From 4dc52f9c5798fa0c01ffecc1421633d258a77df1 Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Mon, 1 Jul 2024 17:45:31 +0200
Subject: [PATCH] updated pom to v2.0.0-a.1, fix classes accordingly to new
architecture, added icon, updated .gitignore
---
.gitignore | 46 ++++--
pom.xml | 10 +-
.../Microscopy/MicroManager/MicroManager.java | 153 ++++++++----------
.../MicroManager/core/AcquisitionHandler.java | 31 ++--
.../MicroManager/core/AcquisitionResult.java | 13 +-
.../event/AcquisitionListener.java | 4 +-
.../MicroManager/event/CoreListener.java | 2 +-
.../MicroManager/event/LiveListener.java | 4 +-
.../MicroManager/gui/AboutPanel.java | 4 +-
.../gui/AcquisitionInfoPanel.java | 10 +-
.../MicroManager/gui/ActionsPanel.java | 46 +++---
.../MicroManager/gui/CameraSettingsPanel.java | 56 +++----
.../MicroManager/gui/ChannelTable.java | 14 +-
.../MicroManager/gui/ConfigurationPanel.java | 35 ++--
.../MicroManager/gui/LiveSettingsPanel.java | 6 +-
.../MicroManager/gui/LoadFrame.java | 35 ++--
.../MicroManager/gui/LoadingFrame.java | 8 +-
.../MicroManager/gui/MMMainFrame.java | 82 ++++------
.../MicroManager/gui/MainPanel.java | 2 +-
.../MicroManager/gui/OptionsPanel.java | 4 +-
.../MicroManager/gui/PluginsToolbar.java | 40 ++---
.../MicroManager/patch/ClassPatcher.java | 45 +++---
.../MicroManager/patch/MMPatcher.java | 4 +-
.../MicroManager/patch/MMStudioMethods.java | 7 +-
.../MicroManager/tools/FrameUtils.java | 56 +------
.../MicroManager/tools/MMUtils.java | 110 ++++++-------
.../MicroManager/tools/StageMover.java | 28 ++--
.../MicromanagerPlugin.java | 10 +-
.../MicroManagerForIcy/MicroscopePlugin.java | 4 +-
src/main/resources/mmj.png | Bin 0 -> 15076 bytes
30 files changed, 403 insertions(+), 466 deletions(-)
create mode 100644 src/main/resources/mmj.png
diff --git a/.gitignore b/.gitignore
index 4d4593d..57f16fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,13 +1,41 @@
-.idea/
-.settings/
-workspace/
-build/
+/build*
+/workspace
+setting.xml
+release/
target/
-bin/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
-*.eml
-*.jar
-.project
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
-export.jardesc
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index e8a2787..3c35a3a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,11 +7,11 @@
<parent>
<artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<artifactId>micromanager</artifactId>
- <version>2.0.0</version>
+ <version>2.0.0-a.1</version>
<name>MicroManager for Icy</name>
<description>
@@ -20,10 +20,6 @@
Compatible with Micro-Manager 1.4.19 or above but we recommend to use the current last (1.4.23 / nightly build)
</description>
- <properties>
- <artifact-to-extract>MMCoreJ,MMJ_</artifact-to-extract>
- </properties>
-
<dependencies>
<dependency>
<groupId>org.micromanager</groupId>
@@ -40,7 +36,7 @@
<repositories>
<repository>
<id>icy</id>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java
index 91a6305..f695b7a 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,21 +18,24 @@
package plugins.tprovoost.Microscopy.MicroManager;
-import icy.common.Version;
-import icy.file.FileUtil;
-import icy.gui.dialog.MessageDialog;
-import icy.gui.frame.progress.FailedAnnounceFrame;
-import icy.image.IcyBufferedImage;
-import icy.main.Icy;
-import icy.sequence.Sequence;
-import icy.system.IcyExceptionHandler;
-import icy.system.thread.ThreadUtil;
-import icy.util.ClassUtil;
-import icy.util.StringUtil;
import mmcorej.CMMCore;
import mmcorej.MMCoreJ;
import mmcorej.StrVector;
import mmcorej.TaggedImage;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.Version;
+import org.bioimageanalysis.icy.common.reflect.ClassUtil;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.gui.dialog.MessageDialog;
+import org.bioimageanalysis.icy.gui.frame.progress.FailedAnnounceFrame;
+import org.bioimageanalysis.icy.io.FileUtil;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
import org.json.JSONObject;
import org.micromanager.MMStudio;
import org.micromanager.MMVersion;
@@ -85,6 +88,7 @@ public class MicroManager {
/**
* @return the MicroManager main frame instance.
*/
+ @Contract(pure = true)
public static MMMainFrame getInstance() {
// initialize micro manager if needed --> NO ! we need to init ourself
// if (instance == null)
@@ -96,14 +100,16 @@ public class MicroManager {
/**
* @return the MicroManager version
*/
- public static Version getMMVersion() {
+ @Contract(value = " -> new", pure = true)
+ public static @NotNull Version getMMVersion() {
// is this method really safe ??
- return new Version(MMVersion.VERSION_STRING);
+ return Version.fromString(MMVersion.VERSION_STRING);
}
/**
* @return the core listener list.
*/
+ @Contract(pure = true)
public static List<CoreListener> getCoreListeners() {
final List<CoreListener> result;
@@ -136,6 +142,7 @@ public class MicroManager {
/**
* @return the acquisition listener list.
*/
+ @Contract(pure = true)
public static List<AcquisitionListener> getAcquisitionListeners() {
final List<AcquisitionListener> result;
@@ -170,6 +177,7 @@ public class MicroManager {
/**
* @return the live listener list.
*/
+ @Contract(pure = true)
public static List<LiveListener> getLiveListeners() {
final List<LiveListener> result;
@@ -210,49 +218,13 @@ public class MicroManager {
}
}
- /**
- * @param listener the <i>acquisition</i> listener to register
- * @deprecated Use {@link #addAcquisitionListener(AcquisitionListener)} instead.
- */
- @Deprecated
- public static void registerListener(final AcquisitionListener listener) {
- addAcquisitionListener(listener);
- }
-
- /**
- * @param listener the <i>acquisition</i> listener to remove
- * @deprecated Use {@link #removeAcquisitionListener(AcquisitionListener)} instead.
- */
- @Deprecated
- public static void removeListener(final AcquisitionListener listener) {
- removeAcquisitionListener(listener);
- }
-
- /**
- * @param listener the <i>live</i> listener to register
- * @deprecated Use {@link #addLiveListener(LiveListener)} instead.
- */
- @Deprecated
- public static void registerListener(final LiveListener listener) {
- addLiveListener(listener);
- }
-
- /**
- * @param listener the <i>live</i> listener to remove
- * @deprecated Use {@link #removeLiveListener(LiveListener)} instead.
- */
- @Deprecated
- public static void removeListener(final LiveListener listener) {
- removeLiveListener(listener);
- }
-
/**
* Use this to access micro-manager main object to access low level function that
* are not been implemented in Icy's micro-Manager.
*
* @return The micro-manager main studio object.
*/
- public static MMStudio getMMStudio() {
+ public static @Nullable MMStudio getMMStudio() {
final MMMainFrame inst = getInstance();
if (inst == null)
return null;
@@ -271,7 +243,7 @@ public class MicroManager {
*
* @return The micro-manager core object
*/
- public static CMMCore getCore() {
+ public static @Nullable CMMCore getCore() {
final MMStudio mmstudio = getMMStudio();
if (mmstudio == null)
return null;
@@ -389,7 +361,7 @@ public class MicroManager {
/**
* @return The acquisition engine wrapper from MicroManager.
*/
- public static AcquisitionWrapperEngine getAcquisitionEngine() {
+ public static @Nullable AcquisitionWrapperEngine getAcquisitionEngine() {
final MMStudio mmstudio = getMMStudio();
if (mmstudio == null)
return null;
@@ -400,7 +372,7 @@ public class MicroManager {
/**
* @return The internal new acquisition engine from MicroManager.
*/
- public static IAcquisitionEngine2010 getAcquisitionEngine2010() {
+ public static @Nullable IAcquisitionEngine2010 getAcquisitionEngine2010() {
final MMStudio mmstudio = getMMStudio();
if (mmstudio == null)
return null;
@@ -412,7 +384,7 @@ public class MicroManager {
* @return The engine settings for the most recently started acquisition sequence, or return
* null if you never started an acquisition.
*/
- public static SequenceSettings getAcquisitionSettings() {
+ public static @Nullable SequenceSettings getAcquisitionSettings() {
final AcquisitionWrapperEngine acqEngine = getAcquisitionEngine();
if (acqEngine == null)
return null;
@@ -424,7 +396,7 @@ public class MicroManager {
* @return The summaryMetadata for the most recently started acquisition sequence, or return
* null if you never started an acquisition.
*/
- public static JSONObject getAcquisitionMetaData() {
+ public static @Nullable JSONObject getAcquisitionMetaData() {
final AcquisitionWrapperEngine acqEngine = getAcquisitionEngine();
if (acqEngine == null)
return null;
@@ -499,7 +471,7 @@ public class MicroManager {
* {@link #addAcquisitionListener(AcquisitionListener)}<br>
* @throws Exception if an error occurred while retrieved last tagged images
*/
- public static List<TaggedImage> getLastTaggedImage() throws Exception {
+ public static @NotNull List<TaggedImage> getLastTaggedImage() throws Exception {
final CMMCore core = MicroManager.getCore();
if (core == null || !core.isSequenceRunning())
@@ -567,7 +539,7 @@ public class MicroManager {
* @return next captured image as List of {@link TaggedImage} or an empty list if the continuous acquisition is not running
* @throws Exception if an error occurred
*/
- public static List<TaggedImage> getNextTaggedImage() throws Exception {
+ public static @NotNull List<TaggedImage> getNextTaggedImage() throws Exception {
final CMMCore core = MicroManager.getCore();
if (core == null || !core.isSequenceRunning())
@@ -575,16 +547,19 @@ public class MicroManager {
final boolean[] done = new boolean[]{false};
final LiveListener listener = new LiveListener() {
+ @Contract(pure = true)
@Override
public void liveStopped() {
done[0] = true;
}
+ @Contract(pure = true)
@Override
public void liveStarted() {
// nothing here
}
+ @Contract(pure = true)
@Override
public void liveImgReceived(final List<TaggedImage> images) {
done[0] = true;
@@ -642,7 +617,7 @@ public class MicroManager {
* @return the captured image as List of {@link TaggedImage}
* @throws Exception if an error occurred
*/
- public static List<TaggedImage> snapTaggedImage() throws Exception {
+ public static @NotNull List<TaggedImage> snapTaggedImage() throws Exception {
final CMMCore core = MicroManager.getCore();
if (core == null)
return new ArrayList<>();
@@ -846,7 +821,7 @@ public class MicroManager {
* @return the list of sequence corresponding to the last sequence acquisition or * <code>null</code> if no acquisition was done.
