diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java
index ca133834871c64bea8202f5a2ad81a085e280f3e..2a6a8fa70c8f0d1aa68416c4fd875980b8447238 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java
@@ -1,17 +1,5 @@
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 java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@@ -33,6 +21,17 @@ import org.micromanager.api.TaggedImageAnalyzer;
import org.micromanager.utils.MDUtils;
import org.micromanager.utils.ReportingUtils;
+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;
@@ -63,7 +62,7 @@ public class MicroManager
static Thread liveManager = null;
/**
- * Retrieve the MicroManager main frame instance.
+ * @return the MicroManager main frame instance.
*/
public static MMMainFrame getInstance()
{
@@ -75,7 +74,7 @@ public class MicroManager
}
/**
- * Retrieve the MicroManager version
+ * @return the MicroManager version
*/
public static Version getMMVersion()
{
@@ -101,7 +100,7 @@ public class MicroManager
/**
* Every {@link MicroscopePlugin} shares the same core, so you will receive every acquisition
- * even if it was not asked by you.<br/>
+ * even if it was not asked by you.<br>
* You should register your listener only when you need image and remove it when your done.
*
* @param listener
@@ -141,11 +140,13 @@ public class MicroManager
}
/**
- * Every {@link MicroscopePlugin} shares the same core, so the same live,<br/>
- * when your plugin start, a live may have been already started and your {@link LiveListener}
- * <br/>
- * could receive images at the moment you call this method. <br />
- * You should register your listener only when you need image and remove it when your done.
+ * Every {@link MicroscopePlugin} shares the same core, so the same live,<br>
+ * when your plugin start, a live may have been already started and your {@link LiveListener}<br>
+ * could receive images at the moment you call this method.<br>
+ * You should register your listener only when you need image and remove it when you're done.
+ *
+ * @param listener
+ * the <i>live</i> listener to add
*/
public static void addLiveListener(LiveListener listener)
{
@@ -156,6 +157,15 @@ public class MicroManager
}
}
+ /**
+ * Every {@link MicroscopePlugin} shares the same core, so the same live,<br>
+ * when your plugin start, a live may have been already started and your {@link LiveListener}<br>
+ * could receive images at the moment you call this method.<br>
+ * You should register your listener only when you need image and remove it when you're done.
+ *
+ * @param listener
+ * the <i>live</i> listener to remove
+ */
public static void removeLiveListener(LiveListener listener)
{
synchronized (liveListeners)
@@ -165,6 +175,8 @@ public class MicroManager
}
/**
+ * @param listener
+ * the <i>acquisition</i> listener to register
* @deprecated Use {@link #addAcquisitionListener(AcquisitionListener)} instead.
*/
@Deprecated
@@ -174,6 +186,8 @@ public class MicroManager
}
/**
+ * @param listener
+ * the <i>acquisition</i> listener to remove
* @deprecated Use {@link #removeAcquisitionListener(AcquisitionListener)} instead.
*/
@Deprecated
@@ -183,6 +197,8 @@ public class MicroManager
}
/**
+ * @param listener
+ * the <i>live</i> listener to register
* @deprecated Use {@link #addLiveListener(LiveListener)} instead.
*/
@Deprecated
@@ -192,6 +208,8 @@ public class MicroManager
}
/**
+ * @param listener
+ * the <i>live</i> listener to remove
* @deprecated Use {@link #removeLiveListener(LiveListener)} instead.
*/
@Deprecated
@@ -217,12 +235,14 @@ public class MicroManager
/**
* Use this to access micro-manager core and to be able to use function that
- * are not been implemented in Micro-Manger for Icy. </br>
- * </br>
+ * are not been implemented in Micro-Manger for Icy. <br>
+ * <br>
* Be careful, if you use core functions instead of the integrated {@link MicroManager} methods
* or utility class as {@link StageMover} you will have to handle synchronization of the
- * core and catch all exception. </br>
+ * core and catch all exception. <br>
* In most of case you don't need to use it, but only if you want to make fancy things.
+ *
+ * @return The micro-manager core object
*/
public static CMMCore getCore()
{
@@ -234,7 +254,7 @@ public class MicroManager
}
/**
- * Get exclusive access to micro manager.</br>
+ * Get exclusive access to micro manager.<br>
*
* @param wait
* number of milli second to wait to retrieve exclusive access if micro manager is
@@ -243,6 +263,7 @@ public class MicroManager
* @return <code>true</code> if you obtained exclusive access and <code>false</code> if micro
* manager is already locked by another thread and wait time elapsed.
* @throws InterruptedException
+ * if thread was interrupt while waiting for lock
* @see #lock()
* @see #unlock()
*/
@@ -256,7 +277,7 @@ public class MicroManager
}
/**
- * Get exclusive access to micro manager.</br>
+ * Get exclusive access to micro manager.<br>
* If another thread already has exclusive access then it will wait until it release it.
*
* @see #lock(long)
@@ -285,10 +306,12 @@ public class MicroManager
inst.unlock();
}
-
+
/**
* Wait for a MM device to be ready.
*
+ * @param device
+ * the device name
* @throws Exception
* if an error occurs
*/
@@ -335,7 +358,7 @@ public class MicroManager
}
/**
- * Get the default config file name
+ * @return the default config file name
*/
public static String getDefaultConfigFileName()
{
@@ -344,6 +367,9 @@ public class MicroManager
/**
* Set the default config file name
+ *
+ * @param fileName
+ * the config filename
*/
public static void setDefaultConfigFileName(String fileName)
{
@@ -403,7 +429,7 @@ public class MicroManager
/**
* @return Returns the number of channel of the camera device (usually 3 for color camera and 1
- * in other case).</br>
+ * in other case).<br>
* Just a shortcut for <code>getCore().getNumberOfCameraChannels()</code>
*/
public static long getCameraChannelCount()
@@ -416,11 +442,9 @@ public class MicroManager
}
/**
- * Returns the metadata object associated to the last image retrieved with
- * {@link #getLastImage()} or
- * {@link #snapImage()}.</br>
- * Returns <code>null</code> if there is no metadata associated to the specified channel.
- *
+ * @return the metadata object associated to the last image retrieved with
+ * {@link #getLastImage()} or {@link #snapImage()}<br>
+ * Returns <code>null</code> if there is no metadata associated to the specified channel.
* @param channel
* channel index for multi channel camera
* @see #getLastImage()
@@ -434,11 +458,9 @@ public class MicroManager
}
/**
- * Returns the metadata object associated to the last image retrieved with
- * {@link #getLastImage()} or
- * {@link #snapImage()}.</br>
- * Returns <code>null</code> if there is no image has been retrieved yet.
- *
+ * @return the metadata object associated to the last image retrieved with
+ * {@link #getLastImage()} or {@link #snapImage()}.<br>
+ * Returns <code>null</code> if there is no image has been retrieved yet.
* @see #getLastImage()
* @see #snapImage()
* @see #getMetadata(int)
@@ -450,16 +472,16 @@ public class MicroManager
}
/**
- * Returns the last image captured from the micro manager continuous acquisition.</br>
- * Returns <code>null</code> if the continuous acquisition is not running.</br>
- * </br>
- * You can listen new image event from acquisition or live mode by using these methods:</br>
- * {@link #addLiveListener(LiveListener)}</br>
- * {@link #addAcquisitionListener(AcquisitionListener)}</br>
- * </br>
- * You can retrieve the associated metadata by using {@link #getMetadata(int)} method.
- *
+ * @return the last image captured from the micro manager continuous acquisition.<br>
+ * Returns <code>null</code> if the continuous acquisition is not running.<br>
+ * <br>
+ * You can listen new image event from acquisition or live mode by using these methods:<br>
+ * {@link #addLiveListener(LiveListener)}<br>
+ * {@link #addAcquisitionListener(AcquisitionListener)}<br>
+ * <br>
+ * You can retrieve the associated metadata by using {@link #getMetadata(int)} method.
* @throws Exception
+ * if an error occurred while retrieved last image
*/
public static IcyBufferedImage getLastImage() throws Exception
{
@@ -467,17 +489,17 @@ public class MicroManager
}
/**
- * Returns a list of {@link TaggedImage} representing the last image captured from the micro
- * manager continuous acquisition. The list contains as many image than camera channel (see
- * {@link #getCameraChannelCount()}).</br>
- * Returns an empty list if the continuous acquisition is not running or if image buffer is
- * empty</br>
- * </br>
- * You can listen new image event from acquisition or live mode by using these methods:</br>
- * {@link #addLiveListener(LiveListener)}</br>
- * {@link #addAcquisitionListener(AcquisitionListener)}</br>
- *
+ * @return a list of {@link TaggedImage} representing the last image captured from the micro
+ * manager continuous acquisition. The list contains as many image than camera channel (see
+ * {@link #getCameraChannelCount()}).<br>
+ * Returns an empty list if the continuous acquisition is not running or if image buffer is
+ * empty<br>
+ * <br>
+ * You can listen new image event from acquisition or live mode by using these methods:<br>
+ * {@link #addLiveListener(LiveListener)}<br>
+ * {@link #addAcquisitionListener(AcquisitionListener)}<br>
* @throws Exception
+ * if an error occurred while retrieved last tagged images
*/
public static List<TaggedImage> getLastTaggedImage() throws Exception
{
@@ -524,14 +546,17 @@ public class MicroManager
/**
* This method waits for the next image captured from the micro manager continuous acquisition
- * and returns it.</br>
- * Returns <code>null</code> if the continuous acquisition is not running.</br>
- * </br>
- * You can listen new image event from acquisition or live mode by using these methods:</br>
- * {@link #addLiveListener(LiveListener)}</br>
- * {@link #addAcquisitionListener(AcquisitionListener)}</br>
- * </br>
+ * and returns it.<br>
+ * <br>
+ * You can listen new image event from acquisition or live mode by using these methods:<br>
+ * {@link #addLiveListener(LiveListener)}<br>
+ * {@link #addAcquisitionListener(AcquisitionListener)}<br>
+ * <br>
* You can retrieve the associated metadata by using {@link #getMetadata(int)} method.
