diff --git a/.gitmodules b/.gitmodules index 5d7c8f02c0..4ba10345c3 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,4 +1,4 @@ [submodule "mmCoreAndDevices"] path = mmCoreAndDevices - url=https://github.com/micro-manager/mmCoreAndDevices.git - branch = main + url=https://github.com/microcombustion/mmCoreAndDevices.git + branch = teledyne-dalsa-genie-GigE diff --git a/mmCoreAndDevices b/mmCoreAndDevices index fee2c1e310..514ba2089f 160000 --- a/mmCoreAndDevices +++ b/mmCoreAndDevices @@ -1 +1 @@ -Subproject commit fee2c1e310e2d237c1f6dda412c262efaecdf094 +Subproject commit 514ba2089fcba36259f0f462e5cb35f36b1d6bf7 diff --git a/mmstudio/src/main/java/org/micromanager/Application.java b/mmstudio/src/main/java/org/micromanager/Application.java index bfd68b543c..abc9716020 100644 --- a/mmstudio/src/main/java/org/micromanager/Application.java +++ b/mmstudio/src/main/java/org/micromanager/Application.java @@ -41,7 +41,7 @@ public interface Application { * poll each device in the system for its current state, which may take * significant time. Compare refreshGUIFromCache(). */ - public void refreshGUI(); + void refreshGUI(); /** * Updates the GUI so that its state reflects the current state of the @@ -49,14 +49,14 @@ public interface Application { * pull values from the Core's System State Cache, which is fast but may not * necessarily reflect the actual state of hardware. */ - public void refreshGUIFromCache(); + void refreshGUIFromCache(); /** * Set the exposure time for the current channel (if any). Equivalent to * updating the exposure time field in the main window. * @param exposureMs Exposure time, in milliseconds. */ - public void setExposure(double exposureMs); + void setExposure(double exposureMs); /** * Updates the exposure time associated with the given preset. If the @@ -68,7 +68,7 @@ public interface Application { * channel that should be updated. * @param exposure New exposure time to set. */ - public void setChannelExposureTime(String channelGroup, String channel, + void setChannelExposureTime(String channelGroup, String channel, double exposure); /** @@ -80,7 +80,7 @@ public void setChannelExposureTime(String channelGroup, String channel, * @param defaultExp Default value to return if no exposure time is found. * @return Exposure time for the channel, or the provided default value. */ - public double getChannelExposureTime(String channelGroup, String channel, + double getChannelExposureTime(String channelGroup, String channel, double defaultExp); /** @@ -93,18 +93,18 @@ public double getChannelExposureTime(String channelGroup, String channel, * @throws IOException If shouldOverwrite is false and there is already a * file at the chosen path. */ - public void saveConfigPresets(String path, boolean allowOverwrite) throws IOException; + void saveConfigPresets(String path, boolean allowOverwrite) throws IOException; /** * Pop up the dialog used to configure the autofocus settings for the * current autofocus device. */ - public void showAutofocusDialog(); + void showAutofocusDialog(); /** * Display the position list dialog. */ - public void showPositionList(); + void showPositionList(); /** * Set the default camera's ROI -- a convenience function. Will stop and @@ -113,12 +113,12 @@ public double getChannelExposureTime(String channelGroup, String channel, * @param rect Rectangle defining the ROI * @throws Exception if there is an error in the Core when setting the ROI */ - public void setROI(Rectangle rect) throws Exception; + void setROI(Rectangle rect) throws Exception; /** * Move the main Micro-Manager window to the top of the user interface. */ - public void makeActive(); + void makeActive(); /** * Provide access to the main window of the program. This is largely @@ -126,19 +126,19 @@ public double getChannelExposureTime(String channelGroup, String channel, * to the main window. * @return the main Window */ - public JFrame getMainWindow(); + JFrame getMainWindow(); /** * Provides access to the application skin API for determining colors for * various GUI components. * @return ApplicationSkin instance. */ - public ApplicationSkin skin(); + ApplicationSkin skin(); /** * Provides access to the application skin API for determining colors for * various GUI components. Identical to skin() except in name. * @return ApplicationSkin instance. */ - public ApplicationSkin