* @see #startAcquisition(int, double)
*/
- public static List<Sequence> getAcquisitionResult() {
+ public static @Nullable List<Sequence> getAcquisitionResult() {
if ((acquisitionManager == null) || acquisitionManager.getSequences().isEmpty())
return null;
@@ -923,7 +898,7 @@ public class MicroManager {
* @return the current camera binning mode (String format)
* @throws Exception if an error occurred
*/
- private static String getBinningAsString(final CMMCore core, final String camera) throws Exception {
+ private static String getBinningAsString(final @NotNull CMMCore core, final String camera) throws Exception {
return core.getProperty(camera, MMCoreJ.getG_Keyword_Binning());
}
@@ -1175,7 +1150,7 @@ public class MicroManager {
/**
* @return all available config group
*/
- public static List<String> getConfigGroups() {
+ public static @NotNull List<String> getConfigGroups() {
final CMMCore core = getCore();
if (core == null)
return new ArrayList<>();
@@ -1193,7 +1168,7 @@ public class MicroManager {
* @param group group name
* @return all available config preset for the specified group
*/
- public static List<String> getConfigs(final String group) {
+ public static @NotNull List<String> getConfigs(final String group) {
final CMMCore core = getCore();
if (core == null)
return new ArrayList<>();
@@ -1278,6 +1253,7 @@ public class MicroManager {
/**
* @return internal preset name set on last call to {@link #setConfigForGroup(String, String, boolean)} method (workaround for MM empty preset name bug)
*/
+ @Contract(pure = true)
public static String getInternalSetPreset() {
if (inConfigSet)
return lastPresetSet;
@@ -1336,7 +1312,7 @@ public class MicroManager {
* @see #getChannelGroup()
* @see #getConfigs(String)
*/
- public static List<String> getChannelConfigs() {
+ public static @NotNull List<String> getChannelConfigs() {
return getConfigs(MicroManager.getChannelGroup());
}
@@ -1408,6 +1384,7 @@ public class MicroManager {
* @return <code>true</code> if Micro-Manager is initialized / loaded.<br>
* @see MicromanagerPlugin#init()
*/
+ @Contract(pure = true)
public static boolean isInitialized() {
return instance != null;
}
@@ -1450,17 +1427,19 @@ public class MicroManager {
}
catch (final Throwable t) {
// an fatal error occurred, force error on version checking then...
- version = new Version("1");
+ version = new Version(1);
}
// cannot get version or wrong version ?
- if ((version == null) || version.isLower(new Version("1.4.19")))
+ if ((version == null) || version.isLower(new Version(1, 4, 19)))
// || version.isGreater(new Version("1.4.22")))
{
MessageDialog.showDialog("Error while loading Micro-Manager",
- "Your version of Micro-Manager seems to not be compatible !\n" + "This plugin is only compatible with version 1.4.19 or above.\n"
- + "Also check that you are using the same architecture for Icy and Micro-Manager (32/64 bits)\n"
- + "You need to restart Icy to redefine the Micro-Manager folder.",
+ """
+ Your version of Micro-Manager seems to not be compatible !
+ This plugin is only compatible with version 1.4.19 or above.
+ Also check that you are using the same architecture for Icy and Micro-Manager (32/64 bits)
+ You need to restart Icy to redefine the Micro-Manager folder.""",
MessageDialog.ERROR_MESSAGE);
// so user can change the defined MM folder
MMUtils.resetLibrayPath();
@@ -1480,9 +1459,7 @@ public class MicroManager {
instance = new MMMainFrame();
}
catch (final Throwable e) {
- IcyExceptionHandler.showErrorMessage(e, true, true);
- MessageDialog.showDialog("Error while loading Micro-Manager", e.getMessage() + "\nYou may try to restart Icy to fix the issue.",
- MessageDialog.ERROR_MESSAGE);
+ IcyLogger.error(MicroManager.class, e, "Error while loading Micro-Manager.", "You may try to restart Icy to fix the issue.");
return;
}
@@ -1529,8 +1506,7 @@ public class MicroManager {
cleanOldMM();
}
catch (final Throwable e) {
- IcyExceptionHandler.showErrorMessage(e, true, true);
- new FailedAnnounceFrame("An error occurred while initializing Micro-Manager (see console output for more details).");
+ IcyLogger.error(MicroManager.class, e, "Error while initializing Micro-Manager.");
// shutdown everything
shutdown();
@@ -1543,8 +1519,10 @@ public class MicroManager {
// cannot load class --> version mismatch probably
MessageDialog
.showDialog("Cannot load Micro-Manager",
- "Your version of Micro-Manager seems to not be compatible !\n" + "This plugin is only compatible with version 1.4.19 or above.\n"
- + "Also check that you are using the same architecture for Icy and Micro-Manager (32/64 bits).",
+ """
+ Your version of Micro-Manager seems to not be compatible !
+ This plugin is only compatible with version 1.4.19 or above.
+ Also check that you are using the same architecture for Icy and Micro-Manager (32/64 bits).""",
MessageDialog.ERROR_MESSAGE);
}
}
@@ -1609,17 +1587,17 @@ public class MicroManager {
stopLiveMode();
}
catch (final Throwable t) {
- IcyExceptionHandler.showErrorMessage(t, true);
+ IcyLogger.error(MicroManager.class, t);
}
}
- if (liveListeners != null)
- liveListeners.clear();
- if (acqListeners != null)
- acqListeners.clear();
+ //if (liveListeners != null)
+ liveListeners.clear();
+ //if (acqListeners != null)
+ acqListeners.clear();
StageMover.clearListener();
- if (metadatas != null)
- metadatas.clear();
+ //if (metadatas != null)
+ metadatas.clear();
// stop live listener
if (liveManager != null) {
@@ -1674,8 +1652,7 @@ public class MicroManager {
final JSONObject tags = image.tags;
- final boolean firstImage = (MDUtils.getPositionIndex(tags) == 0) && (MDUtils.getFrameIndex(tags) == 0) && (MDUtils.getChannelIndex(tags) == 0)
- && (MDUtils.getSliceIndex(tags) == 0);
+ final boolean firstImage = (MDUtils.getPositionIndex(tags) == 0) && (MDUtils.getFrameIndex(tags) == 0) && (MDUtils.getChannelIndex(tags) == 0) && (MDUtils.getSliceIndex(tags) == 0);
final boolean newAcquisition = (acquisitionManager == null) || acquisitionManager.isDone();
// first acquisition image or new acquisition --> create the new acquisition
@@ -1717,7 +1694,7 @@ public class MicroManager {
l.acqImgReveived(image);
}
catch (final Exception e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(MicroManager.class, e);
}
}
}
@@ -1753,7 +1730,7 @@ public class MicroManager {
catch (final Exception e) {
// can happen with advanced acquisition set with a lower time
// interval than current exposure time
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(MicroManager.class, e);
}
}
}
@@ -1769,7 +1746,7 @@ public class MicroManager {
}
catch (final Exception e) {
// should not happen
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(MicroManager.class, e);
}
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionHandler.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionHandler.java
index fe236a8..f5c973d 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionHandler.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionHandler.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,15 +18,16 @@
package plugins.tprovoost.Microscopy.MicroManager.core;
-import icy.gui.frame.IcyFrame;
-import icy.gui.frame.IcyFrameAdapter;
-import icy.gui.frame.IcyFrameEvent;
-import icy.gui.util.GuiUtil;
-import icy.sequence.Sequence;
-import icy.system.IcyExceptionHandler;
-import icy.system.thread.ThreadUtil;
-import icy.util.ReflectionUtil;
import mmcorej.TaggedImage;
+import org.bioimageanalysis.icy.common.reflect.ReflectionUtil;
+import org.bioimageanalysis.icy.gui.GuiUtil;
+import org.bioimageanalysis.icy.gui.frame.IcyFrame;
+import org.bioimageanalysis.icy.gui.frame.IcyFrameAdapter;
+import org.bioimageanalysis.icy.gui.frame.IcyFrameEvent;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
+import org.jetbrains.annotations.NotNull;
import org.json.JSONException;
import org.json.JSONObject;
import org.micromanager.MMStudio;
@@ -65,7 +66,7 @@ public class AcquisitionHandler implements AcquisitionListener {
MicroManager.addAcquisitionListener(this);
}
- private void initDialog(final MMMainFrame mainFrame) {
+ private void initDialog(final @NotNull MMMainFrame mainFrame) {
final MMStudio mmstudio = mainFrame.getMMStudio();
try {
@@ -73,7 +74,7 @@ public class AcquisitionHandler implements AcquisitionListener {
advAcqDialog = (AcqControlDlg) ReflectionUtil.getFieldObject(mmstudio, "acqControlWin_");
}
catch (final Exception ex) {
- System.err.println("Warning: cannot retrieve AcqControlDlg from Micro-Manager.");
+ IcyLogger.warn(this.getClass(), ex, "Cannot retrieve AcqControlDlg from Micro-Manager.");
}
// not existing yet ? --> create it now