+ *
+ * @return next captured image or <code>null</code> if the continuous acquisition is not running
+ * @throws Exception
+ * if an error occurred
*/
public static IcyBufferedImage getNextImage() throws Exception
{
@@ -541,12 +566,16 @@ public class MicroManager
/**
* This method waits for the next image captured from the micro manager continuous acquisition
* and returns the result as a list of {@link TaggedImage}. The list contains as many image than
- * camera channel (see {@link #getCameraChannelCount()}).</br>
- * Returns an empty list if the continuous acquisition is not running.</br>
- * </br>
- * You can listen new image event from acquisition or live mode by using these methods:</br>
- * {@link #addLiveListener(LiveListener)}</br>
- * {@link #addAcquisitionListener(AcquisitionListener)}</br>
+ * camera channel (see {@link #getCameraChannelCount()}).<br>
+ * Returns an empty list if the continuous acquisition is not running.<br>
+ * <br>
+ * You can listen new image event from acquisition or live mode by using these methods:<br>
+ * {@link #addLiveListener(LiveListener)}<br>
+ * {@link #addAcquisitionListener(AcquisitionListener)}<br>
+ *
+ * @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
{
@@ -611,6 +640,10 @@ public class MicroManager
* will wait for and return the next image from the image acquisition buffer.<br>
* In other case it just snaps a new image from the camera device and returns it.<br>
* You can retrieve the associated metadata by using {@link #getMetadata(int)} method.
+ *
+ * @return the captured image or <code>null</code> if conversion failed
+ * @throws Exception
+ * if an error occurred
*/
public static IcyBufferedImage snapImage() throws Exception
{
@@ -625,6 +658,10 @@ public class MicroManager
* This function return a list of image as the camera device can have several channel (see
* {@link #getCameraChannelCount()}) in which case we have one image per channel.<br>
* You can retrieve the associated metadata by using {@link #getMetadata(int)} method.
+ *
+ * @return the captured image as List of {@link TaggedImage}
+ * @throws Exception
+ * if an error occurred
*/
public static List<TaggedImage> snapTaggedImage() throws Exception
{
@@ -676,7 +713,7 @@ public class MicroManager
}
/**
- * Use this method to know if the continuous acquisition (live mode) is running.
+ * @return <code>true</code> if the continuous acquisition (live mode) is running, <code>false</code> otherwise
*/
public static boolean isLiveRunning()
{
@@ -689,22 +726,20 @@ public class MicroManager
/**
* Use this method to start the continuous acquisition mode (live mode) and retrieve images with
- * {@link LiveListener}.</br>
+ * {@link LiveListener}.<br>
* This command does not block the calling thread for the duration of the acquisition.
* The GUI will draw the indeterminate progress bar representing a live acquisition running,
- * in the Running Acquisition tab panel.<br/>
- * <b>There is only one "live" progress bar for all plugin<b/>.<br/>
+ * in the Running Acquisition tab panel.<br>
+ * <b>There is only one "live" progress bar for all plugin</b>.<br>
*
* @throws Exception
* If a sequence acquisition is running (see {@link #startAcquisition(int, double)}) or
- * if the core
- * doesn't respond.
+ * if the core doesn't respond.
* @see #stopLiveMode()
* @see #addLiveListener(LiveListener)
* @see #isLiveRunning()
* @return <code>true</code> if the method actually started the live mode and <code>false</code>
- * if it was already
- * running.
+ * if it was already running
*/
public static boolean startLiveMode() throws Exception
{
@@ -738,9 +773,9 @@ public class MicroManager
}
/**
- * Use this method to stop the continuous acquisition mode (live mode).<br/>
+ * Use this method to stop the continuous acquisition mode (live mode).<br>
* The GUI will remove indeterminate progress bar representing a live acquisition running,
- * in the Running Acquisition tab panel, if live have been stopped. <br/>
+ * in the Running Acquisition tab panel, if live have been stopped. <br>
*
* @throws Exception
* If the core can't stop the continuous acquisition mode.
@@ -776,6 +811,7 @@ public class MicroManager
*
* @see #startAcquisition(int, double)
* @see #stopAcquisition()
+ * @return <code>true</code> if the continuous is currently in process, <code>false</code> otherwise
*/
public static boolean isAcquisitionRunning()
{
@@ -788,8 +824,8 @@ public class MicroManager
/**
* Use this method to start an acquisition on the current camera device and retrieve images with
- * {@link AcquisitionListener}.</br>
- * This command does not block the calling thread for the duration of the acquisition.</br>
+ * {@link AcquisitionListener}.<br>
+ * This command does not block the calling thread for the duration of the acquisition.<br>
* Note that you have to stop the live mode (see {@link #stopLiveMode()}) before calling this
* method.
*
@@ -798,8 +834,7 @@ public class MicroManager
* @param intervalMs
* The interval between images
* @throws Exception
- * if live is running or if a sequence acquisition have been started and is not finished
- * yet.
+ * if live is running or if a sequence acquisition have been started and is not finished yet.
* @see #isAcquisitionRunning()
* @see #getAcquisitionResult()
* @see #stopAcquisition()
@@ -850,12 +885,11 @@ public class MicroManager
/**
* If acquisition storage is enabled (see {@link #setStoreLastAcquisition(boolean)} method) then
- * this method will
- * return the list of sequence corresponding to the last sequence acquisition or
- * <code>null</code> if no acquisition
- * was done.</br>
+ * this method will return the list of sequence corresponding to the last sequence acquisition or
+ * <code>null</code> if no acquisition was done.<br>
* Note you can have severals sequence for acquisition using different XY position.<br>
*
+ * @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()
@@ -867,7 +901,9 @@ public class MicroManager
}
/**
- * Returns the current camera device name
+ * @return the current camera device name
+ * @throws Exception
+ * if an error occurred
*/
public static String getCamera() throws Exception
{
@@ -879,7 +915,9 @@ public class MicroManager
}
/**
- * Get the exposure of the current camera
+ * @return the exposure of the current camera
+ * @throws Exception
+ * if an error occurred
*/
public static double getExposure() throws Exception
{
@@ -892,6 +930,11 @@ public class MicroManager
/**
* Set the exposure of the current camera
+ *
+ * @param exposure
+ * the exposure to set
+ * @throws Exception
+ * if an error occurred
*/
public static void setExposure(double exposure) throws Exception
{
@@ -935,7 +978,9 @@ public class MicroManager
}
/**
- * Get the current camera binning mode (String format)
+ * @return the current camera binning mode (String format)
+ * @throws Exception
+ * if an error occurred
*/
private static String getBinningAsString(CMMCore core, String camera) throws Exception
{
@@ -943,7 +988,9 @@ public class MicroManager
}
/**
- * Get the current camera binning mode (String format)
+ * @return the current camera binning mode (String format)
+ * @throws Exception
+ * if an error occurred
*/
public static String getBinningAsString() throws Exception
{
@@ -961,6 +1008,11 @@ public class MicroManager
/**
* Set the current camera binning mode (String format)
+ *
+ * @param value
+ * the binning value to set
+ * @throws Exception
+ * if an error occurred
*/
public static void setBinning(String value) throws Exception
{
@@ -1003,7 +1055,9 @@ public class MicroManager
}
/**
- * Get the binning in integer format
+ * @return the binning in integer format
+ * @throws Exception
+ * if an error occurred
*/
private static int getBinningAsInt(String value, int def) throws Exception
{
@@ -1017,7 +1071,9 @@ public class MicroManager
}
/**
- * Get the current camera binning mode
+ * @return the current camera binning mode
+ * @throws Exception
+ * if an error occurred
*/
public static int getBinning() throws Exception
{
@@ -1026,6 +1082,11 @@ public class MicroManager
/**
* Set the current camera binning mode
+ *
+ * @param value
+ * the binning value to set
+ * @throws Exception
+ * if an error occurred
*/
public static void setBinning(int value) throws Exception
{
@@ -1080,7 +1141,9 @@ public class MicroManager
}
/**
- * Returns the current shutter device.
+ * @return the current shutter device.
+ * @throws Exception
+ * if an error occurred
*/
public static String getShutter() throws Exception
{
@@ -1093,6 +1156,11 @@ public class MicroManager
/**
* Sets the current shutter device.
+ *
+ * @param value
+ * device name to set for the shutter
+ * @throws Exception
+ * if an error occurred
*/
public static void setShutter(String value) throws Exception
{
@@ -1116,7 +1184,9 @@ public class MicroManager
}
/**
- * Returns the current shutter device open state.
+ * @return the current shutter device open state.
+ * @throws Exception
+ * if an error occurred
*/
public static boolean isShutterOpen() throws Exception
{
@@ -1129,6 +1199,11 @@ public class MicroManager
/**
* Open / close the current shutter device.
+ *
+ * @param value
+ * open state of shutter device
+ * @throws Exception
+ * if an error occurred
*/
public static void setShutterOpen(boolean value) throws Exception
{
@@ -1152,7 +1227,9 @@ public class MicroManager
}
/**
- * Returns the current auto shutter state.
+ * @return the current auto shutter state.
+ * @throws Exception
+ * if an error occurred
*/
public static boolean getAutoShutter() throws Exception
{
@@ -1165,6 +1242,11 @@ public class MicroManager
/**
* Sets the auto shutter state.
