diff --git a/.gitignore b/.gitignore
index 6bf55a6e726d00e9470abd5220a69e2226dcafab..d4c3a6c5e5d37c1d2e1b9bcdddf30fb1530593bd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,4 +8,5 @@ bin/
*.jar
.classpath
.project
-export.jardesc
\ No newline at end of file
+export.jardesc
+**/.DS_Store
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index c5c56e217d6de7d54744491fbcb45bdc0e01843b..1ac5ed60cf6b5586bb20c3aac3bb9a853c90be83 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,42 +1,32 @@
<?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>pom-icy</artifactId>
- <version>2.0.0</version>
- </parent>
+ <artifactId>pom-icy</artifactId>
+ <version>2.2.0</version>
+ </parent>
<artifactId>micromanager-block</artifactId>
- <version>1.0.4</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0</version>
<name>Micro-Manager Block</name>
<description>
Blocks (protocols) for Micro-Manager (Icy plugin).
</description>
-
- <profiles>
- <profile>
- <id>icy-plugin</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- </profile>
- </profiles>
<dependencies>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>micromanager</artifactId>
</dependency>
+
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>blocks</artifactId>
+ <artifactId>protocols</artifactId>
</dependency>
</dependencies>
diff --git a/src/main/java/plugins/stef/micromanager/block/AbstractMicroscopeBlock.java b/src/main/java/plugins/stef/micromanager/block/AbstractMicroscopeBlock.java
index 4ae8f4bed2e0c6c146149ea9a20ad752a5cffbf3..24ba799a9cf2cb5d7ec6726050b7dc47288f1492 100644
--- a/src/main/java/plugins/stef/micromanager/block/AbstractMicroscopeBlock.java
+++ b/src/main/java/plugins/stef/micromanager/block/AbstractMicroscopeBlock.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.stef.micromanager.block;
import icy.gui.dialog.MessageDialog;
@@ -8,9 +23,7 @@ import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
import mmcorej.CMMCore;
-
import org.micromanager.utils.ReportingUtils;
-
import plugins.adufour.blocks.lang.Block;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import plugins.tprovoost.Microscopy.MicroManagerForIcy.MicromanagerPlugin;
@@ -18,10 +31,8 @@ import plugins.tprovoost.Microscopy.MicroManagerForIcy.MicromanagerPlugin;
/**
* @author Stephane
*/
-public abstract class AbstractMicroscopeBlock extends Plugin implements Block, PluginLibrary, PluginBundled
-{
- public AbstractMicroscopeBlock()
- {
+public abstract class AbstractMicroscopeBlock extends Plugin implements Block, PluginLibrary, PluginBundled {
+ public AbstractMicroscopeBlock() {
super();
MicromanagerPlugin.init();
@@ -31,19 +42,15 @@ public abstract class AbstractMicroscopeBlock extends Plugin implements Block, P
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return MicroscopyBlocks.class.getName();
}
- public static CMMCore getMMCore(boolean throwException)
- {
- try
- {
+ public static CMMCore getMMCore(final boolean throwException) {
+ try {
return MicroManager.getCore();
}
- catch (Throwable e)
- {
+ catch (final Throwable e) {
ReportingUtils.logError(e);
if (throwException)
throw new RuntimeException("Cannot retrieve Micro-Manager core !", e);
diff --git a/src/main/java/plugins/stef/micromanager/block/MicroscopyBlocks.java b/src/main/java/plugins/stef/micromanager/block/MicroscopyBlocks.java
index 72b350059b2d8eca903f2d7eac8602bf073849fc..a61fa1725b396379c44e8068577e721b0cecad97 100644
--- a/src/main/java/plugins/stef/micromanager/block/MicroscopyBlocks.java
+++ b/src/main/java/plugins/stef/micromanager/block/MicroscopyBlocks.java
@@ -1,12 +1,28 @@
+/*
+ * 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.stef.micromanager.block;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginLibrary;
-public class MicroscopyBlocks extends Plugin implements PluginLibrary
-{
- public MicroscopyBlocks()
- {
+public class MicroscopyBlocks extends Plugin implements PluginLibrary {
+ public MicroscopyBlocks() {
super();
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeGetMetadata.java b/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeGetMetadata.java
index 3f98172515c6d4825643d87172f5aae4504c9518..bd0f6c2ed13695dbb5f4b7519de54b9f3b174a49 100644
--- a/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeGetMetadata.java
+++ b/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeGetMetadata.java
@@ -1,10 +1,24 @@
-/**
- *
+/*
+ * 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.stef.micromanager.block.capture;
import org.json.JSONObject;
-
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarInteger;
@@ -13,38 +27,33 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
* Retrieve global acquisition metadata and last acquired image metadata (Micro-Manager)
- *
+ *
* @author Stephane
*/
-public class MicroscopeGetMetadata extends AbstractMicroscopeBlock
-{
+public class MicroscopeGetMetadata extends AbstractMicroscopeBlock {
VarInteger channel = new VarInteger("Channel", 0);
- Var<JSONObject> metadata = new Var<JSONObject>("Image metadata", JSONObject.class);
- Var<JSONObject> acqMetadata = new Var<JSONObject>("Acquisition metadata", JSONObject.class);
+ Var<JSONObject> metadata = new Var<>("Image metadata", JSONObject.class);
+ Var<JSONObject> acqMetadata = new Var<>("Acquisition metadata", JSONObject.class);
@Override
- public void run()
- {
- metadata.setValue(MicroManager.getMetadata(channel.getValue().intValue()));
+ public void run() {
+ metadata.setValue(MicroManager.getMetadata(channel.getValue()));
acqMetadata.setValue(MicroManager.getAcquisitionMetaData());
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("channel", channel);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("imageMetadata", metadata);
outputMap.add("acqMetadata", acqMetadata);
}
@Override
- public String getName()
- {
+ public String getName() {
return "Get Micro-Manager Metadata";
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSetTaggedImage.java b/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSetTaggedImage.java
index a118be785210d6b2af4da307058cd137cf0178e7..a6b988253dd3d21afa8df4d37ee23f9111a9bb16 100644
--- a/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSetTaggedImage.java
+++ b/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSetTaggedImage.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.stef.micromanager.block.capture;
import mmcorej.TaggedImage;
@@ -14,13 +29,11 @@ import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
/**
* Set a TaggedImage into a Sequence (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSetTaggedImage extends AbstractMicroscopeBlock
-{
