ.setValue(MetaDataUtil.getPositionZ(meta, s, 0, 0, 0, 0d));
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("Metadata", metadata);
inputMap.add("Serie", serie);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("numSerie", numSerie);
outputMap.add("Name", name);
outputMap.add("Size X", sizeX);
@@ -101,8 +114,7 @@ public class ReadMetadata extends Plugin implements SequenceBlock, PluginLibrary
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelName.java
index 2b94357..336b7f6 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelName.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -14,29 +32,27 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to set channel name of the specified sequence
- *
+ *
* @author Stephane
* @see GetChannelsName
* @see SetChannelName
*/
-public class SetChannelName extends Plugin implements SequenceBlock, PluginBundled
-{
+public class SetChannelName extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
final protected VarString varName = new VarString("Name", "");
final protected VarInteger idx = new VarInteger("Channel", 0);
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
+ public void run() {
+ final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
- int index = idx.getValue().intValue();
+ final int index = idx.getValue();
if (index < 0 || index >= s.getSizeC())
throw new VarException(idx, "Wrong channel index.");
- String name = varName.getName();
+ final String name = varName.getName();
if (StringUtil.isEmpty(name))
throw new VarException(varName, "Name cannot be empty");
@@ -44,22 +60,19 @@ public class SetChannelName extends Plugin implements SequenceBlock, PluginBundl
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
inputMap.add("index", idx);
inputMap.add("name", varName);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelsName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelsName.java
index ce421ee..d735499 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelsName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelsName.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -12,19 +30,17 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to set all channels name of the specified sequence
- *
+ *
* @author Stephane
* @see GetChannelsName
* @see SetChannelName
*/
-public class SetChannelsName extends Plugin implements SequenceBlock, PluginBundled
-{
+public class SetChannelsName extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
- final protected VarArray<String> varNames = new VarArray<String>("Names", String[].class, new String[0]);
+ final protected VarArray<String> varNames = new VarArray<>("Names", String[].class, new String[0]);
@Override
- public void run()
- {
+ public void run() {
final Sequence s = varSequence.getValue();
if (s == null)
throw new VarException(varSequence, "Sequence is null");
@@ -38,21 +54,18 @@ public class SetChannelsName extends Plugin implements SequenceBlock, PluginBund
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
inputMap.add("names", varNames);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormap.java
index 3a7e57c..5abab03 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormap.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormap.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.image.colormap.IcyColorMap;
@@ -12,34 +30,29 @@ import plugins.adufour.vars.lang.VarInteger;
import plugins.adufour.vars.lang.VarSequence;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
-public class SetColormap extends Plugin implements SequenceBlock, PluginBundled
-{
+public class SetColormap extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence sequenceIn = new VarSequence("Sequence", null);
final protected VarInteger numChannel = new VarInteger("Channel", 0);
final protected VarColormap colormap = new VarColormap("Color map", LinearColorMap.gray_);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("input", sequenceIn);
inputMap.add("numChannel", numChannel);
inputMap.add("colormap", colormap);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
// no output here
}
@Override
- public void run()
- {
+ public void run() {
final Sequence seq = sequenceIn.getValue();
- if (seq != null)
- {
- final int ch = numChannel.getValue().intValue();
+ if (seq != null) {
+ final int ch = numChannel.getValue();
final IcyColorMap map = colormap.getValue();
if ((ch < seq.getSizeC()) && (map != null))
@@ -50,8 +63,7 @@ public class SetColormap extends Plugin implements SequenceBlock, PluginBundled
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormaps.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormaps.java
index 9e0d9e5..09c5873 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormaps.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormaps.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.image.colormap.IcyColorMap;
@@ -11,28 +29,23 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
-public class SetColormaps extends Plugin implements SequenceBlock, PluginBundled
-{
+public class SetColormaps extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence sequenceIn = new VarSequence("Input", null);
- final protected VarArray<IcyColorMap> colormaps = new VarArray<IcyColorMap>("Color maps", IcyColorMap[].class,
- new IcyColorMap[0]);
+ final protected VarArray<IcyColorMap> colormaps = new VarArray<>("Color maps", IcyColorMap[].class, new IcyColorMap[0]);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("input", sequenceIn);
inputMap.add("colormaps", colormaps);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
// no output here
}
@Override
- public void run()
- {
+ public void run() {
final Sequence seq = sequenceIn.getValue();
if (seq == null)
throw new VarException(sequenceIn, "Sequence is null");
@@ -46,8 +59,7 @@ public class SetColormaps extends Plugin implements SequenceBlock, PluginBundled