+ *
+ * @param value
+ * <code>true</code> to set the automatic shutter mode, <code>false</code> otherwise
+ * @throws Exception
+ * if an error occurred
*/
public static void setAutoShutter(boolean value) throws Exception
{
@@ -1190,8 +1272,7 @@ public class MicroManager
}
/**
- * Returns current pixel configured pixel size in micro meter.<br/>
- * Returns 0d if pixel size is not defined
+ * @return current pixel configured pixel size in micro meter or <code>0d</code> if pixel size is not defined
*/
public static double getPixelSize()
{
@@ -1203,7 +1284,7 @@ public class MicroManager
}
/**
- * Get all available config group
+ * @return all available config group
*/
public static List<String> getConfigGroups()
{
@@ -1221,7 +1302,9 @@ public class MicroManager
}
/**
- * Get all available config preset for the specified group
+ * @param group
+ * group name
+ * @return all available config preset for the specified group
*/
public static List<String> getConfigs(String group)
{
@@ -1242,7 +1325,11 @@ public class MicroManager
}
/**
- * Get the current config preset for the specified group
+ * @param group
+ * group name
+ * @return the current config preset for the specified group
+ * @throws Exception
+ * if an error occurred
*/
public static String getCurrentConfig(String group) throws Exception
{
@@ -1258,6 +1345,15 @@ public class MicroManager
/**
* Set the specified preset for the given config group
+ *
+ * @param group
+ * group name
+ * @param preset
+ * preset name
+ * @param wait
+ * wait for the preset configuration to be loaded
+ * @throws Exception
+ * if an error occurred
*/
public static void setConfigForGroup(String group, String preset, boolean wait) throws Exception
{
@@ -1299,7 +1395,7 @@ public class MicroManager
}
/**
- * Returns current channel group (camera / channel / objective...)
+ * @return current channel group (camera / channel / objective...)
*/
public static String getChannelGroup()
{
@@ -1312,6 +1408,11 @@ public class MicroManager
/**
* Set the channel group (camera / channel / objective...)
+ *
+ * @param group
+ * channel group name
+ * @throws Exception
+ * if an error occurred
*/
public static void setChannelGroup(String group) throws Exception
{
@@ -1347,8 +1448,7 @@ public class MicroManager
}
/**
- * Returns configurations for current channel group.
- *
+ * @return configurations for current channel group.
* @see #getChannelGroup()
* @see #getConfigs(String)
*/
@@ -1358,8 +1458,7 @@ public class MicroManager
}
/**
- * Returns the "enable storage of last acquisition" state.
- *
+ * @return the "enable storage of last acquisition" state.
* @see #setStoreLastAcquisition(boolean)
* @see #getAcquisitionResult()
*/
@@ -1376,6 +1475,8 @@ public class MicroManager
* {@link #getAcquisitionResult()}.<br>
* Set to <code>true</code> by default.
*
+ * @param value
+ * <code>true</code> to enable storage of last acquisition, <code>false</code> otherwise
* @see #getAcquisitionResult()
*/
public static void setStoreLastAcquisition(boolean value)
@@ -1385,8 +1486,7 @@ public class MicroManager
}
/**
- * Enable immediate display of image acquisition.
- *
+ * @return state of immediate display of image acquisition.
* @see #startAcquisition(int, double)
*/
public static boolean getDisplayAcquisitionSequence()
@@ -1400,6 +1500,8 @@ public class MicroManager
/**
* Enable immediate display of image acquisition.
*
+ * @param value
+ * <code>true</code> to enable immediate display of acquisition, <code>false</code> otherwise
* @see #startAcquisition(int, double)
*/
public static void setDisplayAcquisitionSequence(boolean value)
@@ -1411,10 +1513,11 @@ public class MicroManager
/**
* Use this method to enable logging (disabled by default).<br>
* Log file are in Icy folder and are named this way : CoreLog20140515.txt ; 20140515 is the
- * date of debugging (2014/05/15)<br/>
+ * date of debugging (2014/05/15)<br>
* <b>Be careful, log files can be very huge and take easily 1Gb.</b>
*
* @param enable
+ * <code>true</code> to enable debug logging, <code>false</code> otherwise
*/
public static void enableDebugLogging(boolean enable)
{
@@ -1427,8 +1530,7 @@ public class MicroManager
}
/**
- * Returns <code>true</code> if Micro-Manager is initialized / loaded.<br>
- *
+ * @return <code>true</code> if Micro-Manager is initialized / loaded.<br>
* @see MicromanagerPlugin#init()
*/
public static boolean isInitialized()
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 4534c257066b434055c2ec6ca5d0e9a9dd29bffc..686e8bda53e0886d4390cb495f85ac4e9e5ac4e1 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java
@@ -22,7 +22,7 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
/**
- * This class is to be used by AcquisitionListener.</br>
+ * This class is to be used by AcquisitionListener.<br>
* It initializes an empty icy sequence you need to feed with the {@link #imageReceived(TaggedImage)} method so the
* sequence will be updated with those images.
*
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 6434515e52d171c8c05a2307289ae10c10d2fcf7..48e4be41cba87b7336bc8213ee46e73b5b0f93cd 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java
@@ -1,14 +1,12 @@
package plugins.tprovoost.Microscopy.MicroManager.event;
-import icy.sequence.Sequence;
-
import java.util.List;
-import mmcorej.TaggedImage;
-
import org.json.JSONObject;
import org.micromanager.api.SequenceSettings;
+import icy.sequence.Sequence;
+import mmcorej.TaggedImage;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
import plugins.tprovoost.Microscopy.MicroManagerForIcy.MicroscopePlugin;
@@ -21,7 +19,7 @@ public interface AcquisitionListener
{
/**
* Called when a new image is captured from a core sequence acquisition (not continuous
- * sequence acquisition).</br>
+ * sequence acquisition).<br>
* You can retrieve the current global acquisition result by using {@link MicroManager#getAcquisitionResult()} if
* acquisition storage is enabled.
*
@@ -37,6 +35,11 @@ public interface AcquisitionListener
/**
* Callback when {@link MicroManager#startAcquisition(int, double)} have
* been called by a {@link MicroscopePlugin}
+ *
+ * @param settings
+ * SequenceSetting object
+ * @param metadata
+ * JSON metadata object
*/
public void acquisitionStarted(SequenceSettings settings, JSONObject metadata);
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 c41bc09ad77f86b2f88a4b19a3425bfe5e38812c..cf56aad2995947ca3be098ba0be3506ce8288d2d 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java
@@ -1,9 +1,8 @@
package plugins.tprovoost.Microscopy.MicroManager.event;
-import icy.sequence.Sequence;
-
import java.util.List;
+import icy.sequence.Sequence;
import mmcorej.TaggedImage;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
@@ -15,9 +14,9 @@ import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
public interface LiveListener
{
/**
- * Called when a new image is captured by the core when live mode is on.<br/>
+ * Called when a new image is captured by the core when live mode is on.<br>
* Note that the new image properties may have changed (such as the image size, binning,
- * exposure...)<br/>
+ * exposure...)<br>
* Note that you can easily convert TaggedImage to Icy image by using
* {@link MMUtils#setImage(Sequence, TaggedImage)} or {@link MMUtils#convertToIcyImage(List)} methods.
*
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 85dcc8bdc9359cf369e29badf32ad8c2f619c3fe..1fcdb07afb8aa9bdc574d3eabf19dea5824097fe 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java
@@ -1,7 +1,5 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.network.NetworkUtil;
-
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.event.ActionListener;
@@ -19,6 +17,8 @@ import javax.swing.border.EmptyBorder;
import org.micromanager.MMVersion;
+import icy.network.NetworkUtil;
+
public class AboutPanel extends JPanel
{
/**
@@ -30,6 +30,9 @@ public class AboutPanel extends JPanel
/**
* Create the panel.
+ *
+ * @param OkAction
+ * action to execute on OK button click
*/
public AboutPanel(ActionListener OkAction)
{
@@ -45,18 +48,17 @@ public class AboutPanel extends JPanel
{
setBorder(new EmptyBorder(10, 10, 10, 10));
JPanel center = new JPanel(new BorderLayout());
- final JLabel value = new JLabel(
- "<html><body>"
- + "<h2>About</h2><p>Micro-Manager for Icy is being developed by Stephane Dallongeville, Irsath Nguyen and Thomas Provoost."
- + "<br/>Copyright 2016, Institut Pasteur</p><br/>"
- + "<p>This plugin is based on Micro-Manager? " + MMVersion.VERSION_STRING
- + " which is developed under the following license:<br/>"
- + "<i>This software is distributed free of charge in the hope that it will be<br/>"
- + "useful, but WITHOUT ANY WARRANTY; without even the implied<br/>"
- + "warranty of merchantability or fitness for a particular purpose. In no<br/>"
- + "event shall the copyright owner or contributors be liable for any direct,<br/>"
- + "indirect, incidental spacial, examplary, or consequential damages.<br/>"
- + "Copyright University of California San Francisco, 2010. All rights reserved.</i>" + "</p>" + "</body></html>");
+ final JLabel value = new JLabel("<html><body>"
+ + "<h2>About</h2><p>Micro-Manager for Icy is being developed by Stephane Dallongeville, Irsath Nguyen and Thomas Provoost."