getApplicationSkin(); + ApplicationSkin getApplicationSkin(); } diff --git a/mmstudio/src/main/java/org/micromanager/ApplicationSkin.java b/mmstudio/src/main/java/org/micromanager/ApplicationSkin.java index febe67f2e6..c8fa139564 100644 --- a/mmstudio/src/main/java/org/micromanager/ApplicationSkin.java +++ b/mmstudio/src/main/java/org/micromanager/ApplicationSkin.java @@ -41,7 +41,7 @@ public interface ApplicationSkin { /** * Available skins used by the application. */ - public enum SkinMode { + enum SkinMode { DAY("Day"), NIGHT("Night"); private final String desc_; @@ -80,43 +80,43 @@ public static SkinMode fromString(String desc) { * application-wide event bus. * @param mode The mode to use. */ - public void setSkin(SkinMode mode); + void setSkin(SkinMode mode); /** * @return the current Micro-Manager skin. */ - public SkinMode getSkin(); + SkinMode getSkin(); /** * Return the current background color for normal GUI elements. * @return current background color */ - public Color getBackgroundColor(); + Color getBackgroundColor(); /** * Return the current "lighter" background color for highlighted or * otherwise differentiated GUI elements. * @return light background color */ - public Color getLightBackgroundColor(); + Color getLightBackgroundColor(); /** * Return the current "disabled" background color. * @return "disabled" background color */ - public Color getDisabledBackgroundColor(); + Color getDisabledBackgroundColor(); /** * Return the current color for enabled text. * @return current color for enabled text */ - public Color getEnabledTextColor(); + Color getEnabledTextColor(); /** * Return the current color for disabled text. * @return current color for disabled text. */ - public Color getDisabledTextColor(); + Color getDisabledTextColor(); /** * If the specified mode is not currently active, then we switch to that @@ -124,10 +124,10 @@ public static SkinMode fromString(String desc) { * with a nonstandard look-and-feel. * @param mode SkinMode to switch to (but without updating the UI) */ - public void suspendToMode(SkinMode mode); + void suspendToMode(SkinMode mode); /** * Restores the mode that was active before suspendToMode was called. */ - public void resume(); + void resume(); } diff --git a/mmstudio/src/main/java/org/micromanager/PropertyManager.java b/mmstudio/src/main/java/org/micromanager/PropertyManager.java new file mode 100644 index 0000000000..152e4744f9 --- /dev/null +++ b/mmstudio/src/main/java/org/micromanager/PropertyManager.java @@ -0,0 +1,47 @@ +package org.micromanager; + +import java.io.File; +import java.io.IOException; + +/** + * Provides access to PropertyMaps. And instance of this interface is obtained + * through Studio.properties() and Studio.propertyManager(); + */ +public interface PropertyManager { + + /** + * Provides an easy way for a script to obtain a PropertyMap Builder + * @return PropertyMap Builder + */ + PropertyMap.Builder propertyMapBuilder(); + + /** + * Returns an empty property map. + * @return empty property map + */ + PropertyMap emptyPropertyMap(); + + /** + * Creates a property map from its JSON-serialized form. + * JSON format is described in {@link org.micromanager.internal.propertymap.PropertyMapJSONSerializer} + * @param json json formatted String to be converted into a PropertyMap + * @return PropertyMap result from conversion + * @throws IOException if {@code json} is invalid JSON or if it does not + * represent a valid property map + */ + PropertyMap fromJSON(String json) throws IOException; + + /** + * Create a property map from its JSON-serialized form stored in a file. + * + * JSON format is described in {@link org.micromanager.internal.propertymap.PropertyMapJSONSerializer} + * @param file File containing JSON serialized Properties. + * @return PropertyMap resulting from conversion fo JSON in file. + * @throws IOException if there was a problem reading {@code file} or if the + * file contained invalid JSON or if the JSON did not represent a valid + * property map + * @throws java.io.FileNotFoundException this subclass of {@code IOException} + * is thrown if {@code file} does not exist + */ + PropertyMap loadJSON(File file) throws IOException; +} diff --git a/mmstudio/src/main/java/org/micromanager/PropertyMap.java b/mmstudio/src/main/java/org/micromanager/PropertyMap.java index 6f027ce12b..678b34ebfc 