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetName.java
index 2cf4be8..82085ef 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetName.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -13,41 +31,34 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class SetName extends Plugin implements SequenceBlock, PluginBundled
-{
+public class SetName extends Plugin implements SequenceBlock, PluginBundled {
final protected VarSequence varSequence = new VarSequence("Sequence", null);
final protected VarString name = new VarString("Name", "");
@Override
- public void run()
- {
- Sequence s = varSequence.getValue();
- if (s != null)
- {
+ public void run() {
+ final Sequence s = varSequence.getValue();
+ if (s != null) {
s.setName(name.getValue());
}
- else
- {
+ else {
throw new VarException(varSequence, "Sequence is null");
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", varSequence);
inputMap.add("name", name);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetResolution.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetResolution.java
index 2fb2bbc..669aa86 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetResolution.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetResolution.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.math.UnitUtil;
@@ -14,58 +32,52 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* @author thomasprovoost
*/
-public class SetResolution extends Plugin implements SequenceBlock, PluginBundled
-{
- final protected VarSequence varSequence = new VarSequence("Sequence", null);
- final protected VarDouble pxSizeX = new VarDouble("Pixel Size X (" + UnitUtil.MICRO_STRING + "m)", 1d);
- final protected VarDouble pxSizeY = new VarDouble("Pixel Size Y (" + UnitUtil.MICRO_STRING + "m)", 1d);
- final protected VarDouble pxSizeZ = new VarDouble("Pixel Size Z (" + UnitUtil.MICRO_STRING + "m)", 1d);
- final protected VarDouble timeIntT = new VarDouble("Time interval T (s)", 100d);
+public class SetResolution extends Plugin implements SequenceBlock, PluginBundled {
+ final protected VarSequence varSequence = new VarSequence("Sequence", null);
+ final protected VarDouble pxSizeX = new VarDouble("Pixel Size X (" + UnitUtil.MICRO_STRING + "m)", 1d);
+ final protected VarDouble pxSizeY = new VarDouble("Pixel Size Y (" + UnitUtil.MICRO_STRING + "m)", 1d);
+ final protected VarDouble pxSizeZ = new VarDouble("Pixel Size Z (" + UnitUtil.MICRO_STRING + "m)", 1d);
+ final protected VarDouble timeIntT = new VarDouble("Time interval T (s)", 100d);
- @Override
- public void run()
- {
- Sequence s = varSequence.getValue();
+ @Override
+ public void run() {
+ final Sequence s = varSequence.getValue();
- if (s != null)
- {
- double x = pxSizeX.getValue().doubleValue();
- double y = pxSizeY.getValue().doubleValue();
- double z = pxSizeZ.getValue().doubleValue();
- double ti = timeIntT.getValue().doubleValue();
- if (x != -1)
- s.setPixelSizeX(x);
- if (y != -1)
- s.setPixelSizeY(y);
- if (z != -1)
- s.setPixelSizeZ(z);
- if (ti != -1)
- s.setTimeInterval(ti);
- } else
- {
- throw new VarException(varSequence, "Sequence is null");
- }
- }
+ if (s != null) {
+ final double x = pxSizeX.getValue();
+ final double y = pxSizeY.getValue();
+ final double z = pxSizeZ.getValue();
+ final double ti = timeIntT.getValue();
+ if (x != -1)
+ s.setPixelSizeX(x);
+ if (y != -1)
+ s.setPixelSizeY(y);
+ if (z != -1)
+ s.setPixelSizeZ(z);
+ if (ti != -1)
+ s.setTimeInterval(ti);
+ }
+ else {
+ throw new VarException(varSequence, "Sequence is null");
+ }
+ }
- @Override
- public void declareInput(VarList inputMap)
- {
- inputMap.add("sequence", varSequence);
- inputMap.add("PxSize X (" + UnitUtil.MICRO_STRING + "m)", pxSizeX);
- inputMap.add("PxSize Y (" + UnitUtil.MICRO_STRING + "m)", pxSizeY);
- inputMap.add("PxSize Z (" + UnitUtil.MICRO_STRING + "m)", pxSizeZ);
- inputMap.add("Time interval T (s)", timeIntT);
- }
+ @Override
+ public void declareInput(final VarList inputMap) {
+ inputMap.add("sequence", varSequence);
+ inputMap.add("PxSize X (" + UnitUtil.MICRO_STRING + "m)", pxSizeX);
+ inputMap.add("PxSize Y (" + UnitUtil.MICRO_STRING + "m)", pxSizeY);
+ inputMap.add("PxSize Z (" + UnitUtil.MICRO_STRING + "m)", pxSizeZ);
+ inputMap.add("Time interval T (s)", timeIntT);
+ }
- @Override
- public void declareOutput(VarList outputMap)
- {
- //
- }
+ @Override
+ public void declareOutput(final VarList outputMap) {
+ //
+ }
- @Override
- public String getMainPluginClassName()
- {
- return SequenceBlocks.class.getName();
- }
+ @Override
+ public String getMainPluginClassName() {
+ return SequenceBlocks.class.getName();
+ }
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetSequenceProperty.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetSequenceProperty.java
index 21aa719..a1ac68a 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetSequenceProperty.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetSequenceProperty.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.infos;
import icy.plugin.abstract_.Plugin;
@@ -29,18 +47,16 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
* <li><i>userName</i> = user who generated / acquired the dataset</li>
* <li><i>virtual</i> = virtual mode enabled on the dataset</li>
* </ul>
- *
+ *
* @author Stephane
*/
-public class SetSequenceProperty extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class SetSequenceProperty extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
protected VarSequence sequence = new VarSequence("Sequence", null);
protected VarString propertyName = new VarString("Property", "name");
protected VarString value = new VarString("Value", "");
@Override
- public void run()
- {
+ public void run() {
final Sequence seq = sequence.getValue();
if (seq != null)
@@ -48,22 +64,19 @@ public class SetSequenceProperty extends Plugin implements SequenceBlock, Plugin