@@ -85,7 +86,7 @@ public class AcquisitionHandler implements AcquisitionListener {
ReflectionUtil.getField(mmstudio.getClass(), "acqControlWin_").set(mmstudio, advAcqDialog);
}
catch (final Exception ex) {
- System.err.println("Warning: cannot set AcqControlDlg from Micro-Manager.");
+ IcyLogger.warn(this.getClass(), ex, "Cannot set AcqControlDlg from Micro-Manager.");
}
}
@@ -199,7 +200,7 @@ public class AcquisitionHandler implements AcquisitionListener {
MicroManager.stopLiveMode();
}
catch (final Exception e) {
- IcyExceptionHandler.showErrorMessage(e, false);
+ IcyLogger.error(this.getClass(), e);
}
}
@@ -229,7 +230,7 @@ public class AcquisitionHandler implements AcquisitionListener {
});
}
catch (final JSONException e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e);
}
}
@@ -246,7 +247,7 @@ public class AcquisitionHandler implements AcquisitionListener {
MicroManager.startLiveMode();
}
catch (final Exception e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e);
}
liveModeWasRunning = false;
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java
index 23cfb5a..5c75c65 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,11 +18,12 @@
package plugins.tprovoost.Microscopy.MicroManager.core;
-import icy.gui.viewer.Viewer;
-import icy.main.Icy;
-import icy.sequence.Sequence;
-import icy.util.StringUtil;
import mmcorej.TaggedImage;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.gui.viewer.Viewer;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.jetbrains.annotations.NotNull;
import org.json.JSONException;
import org.json.JSONObject;
import org.micromanager.api.SequenceSettings;
@@ -61,7 +62,7 @@ public class AcquisitionResult {
return new ArrayList<>(sequences.values());
}
- public void imageReceived(final TaggedImage taggedImage) throws JSONException, MMScriptException {
+ public void imageReceived(final @NotNull TaggedImage taggedImage) throws JSONException, MMScriptException {
final JSONObject tags = taggedImage.tags;
final Integer position = MDUtils.getPositionIndex(tags);
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java
index f1c04f5..083ea0f 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,8 +18,8 @@
package plugins.tprovoost.Microscopy.MicroManager.event;
-import icy.sequence.Sequence;
import mmcorej.TaggedImage;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
import org.json.JSONObject;
import org.micromanager.api.SequenceSettings;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/CoreListener.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/CoreListener.java
index f466c01..53936b0 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/CoreListener.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/CoreListener.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java
index 8d2b2d8..585c6ad 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,8 +18,8 @@
package plugins.tprovoost.Microscopy.MicroManager.event;
-import icy.sequence.Sequence;
import mmcorej.TaggedImage;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java
index 1067b46..12f9fc6 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,7 +18,7 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.network.NetworkUtil;
+import org.bioimageanalysis.icy.network.NetworkUtil;
import org.micromanager.MMVersion;
import javax.swing.*;
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java
index c46f9ff..b36d1e7 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,9 +18,10 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.math.MathUtil;
-import icy.system.thread.ThreadUtil;
import mmcorej.CMMCore;
+import org.bioimageanalysis.icy.common.math.MathUtil;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import plugins.tprovoost.Microscopy.MicroManager.tools.StageMover;
@@ -251,8 +252,7 @@ public class AcquisitionInfoPanel extends JPanel implements Runnable {
setPixelSize(core.getPixelSizeUm());
}
catch (final Throwable t) {
- System.err.println("Warning: can't read camera informations from Micro-Manager");
- System.err.println("Cause: " + t);
+ IcyLogger.warn(this.getClass(), t, "Cannot read camera information from Micro-Manager.");
}
}
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java
index f28a4e1..f41c073 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,20 +18,20 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.gui.component.button.IcyButton;
-import icy.gui.component.button.IcyToggleButton;
-import icy.gui.dialog.MessageDialog;
-import icy.main.Icy;
-import icy.math.FPSMeter;
-import icy.resource.ResourceUtil;
-import icy.resource.icon.IcyIcon;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceEvent;
-import icy.sequence.SequenceListener;
-import icy.system.IcyExceptionHandler;
-import icy.util.StringUtil;
import mmcorej.CMMCore;
import mmcorej.TaggedImage;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.math.FPSMeter;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.gui.component.button.IcyButton;
+import org.bioimageanalysis.icy.gui.component.button.IcyToggleButton;
+import org.bioimageanalysis.icy.gui.component.icon.SVGIcon;
+import org.bioimageanalysis.icy.gui.dialog.MessageDialog;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceEvent;
+import org.bioimageanalysis.icy.model.sequence.SequenceListener;
+import org.bioimageanalysis.icy.system.IcyExceptionHandler;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import org.json.JSONObject;
import org.micromanager.MMStudio;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
@@ -116,7 +116,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
gridBagLayout.rowWeights = new double[]{1.0, 1.0, 1.0, 1.0, 1.0, Double.MIN_VALUE};
setLayout(gridBagLayout);
- snapBtn = new IcyButton("Snap", new IcyIcon(ResourceUtil.ICON_PHOTO));
+ snapBtn = new IcyButton("Snap", SVGIcon.PHOTO_CAMERA);
snapBtn.setToolTipText("Snap an image");
snapBtn.setIconTextGap(12);
final GridBagConstraints gbc_snapBtn = new GridBagConstraints();
@@ -126,7 +126,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
gbc_snapBtn.gridy = 0;
add(snapBtn, gbc_snapBtn);
- liveBtn = new IcyToggleButton("Live", new IcyIcon("camera"));
+ liveBtn = new IcyToggleButton("Live", SVGIcon.VIDEOCAM);
liveBtn.setToolTipText("Enable / Disable the live display");
liveBtn.setIconTextGap(12);
final GridBagConstraints gbc_liveBtn = new GridBagConstraints();
@@ -136,7 +136,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
gbc_liveBtn.gridy = 1;
add(liveBtn, gbc_liveBtn);
- albumBtn = new IcyButton("Album", new IcyIcon("movie"));
+ albumBtn = new IcyButton("Album", SVGIcon.CAMERA_ROLL);
albumBtn.setToolTipText("Snap an image and store it in the album");
albumBtn.setIconTextGap(12);
final GridBagConstraints gbc_albumBtn = new GridBagConstraints();
@@ -146,7 +146,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
gbc_albumBtn.gridy = 2;
add(albumBtn, gbc_albumBtn);
- advAcqBtn = new IcyButton("Multi-D Acq.", new IcyIcon(ResourceUtil.ICON_LAYER_V1));
+ advAcqBtn = new IcyButton("Multi-D Acq.", SVGIcon.LAYERS);
advAcqBtn.setToolTipText("Multi dimension acquisition");
advAcqBtn.setIconTextGap(8);
final GridBagConstraints gbc_advAcqBtn = new GridBagConstraints();
@@ -156,7 +156,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
gbc_advAcqBtn.gridy = 3;
add(advAcqBtn, gbc_advAcqBtn);
- refreshBtn = new IcyButton("Refresh", new IcyIcon(ResourceUtil.ICON_RELOAD));
+ refreshBtn = new IcyButton("Refresh", SVGIcon.REPLAY);
refreshBtn.setToolTipText("Force GUI refresh");
refreshBtn.setIconTextGap(12);
final GridBagConstraints gbc_refreshBtn = new GridBagConstraints();
@@ -403,7 +403,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
liveSequence.beginUpdate();
try {
// format not anymore compatible --> need to clear sequence first
- if (!MMUtils.isCompatible(liveSequence, images.get(0).tags))
+ if (!MMUtils.isCompatible(liveSequence, images.getFirst().tags))
liveSequence.removeAllImages();
final LiveSettingsPanel livePanel = mainFrame.livePanel;
@@ -474,8 +474,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
}
}
catch (final Exception e) {
- System.err.println("MicroManager: cannot update live image.");
- IcyExceptionHandler.showErrorMessage(e, false, true);
+ IcyLogger.error(this.getClass(), e, "Cannot update live image.");
}
finally {
liveSequence.endUpdate();
@@ -499,7 +498,6 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
@Override
public void sequenceChanged(final SequenceEvent sequenceEvent) {
// ignore this event
-
}
@Override
@@ -511,7 +509,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
if (sequence == albumSequence) {
// album not saved ?