- VarArray<TaggedImage> taggedImages = new VarArray<TaggedImage>("Tagged image(s)", TaggedImage[].class,
- new TaggedImage[0]);
+public class MicroscopeSetTaggedImage extends AbstractMicroscopeBlock {
+ VarArray<TaggedImage> taggedImages = new VarArray<>("Tagged image(s)", TaggedImage[].class, new TaggedImage[0]);
VarSequence seq = new VarSequence("Sequence", null);
VarInteger posT = new VarInteger("T", -1);
VarInteger posZ = new VarInteger("Z", -1);
@@ -30,28 +43,30 @@ public class MicroscopeSetTaggedImage extends AbstractMicroscopeBlock
VarInteger sizeC = new VarInteger("Size C", -1);
@Override
- public void run()
- {
- try
- {
- for (TaggedImage image : taggedImages.getValue())
- {
+ public void run() {
+ try {
+ for (final TaggedImage image : taggedImages.getValue()) {
// set image position metadata
- MMUtils.setImageMetadata(image, posT.getValue().intValue(), posZ.getValue().intValue(), posC
- .getValue().intValue(), sizeT.getValue().intValue(), sizeZ.getValue().intValue(), sizeC.getValue().intValue());
+ MMUtils.setImageMetadata(
+ image,
+ posT.getValue(),
+ posZ.getValue(),
+ posC.getValue(),
+ sizeT.getValue(),
+ sizeZ.getValue(),
+ sizeC.getValue()
+ );
// store image in sequence
MMUtils.setImage(seq.getValue(), image);
}
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(taggedImages, t.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("taggedImage", taggedImages);
inputMap.add("seq", seq);
inputMap.add("t", posT);
@@ -63,15 +78,12 @@ public class MicroscopeSetTaggedImage extends AbstractMicroscopeBlock
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
-
}
@Override
- public String getName()
- {
+ public String getName() {
return "Set Tagged Image(s)";
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapChannels.java b/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapChannels.java
index e0f6b298f8cc853cb5a490b9c9d13668cb6aeedd..05c7845fb8001282c1013b2356e56bed0f519ba4 100644
--- a/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapChannels.java
+++ b/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapChannels.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.stef.micromanager.block.capture;
import java.util.ArrayList;
@@ -25,55 +43,48 @@ import plugins.tprovoost.Microscopy.MicroManager.tools.StageMover;
*
* @author Stephane
*/
-public class MicroscopeSnapChannels extends AbstractMicroscopeBlock
-{
+public class MicroscopeSnapChannels extends AbstractMicroscopeBlock {
VarObject trigger;
VarMMGroup group;
VarChannels channels;
VarArray<TaggedImage> out;
- public MicroscopeSnapChannels()
- {
+ public MicroscopeSnapChannels() {
super();
trigger = new VarObject("Trigger", null);
group = new VarMMGroup();
channels = new VarChannels(group);
- out = new VarArray<TaggedImage>("Tagged image(s)", TaggedImage[].class, new TaggedImage[0]);
+ out = new VarArray<>("Tagged image(s)", TaggedImage[].class, new TaggedImage[0]);
}
@Override
- public void run()
- {
+ public void run() {
// default
out.setValue(new TaggedImage[0]);
final ChannelSpec[] specs = channels.getValue();
// no channel to process
- if (specs.length <= 0)
+ if (specs.length == 0)
return;
- try
- {
+ try {
MicroManager.setChannelGroup(group.getValue());
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(group, "Group value is not valid.");
}
- final List<TaggedImage> result = new ArrayList<TaggedImage>();
+ final List<TaggedImage> result = new ArrayList<>();
- for (int ch = 0; ch < specs.length; ch++)
- {
+ for (int ch = 0; ch < specs.length; ch++) {
final ChannelSpec cs = specs[ch];
// channel not used --> skip
if (!cs.useChannel)
continue;
- try
- {
+ try {
final String configName = cs.config;
// set config
@@ -82,7 +93,7 @@ public class MicroscopeSnapChannels extends AbstractMicroscopeBlock
// set exposure
MicroManager.setExposure(cs.exposure);
// doing Z-Stack ? --> apply Z-offset
- if (cs.doZStack.booleanValue() && (cs.zOffset != 0d))
+ if (cs.doZStack && (cs.zOffset != 0d))
StageMover.moveZRelative(cs.zOffset, true);
// do image acquisition
@@ -90,7 +101,7 @@ public class MicroscopeSnapChannels extends AbstractMicroscopeBlock
final List<TaggedImage> images = MicroManager.snapTaggedImage();
// restore Z position if needed
- if (cs.doZStack.booleanValue() && (cs.zOffset != 0d))
+ if (cs.doZStack && (cs.zOffset != 0d))
StageMover.moveZRelative(-cs.zOffset, true);
// no image ? --> error
@@ -98,8 +109,7 @@ public class MicroscopeSnapChannels extends AbstractMicroscopeBlock
throw new Exception("Cannot snap image from Micro-Manager !");
// set metadata
- for (TaggedImage image : images)
- {
+ for (final TaggedImage image : images) {
final JSONObject tags = image.tags;
MDUtils.setNumChannels(tags, specs.length);
@@ -110,33 +120,29 @@ public class MicroscopeSnapChannels extends AbstractMicroscopeBlock
// add to result
result.addAll(images);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(out, t.getMessage());
}
}
// set result
- out.setValue(result.toArray(new TaggedImage[result.size()]));
+ out.setValue(result.toArray(new TaggedImage[0]));
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
inputMap.add("group", group);
inputMap.add("channels", channels);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("out", out);
}
@Override
- public String getName()
- {
+ public String getName() {
return "Snap Channel(s)";
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapImage.java b/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapImage.java
index baf19d0cda1bc450ab623a170332e930b06b72ff..7105ac8bd0e039ebe3a7c810ce706b932c2778c3 100644
--- a/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapImage.java
+++ b/src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapImage.java
@@ -1,6 +1,22 @@
-package plugins.stef.micromanager.block.capture;
+/*
+ * 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.stef.micromanager.block.capture;
import mmcorej.TaggedImage;
import plugins.adufour.blocks.util.VarList;
@@ -10,48 +26,43 @@ import plugins.adufour.vars.util.VarException;
import plugins.stef.micromanager.block.AbstractMicroscopeBlock;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
+import java.util.List;
+
/**
* Snap single channel image (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSnapImage extends AbstractMicroscopeBlock
-{
- VarArray<TaggedImage> out = new VarArray<TaggedImage>("Tagged image(s)", TaggedImage[].class, new TaggedImage[0]);
+public class MicroscopeSnapImage extends AbstractMicroscopeBlock {
+ VarArray<TaggedImage> out = new VarArray<>("Tagged image(s)", TaggedImage[].class, new TaggedImage[0]);
VarObject trigger = new VarObject("Trigger", null);
@Override
- public void run()
- {
- try
- {
+ public void run() {