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", sequence);
inputMap.add("property", propertyName);
inputMap.add("value", value);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/infos/VarColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/VarColormap.java
index bd81d7b..41ac152 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/infos/VarColormap.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/VarColormap.java
@@ -1,35 +1,48 @@
-package plugins.tprovoost.sequenceblocks.infos;
-
-import javax.swing.JComboBox;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import org.w3c.dom.Node;
+package plugins.tprovoost.sequenceblocks.infos;
import icy.gui.component.renderer.ColormapComboBoxRenderer;
import icy.image.colormap.IcyColorMap;
import icy.image.colormap.LinearColorMap;
import icy.util.XMLUtil;
+import org.w3c.dom.Node;
import plugins.adufour.vars.gui.VarEditor;
import plugins.adufour.vars.gui.model.ValueSelectionModel;
import plugins.adufour.vars.gui.swing.ComboBox;
import plugins.adufour.vars.lang.Var;
+import javax.swing.*;
+
/**
* Define a specific Var type for ColorMap object
- *
+ *
* @author emilie
*/
-public class VarColormap extends Var<IcyColorMap>
-{
- public static class ColormapSelectionModel extends ValueSelectionModel<IcyColorMap>
- {
- public ColormapSelectionModel()
- {
+public class VarColormap extends Var<IcyColorMap> {
+ public static class ColormapSelectionModel extends ValueSelectionModel<IcyColorMap> {
+ public ColormapSelectionModel() {
super(IcyColorMap.getAllColorMaps(true, true).toArray(new IcyColorMap[0]), LinearColorMap.gray_, false);
}
@Override
- public boolean isValid(IcyColorMap value)
- {
+ public boolean isValid(final IcyColorMap value) {
return true;
}
}
@@ -38,21 +51,20 @@ public class VarColormap extends Var<IcyColorMap>
/**
* Create a new VarColormap with given name and default value
- * @param name String
+ *
+ * @param name String
* @param defaultValue IcyColorMap
*/
- public VarColormap(String name, IcyColorMap defaultValue)
- {
+ public VarColormap(final String name, final IcyColorMap defaultValue) {
super(name, new ColormapSelectionModel());
}
@Override
- public VarEditor<IcyColorMap> createVarEditor()
- {
+ public VarEditor<IcyColorMap> createVarEditor() {
// create the var editor (combo box type here)
- final ComboBox<IcyColorMap> result = new ComboBox<IcyColorMap>(this);
+ final ComboBox<IcyColorMap> result = new ComboBox<>(this);
// get the editor component
- final JComboBox combo = result.getEditorComponent();
+ final JComboBox<IcyColorMap> combo = result.getEditorComponent();
// and set a specific renderer
combo.setRenderer(new ColormapComboBoxRenderer(combo));
@@ -60,32 +72,26 @@ public class VarColormap extends Var<IcyColorMap>
}
@Override
- public boolean loadFromXML(Node node)
- {
- try
- {
+ public boolean loadFromXML(final Node node) {
+ try {
final IcyColorMap map = new IcyColorMap();
map.loadFromXML(XMLUtil.setElement(node, ID_NODE));
setValue(map);
return true;
}
- catch (Exception e)
- {
+ catch (final Exception e) {
return false;
}
}
@Override
- public boolean saveToXML(Node node) throws UnsupportedOperationException
- {
- try
- {
+ public boolean saveToXML(final Node node) throws UnsupportedOperationException {
+ try {
getValue().saveToXML(XMLUtil.setElement(node, ID_NODE));
return true;
}
- catch (Exception e)
- {
+ catch (final Exception e) {
return false;
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
index ed0dbe8..14c7b67 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.loop;
import icy.plugin.interface_.PluginBundled;
@@ -12,18 +30,16 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Simple batch loop to iterate over all C channel from an input Sequence.
- *
+ *
* @author Stephane
*/
-public class SequenceChannelBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class SequenceChannelBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled {
// important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
@Override
- public VarSequence getBatchSource()
- {
+ public VarSequence getBatchSource() {
// initialize variable if needed
if (inputSequence == null)
inputSequence = new VarSequence("Sequence", null);
@@ -32,8 +48,7 @@ public class SequenceChannelBatch extends Batch implements SequenceBlock, Plugin
}
@Override
- public VarSequence getBatchElement()
- {
+ public VarSequence getBatchElement() {
// initialize element if needed
if (element == null)
element = new VarSequence("Channel Sequence", null);
@@ -42,8 +57,7 @@ public class SequenceChannelBatch extends Batch implements SequenceBlock, Plugin
}
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
final Sequence value = inputSequence.getValue();
if (value == null)
@@ -51,28 +65,23 @@ public class SequenceChannelBatch extends Batch implements SequenceBlock, Plugin
}
@Override
- public void beforeIteration()
- {
- try
- {
+ public void beforeIteration() {
+ try {
// set result in element
- element.setValue(SequenceUtil.extractChannel(inputSequence.getValue(), getIterationCounter().getValue().intValue()));
+ element.setValue(SequenceUtil.extractChannel(inputSequence.getValue(), getIterationCounter().getValue()));
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= inputSequence.getValue().getSizeC();
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= inputSequence.getValue().getSizeC();
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
index d487731..6343962 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.loop;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.util.List;
+package plugins.tprovoost.sequenceblocks.loop;
import icy.file.SequenceFileImporter;
import icy.plugin.interface_.PluginBundled;
@@ -14,13 +30,14 @@ import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
+import java.util.List;
+
/**
* Base abstract class for {@link SequenceFileImporter} batch loop.