+ + "<br/>Copyright 2016, Institut Pasteur</p><br/>" + "<p>This plugin is based on Micro-Manager? "
+ + MMVersion.VERSION_STRING + " which is developed under the following license:<br/>"
+ + "<i>This software is distributed free of charge in the hope that it will be<br/>"
+ + "useful, but WITHOUT ANY WARRANTY; without even the implied<br/>"
+ + "warranty of merchantability or fitness for a particular purpose. In no<br/>"
+ + "event shall the copyright owner or contributors be liable for any direct,<br/>"
+ + "indirect, incidental spacial, examplary, or consequential damages.<br/>"
+ + "Copyright University of California San Francisco, 2010. All rights reserved.</i>" + "</p>"
+ + "</body></html>");
JLabel link = new JLabel("<html><a href=\"\">For more information, please follow this link.</a></html>");
link.addMouseListener(new MouseAdapter()
{
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 d24a3b894f78dd78d3069a28cbb24e31161effe6..f86d481cdc5c8ec4894a71e16f77abfd4920ac84 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java
@@ -38,6 +38,8 @@ public class AcquisitionInfoPanel extends JPanel implements Runnable
/**
* Create the panel.
+ *
+ * @param mainFrame the attached {@link MMMainFrame} object
*/
public AcquisitionInfoPanel(MMMainFrame mainFrame)
{
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 2e1b1b64046b95a69ce9fc6c9084e312088ef1dc..05f3e81866b6c9b452e40c6171d7e865b99e2004 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java
@@ -64,6 +64,9 @@ public class ActionsPanel extends JPanel implements LiveListener, SequenceListen
/**
* Create the panel.
+ *
+ * @param mainFrame
+ * the attached {@link MMMainFrame} object
*/
public ActionsPanel(MMMainFrame mainFrame)
{
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 8eea7b4965b2003870057294e1dac9b8aa7df886..97439afe75511e92623d09bb61021c64be14e151 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java
@@ -1,15 +1,5 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.gui.component.NumberTextField;
-import icy.gui.component.NumberTextField.ValueChangeListener;
-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 java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
@@ -27,6 +17,15 @@ import javax.swing.border.TitledBorder;
import org.micromanager.MMStudio;
+import icy.gui.component.NumberTextField;
+import icy.gui.component.NumberTextField.ValueChangeListener;
+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;
@@ -67,6 +66,9 @@ public class CameraSettingsPanel extends JPanel implements Runnable
/**
* Create the panel.
+ *
+ * @param mainFrame
+ * the attached {@link MMMainFrame} object
*/
public CameraSettingsPanel(MMMainFrame mainFrame)
{
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 81d2caa26d210771eafc9cdb0524d633e062d08d..2a92aee27013bebd1ba9dc16417a16a631e7c11b 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java
@@ -1,13 +1,5 @@
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.thread.ThreadUtil;
-import icy.util.StringUtil;
-
import java.awt.BorderLayout;
import java.awt.Font;
import java.awt.GridBagConstraints;
@@ -23,13 +15,19 @@ import javax.swing.JPanel;
import javax.swing.border.EmptyBorder;
import javax.swing.border.TitledBorder;
-import mmcorej.CMMCore;
-
import org.micromanager.ConfigGroupPad;
import org.micromanager.MMStudio;
import org.micromanager.dialogs.GroupEditor;
import org.micromanager.dialogs.PresetEditor;
+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.thread.ThreadUtil;
+import icy.util.StringUtil;
+import mmcorej.CMMCore;
import plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
public class ConfigurationPanel extends JPanel
@@ -51,6 +49,9 @@ public class ConfigurationPanel extends JPanel
/**
* Create the panel.
+ *
+ * @param mainFrame
+ * the attached {@link MMMainFrame} object
*/
public ConfigurationPanel(MMMainFrame mainFrame)
{
@@ -190,12 +191,12 @@ public class ConfigurationPanel extends JPanel
final String groupName = MMUtils.getSelectedGroupName(groupPad);
if (StringUtil.isEmpty(groupName))
- MessageDialog
- .showDialog("To remove a group, please select it first then press the remove group button.");
+ MessageDialog.showDialog(
+ "To remove a group, please select it first then press the remove group button.");
else
{
- if (ConfirmDialog.confirm("Remove group", "Are you sure you want to remove group " + groupName
- + " and all associated presets ?"))
+ if (ConfirmDialog.confirm("Remove group",
+ "Are you sure you want to remove group " + groupName + " and all associated presets ?"))
{
try
{
@@ -242,8 +243,8 @@ public class ConfigurationPanel extends JPanel
final String groupName = MMUtils.getSelectedGroupName(groupPad);
if (StringUtil.isEmpty(groupName))
- MessageDialog
- .showDialog("To add a preset to a group, please select the group first then press the add preset button.");
+ MessageDialog.showDialog(
+ "To add a preset to a group, please select the group first then press the add preset button.");
else
{
final PresetEditor pe = new PresetEditor(groupName, "", getMMStudio(), getCore(), true);
@@ -275,8 +276,8 @@ public class ConfigurationPanel extends JPanel
final String presetName = MMUtils.getSelectedPresetName(groupPad);
if (StringUtil.isEmpty(groupName) || StringUtil.isEmpty(presetName))
- MessageDialog
- .showDialog("To edit a preset, please select the preset first then press the edit preset button.");
+ MessageDialog.showDialog(
+ "To edit a preset, please select the preset first then press the edit preset button.");
else
{
final PresetEditor pe = new PresetEditor(groupName, presetName, getMMStudio(), getCore(), false);
@@ -301,15 +302,15 @@ public class ConfigurationPanel extends JPanel
final String presetName = MMUtils.getSelectedPresetName(groupPad);
if (StringUtil.isEmpty(groupName) || StringUtil.isEmpty(presetName))
- MessageDialog
- .showDialog("To remove a preset from a group, please select preset first then press the remove button.");
+ MessageDialog.showDialog(
+ "To remove a preset from a group, please select preset first then press the remove button.");
else
{
if (getCore().getAvailableConfigs(groupName).size() == 1L)
{
- if (ConfirmDialog.confirm("Remove last preset in group", "'" + presetName
- + "' is the last preset for the '" + groupName
- + "' group.\nDelete both preset and group ?"))
+ if (ConfirmDialog.confirm("Remove last preset in group",
+ "'" + presetName + "' is the last preset for the '" + groupName
+ + "' group.\nDelete both preset and group ?"))
{
try
{
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 4e84235f6e5da639b323cbe983b59d34f57c1789..1aec464a6d4f3d174a41ad76dd372c45747cb74e 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java
@@ -26,6 +26,12 @@ public class LiveSettingsPanel extends JPanel
private JLabel lblNewLabel;
private NumberTextField zStepField;
+ /**
+ * Create the panel.
+ *
+ * @param mainFrame
+ * the attached {@link MMMainFrame} object
+ */
public LiveSettingsPanel(MMMainFrame mainFrame)
{
super();
@@ -37,7 +43,8 @@ public class LiveSettingsPanel extends JPanel
private void initialize()
{
- setBorder(new TitledBorder(null, "Snap / Live / Album settings", TitledBorder.LEADING, TitledBorder.TOP, null, null));
+ setBorder(new TitledBorder(null, "Snap / Live / Album settings", TitledBorder.LEADING, TitledBorder.TOP, null,
+ null));
GridBagLayout gridBagLayout = new GridBagLayout();
gridBagLayout.columnWidths = new int[] {60, 0, 60, 0, 60, 0, 0};
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 6805976f81f294fe859eaee315171d1b52be24c1..c494bcbfceaf47dd662d6582ed7a5078a0c68a2e 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java
@@ -1,16 +1,5 @@
package plugins.tprovoost.Microscopy.MicroManager.gui;
-import icy.action.IcyAbstractAction;
-import icy.file.FileUtil;
-import icy.gui.component.button.IcyButton;
-import icy.gui.dialog.MessageDialog;
-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 java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.Font;
@@ -40,6 +29,16 @@ import javax.swing.border.EmptyBorder;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
+import icy.action.IcyAbstractAction;
+import icy.file.FileUtil;
+import icy.gui.component.button.IcyButton;
+import icy.gui.dialog.MessageDialog;
+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 plugins.tprovoost.Microscopy.MicroManager.tools.MMUtils;
import plugins.tprovoost.Microscopy.MicroManagerForIcy.MicromanagerPlugin;
@@ -48,7 +47,9 @@ import plugins.tprovoost.Microscopy.MicroManagerForIcy.MicromanagerPlugin;
* visible the first time the user launches the plugin, and when he hits the "Load Configuration"
* button in the {@link MMMainFrame}.