+ try {
final List<TaggedImage> images = MicroManager.snapTaggedImage();
if (images.isEmpty())
throw new Exception("Cannot snap image from Micro-Manager !");
- out.setValue(images.toArray(new TaggedImage[images.size()]));
+ out.setValue(images.toArray(new TaggedImage[0]));
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(out, t.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("out", out);
}
@Override
- public String getName()
- {
+ public String getName() {
return "Snap Image";
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/lang/VarChannels.java b/src/main/java/plugins/stef/micromanager/block/lang/VarChannels.java
index ee0aca09eb0ce813604d3ea008cba4597982b0c0..005b165619417e9164e1c0ece5f42c99c78c3977 100644
--- a/src/main/java/plugins/stef/micromanager/block/lang/VarChannels.java
+++ b/src/main/java/plugins/stef/micromanager/block/lang/VarChannels.java
@@ -1,8 +1,25 @@
-package plugins.stef.micromanager.block.lang;
+/*
+ * 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.micromanager.utils.ChannelSpec;
+package plugins.stef.micromanager.block.lang;
import icy.type.collection.CollectionUtil;
+import org.micromanager.utils.ChannelSpec;
import plugins.adufour.vars.gui.VarEditor;
import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarArray;
@@ -11,12 +28,10 @@ import plugins.adufour.vars.util.VarListener;
/**
* Class in standby until an EzPlug fix
*/
-public class VarChannels extends VarArray<ChannelSpec>
-{
+public class VarChannels extends VarArray<ChannelSpec> {
VarChannelsEditor editor;
- public VarChannels(String name, VarMMGroup groupVar)
- {
+ public VarChannels(final String name, final VarMMGroup groupVar) {
super(name, ChannelSpec[].class, null);
// can be initialized by super constructor
@@ -25,31 +40,25 @@ public class VarChannels extends VarArray<ChannelSpec>
setGroup(groupVar.getValue());
- groupVar.addListener(new VarListener<String>()
- {
+ groupVar.addListener(new VarListener<>() {
@Override
- public void valueChanged(Var<String> source, String oldValue, String newValue)
- {
+ public void valueChanged(final Var<String> source, final String oldValue, final String newValue) {
setGroup(newValue);
}
@Override
- public void referenceChanged(Var<String> source, Var<? extends String> oldReference,
- Var<? extends String> newReference)
- {
+ public void referenceChanged(final Var<String> source, final Var<? extends String> oldReference, final Var<? extends String> newReference) {
//
}
});
}
- public VarChannels(VarMMGroup groupVar)
- {
+ public VarChannels(final VarMMGroup groupVar) {
this("Channels", groupVar);
}
@Override
- public VarEditor<ChannelSpec[]> createVarEditor()
- {
+ public VarEditor<ChannelSpec[]> createVarEditor() {
if (editor == null)
editor = new VarChannelsEditor(this);
@@ -57,59 +66,16 @@ public class VarChannels extends VarArray<ChannelSpec>
}
@Override
- public ChannelSpec[] getValue()
- {
+ public ChannelSpec[] getValue() {
return editor.table.getChannels().toArray(new ChannelSpec[0]);
}
@Override
- public void setValue(ChannelSpec[] value)
- {
+ public void setValue(final ChannelSpec[] value) {
editor.table.setChannels(CollectionUtil.asArrayList(value));
}
- public void setGroup(String groupName)
- {
+ public void setGroup(final String groupName) {
editor.setGroup(groupName);
}
-
- // public static List<ChannelSpec> generateChannels(String groupName)
- // {
- // final List<ChannelSpec> toReturn = new ArrayList<ChannelSpec>();
- // if (groupName == null)
- // return toReturn;
- //
- // final List<String> presets = MicroManager.getConfigs(groupName);
- //
- // if (presets != null)
- // {
- // try
- // {
- // final String cam = MicroManager.getCamera();
- //
- // for (String s : presets)
- // {
- // ChannelSpec cs = new ChannelSpec();
- //
- // cs.config = s;
- // cs.camera = cam;
- // cs.color = Color.WHITE;
- // cs.doZStack = true;
- // cs.skipFactorFrame = 0;
- // cs.zOffset = 0D;
- // cs.exposure = 10;
- // cs.useChannel = true;
- //
- // toReturn.add(cs);
- // }
- // }
- // catch (Throwable t)
- // {
- // ReportingUtils.logError(t);
- // }
- // }
- //
- // return toReturn;
- // }
-
}
diff --git a/src/main/java/plugins/stef/micromanager/block/lang/VarChannelsEditor.java b/src/main/java/plugins/stef/micromanager/block/lang/VarChannelsEditor.java
index 7137301767e26dbde87efa55fc06c95f4508abc5..67d70d78501e4ea21cf160b4fac482848c739278 100644
--- a/src/main/java/plugins/stef/micromanager/block/lang/VarChannelsEditor.java
+++ b/src/main/java/plugins/stef/micromanager/block/lang/VarChannelsEditor.java
@@ -1,34 +1,41 @@
-package plugins.stef.micromanager.block.lang;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+/*
+ * 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 javax.swing.BoxLayout;
-import javax.swing.JButton;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.ScrollPaneConstants;
+package plugins.stef.micromanager.block.lang;
import org.micromanager.dialogs.ChannelTableModel;
import org.micromanager.utils.ChannelSpec;
import org.micromanager.utils.TooltipTextMaker;
-
import plugins.adufour.vars.gui.VarEditor;
import plugins.adufour.vars.lang.Var;
import plugins.tprovoost.Microscopy.MicroManager.gui.ChannelTable;
+import javax.swing.*;
+import java.awt.*;
+
/**
* Class in standby until an EzPlug fix
*/
-public class VarChannelsEditor extends VarEditor<ChannelSpec[]>
-{
+public class VarChannelsEditor extends VarEditor<ChannelSpec[]> {
protected JPanel mainPanel;
protected ChannelTable table;
- public VarChannelsEditor(Var<ChannelSpec[]> variable)
- {
+ public VarChannelsEditor(final Var<ChannelSpec[]> variable) {
super(variable);
// can be done by super constructor
@@ -39,8 +46,7 @@ public class VarChannelsEditor extends VarEditor<ChannelSpec[]>
}
@Override
- protected JPanel createEditorComponent()
- {
+ protected JPanel createEditorComponent() {
// initialize if needed
if (mainPanel == null)
initialize();
@@ -48,91 +54,65 @@ public class VarChannelsEditor extends VarEditor<ChannelSpec[]>
return mainPanel;
}
- private void initialize()
- {
+ private void initialize() {
table = new ChannelTable();
- JScrollPane scroll = new JScrollPane(table);
+ final JScrollPane scroll = new JScrollPane(table);
scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
// better to give it a very small size
scroll.setMinimumSize(new Dimension(240, 60));
scroll.setPreferredSize(new Dimension(240, 100));
- JButton btnAddChannel = new JButton("Add Channel");
+ final JButton btnAddChannel = new JButton("Add Channel");
btnAddChannel.setToolTipText("Create new channel for currently selected channel group");