- *
+ *
* @author Stephane
*/
-public abstract class SequenceFileImporterBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public abstract class SequenceFileImporterBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled {
// important to not initialize and create them in getBatchSource() and getBatchElement()
protected Var<PositionedSequenceFileImporter> positionedImporter;
protected Var<PositionedSequenceFileImporter> element;
@@ -30,29 +47,26 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
protected int limit;
@Override
- public Var<PositionedSequenceFileImporter> getBatchSource()
- {
+ public Var<PositionedSequenceFileImporter> getBatchSource() {
// initialize variable if needed
if (positionedImporter == null)
- positionedImporter = new Var<PositionedSequenceFileImporter>("Importer",
+ positionedImporter = new Var<>("Importer",
PositionedSequenceFileImporter.class);
return positionedImporter;
}
@Override
- public Var<PositionedSequenceFileImporter> getBatchElement()
- {
+ public Var<PositionedSequenceFileImporter> getBatchElement() {
// initialize element if needed
if (element == null)
- element = new Var<PositionedSequenceFileImporter>("Loop importer", PositionedSequenceFileImporter.class);
+ element = new Var<>("Loop importer", PositionedSequenceFileImporter.class);
return element;
}
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
final PositionedSequenceFileImporter value = positionedImporter.getValue();
if (value == null)
@@ -66,7 +80,7 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
// create new positioned importer for element initialization
final PositionedSequenceFileImporter pi = new PositionedSequenceFileImporter(value);
- final int s = series.getValue().intValue();
+ final int s = series.getValue();
// defined series ? --> set series position
if (s != -1)
@@ -77,8 +91,7 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
super.declareInput(inputMap);
// lazy creation
@@ -89,8 +102,7 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
}
@Override
- public void declareLoopVariables(List<Var<?>> loopVariables)
- {
+ public void declareLoopVariables(final List<Var<?>> loopVariables) {
// need to be called after
super.declareLoopVariables(loopVariables);
@@ -102,8 +114,7 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
index afc3b04..bf0d032 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.loop;
import icy.file.SequenceFileImporter;
@@ -7,49 +25,41 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
/**
* Simple batch loop to iterate over all C channel from specified opened {@link SequenceFileImporter} object.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterChannelBatch extends SequenceFileImporterBatch
-{
+public class SequenceFileImporterChannelBatch extends SequenceFileImporterBatch {
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
super.initializeLoop();
// can take position from element which should have been initialized here
final PositionedSequenceFileImporter pi = element.getValue();
- try
- {
+ try {
// can iterate over C dimension ?
if (pi.c == -1)
limit = MetaDataUtil.getSizeC(pi.getMetadata(), (pi.s == -1) ? 0 : pi.s);
else
limit = 1;
}
- catch (Exception e)
- {
- throw new VarException(element,
- "Error while initializing SequenceFileImporter channel batch: " + e.getMessage());
+ catch (final Exception e) {
+ throw new VarException(element, "Error while initializing SequenceFileImporter channel batch: " + e.getMessage());
}
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set current position C
- if (positionedImporter.getValue().c == -1)
- {
- element.getValue().c = getIterationCounter().getValue().intValue();
+ if (positionedImporter.getValue().c == -1) {
+ element.getValue().c = getIterationCounter().getValue();
// force element changed event so loop get correctly executed
element.valueChanged(element, element.getValue(), element.getValue());
}
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= limit;
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= limit;
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
index ba8bf10..9c55471 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.loop;
import icy.file.SequenceFileImporter;
@@ -7,49 +25,41 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
/**
* Simple batch loop to iterate over all T frame from the specified opened {@link SequenceFileImporter} object.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterFrameBatch extends SequenceFileImporterBatch
-{
+public class SequenceFileImporterFrameBatch extends SequenceFileImporterBatch {
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
super.initializeLoop();
// can take position from element which should have been initialized here
final PositionedSequenceFileImporter pi = element.getValue();
- try
- {
+ try {
// can iterate over T dimension ?
if (pi.t == -1)
limit = MetaDataUtil.getSizeT(pi.getMetadata(), (pi.s == -1) ? 0 : pi.s);
else
limit = 1;
}
- catch (Exception e)
- {
- throw new VarException(element,
- "Error while initializing SequenceFileImporter frame batch: " + e.getMessage());
+ catch (final Exception e) {
+ throw new VarException(element, "Error while initializing SequenceFileImporter frame batch: " + e.getMessage());
}
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set current position T
- if (positionedImporter.getValue().t == -1)
- {
- element.getValue().t = getIterationCounter().getValue().intValue();
+ if (positionedImporter.getValue().t == -1) {
+ element.getValue().t = getIterationCounter().getValue();
// force element changed event so loop get correctly executed
element.valueChanged(element, element.getValue(), element.getValue());
}
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= limit;
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= limit;
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
index 05f0518..3cf4b94 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
@@ -1,9 +1,22 @@
-package plugins.tprovoost.sequenceblocks.loop;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.awt.Rectangle;
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.List;
+package plugins.tprovoost.sequenceblocks.loop;
import icy.file.SequenceFileImporter;
import icy.roi.ROI;
@@ -16,14 +29,18 @@ import plugins.adufour.vars.lang.VarROIArray;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
+import java.awt.*;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Simple batch loop to iterate over a set of XY region defined by ROIs from the specified opened
* {@link SequenceFileImporter} object.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
-{
+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;
@@ -31,27 +48,22 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
protected List<Rectangle> regions;
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
super.initializeLoop();
// 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))
- {
+ if ((pi.xyRegion == null) && (rois.getValue() != null)) {
final int s = (pi.s == -1) ? 0 : pi.s;
final Rectangle regionMask;
- try
- {
+ try {
// mask for region
- regionMask = new Rectangle(0, 0, MetaDataUtil.getSizeX(pi.getMetadata(), s),
- MetaDataUtil.getSizeY(pi.getMetadata(), s));
+ regionMask = new Rectangle(0, 0, MetaDataUtil.getSizeX(pi.getMetadata(), s), MetaDataUtil.getSizeY(pi.getMetadata(), s));
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(element,
"Error while initializing SequenceFileImporter region batch: " + e.getMessage());
}
@@ -60,9 +72,8 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
final double margeFactor = 1d + (inputRoisMargin.getValue().doubleValue() / 100d);
// build 2D regions from ROI
- regions = new ArrayList<Rectangle>();
- for (ROI roi : rois.getValue())
- {
+ regions = new ArrayList<>();
+ for (final ROI roi : rois.getValue()) {
Rectangle2D region = roi.getBounds5D().toRectangle2D();
// convert to full resolution if needed
@@ -84,20 +95,17 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set current position XY region
- if (positionedImporter.getValue().xyRegion == null)
- {
- element.getValue().xyRegion = regions.get(getIterationCounter().getValue().intValue());
+ if (positionedImporter.getValue().xyRegion == null) {
+ element.getValue().xyRegion = regions.get(getIterationCounter().getValue());
// force element changed event so loop get correctly executed
element.valueChanged(element, element.getValue(), element.getValue());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
super.declareInput(inputMap);
// lazy creation
@@ -114,8 +122,7 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
}
@Override
- public void declareLoopVariables(List<Var<?>> loopVariables)
- {
+ public void declareLoopVariables(final List<Var<?>> loopVariables) {
super.declareLoopVariables(loopVariables);
// lazy creation
@@ -132,8 +139,7 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= limit;
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= limit;
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
index ffb8e57..e9d9950 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.loop;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.util.List;
+package plugins.tprovoost.sequenceblocks.loop;
import icy.file.SequenceFileImporter;
import icy.sequence.MetaDataUtil;
@@ -9,39 +25,36 @@ import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
+import java.util.List;
+
/**
* Simple batch loop to iterate over all series from the specified opened {@link SequenceFileImporter} object.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
-{
+public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch {
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
super.initializeLoop();
// can take position from element which should have been initialized here
final PositionedSequenceFileImporter pi = element.getValue();
- try
- {
+ try {
// can iterate over S dimension ?