//if (StringUtil.isEmpty(sequence.getFilename())) {
- // ask user if he want to save it
+ // ask user if he wants to save it
//}
// clear it
@@ -561,7 +559,7 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
}
}
catch (final Exception e) {
- System.err.println("MicroManager: cannot process stack acquisition.");
+ //IcyLogger.error(this.getClass(), e, "Stack acquisition failed.");
IcyExceptionHandler.handleException(e, true);
}
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java
index 48a128a..48183ad 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,18 +18,17 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.gui.component.NumberTextField;
-import icy.gui.component.button.IcyButton;
-import icy.gui.component.button.IcyToggleButton;
-import icy.gui.dialog.MessageDialog;
-import icy.resource.icon.IcyIcon;
-import icy.system.IcyExceptionHandler;
-import icy.system.thread.ThreadUtil;
-import icy.util.StringUtil;
import mmcorej.CMMCore;
import mmcorej.DeviceType;
import mmcorej.MMCoreJ;
import mmcorej.StrVector;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.gui.component.button.IcyButton;
+import org.bioimageanalysis.icy.gui.component.button.IcyToggleButton;
+import org.bioimageanalysis.icy.gui.component.field.NumberTextField;
+import org.bioimageanalysis.icy.gui.component.icon.SVGIcon;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
import org.micromanager.MMStudio;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
@@ -116,8 +115,7 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
refreshOpenShutterButton(open);
}
catch (final Throwable t) {
- MessageDialog.showDialog("Cannot change shutter state: " + t, MessageDialog.ERROR_MESSAGE);
- System.err.println("Cannot change shutter state: " + t);
+ IcyLogger.error(this.getClass(), t, "Cannot change shutter state.");
}
});
lblAutoShutter.addMouseListener(new MouseAdapter() {
@@ -145,8 +143,7 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
shutterOpenBtn.setEnabled(!autoshutter);
}
catch (final Throwable t) {
- MessageDialog.showDialog("Cannot set auto shutter: " + t, MessageDialog.ERROR_MESSAGE);
- System.err.println("Cannot set auto shutter: " + t);
+ IcyLogger.error(this.getClass(), t, "Cannot set auto shutter.");
}
});
autofocusBtn.addActionListener(e -> {
@@ -154,14 +151,14 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
if (studio != null)
studio.autofocusNow();
else
- System.err.println("MMStudio is null, cannot autofocus");
+ IcyLogger.error(this.getClass(), "Cannot autofocus now (MMStudio is null).");
});
autofocusSettingBtn.addActionListener(e -> {
final MMStudio studio = MicroManager.getMMStudio();
if (studio != null)
studio.showAutofocusDialog();
else
- System.err.println("MMStudio is null, cannot open autofocus setting panel");
+ IcyLogger.error(this.getClass(), "Cannot show autofocus dialog (MMStudio is null).");
});
}
@@ -226,7 +223,7 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
gbc_shuttersCombo.gridy = 2;
add(shuttersCombo, gbc_shuttersCombo);
- shutterOpenBtn = new IcyToggleButton("Open", new IcyIcon("shutter"));
+ shutterOpenBtn = new IcyToggleButton("Open", SVGIcon.CAMERA);
shutterOpenBtn.setIconTextGap(10);
shutterOpenBtn.setToolTipText("Open / close the shutter");
@@ -265,7 +262,7 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
gbc_lblAutofocus.gridy = 4;
add(lblAutofocus, gbc_lblAutofocus);
- autofocusBtn = new IcyButton(new IcyIcon("autofocus"));
+ autofocusBtn = new IcyButton(SVGIcon.CENTER_FOCUS_STRONG);
autofocusBtn.setToolTipText("Perform autofocus now");
final GridBagConstraints gbc_autofocusBtn = new GridBagConstraints();
gbc_autofocusBtn.fill = GridBagConstraints.BOTH;
@@ -274,7 +271,7 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
gbc_autofocusBtn.gridy = 4;
add(autofocusBtn, gbc_autofocusBtn);
- autofocusSettingBtn = new IcyButton(new IcyIcon("af_setting"));
+ autofocusSettingBtn = new IcyButton(SVGIcon.SETTINGS_PHOTO_CAMERA);
autofocusSettingBtn.setToolTipText("Autofocus settings");
final GridBagConstraints gbc_autoFocusSettingBtn = new GridBagConstraints();
gbc_autoFocusSettingBtn.fill = GridBagConstraints.BOTH;
@@ -299,13 +296,15 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
mainFrame.unlock();
}
+ /*@Deprecated(forRemoval = true)
public void logError(final Exception e) {
getMMStudio().logError(e);
- }
+ }*/
+ /*@Deprecated(forRemoval = true)
public void logError(final Exception e, final String msg) {
getMMStudio().logError(e, msg);
- }
+ }*/
public String getCameraName() {
return cameraName;
@@ -343,8 +342,8 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
MicroManager.setExposure(exposure);
}
catch (final Exception e) {
- logError(e, "Couldn't set exposure time.");
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e, "Cannot set exposure time.");
+ //logError(e, "Couldn't set exposure time.");
}
}
@@ -360,8 +359,8 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
MicroManager.setBinning(binning);
}
catch (final Exception e) {
- logError(e, "Couldn't set camera binning.");
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e, "Cannot set camera binning.");
+ //logError(e, "Couldn't set camera binning.");
}
}
@@ -420,7 +419,8 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
}
}
catch (final Exception e) {
- logError(e);
+ IcyLogger.error(this.getClass(), e);
+ //logError(e);
}
}
@@ -463,7 +463,8 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
}
}
catch (final Exception e) {
- logError(e);
+ IcyLogger.error(this.getClass(), e);
+ //logError(e);
}
}
@@ -512,7 +513,8 @@ public class CameraSettingsPanel extends JPanel implements Runnable {
autoShutterCheckbox.setSelected(autoShutter);
}
catch (final Exception e) {
- logError(e);
+ IcyLogger.error(this.getClass(), e);
+ //logError(e);
}
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ChannelTable.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ChannelTable.java
index bb67d21..62c1426 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ChannelTable.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ChannelTable.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,10 +18,10 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.system.IcyExceptionHandler;
import mmcorej.CMMCore;
import mmcorej.Configuration;
import mmcorej.PropertySetting;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import org.micromanager.acquisition.AcquisitionWrapperEngine;
import org.micromanager.dialogs.ChannelCellEditor;
import org.micromanager.dialogs.ChannelCellRenderer;
@@ -42,7 +42,7 @@ import java.util.List;
/**
* Custom table representing channel definition for Micro-Manager advanced acquisition
*
- * @author Stephane
+ * @author Stephane Dallongeville
*/
public class ChannelTable extends JTable {
final protected ChannelTableModel model;
@@ -118,8 +118,7 @@ public class ChannelTable extends JTable {
return true;
}
catch (final Throwable t) {
- System.err.println("Cannot set channel group in Micro-Manager.");
- IcyExceptionHandler.showErrorMessage(t, true);
+ IcyLogger.error(ChannelTable.class, t, "Cannot set channel group in Micro-Manager.");
}
}
@@ -135,7 +134,7 @@ public class ChannelTable extends JTable {
if (!cfgs.isEmpty()) {
try {
- final Configuration presetData = core.getConfigData(group, cfgs.get(0));
+ final Configuration presetData = core.getConfigData(group, cfgs.getFirst());
if (presetData.size() >= 1L) {
final PropertySetting setting = presetData.getSetting(0L);
@@ -147,8 +146,7 @@ public class ChannelTable extends JTable {
}
}
catch (final Exception e) {
- System.err.println("Error with Micro-Manager:");
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(ChannelTable.class, e, "Error with Micro-Manager");
return false;
}
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java
index d8b61bf..dcc7a0c 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,15 +18,14 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.gui.component.button.IcyButton;
-import icy.gui.dialog.ConfirmDialog;
-import icy.gui.dialog.MessageDialog;
-import icy.resource.ResourceUtil;
-import icy.resource.icon.IcyIcon;
-import icy.system.IcyExceptionHandler;
-import icy.system.thread.ThreadUtil;
-import icy.util.StringUtil;
import mmcorej.CMMCore;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.gui.component.button.IcyButton;
+import org.bioimageanalysis.icy.gui.component.icon.SVGIcon;
+import org.bioimageanalysis.icy.gui.dialog.ConfirmDialog;
+import org.bioimageanalysis.icy.gui.dialog.MessageDialog;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
import org.micromanager.ConfigGroupPad;
import org.micromanager.MMStudio;
import org.micromanager.dialogs.GroupEditor;
@@ -81,7 +80,7 @@ public class ConfigurationPanel extends JPanel {
ThreadUtil.invokeLater(() -> refreshGroupNow(groupNameRefresh, configName));
}
catch (final Exception e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e);
}
};
}
@@ -104,7 +103,7 @@ public class ConfigurationPanel extends JPanel {
gbl_configButtonPanel.rowWeights = new double[]{0.0, Double.MIN_VALUE};
configButtonPanel.setLayout(gbl_configButtonPanel);
- final IcyButton addGroupBtn = new IcyButton(new IcyIcon("sq_plus"));
+ final IcyButton addGroupBtn = new IcyButton(SVGIcon.ADD);
addGroupBtn.addActionListener(e -> {
final GroupEditor ge = new GroupEditor("", "", getMMStudio(), getCore(), true);
if (ge.getWidth() < 580)
@@ -132,10 +131,10 @@ public class ConfigurationPanel extends JPanel {
gbc_addGroupBtn.gridx = 1;
gbc_addGroupBtn.gridy = 0;
configButtonPanel.add(addGroupBtn, gbc_addGroupBtn);
- final IcyButton editGroupBtn = new IcyButton(new IcyIcon("doc_edit"));
+ final IcyButton editGroupBtn = new IcyButton(SVGIcon.EDIT);
editGroupBtn.addActionListener(e -> {
final String groupName = MMUtils.getSelectedGroupName(groupPad);