- btnAddChannel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- final ChannelTableModel model = (ChannelTableModel) table.getModel();
- model.addNewChannel();
- model.fireTableDataChanged();
- }
+ btnAddChannel.addActionListener(e -> {
+ final ChannelTableModel model = (ChannelTableModel) table.getModel();
+ model.addNewChannel();
+ model.fireTableDataChanged();
});
- JButton btnRemoveChannel = new JButton("Remove Channel");
+ final JButton btnRemoveChannel = new JButton("Remove Channel");
btnRemoveChannel.setToolTipText("Remove currently selected channel");
- btnRemoveChannel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- int sel = table.getSelectedRow();
-
- if (sel > -1)
- {
- final ChannelTableModel model = (ChannelTableModel) table.getModel();
- model.removeChannel(sel);
- model.fireTableDataChanged();
- if (table.getRowCount() > sel)
- table.setRowSelectionInterval(sel, sel);
- }
+ btnRemoveChannel.addActionListener(e -> {
+ final int sel = table.getSelectedRow();
+
+ if (sel > -1) {
+ final ChannelTableModel model = (ChannelTableModel) table.getModel();
+ model.removeChannel(sel);
+ model.fireTableDataChanged();
+ if (table.getRowCount() > sel)
+ table.setRowSelectionInterval(sel, sel);
}
});
final JButton upButton = new JButton("Up");
upButton.setToolTipText(TooltipTextMaker
.addHTMLBreaksForTooltip("Move currently selected channel up (Channels higher on list are acquired first)"));
- upButton.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- int sel = table.getSelectedRow();
-
- if (sel > -1)
- {
- final ChannelTableModel model = (ChannelTableModel) table.getModel();
- int newSel = model.rowUp(sel);
- model.fireTableDataChanged();
- table.setRowSelectionInterval(newSel, newSel);
- }
+ upButton.addActionListener(e -> {
+ final int sel = table.getSelectedRow();
+
+ if (sel > -1) {
+ final ChannelTableModel model = (ChannelTableModel) table.getModel();
+ final int newSel = model.rowUp(sel);
+ model.fireTableDataChanged();
+ table.setRowSelectionInterval(newSel, newSel);
}
});
final JButton downButton = new JButton("Down");
- downButton
- .setToolTipText(TooltipTextMaker
- .addHTMLBreaksForTooltip("Move currently selected channel down (Channels lower on list are acquired later)"));
- downButton.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- int sel = table.getSelectedRow();
-
- if (sel > -1)
- {
- final ChannelTableModel model = (ChannelTableModel) table.getModel();
- int newSel = model.rowDown(sel);
- model.fireTableDataChanged();
- table.setRowSelectionInterval(newSel, newSel);
- }
+ downButton.setToolTipText(TooltipTextMaker.addHTMLBreaksForTooltip("Move currently selected channel down (Channels lower on list are acquired later)"));
+ downButton.addActionListener(e -> {
+ final int sel = table.getSelectedRow();
+
+ if (sel > -1) {
+ final ChannelTableModel model = (ChannelTableModel) table.getModel();
+ final int newSel = model.rowDown(sel);
+ model.fireTableDataChanged();
+ table.setRowSelectionInterval(newSel, newSel);
}
});
- JPanel panelButtons = new JPanel();
+ final JPanel panelButtons = new JPanel();
panelButtons.setLayout(new BoxLayout(panelButtons, BoxLayout.X_AXIS));
panelButtons.add(btnAddChannel);
panelButtons.add(btnRemoveChannel);
@@ -146,31 +126,26 @@ public class VarChannelsEditor extends VarEditor<ChannelSpec[]>
}
@Override
- protected void activateListeners()
- {
+ protected void activateListeners() {
//
}
@Override
- protected void deactivateListeners()
- {
+ protected void deactivateListeners() {
//
}
@Override
- protected void updateInterfaceValue()
- {
+ protected void updateInterfaceValue() {
//
}
- public void setGroup(String group)
- {
+ public void setGroup(final String group) {
table.setGroup(group);
}
@Override
- public Dimension getPreferredSize()
- {
+ public Dimension getPreferredSize() {
if (mainPanel != null)
return mainPanel.getPreferredSize();
@@ -178,15 +153,13 @@ public class VarChannelsEditor extends VarEditor<ChannelSpec[]>
}
@Override
- public void setComponentToolTipText(String s)
- {
+ public void setComponentToolTipText(final String s) {
if (mainPanel != null)
mainPanel.setToolTipText(s);
}
@Override
- protected void setEditorEnabled(boolean enabled)
- {
+ protected void setEditorEnabled(final boolean enabled) {
if (mainPanel != null)
mainPanel.setEnabled(enabled);
}
diff --git a/src/main/java/plugins/stef/micromanager/block/lang/VarMMGroup.java b/src/main/java/plugins/stef/micromanager/block/lang/VarMMGroup.java
index b94129e403ec351babafdf6b88ac15897831378f..ecf62f70255c452ec7944330378474461af54471 100644
--- a/src/main/java/plugins/stef/micromanager/block/lang/VarMMGroup.java
+++ b/src/main/java/plugins/stef/micromanager/block/lang/VarMMGroup.java
@@ -1,33 +1,45 @@
-/**
- *
+/*
+ * 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.stef.micromanager.block.lang;
-import java.util.List;
+package plugins.stef.micromanager.block.lang;
import plugins.adufour.vars.gui.model.ValueSelectionModel;
import plugins.adufour.vars.lang.VarString;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
+import java.util.List;
+
/**
* EzVar representing Micro-Manager config group.
- *
+ *
* @author Stephane
*/
-public class VarMMGroup extends VarString
-{
- public VarMMGroup(String name)
- {
+public class VarMMGroup extends VarString {
+ public VarMMGroup(final String name) {
super(name, "");
-
+
final List<String> groups = MicroManager.getConfigGroups();
-
- if (groups.size() > 0)
- setDefaultEditorModel(new ValueSelectionModel<String>(groups.toArray(new String[groups.size()]), groups.get(0), false));
+
+ if (!groups.isEmpty())
+ setDefaultEditorModel(new ValueSelectionModel<>(groups.toArray(new String[0]), groups.get(0), false));
}
- public VarMMGroup()
- {
+ public VarMMGroup() {
this("Group");
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/lang/VarMMPreset.java b/src/main/java/plugins/stef/micromanager/block/lang/VarMMPreset.java
index 5fbbee36e0c7e34010039f39fb5311f48ff99a2c..f6952b4d81c101788ddc6e0b0c5fcfc95af30e8a 100644
--- a/src/main/java/plugins/stef/micromanager/block/lang/VarMMPreset.java
+++ b/src/main/java/plugins/stef/micromanager/block/lang/VarMMPreset.java
@@ -1,9 +1,22 @@
-/**
- *
+/*
+ * 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.stef.micromanager.block.lang;
-import java.util.List;
+package plugins.stef.micromanager.block.lang;
import plugins.adufour.vars.gui.model.ValueSelectionModel;
import plugins.adufour.vars.lang.Var;
@@ -11,51 +24,44 @@ import plugins.adufour.vars.lang.VarString;
import plugins.adufour.vars.util.VarListener;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
+import java.util.List;
+
/**
* EzVar representing Micro-Manager config preset.