if (pi.s == -1)
limit = MetaDataUtil.getNumSeries(pi.getMetadata());
else
limit = 1;
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(element,
"Error while initializing SequenceFileImporter series batch: " + e.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
super.declareInput(inputMap);
// we don't want it here
@@ -49,8 +62,7 @@ public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
}
@Override
- public void declareLoopVariables(List<Var<?>> loopVariables)
- {
+ public void declareLoopVariables(final List<Var<?>> loopVariables) {
super.declareLoopVariables(loopVariables);
// we don't want it here
@@ -58,20 +70,17 @@ public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set current position S
- if (positionedImporter.getValue().s == -1)
- {
- element.getValue().s = getIterationCounter().getValue().intValue();
+ if (positionedImporter.getValue().s == -1) {
+ element.getValue().s = getIterationCounter().getValue();
// force element changed event so loop get correctly executed
element.valueChanged(element, element.getValue(), element.getValue());
}
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= limit;
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= limit;
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
index 16f1dad..2abea99 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.loop;
import icy.file.SequenceFileImporter;
@@ -7,49 +25,41 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
/**
* Simple batch loop to iterate over all Z slice from specified opened {@link SequenceFileImporter} object.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterSliceBatch extends SequenceFileImporterBatch
-{
+public class SequenceFileImporterSliceBatch extends SequenceFileImporterBatch {
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
super.initializeLoop();
// can take position from element which should have been initialized here
final PositionedSequenceFileImporter pi = element.getValue();
-
- try
- {
+
+ try {
// can iterate over Z dimension ?
if (pi.z == -1)
limit = MetaDataUtil.getSizeZ(pi.getMetadata(), (pi.s == -1) ? 0 : pi.s);
else
limit = 1;
}
- catch (Exception e)
- {
- throw new VarException(element,
- "Error while initializing SequenceFileImporter slice batch: " + e.getMessage());
+ catch (final Exception e) {
+ throw new VarException(element, "Error while initializing SequenceFileImporter slice batch: " + e.getMessage());
}
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set current position Z
- if (positionedImporter.getValue().z == -1)
- {
- element.getValue().z = getIterationCounter().getValue().intValue();
+ if (positionedImporter.getValue().z == -1) {
+ element.getValue().z = getIterationCounter().getValue();
// force element changed event so loop get correctly executed
element.valueChanged(element, element.getValue(), element.getValue());
}
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= limit;
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= limit;
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
index 4d6e434..ffdeb1c 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
@@ -1,7 +1,22 @@
-package plugins.tprovoost.sequenceblocks.loop;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.awt.Rectangle;
-import java.util.List;
+package plugins.tprovoost.sequenceblocks.loop;
import icy.file.SequenceFileImporter;
import icy.image.ImageUtil;
@@ -12,13 +27,15 @@ import plugins.adufour.vars.lang.VarInteger;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
+import java.awt.*;
+import java.util.List;
+
/**
* Simple batch loop to iterate over all XY tile from the specified opened {@link SequenceFileImporter} object.