*
- * @author Irsath Nguyen & Thomas Provoost
+ * @author Irsath Nguyen
+ * @author Thomas Provoost
+ * @author Stephane Dallongeville
*/
public class LoadFrame extends JDialog
{
@@ -164,8 +165,8 @@ public class LoadFrame extends JDialog
}
}
else
- _list_files
- .setToolTipText("Double click on a file or select it then click on 'Open File' to open it.");
+ _list_files.setToolTipText(
+ "Double click on a file or select it then click on 'Open File' to open it.");
}
});
_list_files.addMouseListener(new MouseAdapter()
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 01139d040b4514ad675be4b08062edaf1b1b987c..87ae10848f21623723c6ba5ce13041bd2701407b 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java
@@ -1,28 +1,5 @@
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.SystemUtil;
-import icy.system.thread.ThreadUtil;
-import icy.util.ReflectionUtil;
-import icy.util.StringUtil;
-
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
@@ -51,6 +28,28 @@ import org.micromanager.conf2.MicroscopeModel;
import org.micromanager.dialogs.CalibrationListDlg;
import org.micromanager.utils.ReportingUtils;
+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.SystemUtil;
+import icy.system.thread.ThreadUtil;
+import icy.util.ReflectionUtil;
+import icy.util.StringUtil;
import mmcorej.CMMCore;
import mmcorej.MMCoreJ;
import mmcorej.MMEventCallback;
@@ -602,17 +601,17 @@ public class MMMainFrame extends IcyFrame
}
});
-// JMenuItem mmConfigProcessors = new JMenuItem("Configure processors...");
-// mmConfigProcessors.setIcon(new IcyIcon(ResourceUtil.ICON_LIGHTING, true));
-// mmConfigProcessors.setToolTipText("Configure on the fly image processors...");
-// mmConfigProcessors.addActionListener(new ActionListener()
-// {
-// @Override
-// public void actionPerformed(ActionEvent e)
-// {
-// mmstudio.showPipelinePanel();
-// }
-// });
+ // JMenuItem mmConfigProcessors = new JMenuItem("Configure processors...");
+ // mmConfigProcessors.setIcon(new IcyIcon(ResourceUtil.ICON_LIGHTING, true));
+ // mmConfigProcessors.setToolTipText("Configure on the fly image processors...");
+ // mmConfigProcessors.addActionListener(new ActionListener()
+ // {
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // mmstudio.showPipelinePanel();
+ // }
+ // });
JMenuItem mmScriptPanel = new JMenuItem("Script panel");
mmScriptPanel.setIcon(new IcyIcon(ResourceUtil.getAlphaIconAsImage("text_curstor"), true));
@@ -637,7 +636,7 @@ public class MMMainFrame extends IcyFrame
// toReturn.insertSeparator(idx++);
toReturn.insert(propertyBrowserItem, idx++);
toReturn.insert(menuPxSizeConfigItem, idx++);
-// toReturn.insert(mmConfigProcessors, idx++);
+ // toReturn.insert(mmConfigProcessors, idx++);
toReturn.insert(mmScriptPanel, idx++);
toReturn.insert(mmSettingItem, idx++);
toReturn.insertSeparator(idx++);
@@ -746,34 +745,48 @@ public class MMMainFrame extends IcyFrame
}
}
+ /**
+ * @return the {@link MMStudio} object
+ */
public MMStudio getMMStudio()
{
return mmstudio;
}
+ /**
+ * @return the {@link AcquisitionHandler} object
+ */
public AcquisitionHandler getAcquisitionHandler()
{
return acquisitionHandler;
}
+ /**
+ * @return the {@link MMOptions} object
+ */
public MMOptions getOptions()
{
return options;
}
+ /**
+ * @return the {@link Preferences} object
+ */
public Preferences getMainPreferences()
{
return mainPreferences;
}
+ /**
+ * @return the {@link XMLPreferences} object
+ */
public XMLPreferences getPreferences()
{
return preferences;
}
/**
- * Returns the "enable storage of last acquisition" state.
- *
+ * @return the "enable storage of last acquisition" state.
* @see #setStoreLastAcquisition(boolean)
* @see MicroManager#getAcquisitionResult()
*/
@@ -786,6 +799,8 @@ public class MMMainFrame extends IcyFrame
* Enable storage of last acquisition so it can be retrieved with {@link MicroManager#getAcquisitionResult()}.<br>
* Set to <code>true</code> by default.
*
+ * @param value
+ * <code>true</code> to enable storage of last acquisition, <code>false</code> otherwise
* @see MicroManager#getAcquisitionResult()
*/
public void setStoreLastAcquisition(boolean value)
@@ -794,8 +809,7 @@ public class MMMainFrame extends IcyFrame
}
/**
- * Enable immediate display of image acquisition.
- *
+ * @return state of immediate display of image acquisition.
* @see MicroManager#startAcquisition(int, double)
*/
public boolean getDisplayAcquisitionSequence()
@@ -806,6 +820,8 @@ public class MMMainFrame extends IcyFrame
/**
* Enable immediate display of image acquisition.
*
+ * @param value
+ * <code>true</code> to enable immediate display of acquisition, <code>false</code> otherwise
* @see MicroManager#startAcquisition(int, double)
*/
public void setDisplayAcquisitionSequence(boolean value)
@@ -831,7 +847,7 @@ public class MMMainFrame extends IcyFrame
* Adds the plugin to the plugin list of MMMainFrame.
*
* @param plugin
- * : plugin to be added.
+ * plugin to be added
* @see #removePlugin(MicroscopePlugin)
*/
public void addPlugin(MicroscopePlugin plugin)
@@ -845,7 +861,7 @@ public class MMMainFrame extends IcyFrame
* using the acquisition is running, acquisition is stopped.
*
* @param plugin
- * : plugin to be removed.
+ * plugin to be removed.
* @see #addPlugin(MicroscopePlugin)
*/
public void removePlugin(MicroscopePlugin plugin)
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 4e9b38e338afa7ad4d6f00e970720597b6a91f07..9d75dcd4d7b754b8cd267ed18f868445966a7b47 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java
@@ -25,6 +25,12 @@ public class MainPanel extends JPanel
public AcquisitionInfoPanel acquisitionInfoPanel;
public PluginsToolbar pluginsPanel;
+ /**
+ * Create the panel.
+ *
+ * @param mainFrame
+ * the attached {@link MMMainFrame} object
+ */
public MainPanel(MMMainFrame mainFrame)
{
super();
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 1ade4b785259a83d19ce8429cd63f963623cb6b6..0787b65dc2cfa68c243388c1eef3480be1d554d9 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java
@@ -32,6 +32,9 @@ public class PluginsToolbar extends JPanel
/**
* Create the panel.
+ *
+ * @param mainFrame
+ * the attached {@link MMMainFrame} object
*/
public PluginsToolbar(MMMainFrame mainFrame)
{
@@ -70,15 +73,15 @@ public class PluginsToolbar extends JPanel
}));
}
-// 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");
-// }
+ // 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"));
@@ -107,7 +110,7 @@ public class PluginsToolbar extends JPanel
* Adds the plugin to the active plugin list of MMMainFrame.
*
* @param plugin
- * : plugin to be added.
+ * plugin to be added.
* @see #removePlugin(MicroscopePlugin)
*/
public void addPlugin(MicroscopePlugin plugin)
@@ -120,7 +123,7 @@ public class PluginsToolbar extends JPanel
* Removes the plugin from the active plugin list of MMMainFrame.
*
* @param plugin
- * : plugin to be removed.
+ * plugin to be removed.
* @see #addPlugin(MicroscopePlugin)
*/
public void removePlugin(MicroscopePlugin plugin)
@@ -130,7 +133,7 @@ public class PluginsToolbar extends JPanel
}
/**
- * Returns list of active Microscope Plugin
+ * @return list of active Microscope Plugin
*/
public List<MicroscopePlugin> getRunningPlugins()
{
@@ -138,7 +141,7 @@ public class PluginsToolbar extends JPanel
}
/**
- * Returns number of active Microscope Plugin
+ * @return number of active Microscope Plugin
*/
public int getRunningPluginsCount()
{
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 a135ef708d741f8b2346a8a7b76318a962591c2e..07bf2edbf40d021d5d71f4c57c0d1e3d901d366b 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java
@@ -63,13 +63,26 @@ import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
*/
public class MMStudioMethods
{
- /** Replaces <code>MMStudio.isLiveModeOn()</code> method */
+ /**
+ * @deprecated Use {@link MicroManager#isLiveRunning()} instead
+ * @param obj
+ * MMStudio object
+ * @return live mode state
+ */
+ @Deprecated
public static boolean isLiveModeOn(final MMStudio obj)
{
return MicroManager.isLiveRunning();
}
- /** Replaces <code>MMStudio.enableLiveMode(boolean enable)</code> method */
+ /**
+ * @deprecated Use {@link MicroManager#startLiveMode()} / {@link MicroManager#startLiveMode()} instead
+ * @param obj
+ * MMStudio object
+ * @param enable
+ * enable state
+ */
+ @Deprecated
public static void enableLiveMode(final MMStudio obj, final boolean enable)
{
try
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 83a7c98889cf5ad6f6d1ead7e8c611ec538184c3..2856b889908b20106dbf35172f9cb6abe4c1a6d3 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java
@@ -23,6 +23,13 @@ import icy.resource.icon.IcyIcon;
*/
public class FrameUtils
{
+ /**
+ * Add the specified MM window to Icy desktop pane (transforming it as an {@link IcyFrame} in the process)
+ *
+ * @param window
+ * the window to add to the main pane
+ * @return the window converted as an {@link IcyFrame}
+ */
public static IcyFrame addMMWindowToDesktopPane(Window window)
{
IcyFrame frame = GuiUtil.createIcyFrameFromWindow(window);
@@ -30,7 +37,16 @@ public class FrameUtils
frame.setVisible(true);
return frame;
}
-
+
+ /**
+ * Find a button from its label in the specified container
+ *
+ * @param container
+ * the container containing the button we are looking for
+ * @param label
+ * button label
+ * @return the button searched or <code>null</code> if was not found
+ */
public static JButton findButtonComponents(Container container, String label)
{
for (Component c : container.getComponents())
@@ -47,13 +63,16 @@ public class FrameUtils
return null;
}
-
/**
+ * Create an {@link IcyButton} from given information
+ *
* @param buttonText
+ * button text
* @param iconPath
- * may be null, if no icon wanted
+ * the icon path. Can be null if no icon wanted
* @param action
- * @return an IcyButton with buttonText and an icon on it if iconPath not null.<br />
+ * 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(String buttonText, String iconPath, final Runnable action)
@@ -75,6 +94,12 @@ public class FrameUtils
}
/**
+ * 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(PluginDescriptor plugin, ActionListener action)
@@ -87,5 +112,4 @@ public class FrameUtils
return result;
}
-
}
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/ImageGetter.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/ImageGetter.java
index e9b6eeff719b89c41378e8ebc9c4003670627f81..ff18948b87edb3e16cf6ef9789f6d65c956c5709 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/ImageGetter.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/ImageGetter.java
@@ -1,15 +1,13 @@
package plugins.tprovoost.Microscopy.MicroManager.tools;
-import icy.image.IcyBufferedImage;
-import icy.type.collection.array.Array1DUtil;
-
import java.util.List;
-import mmcorej.CMMCore;
-import mmcorej.TaggedImage;
-
import org.json.JSONException;
+import icy.image.IcyBufferedImage;
+import icy.type.collection.array.Array1DUtil;
+import mmcorej.CMMCore;
+import mmcorej.TaggedImage;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
@@ -20,6 +18,11 @@ public class ImageGetter
{
/**
* @deprecated Use {@link MMUtils#convertToIcyImage(List)} instead.