- *
+ *
* @author Stephane
*/
-public class VarMMPreset extends VarString
-{
- public VarMMPreset(String name, VarMMGroup groupVar)
- {
+public class VarMMPreset extends VarString {
+ public VarMMPreset(final String name, final VarMMGroup groupVar) {
super(name, "");
// set values
refreshPresets(groupVar.getValue());
// listen group var change
- groupVar.addListener(new VarListener<String>()
- {
+ groupVar.addListener(new VarListener<>() {
@Override
- public void valueChanged(Var<String> source, String oldValue, String newValue)
- {
+ public void valueChanged(final Var<String> source, final String oldValue, final String newValue) {
refreshPresets(newValue);
}
@Override
- public void referenceChanged(Var<String> source, Var<? extends String> oldReference,
- Var<? extends String> newReference)
- {
+ public void referenceChanged(final Var<String> source, final Var<? extends String> oldReference, final Var<? extends String> newReference) {
//
}
});
}
- public VarMMPreset(VarMMGroup groupVar)
- {
+ public VarMMPreset(final VarMMGroup groupVar) {
this("Preset", groupVar);
}
- public void refreshPresets(String group)
- {
+ public void refreshPresets(final String group) {
final List<String> presets = MicroManager.getConfigs(group);
- if (presets.size() > 0)
- setDefaultEditorModel(new ValueSelectionModel<String>(presets.toArray(new String[presets.size()]),
- presets.get(0), false));
- else
- setDefaultEditorModel(new ValueSelectionModel<String>(new String[] {""}, "", false));
+ if (!presets.isEmpty())
+ setDefaultEditorModel(new ValueSelectionModel<>(presets.toArray(new String[0]), presets.get(0), false));
+ else
+ setDefaultEditorModel(new ValueSelectionModel<>(new String[]{""}, "", false));
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/lang/VarMultiStagePosition.java b/src/main/java/plugins/stef/micromanager/block/lang/VarMultiStagePosition.java
index 92f0982dd25eb315c252e6433bbf11566aeb7055..656ff7d2633993be4d31e19e1c03ee490f7ab2aa 100644
--- a/src/main/java/plugins/stef/micromanager/block/lang/VarMultiStagePosition.java
+++ b/src/main/java/plugins/stef/micromanager/block/lang/VarMultiStagePosition.java
@@ -1,25 +1,36 @@
-package plugins.stef.micromanager.block.lang;
-
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+/*
+ * 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 javax.swing.JButton;
-import javax.swing.JComponent;
+package plugins.stef.micromanager.block.lang;
import org.micromanager.api.MultiStagePosition;
-
import plugins.adufour.vars.gui.VarEditor;
import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarArray;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
-public class VarMultiStagePosition extends VarArray<MultiStagePosition>
-{
+import javax.swing.*;
+import java.awt.*;
+
+public class VarMultiStagePosition extends VarArray<MultiStagePosition> {
VarEditorMultiStagePositions pos;
- public VarMultiStagePosition(String name, MultiStagePosition[] defaultValue)
- {
+ public VarMultiStagePosition(final String name, final MultiStagePosition[] defaultValue) {
super(name, MultiStagePosition[].class, defaultValue);
// can be initialized with super constructor
@@ -28,57 +39,42 @@ public class VarMultiStagePosition extends VarArray<MultiStagePosition>
}
@Override
- public VarEditor<MultiStagePosition[]> createVarEditor()
- {
+ public VarEditor<MultiStagePosition[]> createVarEditor() {
if (pos == null)
pos = new VarEditorMultiStagePositions(this);
return pos;
}
- private class VarEditorMultiStagePositions extends VarEditor<MultiStagePosition[]>
- {
+ private static class VarEditorMultiStagePositions extends VarEditor<MultiStagePosition[]> {
JButton btnOpen;
- public VarEditorMultiStagePositions(Var<MultiStagePosition[]> variable)
- {
+ public VarEditorMultiStagePositions(final Var<MultiStagePosition[]> variable) {
super(variable);
}
@Override
- protected JComponent createEditorComponent()
- {
+ protected JComponent createEditorComponent() {
btnOpen = new JButton("Open");
- btnOpen.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- MicroManager.getMMStudio().showXYPositionList();
- }
- });
+ btnOpen.addActionListener(e -> MicroManager.getMMStudio().showXYPositionList());
return btnOpen;
}
@Override
- protected void activateListeners()
- {
+ protected void activateListeners() {
}
@Override
- protected void deactivateListeners()
- {
+ protected void deactivateListeners() {
}
@Override
- protected void updateInterfaceValue()
- {
+ protected void updateInterfaceValue() {
}
@Override
- public Dimension getPreferredSize()
- {
+ public Dimension getPreferredSize() {
if (btnOpen != null)
return btnOpen.getPreferredSize();
@@ -86,15 +82,13 @@ public class VarMultiStagePosition extends VarArray<MultiStagePosition>
}
@Override
- public void setComponentToolTipText(String s)
- {
+ public void setComponentToolTipText(final String s) {
if (btnOpen != null)
btnOpen.setToolTipText(s);
}
@Override
- protected void setEditorEnabled(boolean enabled)
- {
+ protected void setEditorEnabled(final boolean enabled) {
if (btnOpen != null)
btnOpen.setEnabled(enabled);
}
diff --git a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeChannels.java b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeChannels.java
index 6f51e6893b6ac5dc32a84884ff0589e27c0ad5b2..ece292cd08fb9aae1af85a574695e2ed7e0b45ca 100644
--- a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeChannels.java
+++ b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeChannels.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.stef.micromanager.block.setting;
import plugins.adufour.blocks.tools.input.InputBlock;
@@ -9,29 +27,25 @@ import plugins.stef.micromanager.block.lang.VarMMGroup;
/**
* Define a list of channel (Micro-Manager)
* Class in standby until an EzPlug fix
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeChannels extends AbstractMicroscopeBlock implements InputBlock
-{
+public class MicroscopeChannels extends AbstractMicroscopeBlock implements InputBlock {
VarMMGroup group;
VarChannels channels;
- public MicroscopeChannels()
- {
+ public MicroscopeChannels() {
group = new VarMMGroup();
channels = new VarChannels(group);
}
@Override
- public void run()
- {
+ public void run() {
//
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
if (group != null)
inputMap.add("groups", group);
if (channels != null)
@@ -39,8 +53,7 @@ public class MicroscopeChannels extends AbstractMicroscopeBlock implements Input
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeGetBinning.java b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeGetBinning.java
index fd9384fe16b11a41ec56528d495a45e882181390..59c90868601b970be45ec0107f3d806e74f301ab 100644
--- a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeGetBinning.java
+++ b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeGetBinning.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.stef.micromanager.block.setting;
import plugins.adufour.blocks.util.VarList;
@@ -9,35 +27,29 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
* Return camera binning value (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeGetBinning extends AbstractMicroscopeBlock
-{
+public class MicroscopeGetBinning extends AbstractMicroscopeBlock {
VarObject trigger = new VarObject("Trigger", null);
VarInteger binning = new VarInteger("Binning", 1);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("binning", binning);
}
@Override
- public void run()
- {
- try
- {
- binning.setValue(Integer.valueOf(MicroManager.getBinning()));
+ public void run() {
+ try {
+ binning.setValue(MicroManager.getBinning());
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(binning, t.getMessage());
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeGetExposure.java b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeGetExposure.java
index 3701e04014a5e78b000e39bd69c737ec92e00eec..52157d65b52469910a3b1539e755d294c35e6ada 100644
--- a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeGetExposure.java
+++ b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeGetExposure.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.stef.micromanager.block.setting;
import plugins.adufour.blocks.util.VarList;
@@ -9,35 +27,29 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