- *
+ *
* @author Stephane
*/
-public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
-{
+public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch {
// important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
protected VarInteger tileW;
protected VarInteger tileH;
@@ -26,16 +43,14 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
protected List<Rectangle> tiles;
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
super.initializeLoop();
// 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)
- {
+ if (pi.xyRegion == null) {
final SequenceFileImporter imp = pi.importer;
final int s = (pi.s == -1) ? 0 : pi.s;
final int sizeX;
@@ -43,13 +58,12 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
int tw;
int th;
- try
- {
+ try {
sizeX = MetaDataUtil.getSizeX(pi.getMetadata(), s);
sizeY = MetaDataUtil.getSizeY(pi.getMetadata(), s);
- tw = tileW.getValue().intValue();
- th = tileH.getValue().intValue();
+ tw = tileW.getValue();
+ th = tileH.getValue();
// auto ? --> get it from importer
if (tw == -1)
tw = imp.getTileWidth(s);
@@ -57,22 +71,20 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
if (th == -1)
th = imp.getTileHeight(s);
}
- catch (Exception e)
- {
- throw new VarException(element,
- "Error while initializing SequenceFileImporter tile batch: " + e.getMessage());
+ catch (final Exception e) {
+ throw new VarException(element, "Error while initializing SequenceFileImporter tile batch: " + e.getMessage());
}
// any size supported ? --> use 1024 by default
if (tw == -1)
tw = 1024;
- // tile loading not supported ? --> use full width
+ // tile loading not supported ? --> use full width
else if (tw == 0)
tw = sizeX;
// any size supported ? --> use 1024 by default
if (th == -1)
th = 1024;
- // tile loading not supported ? --> use full height
+ // tile loading not supported ? --> use full height
else if (th == 0)
th = sizeY;
@@ -86,10 +98,9 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
super.declareInput(inputMap);
-
+
// lazy creation
if (tileW == null)
tileW = new VarInteger("Tile width (-1 = auto)", -1);
@@ -101,8 +112,7 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
}
@Override
- public void declareLoopVariables(List<Var<?>> loopVariables)
- {
+ public void declareLoopVariables(final List<Var<?>> loopVariables) {
// need to be called after
super.declareLoopVariables(loopVariables);
@@ -117,20 +127,17 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set current position XY region
- if (positionedImporter.getValue().xyRegion == null)
- {
- element.getValue().xyRegion = tiles.get(getIterationCounter().getValue().intValue());
+ if (positionedImporter.getValue().xyRegion == null) {
+ element.getValue().xyRegion = tiles.get(getIterationCounter().getValue());
// force element changed event so loop get correctly executed
element.valueChanged(element, element.getValue(), element.getValue());
}
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= limit;
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= limit;
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
index 2a77e4f..8635b25 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.loop;
import icy.plugin.interface_.PluginBundled;
@@ -11,23 +29,20 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Simple batch loop to iterate over all T frame from an input Sequence.
- *
+ *
* @author Stephane
*/
-public class SequenceFrameBatch extends Batch implements PluginLibrary, PluginBundled
-{
+public class SequenceFrameBatch extends Batch implements PluginLibrary, PluginBundled {
// important to not initialize and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
- public SequenceFrameBatch()
- {
+ public SequenceFrameBatch() {
super();
}
@Override
- public VarSequence getBatchSource()
- {
+ public VarSequence getBatchSource() {
// initialize variable if needed
if (inputSequence == null)
inputSequence = new VarSequence("Sequence", null);
@@ -36,8 +51,7 @@ public class SequenceFrameBatch extends Batch implements PluginLibrary, PluginBu
}
@Override
- public VarSequence getBatchElement()
- {
+ public VarSequence getBatchElement() {
// initialize element if needed
if (element == null)
element = new VarSequence("Frame Sequence", null);
@@ -46,8 +60,7 @@ public class SequenceFrameBatch extends Batch implements PluginLibrary, PluginBu
}
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
final Sequence value = inputSequence.getValue();
if (value == null)
@@ -55,22 +68,18 @@ public class SequenceFrameBatch extends Batch implements PluginLibrary, PluginBu
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set result in element
- element.setValue(
- SequenceUtil.extractFrame(inputSequence.getValue(), getIterationCounter().getValue().intValue()));
+ element.setValue(SequenceUtil.extractFrame(inputSequence.getValue(), getIterationCounter().getValue()));
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= inputSequence.getValue().getSizeT();
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= inputSequence.getValue().getSizeT();
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
index 99fc20a..0409bdd 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
@@ -1,6 +1,22 @@
-package plugins.tprovoost.sequenceblocks.loop;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.util.List;
+package plugins.tprovoost.sequenceblocks.loop;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
@@ -16,27 +32,26 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.util.List;
+
/**
* Simple batch loop to iterate over a set of Region (ROIs) from an input Sequence.
- *
+ *
* @author Stephane
*/
-public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled {
// important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
protected VarROIArray rois;
protected VarROIArray currentRoi;
- public SequenceRegionBatch()
- {
+ public SequenceRegionBatch() {
super();
}
@Override
- public VarROIArray getBatchSource()
- {
+ public VarROIArray getBatchSource() {
if (rois == null)
rois = new VarROIArray("ROI(s)");
@@ -44,8 +59,7 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
}
@Override
- public VarSequence getBatchElement()
- {
+ public VarSequence getBatchElement() {
if (element == null)
element = new VarSequence("Region Sequence", null);
@@ -53,8 +67,7 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
super.declareInput(inputMap);
if (inputSequence == null)
@@ -64,8 +77,7 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
super.declareOutput(outputMap);
if (currentRoi == null)
@@ -75,8 +87,7 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
}
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
final Sequence value = inputSequence.getValue();
if (value == null)
@@ -87,39 +98,33 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set result in element
- final ROI roi = rois.getValue()[getIterationCounter().getValue().intValue()];
+ final ROI roi = rois.getValue()[getIterationCounter().getValue()];
- try
- {
+ try {
element.setValue(SequenceUtil.getSubSequence(inputSequence.getValue(), roi));
- currentRoi.setValue(new ROI[] {roi});
+ currentRoi.setValue(new ROI[]{roi});
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= rois.getValue().length;
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= rois.getValue().length;
}
@Override
- public void declareLoopVariables(List<Var<?>> loopVariables)
- {
+ public void declareLoopVariables(final List<Var<?>> loopVariables) {
super.declareLoopVariables(loopVariables);
loopVariables.add(inputSequence);
loopVariables.add(currentRoi);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
index e8c2003..d5600bb 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.loop;
import icy.plugin.interface_.PluginBundled;
@@ -12,18 +30,16 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Simple batch loop to iterate over all Z slice from an input Sequence.