100644 --- a/mmstudio/src/main/java/org/micromanager/PropertyMap.java +++ b/mmstudio/src/main/java/org/micromanager/PropertyMap.java @@ -83,7 +83,7 @@ public interface PropertyMap { * This is only used for interchange purposes, for example when performing * bulk operations on property maps. */ - public interface OpaqueValue { + interface OpaqueValue { /** * * @return diff --git a/mmstudio/src/main/java/org/micromanager/PropertyMaps.java b/mmstudio/src/main/java/org/micromanager/PropertyMaps.java index 8014bf4ad4..b22b9f9922 100644 --- a/mmstudio/src/main/java/org/micromanager/PropertyMaps.java +++ b/mmstudio/src/main/java/org/micromanager/PropertyMaps.java @@ -48,8 +48,8 @@ public static PropertyMap emptyPropertyMap() { /** * Create a property map from its JSON-serialized form. - * @param json - * @return + * @param json json formatted String to be converted into a PropertyMap + * @return PropertyMap result from conversion * @throws IOException if {@code json} is invalid JSON or if it does not * represent a valid property map */ diff --git a/mmstudio/src/main/java/org/micromanager/Studio.java b/mmstudio/src/main/java/org/micromanager/Studio.java index 6d98b44c8e..044857d86b 100644 --- a/mmstudio/src/main/java/org/micromanager/Studio.java +++ b/mmstudio/src/main/java/org/micromanager/Studio.java @@ -43,7 +43,7 @@ public interface Studio { * implicit, temporary image storage datastore. * @return An implementation of the Album API. */ - public Album album(); + Album album(); /** * Provides access to and control of the contents of the Album, the @@ -51,42 +51,42 @@ public interface Studio { * in name. * @return An implementation of the Album API. */ - public Album getAlbum(); + Album getAlbum(); /** * Provides access to the compatibility layer that exposes some old 1.4 * API methods. * @return An implementation of the compatibility API. */ - public CompatibilityInterface compat(); + CompatibilityInterface compat(); /** * Provides access to the compatibility layer that exposes some old 1.4 * API methods. Identical to compat() in all but name. * @return An implementation of the compatibility API. */ - public CompatibilityInterface getCompatibilityInterface(); + CompatibilityInterface getCompatibilityInterface(); /** * Provides access to Micro-Manager's logging functions, like logError(), * showMessage(), etc. * @return Access to Micro-Manager's logging interface. */ - public LogManager logs(); + LogManager logs(); /** * Provides access to Micro-Manager's logging functions, like logError(), * showMessage(), etc. Identical to logs() except in name. * @return Access to Micro-Manager's logging interface. */ - public LogManager getLogManager(); + LogManager getLogManager(); /** * Provide access to the AcquisitionManager, for running data acquisition * using the Micro-Manager acquisition engine. * @return AcquisitionManager */ - public AcquisitionManager acquisitions(); + AcquisitionManager acquisitions(); /** * Provide access to the AcquisitionManager, for running data acquisition @@ -94,14 +94,14 @@ public interface Studio { * except in name. * @return AcquisitionManager */ - public AcquisitionManager getAcquisitionManager(); + AcquisitionManager getAcquisitionManager(); /** * Provide access to the AlertManager, for creating low-profile, non- * interrupting alerts in the user interface. * @return AlertManager */ - public AlertManager alerts(); + AlertManager alerts(); /** * Provide access to the AlertManager, for creating low-profile, non- @@ -109,62 +109,62 @@ public interface Studio { * in name. * @return AlertManager */ - public AlertManager getAlertManager(); + AlertManager getAlertManager(); /** * Provide access to the AutofocusManager, for performing autofocus * operations. * @return AutofocusManager */ - public AutofocusManager getAutofocusManager(); + AutofocusManager getAutofocusManager(); /** * Provides access to the Core and its functionality. * @return Micro-Manager core object. */ - public CMMCore core(); + CMMCore core(); /** * Provides access to the Core and its functionality. Identical to core() * except in name. * @return Micro-Manager core object. */ - public CMMCore getCMMCore(); + CMMCore getCMMCore(); /** * Provide access to the DataManager instance for accessing Micro-Manager * data constructs. * @return DataManager instance */ - public DataManager