* Return camera exposure value in ms (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeGetExposure extends AbstractMicroscopeBlock
-{
+public class MicroscopeGetExposure extends AbstractMicroscopeBlock {
VarObject trigger = new VarObject("Trigger", null);
VarDouble exposure = new VarDouble("Exposure (ms)", 50d);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("exposure", exposure);
}
@Override
- public void run()
- {
- try
- {
- exposure.setValue(Double.valueOf(MicroManager.getExposure()));
+ public void run() {
+ try {
+ exposure.setValue(MicroManager.getExposure());
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(exposure, t.getMessage());
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopePositions.java b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopePositions.java
index dc87ec8f97df95d198fa5d6858f331be39052980..e4814215097777108cabea81c5b64b4c7366875c 100644
--- a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopePositions.java
+++ b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopePositions.java
@@ -1,9 +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.stef.micromanager.block.setting;
import org.micromanager.MMStudio;
import org.micromanager.api.MultiStagePosition;
import org.micromanager.api.PositionList;
-
import plugins.adufour.blocks.tools.input.InputBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarArray;
@@ -14,42 +31,35 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
* Define a list of stage positions (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopePositions extends AbstractMicroscopeBlock implements InputBlock
-{
+public class MicroscopePositions extends AbstractMicroscopeBlock implements InputBlock {
VarArray<MultiStagePosition> varPositions;
- public MicroscopePositions()
- {
+ public MicroscopePositions() {
super();
varPositions = new VarMultiStagePosition("Positions", null);
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("positions", varPositions);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
//
}
@Override
- public void run()
- {
+ public void run() {
final MMStudio mstudio = MicroManager.getMMStudio();
if (mstudio == null)
- throw new VarException(null,
- "Cannot retrieve Micro-Manager core...\nBe sure you started Micro-Manager plugin before using Micro-Manager blocks !");
+ throw new VarException(null, "Cannot retrieve Micro-Manager core...\nBe sure you started Micro-Manager plugin before using Micro-Manager blocks !");
- try
- {
+ try {
final PositionList list = mstudio.getPositionList();
if (list.getPositions() == null)
@@ -57,8 +67,7 @@ public class MicroscopePositions extends AbstractMicroscopeBlock implements Inpu
varPositions.setValue(list.getPositions());
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(varPositions, e.getMessage());
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetBinning.java b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetBinning.java
index f7929ee4e5cac81cf25df061413d39f0f9cd3180..19ce2c474ced75fc9915381e183517302a8cdc70 100644
--- a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetBinning.java
+++ b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetBinning.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.stef.micromanager.block.setting;
import plugins.adufour.blocks.util.VarList;
@@ -13,40 +28,34 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
* Set the camera binning value (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSetBinning extends AbstractMicroscopeBlock
-{
+public class MicroscopeSetBinning extends AbstractMicroscopeBlock {
VarObject trigger = new VarObject("Trigger", null);
VarInteger binning = new VarInteger("Binning", 1);
VarBoolean done = new VarBoolean("Done", false);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
inputMap.add("binning", binning);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("done", done);
}
@Override
- public void run()
- {
+ public void run() {
done.setValue(Boolean.FALSE);
- try
- {
- MicroManager.setBinning(binning.getValue().intValue());
+ try {
+ MicroManager.setBinning(binning.getValue());
done.setValue(Boolean.TRUE);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(binning, t.getMessage());
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetConfig.java b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetConfig.java
index 4ab9a964f23dac0ed9006a08ac5d4e2a4bcd8859..fbb0c2bea2e7843248dd65ce710dc06dc9eb35fe 100644
--- a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetConfig.java
+++ b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetConfig.java
@@ -1,6 +1,22 @@
-package plugins.stef.micromanager.block.setting;
+/*
+ * 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.stef.micromanager.block.setting;
import plugins.adufour.blocks.lang.BlockDescriptor;
import plugins.adufour.blocks.lang.WorkFlow;
@@ -22,21 +38,21 @@ import plugins.stef.micromanager.block.lang.VarMMGroup;
import plugins.stef.micromanager.block.lang.VarMMPreset;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
+import java.util.List;
+
/**
* Set a preset for a specified group (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSetConfig extends AbstractMicroscopeBlock
-{
+public class MicroscopeSetConfig extends AbstractMicroscopeBlock {
VarObject trigger;
VarMMGroup group;
VarMMPreset preset;
VarBoolean wait;
VarBoolean done;
- public MicroscopeSetConfig()
- {
+ public MicroscopeSetConfig() {
super();
trigger = new VarObject("Trigger", null);
@@ -46,42 +62,34 @@ public class MicroscopeSetConfig extends AbstractMicroscopeBlock
done = new VarBoolean("Done", false);
// listen group var to refresh the preset GUI which is disconnected from preset var
- group.addListener(new VarListener<String>()
- {
+ group.addListener(new VarListener<>() {
@Override
- public void valueChanged(Var<String> source, String oldValue, String newValue)
- {
+ public void valueChanged(final Var<String> source, final String oldValue, final String newValue) {
refreshPresetsGUI(newValue);
}
@Override
- public void referenceChanged(Var<String> source, Var<? extends String> oldReference,
- Var<? extends String> newReference)
- {
+ public void referenceChanged(final Var<String> source, final Var<? extends String> oldReference, final Var<? extends String> newReference) {
//
}
});
}
@Override
- public void run()
- {
+ public void run() {
done.setValue(Boolean.FALSE);
- try
- {
- MicroManager.setConfigForGroup(group.getValue(), preset.getValue(), wait.getValue().booleanValue());
+ try {
+ MicroManager.setConfigForGroup(group.getValue(), preset.getValue(), wait.getValue());
done.setValue(Boolean.TRUE);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(group, t.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
inputMap.add("group", group);
inputMap.add("preset", preset);
@@ -89,42 +97,34 @@ public class MicroscopeSetConfig extends AbstractMicroscopeBlock
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
if (done != null)
outputMap.add("done", done);
}
- @SuppressWarnings("unchecked")
- public void refreshPresetsGUI(String group)
- {
+ public void refreshPresetsGUI(final String group) {
final MainFrame protocols = Protocols.getInstance();
- if (protocols != null)
- {
+ if (protocols != null) {
final ProtocolPanel protocolPanel = protocols.getActiveProtocol();
- if (protocolPanel != null)
- {
+ if (protocolPanel != null) {
final WorkFlowContainer wfc = protocolPanel.getWorkFlowContainer();
final WorkFlow wf = protocolPanel.getWorkFlow();
// get our block descriptor
final BlockDescriptor bd = wf.getInputOwner(preset);
- if (bd != null)
- {
+ if (bd != null) {
// get our block panel
final BlockPanel bp = wfc.getBlockPanel(bd);
- if (bp != null)
- {
+ if (bp != null) {
// get GUI component for preset var
final VarEditor<?> editor = bp.getVarEditor(preset);
// should be a combo box
- if (editor instanceof ComboBox<?>)
- {
- final ComboBox<String> combo = (ComboBox<String>) editor;
+ if (editor instanceof ComboBox<?>) {
+ @SuppressWarnings("unchecked") final ComboBox<String> combo = (ComboBox<String>) editor;
final List<String> presets = MicroManager.getConfigs(group);
- if (presets.size() > 0)
- combo.setDefaultValues(presets.toArray(new String[presets.size()]), 0, false);
+ if (!presets.isEmpty())
+ combo.setDefaultValues(presets.toArray(new String[0]), 0, false);
}