- final String groupName2 = groupPad.getSelectedGroup();
+ //final String groupName2 = groupPad.getSelectedGroup();
if (StringUtil.isEmpty(groupName))
MessageDialog.showDialog("To edit a group, please select it first then press the edit group button.");
@@ -151,7 +150,7 @@ public class ConfigurationPanel extends JPanel {
});
}
});
- final IcyButton removeGroupBtn = new IcyButton(new IcyIcon("sq_minus"));
+ final IcyButton removeGroupBtn = new IcyButton(SVGIcon.REMOVE);
removeGroupBtn.addActionListener(e -> {
final String groupName = MMUtils.getSelectedGroupName(groupPad);
@@ -192,7 +191,7 @@ public class ConfigurationPanel extends JPanel {
gbc_presetLabel.gridy = 0;
configButtonPanel.add(presetLabel, gbc_presetLabel);
- final IcyButton addPresetBtn = new IcyButton(new IcyIcon("sq_plus"));
+ final IcyButton addPresetBtn = new IcyButton(SVGIcon.ADD);
addPresetBtn.addActionListener(e -> {
final String groupName = MMUtils.getSelectedGroupName(groupPad);
@@ -215,7 +214,7 @@ public class ConfigurationPanel extends JPanel {
gbc_addPresetBtn.gridx = 7;
gbc_addPresetBtn.gridy = 0;
configButtonPanel.add(addPresetBtn, gbc_addPresetBtn);
- final IcyButton editPresetBtn = new IcyButton(new IcyIcon("doc_edit"));
+ final IcyButton editPresetBtn = new IcyButton(SVGIcon.EDIT);
editPresetBtn.addActionListener(e -> {
final String groupName = MMUtils.getSelectedGroupName(groupPad);
final String presetName = MMUtils.getSelectedPresetName(groupPad);
@@ -232,7 +231,7 @@ public class ConfigurationPanel extends JPanel {
});
}
});
- final IcyButton removePresetBtn = new IcyButton(new IcyIcon("sq_minus"));
+ final IcyButton removePresetBtn = new IcyButton(SVGIcon.REMOVE);
removePresetBtn.addActionListener(e -> {
final String groupName = MMUtils.getSelectedGroupName(groupPad);
final String presetName = MMUtils.getSelectedPresetName(groupPad);
@@ -282,7 +281,7 @@ public class ConfigurationPanel extends JPanel {
gbc_editPresetBtn.gridy = 0;
configButtonPanel.add(editPresetBtn, gbc_editPresetBtn);
- final IcyButton saveBtn = new IcyButton(new IcyIcon(ResourceUtil.ICON_SAVE));
+ final IcyButton saveBtn = new IcyButton(SVGIcon.SAVE);
saveBtn.setToolTipText("Save current presets to configuration file...");
saveBtn.addActionListener(e -> mainFrame.saveConfig());
final GridBagConstraints gbc_saveBtn = new GridBagConstraints();
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java
index 1ece6a7..4372153 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,8 +18,8 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.gui.component.NumberTextField;
-import icy.util.StringUtil;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.gui.component.field.NumberTextField;
import javax.swing.*;
import javax.swing.border.TitledBorder;
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java
index b6d9e3a..ca334be 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,16 +18,15 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.action.IcyAbstractAction;
-import icy.file.FileUtil;
-import icy.gui.component.button.IcyButton;
-import icy.gui.dialog.OpenDialog;
-import icy.main.Icy;
-import icy.preferences.PluginsPreferences;
-import icy.preferences.XMLPreferences;
-import icy.resource.ResourceUtil;
-import icy.resource.icon.IcyIcon;
-import icy.system.IcyExceptionHandler;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.gui.action.IcyAbstractAction;
+import org.bioimageanalysis.icy.gui.component.button.IcyButton;
+import org.bioimageanalysis.icy.gui.component.icon.SVGIcon;
+import org.bioimageanalysis.icy.gui.dialog.OpenDialog;
+import org.bioimageanalysis.icy.io.FileUtil;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.preferences.PluginsPreferences;
+import org.bioimageanalysis.icy.system.preferences.XMLPreferences;
import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
import plugins.tprovoost.Microscopy.MicroManagerForIcy.MicromanagerPlugin;
@@ -132,7 +131,7 @@ public class LoadFrame extends JDialog {
openButton.setEnabled(true);
}
catch (final IOException e1) {
- IcyExceptionHandler.showErrorMessage(e1, true);
+ IcyLogger.error(this.getClass(), e1);
}
}
else
@@ -232,15 +231,11 @@ public class LoadFrame extends JDialog {
lbl_devices.setFont(lbl_files.getFont().deriveFont(Font.BOLD, 12));
lbl_config_presets.setFont(lbl_files.getFont().deriveFont(Font.BOLD, 12));
- openButton = new IcyButton(openAction);
- openButton.setIcon(new IcyIcon(ResourceUtil.ICON_OPEN));
+ openButton = new IcyButton(openAction, SVGIcon.FOLDER_OPEN);
openButton.setEnabled(false);
- final IcyButton cancelButton = new IcyButton(cancelAction);
- cancelButton.setIcon(new IcyIcon(ResourceUtil.ICON_DELETE));
- final IcyButton addButton = new IcyButton(addAction);
- addButton.setIcon(new IcyIcon(ResourceUtil.ICON_PLUS));
- final IcyButton removeButton = new IcyButton(removeAction);
- removeButton.setIcon(new IcyIcon(ResourceUtil.ICON_MINUS));
+ final IcyButton cancelButton = new IcyButton(cancelAction, SVGIcon.DELETE);
+ final IcyButton addButton = new IcyButton(addAction, SVGIcon.ADD);
+ final IcyButton removeButton = new IcyButton(removeAction, SVGIcon.REMOVE);
final JPanel buttonPanel = new JPanel();
getContentPane().add(buttonPanel, BorderLayout.SOUTH);
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadingFrame.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadingFrame.java
index 800aa72..7603247 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadingFrame.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadingFrame.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,8 +18,8 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.gui.frame.IcyFrame;
-import icy.system.thread.ThreadUtil;
+import org.bioimageanalysis.icy.gui.frame.IcyFrame;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
import javax.swing.*;
import java.awt.*;
@@ -27,7 +27,7 @@ import java.awt.*;
/**
* Simple static Loading Frame for Micro-Manager initialization.
*
- * @author Stephane
+ * @author Stephane Dallongeville
*/
public class LoadingFrame extends IcyFrame {
JProgressBar progressBar;
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java
index 4e8f9d0..9bea7ce 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,30 +18,28 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.common.MenuCallback;
-import icy.file.FileUtil;
-import icy.gui.dialog.ActionDialog;
-import icy.gui.dialog.ConfirmDialog;
-import icy.gui.dialog.MessageDialog;
-import icy.gui.dialog.SaveDialog;
-import icy.gui.frame.IcyFrame;
-import icy.gui.frame.IcyFrameAdapter;
-import icy.gui.frame.IcyFrameEvent;
-import icy.gui.frame.progress.FailedAnnounceFrame;
-import icy.gui.frame.progress.ToolTipFrame;
-import icy.gui.util.ComponentUtil;
-import icy.main.Icy;
-import icy.preferences.PluginPreferences;
-import icy.preferences.XMLPreferences;
-import icy.resource.ResourceUtil;
-import icy.resource.icon.IcyIcon;
-import icy.system.IcyExceptionHandler;
-import icy.system.thread.ThreadUtil;
-import icy.util.ReflectionUtil;
-import icy.util.StringUtil;
import mmcorej.CMMCore;
import mmcorej.MMCoreJ;
import mmcorej.MMEventCallback;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.reflect.ReflectionUtil;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.gui.component.ComponentUtil;
+import org.bioimageanalysis.icy.gui.component.icon.SVGIcon;
+import org.bioimageanalysis.icy.gui.component.menu.IcyMenuItem;
+import org.bioimageanalysis.icy.gui.dialog.ActionDialog;
+import org.bioimageanalysis.icy.gui.dialog.ConfirmDialog;
+import org.bioimageanalysis.icy.gui.dialog.MessageDialog;
+import org.bioimageanalysis.icy.gui.dialog.SaveDialog;
+import org.bioimageanalysis.icy.gui.frame.IcyFrame;
+import org.bioimageanalysis.icy.gui.frame.IcyFrameAdapter;
+import org.bioimageanalysis.icy.gui.frame.IcyFrameEvent;
+import org.bioimageanalysis.icy.gui.frame.progress.ToolTipFrame;
+import org.bioimageanalysis.icy.io.FileUtil;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.preferences.PluginPreferences;
+import org.bioimageanalysis.icy.system.preferences.XMLPreferences;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
import org.micromanager.MMOptions;
import org.micromanager.MMStudio;
import org.micromanager.MainFrame;
@@ -50,7 +48,6 @@ import org.micromanager.conf2.ConfiguratorDlg2;
import org.micromanager.conf2.MMConfigFileException;
import org.micromanager.conf2.MicroscopeModel;
import org.micromanager.dialogs.CalibrationListDlg;
-import org.micromanager.utils.ReportingUtils;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import plugins.tprovoost.Microscopy.MicroManager.core.AcquisitionHandler;
import plugins.tprovoost.Microscopy.MicroManager.event.CoreListener;
@@ -170,7 +167,7 @@ public class MMMainFrame extends IcyFrame {
options.closeOnExit_ = false;
}
catch (final Exception ex) {
- System.err.println("Warning: cannot patch options informations from Micro-Manager.");
+ IcyLogger.warn(MMMainFrame.this.getClass(), ex, "Cannot patch options information from Micro-Manager");
}
try {
@@ -181,7 +178,7 @@ public class MMMainFrame extends IcyFrame {
contrastPrefs = (Preferences) ReflectionUtil.getFieldObject(mmstudio, "contrastPrefs_");
}
catch (final Exception ex) {
- System.err.println("Warning: cannot retrieve Preferences from Micro-Manager.");
+ IcyLogger.warn(MMMainFrame.this.getClass(), ex, "Cannot retrieve Preferences from Micro-Manager");
}
final MainFrame frame = MMStudio.getFrame();
@@ -363,8 +360,7 @@ public class MMMainFrame extends IcyFrame {
final JMenuBar menuBar = new JMenuBar();
menuBar.add(toReturn);
setJMenuBar(menuBar);
- final JMenuItem hconfig = new JMenuItem("Configuration Wizard");
- hconfig.setIcon(new IcyIcon("star.png"));
+ final IcyMenuItem hconfig = new IcyMenuItem("Configuration Wizard", SVGIcon.STAR);
hconfig.addActionListener(e -> {
// we have some plugins running ?