+ * @param images
+ * the list of {@link TaggedImage} to convert
+ * @return the {@link IcyBufferedImage} image
+ * @throws JSONException
+ * if an error occurred while reading the metadata
*/
@Deprecated
public static IcyBufferedImage convertToIcyImage(List<TaggedImage> images) throws JSONException
@@ -29,6 +32,11 @@ public class ImageGetter
/**
* @deprecated Use {@link MMUtils#convertToIcyImage(TaggedImage)} instead.
+ * @param image
+ * the input {@link TaggedImage} to convert
+ * @return the resulting {@link IcyBufferedImage} image
+ * @throws JSONException
+ * if an error occurred while reading the metadata
*/
@Deprecated
public static IcyBufferedImage convertToIcyImage(TaggedImage image) throws JSONException
@@ -56,6 +64,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#getLastImage()} instead.
+ * @return the last image captured from the micro manager continuous acquisition.
+ * @throws Exception
+ * if an error occurred while retrieved last image
*/
@Deprecated
public static IcyBufferedImage getLastImage() throws Exception
@@ -65,6 +76,10 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#getLastTaggedImage()} instead.
+ * @return a list of {@link TaggedImage} representing the last image captured from the micro
+ * manager continuous acquisition.
+ * @throws Exception
+ * if an error occurred while retrieved last tagged images
*/
@Deprecated
public static List<TaggedImage> getLastTaggedImage() throws Exception
@@ -74,6 +89,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#snapImage()} instead.
+ * @return the captured image or <code>null</code> if conversion failed
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static IcyBufferedImage snapImage() throws Exception
@@ -83,6 +101,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#snapTaggedImage()} instead.
+ * @return the captured image as List of {@link TaggedImage}
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static List<TaggedImage> snapTaggedImage() throws Exception
@@ -94,6 +115,7 @@ public class ImageGetter
* Use this method to only get the data of a snapped image. Uses short.
*
* @param core
+ * micro-manager core
* @return Returns data in int. Returns null if an error occurs (Mostly when acquisition is
* running).
* @deprecated use {@link #snapImageFromCore()} instead.
@@ -127,7 +149,7 @@ public class ImageGetter
*
* @deprecated use {@link #snapImageFromLive()} instead.
* @param core
- * : reference to actual core
+ * reference to actual core
* @return Returns a data short[] image. Returns null if an error occurs
* (mostly when acquisition sequence has not yet been run).
*/
@@ -155,6 +177,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#snapImage()} instead.
+ * @return the captured image or <code>null</code> if an error occurred
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static IcyBufferedImage snapIcyImageFromCore() throws Exception
@@ -164,6 +189,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#snapImage()} instead.
+ * @return the captured image from live or <code>null</code> if an error occurred
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static IcyBufferedImage snapImageFromLiveToIcy() throws Exception
@@ -173,6 +201,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#snapImage()} instead.
+ * @return the captured image or <code>null</code> if an error occurred
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static IcyBufferedImage snapImageFromCoreToIcy() throws Exception
@@ -182,6 +213,9 @@ public class ImageGetter
/**
* @deprecated Use {@link #snapImage()} instead.
+ * @return the captured image or <code>null</code> if an error occurred
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static IcyBufferedImage snapIcyImage() throws Exception
@@ -191,6 +225,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#snapImage()} instead.
+ * @return the captured image or <code>null</code> if an error occurred
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static IcyBufferedImage snapToIcy() throws Exception
@@ -200,6 +237,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#snapTaggedImage()} instead.
+ * @return the captured {@link TaggedImage} or <code>null</code> if an error occurred
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static TaggedImage snapImageFromCore() throws Exception
@@ -214,6 +254,11 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#getLastImage()} instead.
+ * @param remove
+ * indicate if we want to remove the image from the acquisition stack
+ * @return the last image captured from the micro manager continuous acquisition.
+ * @throws Exception
+ * if an error occurred while retrieved last image
*/
@Deprecated
public static IcyBufferedImage snapIcyImageFromLive(boolean remove) throws Exception
@@ -223,6 +268,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#getLastImage()} instead.
+ * @return the last image captured from the micro manager continuous acquisition.
+ * @throws Exception
+ * if an error occurred while retrieved last image
*/
@Deprecated
public static IcyBufferedImage snapIcyImageFromLive() throws Exception
@@ -232,6 +280,11 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#getLastTaggedImage()}
+ * @param remove
+ * indicate if we want to remove the image from the acquisition stack
+ * @return the last image captured from the micro manager continuous acquisition.
+ * @throws Exception
+ * if an error occurred while retrieved last image
*/
@Deprecated
public static TaggedImage snapImageFromLive(boolean remove) throws Exception
@@ -246,6 +299,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#getLastTaggedImage()} instead.
+ * @return the last image captured from the micro manager continuous acquisition.
+ * @throws Exception
+ * if an error occurred while retrieved last image
*/
@Deprecated
public static TaggedImage snapImageFromLive() throws Exception
@@ -260,6 +316,9 @@ public class ImageGetter
/**
* @deprecated Use {@link MicroManager#snapTaggedImage()} instead.
+ * @return the captured image as a {@link TaggedImage}
+ * @throws Exception
+ * if an error occurred
*/
@Deprecated
public static TaggedImage snap() throws Exception
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 c9c72d375f1d1b86b2c93d648edeb2419ea24426..40d940d166d5ba7b183a4bb1648158291464a0bb 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java
@@ -70,7 +70,7 @@ public class MMUtils
private static boolean loaded = false;
/**
- * Returns the Micro-Manager folder
+ * @return the Micro-Manager folder
*/
public static String getMicroManagerFolder()
{
@@ -81,11 +81,17 @@ public class MMUtils
return uManagerRep;
}
+ /**
+ * @return <code>true</code> if Micro-Manager library is loaded
+ */
public static boolean isSystemLibrairiesLoaded()
{
return loaded;
}
+ /**
+ * @return <code>true</code> if Micro-Manager path has been correctly updated and library loaded.
+ */
public static boolean fixSystemLibrairies()
{
if (loaded)
@@ -193,6 +199,9 @@ public class MMUtils
return loaded;
}
+ /**
+ * Reset the Micro-Manager library path
+ */
public static void resetLibrayPath()
{
prefs.put(MM_PATH_ID, "");
@@ -200,7 +209,9 @@ public class MMUtils
}
/**
- * Return true if the specified list of TaggedImage contains a <code>null</code> or poison image.
+ * @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(List<TaggedImage> images)
{
@@ -215,7 +226,11 @@ public class MMUtils
* Convert a list of {@link TaggedImage} (Micro Manager) to {@link IcyBufferedImage} (Icy) where each
* {@link TaggedImage} represents one channel of the output image.
*
+ * @param images
+ * the list of {@link TaggedImage} to convert
+ * @return the resulting {@link IcyBufferedImage} image
* @throws JSONException
+ * if an error occurred while reading the metadata
*/
public static IcyBufferedImage convertToIcyImage(List<TaggedImage> images) throws JSONException
{
@@ -265,7 +280,11 @@ public class MMUtils
/**
* Convert a {@link TaggedImage} (Micro-Manager) to {@link IcyBufferedImage} (Icy).
*
+ * @param img
+ * the input {@link TaggedImage} to convert
+ * @return the resulting {@link IcyBufferedImage} image
* @throws JSONException
+ * if an error occurred while reading the metadata
*/
public static IcyBufferedImage convertToIcyImage(TaggedImage img) throws JSONException
{
@@ -275,8 +294,14 @@ public class MMUtils
/**
* Set Sequence metadata from the given JSON metadata object (can be image or summaryMetadata).
*
+ * @param sequence
+ * the sequence we want to set metadata
+ * @param tags
+ * JSON metadata object
* @throws JSONException
+ * if an error occurred while reading the metadata
* @throws MMScriptException
+ * if an error occurred on MM script parsing
*/
public static void setMetadata(Sequence sequence, JSONObject tags) throws JSONException, MMScriptException
{
@@ -433,6 +458,8 @@ public class MMUtils
/**
* Set the TaggedImage metadata.
*
+ * @param taggedImage
+ * the image we want to set metadata
* @param t
* wanted T position (frame) of the image, set to <code>-1</code> to keep current value
* @param z
@@ -446,6 +473,7 @@ 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(TaggedImage taggedImage, int t, int z, int c, int sizeT, int sizeZ, int sizeC)
throws JSONException
@@ -470,7 +498,16 @@ public class MMUtils
}
/**
- * Set image data
+ * Set {@link IcyBufferedImage} data from native Micro-Manager pixels data blob
+ *
+ * @param dest
+ * the {@link IcyBufferedImage} we want to set data
+ * @param pixels
+ * the pixel data in native micro-manager format
+ * @param channel
+ * the channel where we want to set data
+ * @param rgb
+ * <code>true</code> if the source data comes from a RGB image
*/
static void setImageData(IcyBufferedImage dest, Object pixels, int channel, boolean rgb)
{
@@ -515,8 +552,10 @@ public class MMUtils
* metadata), set it to 0 to ignore it.