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetExposure.java b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetExposure.java
index 3f177e7b61a01b7ecbe514d5e0672be2796f0be0..803e6e75f4c81d07b566c88757b7cbc27b39a61a 100644
--- a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetExposure.java
+++ b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetExposure.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.stef.micromanager.block.setting;
import plugins.adufour.blocks.util.VarList;
@@ -10,40 +28,34 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
* Set the camera exposure value (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSetExposure extends AbstractMicroscopeBlock
-{
+public class MicroscopeSetExposure extends AbstractMicroscopeBlock {
VarObject trigger = new VarObject("Trigger", null);
VarDouble exposure = new VarDouble("Exposure", 10d);
VarBoolean done = new VarBoolean("Done", false);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
inputMap.add("exposure", exposure);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("done", done);
}
@Override
- public void run()
- {
+ public void run() {
done.setValue(Boolean.FALSE);
- try
- {
- MicroManager.setExposure(exposure.getValue().doubleValue());
+ try {
+ MicroManager.setExposure(exposure.getValue());
done.setValue(Boolean.TRUE);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(exposure, t.getMessage());
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetShutter.java b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetShutter.java
index 84e1e7e011aed04a79a7d281d54b4a556332c377..82b13e0a5a8cdc2cd9ffefb6ba1248dca58086f8 100644
--- a/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetShutter.java
+++ b/src/main/java/plugins/stef/micromanager/block/setting/MicroscopeSetShutter.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.stef.micromanager.block.setting;
import plugins.adufour.blocks.util.VarList;
@@ -9,41 +27,35 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
* Set the shutter position: open / close (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSetShutter extends AbstractMicroscopeBlock
-{
+public class MicroscopeSetShutter extends AbstractMicroscopeBlock {
VarObject trigger = new VarObject("Trigger", null);
VarBoolean open = new VarBoolean("Open", true);
VarBoolean done = new VarBoolean("Done", false);
@Override
- public void run()
- {
+ public void run() {
done.setValue(Boolean.FALSE);
- try
- {
- MicroManager.setShutterOpen(open.getValue().booleanValue());
+ try {
+ MicroManager.setShutterOpen(open.getValue());
done.setValue(Boolean.TRUE);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(open, t.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
inputMap.add("open", open);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("done", done);
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeGetStageXYZ.java b/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeGetStageXYZ.java
index a67874c466651de9e70936cbd0bc8e814980e716..9f91b3403ff42cf824516e62cacf5aeb87403fee 100644
--- a/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeGetStageXYZ.java
+++ b/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeGetStageXYZ.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.stef.micromanager.block.stage;
import icy.type.point.Point3D;
@@ -11,11 +29,10 @@ import plugins.tprovoost.Microscopy.MicroManager.tools.StageMover;
/**
* Return the stage XYZ position (Micro-Manager)
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeGetStageXYZ extends AbstractMicroscopeBlock
-{
+public class MicroscopeGetStageXYZ extends AbstractMicroscopeBlock {
VarObject trigger = new VarObject("Trigger", null);
VarBoolean wait = new VarBoolean("Wait stage", true);
VarDouble outX = new VarDouble("X", 0d);
@@ -23,32 +40,27 @@ public class MicroscopeGetStageXYZ extends AbstractMicroscopeBlock
VarDouble outZ = new VarDouble("Z", 0d);
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
inputMap.add("wait", wait);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("x", outX);
outputMap.add("y", outY);
outputMap.add("z", outZ);
}
@Override
- public void run()
- {
- try
- {
- Point3D.Double pos = StageMover.getXYZ();
+ public void run() {
+ try {
+ final Point3D.Double pos = StageMover.getXYZ();
outX.setValue(Double.valueOf(pos.x));
outY.setValue(Double.valueOf(pos.y));
outZ.setValue(Double.valueOf(pos.z));
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(outX, t.getMessage());
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStagePosition.java b/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStagePosition.java
index 4e85038c75734b04a938d823722941a867c8bef9..8b08e76c81cad640dfa237945fae51808e5925bd 100644
--- a/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStagePosition.java
+++ b/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStagePosition.java
@@ -1,9 +1,26 @@
-package plugins.stef.micromanager.block.stage;
+/*
+ * 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.micromanager.api.MultiStagePosition;
+package plugins.stef.micromanager.block.stage;
import icy.system.thread.ThreadUtil;
import mmcorej.CMMCore;
+import org.micromanager.api.MultiStagePosition;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarBoolean;
@@ -15,59 +32,45 @@ import plugins.stef.micromanager.block.setting.MicroscopePositions;
* Set the stage to given position (Micro-Manager).<br>
* This block should be used in conjunction with {@link MicroscopePositions} block and an indexer
* so we can move to each position.
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSetStagePosition extends AbstractMicroscopeBlock
-{
+public class MicroscopeSetStagePosition extends AbstractMicroscopeBlock {
Var<MultiStagePosition> input;
VarBoolean waitForStage;
VarBoolean done;
- public MicroscopeSetStagePosition()
- {
+ public MicroscopeSetStagePosition() {
super();
- input = new Var<MultiStagePosition>("Position", MultiStagePosition.class);
+ input = new Var<>("Position", MultiStagePosition.class);
waitForStage = new VarBoolean("Wait stage", true);
done = new VarBoolean("Done", false);
}
@Override
- public void run()
- {
+ public void run() {
done.setValue(Boolean.FALSE);
final CMMCore core = getMMCore(true);
- if (waitForStage.getValue().booleanValue())
- {
- try
- {
+ if (waitForStage.getValue()) {
+ try {
MultiStagePosition.goToPosition(input.getValue(), core);
done.setValue(Boolean.TRUE);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(input, t.getMessage());
}
}
- else
- {
+ else {
// do it in background
- ThreadUtil.bgRun(new Runnable()
- {
- @Override
- public void run()
- {
- try
- {
- MultiStagePosition.goToPosition(input.getValue(), core);
- }
- catch (Throwable t)
- {
- throw new VarException(input, t.getMessage());
- }
+ ThreadUtil.bgRun(() -> {
+ try {
+ MultiStagePosition.goToPosition(input.getValue(), core);
+ }
+ catch (final Throwable t) {
+ throw new VarException(input, t.getMessage());
}
});
@@ -76,8 +79,7 @@ public class MicroscopeSetStagePosition extends AbstractMicroscopeBlock
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
if (input != null)
inputMap.add("position", input);
if (waitForStage != null)
@@ -85,8 +87,7 @@ public class MicroscopeSetStagePosition extends AbstractMicroscopeBlock
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
if (done != null)
outputMap.add("done", done);
}
diff --git a/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStageXY.java b/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStageXY.java
index 0d180fcb1e57917dca86b05f3ebffdd703122dda..97db9cc131badf2003a9099b42457247045bc6ab 100644
--- a/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStageXY.java
+++ b/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStageXY.java
@@ -1,6 +1,22 @@
-package plugins.stef.micromanager.block.stage;
+/*
+ * 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.geom.Point2D;
+package plugins.stef.micromanager.block.stage;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarBoolean;
@@ -10,13 +26,14 @@ import plugins.adufour.vars.util.VarException;
import plugins.stef.micromanager.block.AbstractMicroscopeBlock;
import plugins.tprovoost.Microscopy.MicroManager.tools.StageMover;
+import java.awt.geom.Point2D;
+
/**
* Set the stage to given XY position (Micro-Manager).