- *
+ *
* @author Stephane
*/
-public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled {
// important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
@Override
- public VarSequence getBatchSource()
- {
+ public VarSequence getBatchSource() {
// initialize variable if needed
if (inputSequence == null)
inputSequence = new VarSequence("Sequence", null);
@@ -32,8 +48,7 @@ public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLi
}
@Override
- public VarSequence getBatchElement()
- {
+ public VarSequence getBatchElement() {
// initialize element if needed
if (element == null)
element = new VarSequence("Slice Sequence", null);
@@ -42,8 +57,7 @@ public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLi
}
@Override
- public void initializeLoop()
- {
+ public void initializeLoop() {
final Sequence value = inputSequence.getValue();
if (value == null)
@@ -51,22 +65,19 @@ public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLi
}
@Override
- public void beforeIteration()
- {
+ public void beforeIteration() {
// set result in element
element.setValue(
- SequenceUtil.extractSlice(inputSequence.getValue(), getIterationCounter().getValue().intValue()));
+ SequenceUtil.extractSlice(inputSequence.getValue(), getIterationCounter().getValue()));
}
@Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= inputSequence.getValue().getSizeZ();
+ public boolean isStopConditionReached() {
+ return getIterationCounter().getValue() >= inputSequence.getValue().getSizeZ();
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
index 2ed300e..4e2a833 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
@@ -1,6 +1,21 @@
-/**
- *
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.tprovoost.sequenceblocks.op;
import icy.image.ImageDataIterator;
@@ -21,82 +36,69 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to do additive fill of area inside the ROI regions with the specified value.<br>
* The result of this operation is similar to heatmap production from ROIs.
- *
+ *
* @author Stephane
*/
-public class AdditiveFillSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class AdditiveFillSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarROIArray rois = new VarROIArray("Roi(s)");
@Override
- public void run()
- {
+ public void run() {
final Sequence sequence = inputSequence.getValue();
if (sequence == null)
throw new VarException(inputSequence, "Input sequence is null.");
- try
- {
- if (rois.getValue() != null)
- {
- for (ROI roi : rois.getValue())
+ try {
+ if (rois.getValue() != null) {
+ for (final ROI roi : rois.getValue())
doAdditiveFill(sequence, roi, 1d);
sequence.dataChanged();
}
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
- public static void doAdditiveFill(Sequence sequence, ROI roi, double value) throws InterruptedException
- {
+ public static void doAdditiveFill(final Sequence sequence, final ROI roi, final double value) throws InterruptedException {
doAdditiveFill(new SequenceDataIterator(sequence, roi), value);
}
- public static void doAdditiveFill(DataIterator it, double value) throws InterruptedException
- {
+ public static void doAdditiveFill(final DataIterator it, final double value) throws InterruptedException {
it.reset();
- while (!it.done())
- {
+ while (!it.done()) {
it.set(it.get() + value);
it.next();
}
- try
- {
+ try {
// not really nice to do that here, but it's to preserve backward compatibility
if (it instanceof SequenceDataIterator)
((SequenceDataIterator) it).flush();
else if (it instanceof ImageDataIterator)
((ImageDataIterator) it).flush();
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
// ignore
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("rois", rois);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
index 7dc0f45..7c86437 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
@@ -1,6 +1,21 @@
-/**
- *
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.tprovoost.sequenceblocks.op;
import icy.plugin.abstract_.Plugin;
@@ -20,57 +35,49 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to fill area inside the ROI regions with the specified value
- *
+ *
* @author Stephane
*/
-public class FillInnerSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class FillInnerSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarROIArray rois = new VarROIArray("Roi(s)");
final protected VarDouble fillValue = new VarDouble("Value", 0d);
@Override
- public void run()
- {
+ public void run() {
final Sequence sequence = inputSequence.getValue();
if (sequence == null)
throw new VarException(inputSequence, "Input sequence is null.");
- try
- {
- if (rois.getValue() != null)
- {
- final double value = fillValue.getValue().doubleValue();
+ try {
+ if (rois.getValue() != null) {
+ final double value = fillValue.getValue();
- for (ROI roi : rois.getValue())
+ for (final ROI roi : rois.getValue())
DataIteratorUtil.set(new SequenceDataIterator(sequence, roi), value);
sequence.dataChanged();
}
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("rois", rois);
inputMap.add("value", fillValue);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
index 89d47ed..d5acacf 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
@@ -1,6 +1,21 @@
-/**
- *
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.tprovoost.sequenceblocks.op;
import icy.plugin.abstract_.Plugin;
@@ -19,72 +34,62 @@ import plugins.adufour.vars.lang.VarDouble;
import plugins.adufour.vars.lang.VarROIArray;
import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
-import plugins.kernel.roi.roi5d.ROI5DStackRectangle;
+import plugins.kernel.roi.roi3d.ROI3DBox;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to fill area outside the ROI regions with the specified value
- *
+ *
* @author Stephane
*/
-public class FillOuterSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class FillOuterSequence extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarROIArray rois = new VarROIArray("Roi(s)");
final protected VarDouble fillValue = new VarDouble("Value", 0d);
@Override
- public void run()
- {
+ public void run() {
final Sequence sequence = inputSequence.getValue();
if (sequence == null)
throw new VarException(inputSequence, "Input sequence is null.");
- try
- {
- if (rois.getValue() != null)
- {
- try
- {
+ try {
+ if (rois.getValue() != null) {
+ try {
final ROI roiUnion = ROIUtil.merge(CollectionUtil.asList(rois.getValue()), BooleanOperator.OR);
- final ROI roiSeq = new ROI5DStackRectangle(sequence.getBounds5D());
+ final ROI roiSeq = new ROI3DBox(sequence.getBounds5D().toRectangle3D());
final ROI roi = roiSeq.getSubtraction(roiUnion);
- final double value = fillValue.getValue().doubleValue();
+ final double value = fillValue.getValue();
DataIteratorUtil.set(new SequenceDataIterator(sequence, roi), value);
sequence.dataChanged();
}
- catch (UnsupportedOperationException e)
- {
+ catch (final UnsupportedOperationException e) {
throw new VarException(rois, e.getMessage());
}
}
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("rois", rois);
inputMap.add("value", fillValue);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveAllRois.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveAllRois.java