data(); + DataManager data(); /** * Provide access to the DataManager instance for accessing Micro-Manager * data constructs. Identical to data() except in name. * @return DataManager instance */ - public DataManager getDataManager(); + DataManager getDataManager(); /** * Provides access to the DisplayManager instance for accessing * Micro-Manager display constructs. * @return DisplayManager instance */ - public DisplayManager displays(); + DisplayManager displays(); /** * Provides access to the DisplayManager instance for accessing * Micro-Manager display constructs. Identical to displays() except in name. * @return DisplayManager instance */ - public DisplayManager getDisplayManager(); + DisplayManager getDisplayManager(); /** * Provides access to the EventManager instance for subscribing to and * posting events on the application-wide EventBus. * @return EventManager instance */ - public EventManager events(); + EventManager events(); /** * Provides access to the EventManager instance for subscribing to and @@ -172,114 +172,128 @@ public interface Studio { * except in name. * @return EventManager instance */ - public EventManager getEventManager(); + EventManager getEventManager(); /** * Provides access to some utility methods for use in the Beanshell * scripting panel. * @return ScriptController instance. */ - public ScriptController scripter(); + ScriptController scripter(); /** * Provides access to some utility methods for use in the Beanshell * scripting panel. Identical to scripter() except in name. * @return ScriptController instance. */ - public ScriptController getScriptController(); + ScriptController getScriptController(); /** * Provides access to the Snap/Live display and associated logic. * @return SnapLiveManager instance. */ - public SnapLiveManager live(); + SnapLiveManager live(); /** * Provides access to the Snap/Live display and associated logic. Identical * to live() except in name. * @return SnapLiveManager instance. */ - public SnapLiveManager getSnapLiveManager(); + SnapLiveManager getSnapLiveManager(); /** * Provides access to the UserProfile instance for accessing per-user * profiles. * @return UserProfile instance */ - public UserProfile profile(); + UserProfile profile(); /** * Provides access to the UserProfile instance for accessing per-user * profiles. Identical to profile() except in name. * @return UserProfile instance */ - public UserProfile getUserProfile(); + UserProfile getUserProfile(); /** * Provides access to the PluginManager for accessing plugin instances. * @return PluginManager instance. */ - public PluginManager plugins(); + PluginManager plugins(); /** * Provides access to the PluginManager for accessing plugin instances. * Identical to plugins() except in name. * @return PluginManager instance. */ - public PluginManager getPluginManager(); + PluginManager getPluginManager(); /** * Provides access to the PositionListManager for interacting with the * Stage Position List. * @return PositionListManager instance. */ - public PositionListManager positions(); + PositionListManager positions(); /** * Provides access to the PositionListManager for interacting with the * Stage Position List. Identical to positions() except in name. * @return PositionListManager instance. */ - public PositionListManager getPositionListManager(); + PositionListManager getPositionListManager(); /** * Provides access to the QuickAccessManager for accessing the Quick-Access * Panel system. * @return QuickAccessManager instance. */ - public QuickAccessManager quickAccess(); + QuickAccessManager quickAccess(); /** * Provides access to the QuickAccessManager for accessing the Quick-Access * Panel system. Identical to quickAccess() except in name. * @return QuickAccessManager instance. */ - public QuickAccessManager getQuickAccessManager(); + QuickAccessManager getQuickAccessManager(); /** * Provides access to the ShutterManager for controlling the shutter state. * @return ShutterManager instance. */ - public ShutterManager shutter(); + ShutterManager shutter(); /** * Provides access to the ShutterManager for controlling the shutter state. * Identical to shutter() except in name. * @return ShutterManager instance. */ - public ShutterManager getShutterManager(); + ShutterManager getShutterManager(); /** * Provides access to the application API for controlling