* @return <code>true</code> if the operation succeed and <code>false</code> otherwise.
* @throws JSONException
+ * if an error occurred while reading the metadata
* @throws MMScriptException
- * @see {@link #setImageMetadata(TaggedImage, int, int, int, int, int, int)}
+ * if an error occurred on MM script parsing
+ * @see #setImageMetadata(TaggedImage, int, int, int, int, int, int)
*/
public static boolean setImage(Sequence sequence, TaggedImage taggedImage, long startDate)
throws JSONException, MMScriptException
@@ -634,7 +673,9 @@ public class MMUtils
* Tagged image to set in the sequence
* @return <code>true</code> if the operation succeed and <code>false</code> otherwise.
* @throws JSONException
+ * if an error occurred while reading the metadata
* @throws MMScriptException
+ * if an error occurred on MM script parsing
*/
public static boolean setImage(Sequence sequence, TaggedImage taggedImage) throws JSONException, MMScriptException
{
@@ -642,11 +683,16 @@ public class MMUtils
}
/**
- * Returns <code>true</code> if the sequence data format is compatible with specified JSON metadata (same dimension
- * and same pixel format)
- *
+ * @param sequence
+ * the sequence we want to test compatibility
+ * @param metadata
+ * JSON metadata object
+ * @return <code>true</code> if the sequence data format is compatible with specified JSON metadata (same dimension
+ * and same pixel format)
* @throws JSONException
+ * if an error occurred while reading the metadata
* @throws MMScriptException
+ * if an error occurred on MM script parsing
*/
public static boolean isCompatible(Sequence sequence, JSONObject metadata) throws JSONException, MMScriptException
{
@@ -661,11 +707,14 @@ public class MMUtils
}
/**
- * Create an empty IcyBufferedImage using properties in given JSON metadata object. It can be either the one from
- * TaggedImage or the summaryMetadata (see {@link MicroManager#getAcquisitionMetaData()})
- *
+ * @param metadata
+ * JSON metadata object
+ * @return an empty IcyBufferedImage using properties in given JSON metadata object.<br>
+ * It can be either the one from TaggedImage or the summaryMetadata (see {@link MicroManager#getAcquisitionMetaData()})
* @throws JSONException
+ * if an error occurred while reading the metadata
* @throws MMScriptException
+ * if an error occurred on MM script parsing
*/
public static IcyBufferedImage createEmptyImage(JSONObject metadata) throws JSONException, MMScriptException
{
@@ -694,7 +743,9 @@ public class MMUtils
}
/**
- * Returns the selected group name from specified ConfigGroupPad
+ * @param group
+ * the {@link ConfigGroupPad} name
+ * @return the selected group name from specified ConfigGroupPad
*/
public static String getSelectedGroupName(ConfigGroupPad group)
{
@@ -716,7 +767,9 @@ public class MMUtils
}
/**
- * Returns the selected preset name from specified ConfigGroupPad
+ * @param group
+ * the {@link ConfigGroupPad} name
+ * @return the selected preset name from specified ConfigGroupPad
*/
public static String getSelectedPresetName(ConfigGroupPad group)
{
@@ -805,5 +858,4 @@ public class MMUtils
return true;
}
-
}
\ No newline at end of file
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 5c4c129ed190a05341d544dc32878cf37f50858b..4ee3b5c55b6c61a145c7c105c7bf202980962864 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java
@@ -46,6 +46,12 @@ public class StageMover
/** Constant value of the switch between x and y for stage movement */
private static final String SWITCHXY = "switchxy";
+ /**
+ * Load the preferences.
+ *
+ * @param pref
+ * {@link XMLPreferences} node
+ */
public static void loadPreferences(XMLPreferences pref)
{
prefs = pref;
@@ -60,7 +66,7 @@ public class StageMover
* and focus device (x,y,z).
*
* @param sl
- * : Listener object to be added.
+ * Listener object to be added.
*/
public static void addListener(StageListener sl)
{
@@ -71,76 +77,133 @@ public class StageMover
* Add a listener to the Stage Mover. he stage will update the listeners with the new values.
*
* @param sl
- * : Listener object to be removed.
+ * Listener object to be removed.
*/
public static void removeListener(StageListener sl)
{
_listeners.remove(sl);
}
+ /**
+ * Remove all listeners
+ */
public static void clearListener()
{
_listeners.clear();
}
+ /**
+ * Set inverted X axis state.
+ *
+ * @param invertX
+ * invert X axis state to set
+ */
public static void setInvertX(boolean invertX)
{
StageMover.invertX = invertX;
prefs.putBoolean(INVERTX, invertX);
}
+ /**
+ * Set inverted Y axis state.
+ *
+ * @param invertY
+ * invert Y axis state to set
+ */
public static void setInvertY(boolean invertY)
{
StageMover.invertY = invertY;
prefs.putBoolean(INVERTY, invertY);
}
+ /**
+ * Set inverted Z axis state.
+ *
+ * @param invertZ
+ * invert Z axis state to set
+ */
public static void setInvertZ(boolean invertZ)
{
StageMover.invertZ = invertZ;
prefs.putBoolean(INVERTZ, invertZ);
}
+ /**
+ * @return state of X inverted axis.
+ */
public static boolean isInvertX()
{
return invertX;
}
+ /**
+ * @return state of Y inverted axis.
+ */
public static boolean isInvertY()
{
return invertY;
}
+ /**
+ * @return state of Y inverted axis.
+ */
public static boolean isInvertZ()
{
return invertZ;
}
+ /**
+ * Switch X and Y axis.
+ *
+ * @param switchXY
+ * <code>true</code> to invert X a Y axis, <code>false</code> otherwise
+ */
public static void setSwitchXY(boolean switchXY)
{
StageMover.switchXY = switchXY;
prefs.putBoolean(SWITCHXY, switchXY);
}
+ /**
+ * @return state of X and Y axis inversion.
+ */
public static boolean isSwitchXY()
{
return switchXY;
}
+ /**
+ * Fire Z stage position change event
+ *
+ * @param s
+ * stage devicce name
+ * @param z
+ * Z position
+ */
public static void onStagePositionChanged(String s, double z)
{
for (StageListener l : _listeners)
l.onStagePositionChanged(s, z);
}
- public static void onXYStagePositionChanged(String s, double d, double d1)
+ /**
+ * Fire XY stage position change event
+ *
+ * @param s
+ * stage device name
+ * @param x
+ * X position
+ * @param y
+ * Y position
+ */
+ public static void onXYStagePositionChanged(String s, double x, double y)
{
for (StageListener l : _listeners)
- l.onXYStagePositionChanged(s, d, d1);
+ l.onXYStagePositionChanged(s, x, y);
};
/**
- * Returns current Stage device
+ * @return current XY Stage device
*/
public static String getXYStageDevice()
{
@@ -148,7 +211,7 @@ public class StageMover
}
/**
- * Returns current focus (Z position) device
+ * @return current focus (Z position) device
*/
public static String getZFocusDevice()
{
@@ -156,7 +219,7 @@ public class StageMover
}
/**
- * Blocking method.
+ * Wait XY stage device to reply.
*
* @throws Exception
* if an error occurs
@@ -170,7 +233,7 @@ public class StageMover
}
/**
- * Blocking method.
+ * Wait Z stage device to reply.
*
* @throws Exception
* if an error occurs
@@ -184,9 +247,9 @@ public class StageMover
}
/**
- * This method returns the coordinates x of the current stage device
+ * This method returns the X coordinate of the current stage device
*
- * @return Returns the coordinates x of the current stage device.
+ * @return the X coordinate of the current stage device.
* @throws Exception
* if an error occurs
*/
@@ -202,9 +265,9 @@ public class StageMover
}
/**
- * This method returns the coordinates y of the current stage device
+ * This method returns the Y coordinate of the current stage device
*
- * @return Returns the coordinates y of the current stage device.
+ * @return the Y coordinate of the current stage device.
* @throws Exception
* if an error occurs
*/
@@ -220,9 +283,9 @@ public class StageMover
}
/**
- * This method returns the coordinates z of the current focus device
+ * This method returns the Z coordinates of the current focus device
*
- * @return Returns the coordinates z of the current focus device.
+ * @return the Z coordinate of the current focus device.
* @throws Exception
* if an error occurs
*/
@@ -238,8 +301,9 @@ public class StageMover
}
/**
- * This method returns the coordinates x and y of the current stage device.
+ * This method returns the X and Y coordinates of the current stage device.
*
+ * @return the X and Y coordinates of the current stage device.
* @throws Exception
* if an error occurs
*/
@@ -255,8 +319,9 @@ public class StageMover
}
/**
- * This method returns the coordinates x and y of the current stage deviceand z coordinate of focus device.
+ * This method returns the X and Y coordinates of the current stage device and the Z coordinate of focus device.
*
+ * @return the X, Y and Z coordinates of the current stage/focus device(s).
* @throws Exception
* if an error occurs
*/
@@ -267,9 +332,9 @@ public class StageMover
}
/**
- * This method returns the coordinates x and y of the current stage device and z coordinate of focus device.
+ * This method returns the X and Y coordinates of the current stage device and the Z coordinate of focus device.
*
- * @return Returns [x, y, z]
+ * @return the X, Y and Z coordinates of the current stage/focus device(s) in double[3] format
* @throws Exception
* if an error occurs
*/
@@ -283,6 +348,8 @@ public class StageMover
* Wait while stage device (XY position) is changing (blocking method).
*
* @return <code>false</code> if more than 5 seconds passed or <code>true</code> if the movement is done.