if (pluginsPanel.getRunningPluginsCount() > 0) {
@@ -394,8 +390,7 @@ public class MMMainFrame extends IcyFrame {
refreshGUI();
});
- final JMenuItem menuPxSizeConfigItem = new JMenuItem("Pixel Size Config");
- menuPxSizeConfigItem.setIcon(new IcyIcon(ResourceUtil.ICON_PROPERTIES));
+ final IcyMenuItem menuPxSizeConfigItem = new IcyMenuItem("Pixel Size Config", SVGIcon.SETTINGS);
menuPxSizeConfigItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_G, InputEvent.SHIFT_DOWN_MASK | InputEvent.CTRL_DOWN_MASK));
menuPxSizeConfigItem.addActionListener(e -> {
final CalibrationListDlg dlg = new CalibrationListDlg(mmstudio.getCore());
@@ -407,9 +402,8 @@ public class MMMainFrame extends IcyFrame {
pixelSizeConfig.setResizable(true);
});
- final JMenuItem loadConfigItem = new JMenuItem("Load Configuration");
+ final IcyMenuItem loadConfigItem = new IcyMenuItem("Load Configuration", SVGIcon.FOLDER_OPEN);
loadConfigItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O, InputEvent.SHIFT_DOWN_MASK | InputEvent.CTRL_DOWN_MASK));
- loadConfigItem.setIcon(new IcyIcon(ResourceUtil.ICON_OPEN));
loadConfigItem.addActionListener(e -> {
final LoadFrame f = new LoadFrame();
@@ -431,13 +425,11 @@ public class MMMainFrame extends IcyFrame {
}
});
- final JMenuItem saveConfigItem = new JMenuItem("Save Configuration");
+ final IcyMenuItem saveConfigItem = new IcyMenuItem("Save Configuration", SVGIcon.SAVE);
saveConfigItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, InputEvent.SHIFT_DOWN_MASK | InputEvent.CTRL_DOWN_MASK));
- saveConfigItem.setIcon(new IcyIcon(ResourceUtil.ICON_SAVE));
saveConfigItem.addActionListener(e -> saveConfig());
- final JMenuItem aboutItem = new JMenuItem("About");
- aboutItem.setIcon(new IcyIcon(ResourceUtil.ICON_INFO));
+ final IcyMenuItem aboutItem = new IcyMenuItem("About", SVGIcon.INFO);
aboutItem.addActionListener(e -> {
final JDialog dialog = new JDialog(Icy.getMainInterface().getMainFrame(), "About");
@@ -449,9 +441,8 @@ public class MMMainFrame extends IcyFrame {
dialog.setVisible(true);
});
- final JMenuItem propertyBrowserItem = new JMenuItem("Property Browser");
+ final IcyMenuItem propertyBrowserItem = new IcyMenuItem("Property Browser", SVGIcon.DATABASE);
propertyBrowserItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_COMMA, InputEvent.CTRL_DOWN_MASK));
- propertyBrowserItem.setIcon(new IcyIcon(ResourceUtil.ICON_DATABASE));
propertyBrowserItem.addActionListener(e -> {
final PropertyEditor editor = new PropertyEditor();
editor.setGui(mmstudio);
@@ -463,13 +454,11 @@ public class MMMainFrame extends IcyFrame {
propertyBrowser.setResizable(true);
});
- final JMenuItem resetMMPath = new JMenuItem("Reset Micro-Manager path");
- resetMMPath.setIcon(new IcyIcon("folder"));
+ final IcyMenuItem resetMMPath = new IcyMenuItem("Reset Micro-Manager path", SVGIcon.FOLDER);
resetMMPath.addActionListener(e -> {
// so user can change the defined MM folder
MMUtils.resetLibrayPath();
- MessageDialog.showDialog("Information", "You need to restart Icy now to change the defined Micro-Manager folder.",
- MessageDialog.INFORMATION_MESSAGE);
+ MessageDialog.showDialog("Information", "You need to restart Icy now to change the defined Micro-Manager folder.", MessageDialog.INFORMATION_MESSAGE);
});
// JMenuItem loadPresetConfigItem = new JMenuItem("Load Core properties from XML");
@@ -494,8 +483,7 @@ public class MMMainFrame extends IcyFrame {
// }
// });
//
- final JMenuItem mmSettingItem = new JMenuItem("Micro-Manager options");
- mmSettingItem.setIcon(new IcyIcon(ResourceUtil.ICON_COG, true));
+ final IcyMenuItem mmSettingItem = new IcyMenuItem("Micro-Manager options", SVGIcon.SETTINGS);
mmSettingItem.setToolTipText("Set a variety of Micro-Manager configuration options");
mmSettingItem.addActionListener(e -> {
if (options == null)
@@ -522,8 +510,7 @@ public class MMMainFrame extends IcyFrame {
// }
// });
- final JMenuItem mmScriptPanel = new JMenuItem("Script panel");
- mmScriptPanel.setIcon(new IcyIcon(ResourceUtil.getAlphaIconAsImage("text_curstor"), true));
+ final IcyMenuItem mmScriptPanel = new IcyMenuItem("Script panel", SVGIcon.EDIT);
mmScriptPanel.setToolTipText("Open Micro-Manager script panel");
mmScriptPanel.addActionListener(e -> mmstudio.showScriptPanel());
@@ -621,9 +608,8 @@ public class MMMainFrame extends IcyFrame {
model.saveToFile(path);
}
catch (final MMConfigFileException e) {
- ReportingUtils.logError(e);
- IcyExceptionHandler.showErrorMessage(e, false);
- new FailedAnnounceFrame("Unable to save configuration file");
+ IcyLogger.error(this.getClass(), e, "Error while saving Micro-Manager configuration.");
+ //ReportingUtils.logError(e);
}
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java
index a353018..1b33279 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/OptionsPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/OptionsPanel.java
index cf25b00..7f09f49 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/OptionsPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/OptionsPanel.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,8 +18,8 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.gui.dialog.ConfirmDialog;
import mmcorej.CMMCore;
+import org.bioimageanalysis.icy.gui.dialog.ConfirmDialog;
import org.micromanager.MMOptions;
import org.micromanager.logging.LogFileManager;
import org.micromanager.utils.NumberUtils;
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java
index 079fed1..7c6beac 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,10 +18,12 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.plugin.PluginDescriptor;
-import icy.plugin.PluginLauncher;
-import icy.plugin.PluginLoader;
-import plugins.tprovoost.Microscopy.MicroManager.tools.FrameUtils;
+import org.bioimageanalysis.icy.extension.plugin.PluginDescriptor;
+import org.bioimageanalysis.icy.extension.plugin.PluginLauncher;
+import org.bioimageanalysis.icy.extension.plugin.PluginLoader;
+import org.bioimageanalysis.icy.gui.component.button.IcyButton;
+import org.bioimageanalysis.icy.gui.component.icon.SVGIcon;
+import org.jetbrains.annotations.NotNull;
import plugins.tprovoost.Microscopy.MicroManagerForIcy.MicroscopePlugin;
import javax.swing.*;
@@ -53,14 +55,23 @@ public class PluginsToolbar extends JPanel {
initialize(PluginLoader.getPlugins(MicroscopePlugin.class));
}
- private void initialize(final List<PluginDescriptor> plugins) {
+ private void initialize(final @NotNull List<PluginDescriptor> plugins) {
pluginToolbar = new JToolBar(SwingConstants.HORIZONTAL);
pluginToolbar.setRollover(true);
pluginToolbar.setFloatable(false);
pluginToolbar.setToolTipText("Micro Manager plugins for Icy");
for (final PluginDescriptor plugin : plugins) {
- pluginToolbar.add(FrameUtils.createPluginButton(plugin, e -> {
+ final JButton pluginButton;
+ final SVGIcon pluginSVGIcon = plugin.getSVGIcon();
+ if (pluginSVGIcon != null)
+ pluginButton = new IcyButton(pluginSVGIcon);
+ else
+ pluginButton = new JButton(plugin.getIcon());
+
+ pluginButton.setToolTipText(plugin.getName());
+
+ pluginButton.addActionListener(e -> {
// create the microscope plugin
final MicroscopePlugin microscopePlugin = (MicroscopePlugin) PluginLauncher.start(plugin);
@@ -69,19 +80,10 @@ public class PluginsToolbar extends JPanel {
addPlugin(microscopePlugin);
microscopePlugin.start();
}
- }));
+ });
+ pluginToolbar.add(pluginButton);
}
- // if (plugins.size() == 0)
- // {
- // MessageDialog.showDialog("Information",
- // "You don't have any Micro manager plugins installed, use the search bar to install some",
- // MessageDialog.INFORMATION_MESSAGE);
- //
- // // search for micro manager plugin
- // // Icy.getMainInterface().getSearchEngine().search("micro-manager");
- // }
-
setLayout(new BorderLayout());
setBorder(new TitledBorder("Plugins"));
add(pluginToolbar, BorderLayout.CENTER);
@@ -139,7 +141,7 @@ public class PluginsToolbar extends JPanel {
}
/**
- * Shutdown all running plugins (should automatically call removePlugin(..))
+ * Shutdown all running plugins (should automatically call removePlugin(...))
*/
public void shutdownPlugins() {
for (final MicroscopePlugin plugin : getRunningPlugins())
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/ClassPatcher.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/ClassPatcher.java
index c6d55b5..9ccf1fa 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/ClassPatcher.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/ClassPatcher.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,23 +18,16 @@
package plugins.tprovoost.Microscopy.MicroManager.patch;
-import java.security.ProtectionDomain;
-import java.util.ArrayList;
-
-import icy.system.IcyExceptionHandler;
-import icy.system.SystemUtil;
-import icy.util.StringUtil;
-import javassist.CannotCompileException;
-import javassist.ClassClassPath;
-import javassist.ClassPool;
-import javassist.CtClass;
-import javassist.CtField;
-import javassist.CtMethod;
-import javassist.CtNewMethod;
-import javassist.LoaderClassPath;
-import javassist.NotFoundException;
+import javassist.*;
import javassist.bytecode.AccessFlag;
import javassist.bytecode.FieldInfo;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.system.SystemUtil;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.NotNull;
+
+import java.security.ProtectionDomain;
+import java.util.ArrayList;
/**
* The code hacker provides a mechanism for altering the behavior of classes
@@ -239,8 +232,7 @@ public class ClassPatcher {
return pool.toClass(classRef);
}
catch (final CannotCompileException e) {
- IcyExceptionHandler.showErrorMessage(e, false);
- System.err.println("Cannot load class: " + fullClass);
+ IcyLogger.error(this.getClass(), e, "Cannot load class: " + fullClass);
return null;
}
}
@@ -265,8 +257,7 @@ public class ClassPatcher {
return pool.toClass(classRef, neighbor, classLoader, protectionDomain);
}
catch (final CannotCompileException e) {
- IcyExceptionHandler.showErrorMessage(e, false);
- System.err.println("Cannot load class: " + fullClass);
+ IcyLogger.error(this.getClass(), e, "Cannot load class: " + fullClass);
return null;
}
}
@@ -323,7 +314,7 @@ public class ClassPatcher {
* Generates a new line of code calling the <code>imagej.legacy.patches</code> class and method
* corresponding to the given method signature.
*/
- private String newCode(final String fullClass, final String methodSig) {
+ private @NotNull String newCode(final @NotNull String fullClass, final String methodSig) {
final int dotIndex = fullClass.lastIndexOf(".");
final String className = fullClass.substring(dotIndex + 1);
@@ -360,13 +351,13 @@ public class ClassPatcher {
/**
* Extracts the method name from the given method signature.
*/
- private String getMethodName(final String methodSig) {
+ private @NotNull String getMethodName(final @NotNull String methodSig) {
final int parenIndex = methodSig.indexOf("(");
final int spaceIndex = methodSig.lastIndexOf(" ", parenIndex);
return methodSig.substring(spaceIndex + 1, parenIndex);
}
- private String[] getMethodArgs(final String methodSig, final boolean wantResult) {
+ private String @NotNull [] getMethodArgs(final @NotNull String methodSig, final boolean wantResult) {
final ArrayList<String> result = new ArrayList<>();
final int parenIndex = methodSig.indexOf("(");
@@ -381,14 +372,14 @@ public class ClassPatcher {
return result.toArray(new String[0]);
}
- private String[] getMethodArgTypes(final String methodSig, final boolean wantResult) {
+ private String @NotNull [] getMethodArgTypes(final String methodSig, final boolean wantResult) {
final String[] args = getMethodArgs(methodSig, wantResult);
for (int i = 0; i < args.length; i++)
args[i] = args[i].split(" ")[0];
return args;
}
- private String[] getMethodArgNames(final String methodSig, final boolean wantResult) {
+ private String @NotNull [] getMethodArgNames(final String methodSig, final boolean wantResult) {
final String[] args = getMethodArgs(methodSig, wantResult);
for (int i = 0; i < args.length; i++)
args[i] = args[i].split(" ")[1];
@@ -398,7 +389,7 @@ public class ClassPatcher {
/**
* Returns true if the given method signature is static.