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSetStageXY extends AbstractMicroscopeBlock
-{
+public class MicroscopeSetStageXY extends AbstractMicroscopeBlock {
VarDouble inX;
VarDouble inY;
VarObject trigger = new VarObject("Trigger", null);
@@ -24,48 +41,39 @@ public class MicroscopeSetStageXY extends AbstractMicroscopeBlock
VarBoolean relative = new VarBoolean("Relative", true);
VarBoolean done = new VarBoolean("Done", false);
- public MicroscopeSetStageXY()
- {
+ public MicroscopeSetStageXY() {
super();
- try
- {
- Point2D.Double pos = StageMover.getXY();
+ try {
+ final Point2D.Double pos = StageMover.getXY();
inX = new VarDouble("X", pos.x);
inY = new VarDouble("Y", pos.y);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
inX = new VarDouble("X", 0d);
inY = new VarDouble("Y", 0d);
}
}
@Override
- public void run()
- {
+ public void run() {
done.setValue(Boolean.FALSE);
- try
- {
- if (relative.getValue().booleanValue())
- StageMover.moveXYRelative(inX.getValue().doubleValue(), inY.getValue().doubleValue(), wait.getValue()
- .booleanValue());
+ try {
+ if (relative.getValue())
+ StageMover.moveXYRelative(inX.getValue(), inY.getValue(), wait.getValue());
else
- StageMover.moveXYAbsolute(inX.getValue().doubleValue(), inY.getValue().doubleValue(), wait.getValue()
- .booleanValue());
+ StageMover.moveXYAbsolute(inX.getValue(), inY.getValue(), wait.getValue());
done.setValue(Boolean.TRUE);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(relative, t.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
inputMap.add("x", inX);
inputMap.add("y", inY);
@@ -74,8 +82,7 @@ public class MicroscopeSetStageXY extends AbstractMicroscopeBlock
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("done", done);
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStageZ.java b/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStageZ.java
index c0f8d84609cc1de5fecb515ae25cd1fad8c8868f..71084a044c126b5906e54ebdfa7a51bf82eddf3f 100644
--- a/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStageZ.java
+++ b/src/main/java/plugins/stef/micromanager/block/stage/MicroscopeSetStageZ.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.stef.micromanager.block.stage;
import plugins.adufour.blocks.util.VarList;
@@ -10,52 +28,44 @@ import plugins.tprovoost.Microscopy.MicroManager.tools.StageMover;
/**
* Set the Z stage to given Z position (Micro-Manager).
- *
+ *
* @author Stephane Dallongeville
*/
-public class MicroscopeSetStageZ extends AbstractMicroscopeBlock
-{
+public class MicroscopeSetStageZ extends AbstractMicroscopeBlock {
VarDouble inZ;
VarObject trigger = new VarObject("Trigger", null);
VarBoolean varWait = new VarBoolean("Wait stage", true);
VarBoolean varRelative = new VarBoolean("Relative", true);
VarBoolean varDone = new VarBoolean("Done", false);
- public MicroscopeSetStageZ()
- {
- try
- {
- double z = StageMover.getZ();
+ public MicroscopeSetStageZ() {
+ try {
+ final double z = StageMover.getZ();
inZ = new VarDouble("Z", z);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
inZ = new VarDouble("Z", 0d);
}
}
@Override
- public void run()
- {
+ public void run() {
varDone.setValue(Boolean.FALSE);
- try
- {
- if (varRelative.getValue().booleanValue())
- StageMover.moveZRelative(inZ.getValue().doubleValue(), varWait.getValue().booleanValue());
+ try {
+ if (varRelative.getValue())
+ StageMover.moveZRelative(inZ.getValue(), varWait.getValue());
else
- StageMover.moveZAbsolute(inZ.getValue().doubleValue(), varWait.getValue().booleanValue());
+ StageMover.moveZAbsolute(inZ.getValue(), varWait.getValue());
varDone.setValue(Boolean.TRUE);
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(varRelative, t.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("trigger", trigger);
inputMap.add("z", inZ);
inputMap.add("relative", varRelative);
@@ -63,8 +73,7 @@ public class MicroscopeSetStageZ extends AbstractMicroscopeBlock
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("done", varDone);
}
}
diff --git a/src/main/java/plugins/stef/micromanager/block/tool/TaggedImageToIcyImage.java b/src/main/java/plugins/stef/micromanager/block/tool/TaggedImageToIcyImage.java
index 8dd0a27d96e197cedceecaf90f9a7e6044fd9604..7574f55a0c8a3c2b75c2fbddf5d685c9571c4b24 100644
--- a/src/main/java/plugins/stef/micromanager/block/tool/TaggedImageToIcyImage.java
+++ b/src/main/java/plugins/stef/micromanager/block/tool/TaggedImageToIcyImage.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.stef.micromanager.block.tool;
import icy.image.IcyBufferedImage;
@@ -15,42 +30,35 @@ import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
/**
* Block to convert a TaggedImage to an IcyBufferedImage (Micro-Manager)
- *
+ *
* @author Stephane
*/
-public class TaggedImageToIcyImage extends AbstractMicroscopeBlock
-{
- VarArray<TaggedImage> in = new VarArray<TaggedImage>("Tagged Image", TaggedImage[].class, new TaggedImage[0]);
- Var<IcyBufferedImage> out = new Var<IcyBufferedImage>("Icy Image", IcyBufferedImage.class);
+public class TaggedImageToIcyImage extends AbstractMicroscopeBlock {
+ VarArray<TaggedImage> in = new VarArray<>("Tagged Image", TaggedImage[].class, new TaggedImage[0]);
+ Var<IcyBufferedImage> out = new Var<>("Icy Image", IcyBufferedImage.class);
@Override
- public void run()
- {
- try
- {
+ public void run() {
+ try {
out.setValue(MMUtils.convertToIcyImage(CollectionUtil.asList(in.getValue())));
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
throw new VarException(out, t.getMessage());
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("taggedImage", in);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("icyImage", out);
}
@Override
- public String getName()
- {
+ public String getName() {
return "TaggedImage to IcyBufferedImage";
}
}
\ No newline at end of file