+ * @throws Exception
+ * if an error occurs
*/
public static boolean waitXYMoving() throws Exception
{
@@ -307,6 +374,8 @@ public class StageMover
* Wait while focus device (Z position) is changing (blocking method).
*
* @return <code>false</code> if more than 5 seconds passed or <code>true</code> if the movement is done.
+ * @throws Exception
+ * if an error occurs
*/
public static boolean waitZMoving() throws Exception
{
@@ -331,6 +400,7 @@ public class StageMover
* Stops the XY stage Movement.
*
* @throws Exception
+ * if an error occurs
*/
public static void stopXYStage() throws Exception
{
@@ -354,6 +424,7 @@ public class StageMover
* Stops the Z focus Movement.
*
* @throws Exception
+ * if an error occurs
*/
public static void stopZFocus() throws Exception
{
@@ -379,6 +450,7 @@ public class StageMover
* @param position
* Z position (in ?m)
* @throws Exception
+ * if an error occurs
*/
public static void moveZAbsolute(double position) throws Exception
{
@@ -386,7 +458,7 @@ public class StageMover
}
/**
- * Moves the stage on the Z-Axis. <br/>
+ * Moves the stage on the Z-Axis. <br>
* <b>You should wait for the microscope if you are planning to capture image after this call</b>
*
* @param position
@@ -395,6 +467,7 @@ public class StageMover
* wait for device to process command. Note that you can use {@link #waitZMoving()} to ensure Z stage
* complete the movement.
* @throws Exception
+ * if an error occurs
* @see #moveZRelative(double, boolean)
* @see #waitZMoving()
*/
@@ -427,6 +500,7 @@ public class StageMover
* @param posY
* y position wanted
* @throws Exception
+ * if an error occurs
*/
public static void moveXYAbsolute(double posX, double posY) throws Exception
{
@@ -434,7 +508,7 @@ public class StageMover
}
/**
- * Move the stage on the X and Y axes to the absolute position given by posX and posY. <br/>
+ * Move the stage on the X and Y axes to the absolute position given by posX and posY. <br>
* <b>You should wait for the microscope if you are planning to capture image after this call</b>
*
* @param posX
@@ -445,6 +519,7 @@ public class StageMover
* wait for device to process command. Note that you can use {@link #waitXYMoving()} to ensure XY stage
* complete the movement.
* @throws Exception
+ * if an error occurs
* @see #moveXYRelative(double, double, boolean)
* @see #waitXYMoving()
*/
@@ -470,12 +545,13 @@ public class StageMover
}
/**
- * Moves the stage on the Z-axis relative to current position. Wait for movement. <br/>
+ * Moves the stage on the Z-axis relative to current position. Wait for movement. <br>
* <b>Relative move may not be accurate !</b>
*
* @param movement
- * : movement (in ?m)
+ * movement (in um)
* @throws Exception
+ * if an error occurs
*/
public static void moveZRelative(double movement) throws Exception
{
@@ -483,16 +559,17 @@ public class StageMover
}
/**
- * Moves the stage on the Z-axis relative to current position. <br/>
- * <b>Relative move may not be accurate !</b> <br/>
+ * Moves the stage on the Z-axis relative to current position. <br>
+ * <b>Relative move may not be accurate !</b> <br>
* <b>You should wait for the microscope if you are planning to capture image after this call</b>
*
* @param movement
- * Z movement (in ?m)
+ * Z movement (in um)
* @param wait
* wait for device to process command. Note that you can use {@link #waitZMoving()} to ensure Z stage
* complete the movement.
* @throws Exception
+ * if an error occurs
* @see #moveZAbsolute(double, boolean)
* @see #waitZMoving()
*/
@@ -521,14 +598,15 @@ public class StageMover
}
/**
- * Moves the stage on the X and Y axes relative to actual position. Wait for movement. <br/>
+ * Moves the stage on the X and Y axes relative to actual position. Wait for movement. <br>
* <b>Relative move may not be accurate !</b>
*
* @param movX
- * movement on X-Axis (in ?m)
+ * movement on X-Axis (in um)
* @param movY
- * movement on Y-Axis (in ?m)
+ * movement on Y-Axis (in um)
* @throws Exception
+ * if an error occurs
*/
public static void moveXYRelative(double movX, double movY) throws Exception
{
@@ -536,18 +614,19 @@ public class StageMover
}
/**
- * Moves the stage on the X and Y axes relative to actual position. <br/>
- * <b>Relative move may not be accurate !</b> <br/>
+ * Moves the stage on the X and Y axes relative to actual position. <br>
+ * <b>Relative move may not be accurate !</b> <br>
* <b>You should wait for the microscope if you are planning to capture image after this call</b>
*
* @param movX
- * movement on X-Axis (in ?m)
+ * movement on X-Axis (in um)
* @param movY
- * movement on Y-Axis (in ?m)
+ * movement on Y-Axis (in um)
* @param wait
* wait for device to process command. Note that you can use {@link #waitXYMoving()} to ensure XY stage
* complete the movement.
* @throws Exception
+ * if an error occurs
* @see #moveXYAbsolute(double, double, boolean)
* @see #waitXYMoving()
*/
@@ -582,8 +661,8 @@ public class StageMover
/**
* This method will move the stage to the ROI wanted in the Sequence. This call is blocking while the microscope not
* finished it move. <b>Be careful, this method should not be used if the pixelSize configuration is not
- * accurate.</b> <br/>
- * <br/>
+ * accurate.</b> <br>
+ * <br>
* <b>This movement may not be accurate !</b>
*
* @param s
@@ -591,6 +670,7 @@ public class StageMover
* @param roi
* The ROI2D to focus on.
* @throws Exception
+ * if an error occurs
*/
public static void moveStageToROI(Sequence s, ROI2D roi) throws Exception
{
@@ -610,7 +690,7 @@ public class StageMover
/**
* Move the stage to a specific point <b>in the sequence</b>. The movement will be relative to the actual position
* of the stage, and relative to the center in the sequence. This call is blocking while the microscope not
- * finished/ it move. <br/>
+ * finished/ it move. <br>
* <b>This movement may not be accurate !</b>
*
* @param s
@@ -620,6 +700,7 @@ 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(Sequence s, double x, double y) throws Exception
{
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java
index dbf9003513f43412f07035bb5878740dddf58b16..9dd0164806c8b9139e225e459295373dce6c5b24 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java
@@ -34,6 +34,7 @@ public final class MicromanagerPlugin extends PluginActionable implements Plugin
/**
* @deprecated Only provided for backward compatibility. Use {@link MicroManager#getCore()} instead.
+ * @return micro-manager core
*/
@Deprecated
public static CMMCore getCore()
diff --git a/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java
index ebd58e34a0aa63d8d68ccd7cac6467dd13b5bbaf..db051fc25de5bf5e21fb840927f873604c116a93 100644
--- a/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java
+++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java
@@ -4,15 +4,16 @@ import icy.plugin.abstract_.Plugin;
import plugins.tprovoost.Microscopy.MicroManager.MicroManager;
/**
- * This is the class to inherit in order to create a Microscope Plugin.<br/>
+ * This is the class to inherit in order to create a Microscope Plugin.<br>
* Any {@link MicroscopePlugin} has to implement the start() method. That
* way, you will have access to the main interface and the core, and your plugin
- * will automatically wait for the Micro-Manager For Icy to be running.<br/>
+ * will automatically wait for the Micro-Manager For Icy to be running.<br>
* <b>At the end of life of your plugin you should manually call shutdown()</b>
* <p>
- * <b>Example: </b></br> start() { <br/>
- * System.out.println(core.getAPIVersionInfo());<br/>
- * shutdown();<br/>
+ * <b>Example: </b><br>
+ * start() { <br>
+ * System.out.println(core.getAPIVersionInfo());<br>
+ * shutdown();<br>
* }
* </p>
*
@@ -33,18 +34,17 @@ public abstract class MicroscopePlugin extends Plugin
}
/**
- * Method to define in sub-classes in replacement of usual run() method of
- * Icy plugin's
+ * Method to define in sub-classes in replacement of usual run() method of Icy plugin's.
* It is called only <b>AFTER</b> Micro-Manager For Icy is launched.
*/
public abstract void start();
/**
- * Called when main Micro-Manager GUI is closed.<br/>
+ * Called when main Micro-Manager GUI is closed.<br>
* Override this method to compute some special operation / data saving before exiting (like image saving, frame
- * position saving...)<br/>
+ * position saving...)<br>
* <b>You should dispose all your threads / resources using MicroManager in this method, remove all listeners and
- * not use them anymore.</b><br/>
+ * not use them anymore.</b><br>
* Don't delete the call to super.shutdown();
*/
public void shutdown()
@@ -54,6 +54,8 @@ public abstract class MicroscopePlugin extends Plugin
/**
* @deprecated No more supported (not really useful)
+ * @param value
+ * enable state
*/
@Deprecated
public void showProgressBar(boolean value)
@@ -72,6 +74,8 @@ public abstract class MicroscopePlugin extends Plugin
/**
* @deprecated No more supported (not really useful)
+ * @param progress
+ * progress value
*/
@Deprecated
public void notifyProgress(int progress)
@@ -83,6 +87,7 @@ public abstract class MicroscopePlugin extends Plugin
* Override this method in order to listen to exposure changes.
*
* @param newExposure
+ * exposure to set
*/
public void onExposureChanged(double newExposure)
{
@@ -93,9 +98,11 @@ public abstract class MicroscopePlugin extends Plugin
* Override this method in order to listen to core properties changes.
*
* @param deviceName
+ * device name
* @param propName
- * Defined as string's in MMCoreJ.getG_Keyword_[....]
+ * property name
* @param propValue
+ * property value
*/
public void onCorePropertyChanged(String deviceName, String propName, String propValue)
{