*/
- private boolean isStatic(final String methodSig) {
+ private boolean isStatic(final @NotNull String methodSig) {
final int parenIndex = methodSig.indexOf("(");
final String methodPrefix = methodSig.substring(0, parenIndex);
for (final String token : methodPrefix.split(" ")) {
@@ -411,7 +402,7 @@ public class ClassPatcher {
/**
* Returns true if the given method signature returns void.
*/
- private boolean isVoid(final String methodSig) {
+ private boolean isVoid(final @NotNull String methodSig) {
final int parenIndex = methodSig.indexOf("(");
final String methodPrefix = methodSig.substring(0, parenIndex);
return methodPrefix.startsWith("void ") || methodPrefix.indexOf(" void ") > 0;
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMPatcher.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMPatcher.java
index 38cf863..73d993b 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMPatcher.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMPatcher.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,7 +18,7 @@
package plugins.tprovoost.Microscopy.MicroManager.patch;
-import icy.plugin.PluginLoader;
+import org.bioimageanalysis.icy.extension.plugin.PluginLoader;
import org.micromanager.MMVersion;
/**
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java
index 2771b26..203b847 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -21,9 +21,8 @@
package plugins.tprovoost.Microscopy.MicroManager.patch;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import org.micromanager.MMStudio;
-
-import icy.system.IcyExceptionHandler;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
@@ -56,7 +55,7 @@ public class MMStudioMethods {
MicroManager.stopLiveMode();
}
catch (final Throwable t) {
- IcyExceptionHandler.showErrorMessage(t, true);
+ IcyLogger.error(MMStudioMethods.class, t);
}
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java
index d0e519a..f014470 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,15 +18,13 @@
package plugins.tprovoost.Microscopy.MicroManager.tools;
-import icy.gui.component.button.IcyButton;
-import icy.gui.frame.IcyFrame;
-import icy.gui.util.GuiUtil;
-import icy.plugin.PluginDescriptor;
-import icy.resource.icon.IcyIcon;
+import org.bioimageanalysis.icy.gui.GuiUtil;
+import org.bioimageanalysis.icy.gui.frame.IcyFrame;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
import javax.swing.*;
import java.awt.*;
-import java.awt.event.ActionListener;
/**
* Utilities class used for wrapping Micro-Manager Frames and Dialogs in a IcyFrame.
@@ -42,7 +40,7 @@ public class FrameUtils {
* @param window the window to add to the main pane
* @return the window converted as an {@link IcyFrame}
*/
- public static IcyFrame addMMWindowToDesktopPane(final Window window) {
+ public static @NotNull IcyFrame addMMWindowToDesktopPane(final Window window) {
final IcyFrame frame = GuiUtil.createIcyFrameFromWindow(window);
frame.addToDesktopPane();
frame.setVisible(true);
@@ -56,11 +54,9 @@ public class FrameUtils {
* @param label button label
* @return the button searched or <code>null</code> if was not found
*/
- public static JButton findButtonComponents(final Container container, final String label) {
+ public static @Nullable JButton findButtonComponents(final @NotNull Container container, final String label) {
for (final Component c : container.getComponents()) {
- if (c instanceof JButton) {
- final JButton button = (JButton) c;
-
+ if (c instanceof final JButton button) {
if (button.getText().equalsIgnoreCase(label))
return button;
}
@@ -68,40 +64,4 @@ public class FrameUtils {
return null;
}
-
- /**
- * Create an {@link IcyButton} from given information
- *
- * @param buttonText button text
- * @param iconPath the icon path. Can be null if no icon wanted
- * @param action the action to execute when button is clicked
- * @return an IcyButton with buttonText and an icon on it if iconPath not null.<br>
- * The button returned have an actionListener wich execute the runnable.
- */
- public static IcyButton createUIButton(final String buttonText, final String iconPath, final Runnable action) {
- final IcyButton theButton;
- if (iconPath != null && !iconPath.isEmpty())
- theButton = new IcyButton(buttonText, new IcyIcon(iconPath, IcyIcon.DEFAULT_SIZE));
- else
- theButton = new IcyButton(buttonText);
- theButton.addActionListener(e -> action.run());
- return theButton;
- }
-
- /**
- * Create a button to launch the specified plugin
- *
- * @param plugin plugin descriptor
- * @param action the action to execute when we click on the button
- * @return an IcyButton with text and icon describing the specified plugin.
- */
- public static IcyButton createPluginButton(final PluginDescriptor plugin, final ActionListener action) {
- final IcyButton result = new IcyButton(new IcyIcon(plugin.getIconAsImage(), 32, false));
-
- result.setToolTipText(plugin.getName());
- if (action != null)
- result.addActionListener(action);
-
- return result;
- }
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java
index ca4af07..34ba4f2 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,37 +18,38 @@
package plugins.tprovoost.Microscopy.MicroManager.tools;
-import icy.file.FileUtil;
-import icy.gui.dialog.MessageDialog;
-import icy.gui.frame.progress.FailedAnnounceFrame;
-import icy.gui.frame.progress.ProgressFrame;
-import icy.image.IcyBufferedImage;
-import icy.image.colormap.IcyColorMap;
-import icy.main.Icy;
-import icy.network.NetworkUtil;
-import icy.plugin.PluginLoader;
-import icy.plugin.PluginLoader.PluginClassLoader;
-import icy.preferences.PluginsPreferences;
-import icy.preferences.XMLPreferences;
-import icy.sequence.MetaDataUtil;
-import icy.sequence.Sequence;
-import icy.system.IcyExceptionHandler;
-import icy.system.SystemUtil;
-import icy.system.thread.ThreadUtil;
-import icy.type.DataType;
-import icy.type.collection.CollectionUtil;
-import icy.type.collection.array.Array2DUtil;
-import icy.type.collection.array.ArrayUtil;
-import icy.type.point.Point3D;
-import icy.util.DateUtil;
-import icy.util.OMEUtil;
-import icy.util.ReflectionUtil;
-import icy.util.StringUtil;
import mmcorej.TaggedImage;
import ome.xml.meta.OMEXMLMetadata;
import ome.xml.model.Pixels;
import ome.xml.model.primitives.NonNegativeInteger;
import ome.xml.model.primitives.Timestamp;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.collection.CollectionUtil;
+import org.bioimageanalysis.icy.common.collection.array.Array2DUtil;
+import org.bioimageanalysis.icy.common.collection.array.ArrayUtil;
+import org.bioimageanalysis.icy.common.datetime.DateUtil;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.common.type.DataType;
+import org.bioimageanalysis.icy.extension.plugin.PluginLoader;
+import org.bioimageanalysis.icy.gui.dialog.MessageDialog;
+import org.bioimageanalysis.icy.gui.frame.progress.FailedAnnounceFrame;
+import org.bioimageanalysis.icy.gui.frame.progress.ProgressFrame;
+import org.bioimageanalysis.icy.io.FileUtil;
+import org.bioimageanalysis.icy.model.OMEUtil;
+import org.bioimageanalysis.icy.model.colormap.IcyColorMap;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.sequence.MetaDataUtil;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.network.NetworkUtil;
+import org.bioimageanalysis.icy.system.SystemUtil;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.preferences.PluginsPreferences;
+import org.bioimageanalysis.icy.system.preferences.XMLPreferences;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
import org.joda.time.DateTime;
import org.json.JSONArray;
import org.json.JSONException;
@@ -195,7 +196,8 @@ public class MMUtils {
* @param images the list of {@link TaggedImage} to test
* @return <code>true</code> if the specified list of TaggedImage contains a <code>null</code> or poison image.