index 6ce1c1a..8259bb6 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveAllRois.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveAllRois.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.remove;
import icy.plugin.abstract_.Plugin;
@@ -13,16 +31,14 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to remove all the {@link ROI} from a Sequence
- *
+ *
* @author Stephane
*/
-public class RemoveAllRois extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class RemoveAllRois extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
@Override
- public void run()
- {
+ public void run() {
final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
@@ -31,20 +47,17 @@ public class RemoveAllRois extends Plugin implements SequenceBlock, PluginLibrar
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
index 2fb63bf..b4a1fbb 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.remove;
import icy.plugin.abstract_.Plugin;
@@ -14,53 +32,46 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to remove a channel from a Sequence
- *
+ *
* @author Stephane
*/
-public class RemoveChannel extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class RemoveChannel extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarInteger channelIdx = new VarInteger("Channel", 0);
@Override
- public void run()
- {
- Sequence s = inputSequence.getValue();
+ public void run() {
+ final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
if (s.getSizeC() == 1)
throw new VarException(inputSequence, "Cannot remove channel on single channel image");
- int channel = channelIdx.getValue().intValue();
+ final int channel = channelIdx.getValue();
if (channel < 0 || channel >= s.getSizeC())
throw new VarException(channelIdx, "Channel index must be between 0 and " + (s.getSizeC() - 1));
- try
- {
+ try {
SequenceUtil.removeChannel(s, channel);
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
// nothing to do
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("channel", channelIdx);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveFrame.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveFrame.java
index 4583bfd..7157722 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveFrame.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveFrame.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.remove;
import icy.plugin.abstract_.Plugin;
@@ -14,40 +32,35 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to remove a frame from a Sequence
- *
+ *
* @author Stephane
*/
-public class RemoveFrame extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class RemoveFrame extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarInteger frameInd = new VarInteger("Frame", 0);
@Override
- public void run()
- {
- Sequence s = inputSequence.getValue();
+ public void run() {
+ final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- SequenceUtil.removeTAndShift(s, frameInd.getValue().intValue());
+ SequenceUtil.removeTAndShift(s, frameInd.getValue());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("frame", frameInd);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveOverlays.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveOverlays.java
index 78d90d2..16a6de0 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveOverlays.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveOverlays.java
@@ -1,6 +1,21 @@
-/**
- *
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.tprovoost.sequenceblocks.remove;
import icy.painter.Overlay;
@@ -17,53 +32,45 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to remove one or several {@link Overlay} from a {@link Sequence}
- *
+ *
* @author Stephane
*/
-public class RemoveOverlays extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class RemoveOverlays extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
- final protected VarArray<Overlay> overlays = new VarArray<Overlay>("Overlay(s)", Overlay[].class, new Overlay[0]);
+ final protected VarArray<Overlay> overlays = new VarArray<>("Overlay(s)", Overlay[].class, new Overlay[0]);
@Override
- public void run()
- {
+ public void run() {
final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
final Overlay[] o = overlays.getValue();
- if (o != null)
- {
+ if (o != null) {
s.beginUpdate();
- try
- {
- for (Overlay overlay : o)
+ try {
+ for (final Overlay overlay : o)
s.removeOverlay(overlay);
}
- finally
- {
+ finally {
s.endUpdate();
}
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("overlay(s)", overlays);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveRois.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveRois.java
index 2866f0d..eb6c415 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveRois.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveRois.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.remove;
import icy.plugin.abstract_.Plugin;
@@ -5,9 +23,6 @@ import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
import icy.roi.ROI;
import icy.sequence.Sequence;
-
-import java.util.Arrays;
-
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarROIArray;
@@ -15,19 +30,19 @@ import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
+import java.util.Arrays;
+
/**
* Block to remove one or several {@link ROI} from a Sequence
- *
+ *
* @author Stephane
*/
-public class RemoveRois extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class RemoveRois extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarROIArray rois = new VarROIArray("Roi(s)");
@Override
- public void run()
- {
+ public void run() {
final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
@@ -38,21 +53,18 @@ public class RemoveRois extends Plugin implements SequenceBlock, PluginLibrary,
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("rois(s)", rois);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveSlice.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveSlice.java
index 56fecec..30fafeb 100644
--- a/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveSlice.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveSlice.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.tprovoost.sequenceblocks.remove;
import icy.plugin.abstract_.Plugin;
@@ -14,40 +32,35 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
* Block to remove a Z slice from a Sequence
- *
+ *
* @author Stephane
*/
-public class RemoveSlice extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
-{
+public class RemoveSlice extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled {
final protected VarSequence inputSequence = new VarSequence("Sequence", null);
final protected VarInteger sliceInd = new VarInteger("Slice", 0);
@Override
- public void run()
- {
- Sequence s = inputSequence.getValue();
+ public void run() {
+ final Sequence s = inputSequence.getValue();
if (s == null)
throw new VarException(inputSequence, "Input sequence is null.");
- SequenceUtil.removeZAndShift(s, sliceInd.getValue().intValue());
+ SequenceUtil.removeZAndShift(s, sliceInd.getValue());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("sequence", inputSequence);
inputMap.add("slice", sliceInd);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return SequenceBlocks.class.getName();
}
}
\ No newline at end of file
--
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