*/
- public static boolean hasNullOrPoison(final List<TaggedImage> images) {
+ @Contract(pure = true)
+ public static boolean hasNullOrPoison(final @NotNull List<TaggedImage> images) {
for (final TaggedImage image : images)
if ((image == null) || TaggedImageQueue.isPoison(image))
return true;
@@ -218,7 +220,7 @@ public class MMUtils {
* @return the resulting {@link IcyBufferedImage} image
* @throws JSONException if an error occurred while reading the metadata
*/
- public static IcyBufferedImage convertToIcyImage(final List<TaggedImage> images) throws JSONException {
+ public static @Nullable IcyBufferedImage convertToIcyImage(final @NotNull List<TaggedImage> images) throws JSONException {
final List<TaggedImage> goodImages = new ArrayList<>(images.size());
int w, h, bpp;
@@ -246,7 +248,7 @@ public class MMUtils {
if ((!goodImages.isEmpty()) && (w > 0) && (h > 0) && (bpp > 0)) {
// create the data array
- final Object[] data = Array2DUtil.createArray(ArrayUtil.getDataType(goodImages.get(0).pix),
+ final Object[] data = Array2DUtil.createArray(ArrayUtil.getDataType(goodImages.getFirst().pix),
goodImages.size());
for (int i = 0; i < goodImages.size(); i++)
@@ -278,7 +280,7 @@ public class MMUtils {
* @throws JSONException if an error occurred while reading the metadata
* @throws MMScriptException if an error occurred on MM script parsing
*/
- public static void setMetadata(final Sequence sequence, final JSONObject tags) throws JSONException, MMScriptException {
+ public static void setMetadata(final @NotNull Sequence sequence, final JSONObject tags) throws JSONException, MMScriptException {
final OMEXMLMetadata metadata = sequence.getOMEXMLMetadata();
final int numComp = Math.max(1, MDUtils.getNumberOfComponents(tags));
@@ -420,8 +422,7 @@ public class MMUtils {
* @param sizeC wanted global size C (number of channel), set to <code>-1</code> to keep current value
* @throws JSONException if an error occurred while reading the metadata
*/
- public static void setImageMetadata(final TaggedImage taggedImage, final int t, final int z, final int c, final int sizeT, final int sizeZ, final int sizeC)
- throws JSONException {
+ public static void setImageMetadata(final TaggedImage taggedImage, final int t, final int z, final int c, final int sizeT, final int sizeZ, final int sizeC) throws JSONException {
if (taggedImage == null)
return;
@@ -489,8 +490,8 @@ public class MMUtils {
* @throws MMScriptException if an error occurred on MM script parsing
* @see #setImageMetadata(TaggedImage, int, int, int, int, int, int)
*/
- public static boolean setImage(final Sequence sequence, final TaggedImage taggedImage, final long startDate)
- throws JSONException, MMScriptException {
+ @Contract("_, null, _ -> false")
+ public static boolean setImage(final Sequence sequence, final TaggedImage taggedImage, final long startDate) throws JSONException, MMScriptException {
// incorrect image --> do nothing
if ((taggedImage == null) || TaggedImageQueue.isPoison(taggedImage))
return false;
@@ -576,7 +577,7 @@ public class MMUtils {
exposure = MicroManager.getExposure() / 1000d;
}
catch (final Throwable e) {
- IcyExceptionHandler.showErrorMessage(e, false);
+ IcyLogger.error(MMUtils.class, e);
}
metadata.setPlanePositionX(OMEUtil.getLength(pos.getX()), 0, planeIndex);
@@ -599,6 +600,7 @@ public class MMUtils {
* @throws JSONException if an error occurred while reading the metadata
* @throws MMScriptException if an error occurred on MM script parsing
*/
+ @Contract("_, null -> false")
public static boolean setImage(final Sequence sequence, final TaggedImage taggedImage) throws JSONException, MMScriptException {
return setImage(sequence, taggedImage, 0L);
}
@@ -611,7 +613,7 @@ public class MMUtils {
* @throws JSONException if an error occurred while reading the metadata
* @throws MMScriptException if an error occurred on MM script parsing
*/
- public static boolean isCompatible(final Sequence sequence, final JSONObject metadata) throws JSONException, MMScriptException {
+ public static boolean isCompatible(final @NotNull Sequence sequence, final JSONObject metadata) throws JSONException, MMScriptException {
if (sequence.isEmpty())
return true;
@@ -619,7 +621,7 @@ public class MMUtils {
&& (sequence.getSizeY() == MDUtils.getHeight(metadata))
&& (sequence.getSizeC() == (MDUtils.getNumChannels(metadata)
* Math.max(1, MDUtils.getNumberOfComponents(metadata))))
- && (sequence.getDataType_().getSize() == ((MDUtils.getBitDepth(metadata) + 7) / 8));
+ && (sequence.getDataType().getSize() == ((MDUtils.getBitDepth(metadata) + 7) / 8));
}
/**
@@ -629,35 +631,27 @@ public class MMUtils {
* @throws JSONException if an error occurred while reading the metadata
* @throws MMScriptException if an error occurred on MM script parsing
*/
- public static IcyBufferedImage createEmptyImage(final JSONObject metadata) throws JSONException, MMScriptException {
+ @Contract("_ -> new")
+ public static @NotNull IcyBufferedImage createEmptyImage(final JSONObject metadata) throws JSONException, MMScriptException {
final int width = MDUtils.getWidth(metadata);
final int height = MDUtils.getHeight(metadata);
final int numChannels = MDUtils.getNumChannels(metadata) * Math.max(1, MDUtils.getNumberOfComponents(metadata));
final int bpp = MDUtils.getBitDepth(metadata);
final int bytespp = (bpp + 7) / 8;
- switch (bytespp) {
- default:
- case 1:
- return new IcyBufferedImage(width, height, numChannels, DataType.UBYTE);
- case 2:
- return new IcyBufferedImage(width, height, numChannels, DataType.USHORT);
- case 3:
- case 4:
- return new IcyBufferedImage(width, height, numChannels, DataType.UINT);
- case 5:
- case 6:
- case 7:
- case 8:
- return new IcyBufferedImage(width, height, numChannels, DataType.DOUBLE);
- }
+ return switch (bytespp) {
+ default -> new IcyBufferedImage(width, height, numChannels, DataType.UBYTE);
+ case 2 -> new IcyBufferedImage(width, height, numChannels, DataType.USHORT);
+ case 3, 4 -> new IcyBufferedImage(width, height, numChannels, DataType.UINT);
+ case 5, 6, 7, 8 -> new IcyBufferedImage(width, height, numChannels, DataType.DOUBLE);
+ };
}
/**
* @param group the {@link ConfigGroupPad} name
* @return the selected group name from specified ConfigGroupPad
*/
- public static String getSelectedGroupName(final ConfigGroupPad group) {
+ public static String getSelectedGroupName(final @NotNull ConfigGroupPad group) {
/*try {
return (String) ReflectionUtil.invokeMethod(group, "getGroup", true, new Object[]{});
}
@@ -677,7 +671,7 @@ public class MMUtils {
* @param group the {@link ConfigGroupPad} name
* @return the selected preset name from specified ConfigGroupPad
*/
- public static String getSelectedPresetName(final ConfigGroupPad group) {
+ public static String getSelectedPresetName(final @NotNull ConfigGroupPad group) {
/*try {
return (String) ReflectionUtil.invokeMethod(group, "getPreset", true, new Object[]{});
}
@@ -734,7 +728,7 @@ public class MMUtils {
return false;
final ClassLoader cl = PluginLoader.getLoader();
- if (cl instanceof PluginClassLoader) {
+ if (cl instanceof PluginLoader.PluginClassLoader) {
for (final File f : files) {
final String path = f.getAbsolutePath();
final String ext = FileUtil.getFileExtension(path, false).toLowerCase();
@@ -757,7 +751,7 @@ public class MMUtils {
continue;
// we can add it
- ((PluginClassLoader) cl).add(path);
+ ((PluginLoader.PluginClassLoader) cl).add(path);
}
}
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java
index b6c45ee..17dacf0 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,13 +18,15 @@
package plugins.tprovoost.Microscopy.MicroManager.tools;
-import icy.preferences.XMLPreferences;
-import icy.roi.ROI2D;
-import icy.sequence.Sequence;
-import icy.system.thread.ThreadUtil;
-import icy.type.point.Point3D;
-import icy.util.StringUtil;
import mmcorej.CMMCore;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.model.roi.ROI2D;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.preferences.XMLPreferences;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import java.awt.geom.Point2D;
@@ -143,6 +145,7 @@ public class StageMover {
/**
* @return state of X inverted axis.
*/
+ @Contract(pure = true)
public static boolean isInvertX() {
return invertX;
}
@@ -150,6 +153,7 @@ public class StageMover {
/**
* @return state of Y inverted axis.
*/
+ @Contract(pure = true)
public static boolean isInvertY() {
return invertY;
}
@@ -157,6 +161,7 @@ public class StageMover {
/**
* @return state of Y inverted axis.
*/
+ @Contract(pure = true)
public static boolean isInvertZ() {
return invertZ;
}
@@ -174,6 +179,7 @@ public class StageMover {
/**
* @return state of X and Y axis inversion.
*/
+ @Contract(pure = true)
public static boolean isSwitchXY() {
return switchXY;
}
@@ -181,7 +187,7 @@ public class StageMover {
/**
* Fire Z stage position change event
*
- * @param s stage devicce name
+ * @param s stage device name
* @param z Z position
*/
public static void onStagePositionChanged(final String s, final double z) {
@@ -322,7 +328,7 @@ public class StageMover {
* @return the X, Y and Z coordinates of the current stage/focus device(s).
* @throws Exception if an error occurs
*/
- public static Point3D.Double getXYZ() throws Exception {
+ public static Point3D.@NotNull Double getXYZ() throws Exception {
final Point2D.Double pt2d = getXY();
return new Point3D.Double(pt2d.x, pt2d.y, getZ());
}
@@ -333,7 +339,7 @@ public class StageMover {
* @return the X, Y and Z coordinates of the current stage/focus device(s) in double[3] format
* @throws Exception if an error occurs
*/
- public static double[] getXYZAsDoubleArray() throws Exception {
+ public static double @NotNull [] getXYZAsDoubleArray() throws Exception {
final Point3D.Double pt = getXYZ();
return new double[]{pt.x, pt.y, pt.z};
}
@@ -642,7 +648,7 @@ public class StageMover {
* @param y y value of the point we want to go to.
* @throws Exception if an error occurs
*/
- public static void moveToPoint(final Sequence s, final double x, final double y) throws Exception {
+ public static void moveToPoint(final @NotNull Sequence s, final double x, final double y) throws Exception {
final double pxsize;
final double vectx = x - s.getBounds2D().getCenterX();
// Y coordinates are inverted in the sequence
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java
index 737b860..0d954c9 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,11 +18,15 @@
package plugins.tprovoost.Microscopy.MicroManagerForIcy;
-import icy.plugin.abstract_.PluginActionable;
-import icy.plugin.interface_.PluginThreaded;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.PluginActionable;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginThreaded;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
+@IcyPluginName("Micro-Manager")
+@IcyPluginIcon(path = "/mmj.png")
public final class MicromanagerPlugin extends PluginActionable implements PluginThreaded {
/**
* Initialize Micro-Manager sub system.
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java
index 2f7603e..291e932 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,7 +18,7 @@
package plugins.tprovoost.Microscopy.MicroManagerForIcy;
-import icy.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
diff --git a/src/main/resources/mmj.png b/src/main/resources/mmj.png
new file mode 100644
index 0000000000000000000000000000000000000000..9a64c58c2537a9f82c3e99f8f8ec2bc82c754549
GIT binary patch
literal 15076
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zQq}K94yHXMZuWTp_C1cu?(CG-*3yzm7x$uk-C&Q>Z}IHEi<=m^JgJnF6sz0IV`)dn
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zciL@zxZRZC$;nypzS$3XtH1gyfn#f>BY@_jSeu>CW|B2NK7R6;MrE0j?ZJdc3JMow
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HcmV?d00001
--
GitLab