and updating the * GUI. * @return Application instance. */ - public Application app(); + Application app(); /** * Provides access to the application API for controlling and updating the * GUI. Identical to app() except in name. * @return Application instance. */ - public Application getApplication(); + Application getApplication(); + + /** + * Provides access to the PropertyManagerAPI. Provides access to the + * PropertyMap.Builder + * @return PropertyManager instance + */ + PropertyManager properties(); + + /** + * Provides access to the PropertyManagerAPI. Provides access to the + * PropertyMap.Builder + * @return PropertyManager instance + */ + PropertyManager getPropertyManager(); } diff --git a/mmstudio/src/main/java/org/micromanager/UserProfile.java b/mmstudio/src/main/java/org/micromanager/UserProfile.java index 775207619f..3466bab332 100644 --- a/mmstudio/src/main/java/org/micromanager/UserProfile.java +++ b/mmstudio/src/main/java/org/micromanager/UserProfile.java @@ -46,7 +46,7 @@ public interface UserProfile { * Return the name of this profile as displayed to the user * @return the profile name */ - public String getProfileName(); + String getProfileName(); /** * Get an interface to save and retrieve settings. @@ -56,76 +56,76 @@ public interface UserProfile { * @param owner the class that "owns" the settings * @return an object allowing settings to be set and retrieved */ - public MutablePropertyMapView getSettings(Class owner); + MutablePropertyMapView getSettings(Class owner); /** * Reset this user profile, deleting all settings. *

* Do not confuse with {@code getSettings(owner).clear()}! */ - public void clearSettingsForAllClasses(); + void clearSettingsForAllClasses(); // Old methods with weird types /** @deprecated use {@code getSettings(c).getString(key, fallback)} instead */ @Deprecated - public String getString(Class c, String key, String fallback); + String getString(Class c, String key, String fallback); /** @deprecated use {@code getSettings(c).getStringList(key, fallback)} instead */ @Deprecated - public String[] getStringArray(Class c, String key, String[] fallback); + String[] getStringArray(Class c, String key, String[] fallback); /** @deprecated use {@code getSettings(c).putString(key, value)} instead */ @Deprecated - public void setString(Class c, String key, String value); + void setString(Class c, String key, String value); /** @deprecated use {@code getSettings(c).putStringList(key, value)} instead */ @Deprecated - public void setStringArray(Class c, String key, String[] value); + void setStringArray(Class c, String key, String[] value); /** @deprecated use {@code getSettings(c).getInteger(key, fallback)} instead */ @Deprecated - public Integer getInt(Class c, String key, Integer fallback); + Integer getInt(Class c, String key, Integer fallback); /** @deprecated use {@code getSettings(c).getIntegerList(key, fallback)} instead */ @Deprecated - public Integer[] getIntArray(Class c, String key, Integer[] fallback); + Integer[] getIntArray(Class c, String key, Integer[] fallback); /** @deprecated use {@code getSettings(c).putInteger(key, value)} instead */ @Deprecated - public void setInt(Class c, String key, Integer value); + void setInt(Class c, String key, Integer value); /** @deprecated use {@code getSettings(c).putIntegerList(key, value)} instead */ @Deprecated - public void setIntArray(Class c, String key, Integer[] value); + void setIntArray(Class c, String key, Integer[] value); /** @deprecated use {@code getSettings(c).getLong(key, fallback)} instead */ @Deprecated - public Long getLong(Class c, String key, Long fallback); + Long getLong(Class c, String key, Long fallback); /** @deprecated use {@code getSettings(c).getLongList(key, fallback)} instead */ @Deprecated - public Long[] getLongArray(Class c, String key, Long[] fallback); + Long[] getLongArray(Class c, String key, Long[] fallback); /** @deprecated use {@code getSettings(c).putLong(key, value)} instead */ @Deprecated - public void setLong(Class c, String key, Long value); + void setLong(Class c, String key, Long value); /** @deprecated use {@code getSettings(c).putLongList(key, value)} instead */ @Deprecated - public void setLongArray(Class c, String key, Long[] value); + void setLongArray(Class c, String key, Long[] value); /** @deprecated use {@code getSettings(c).getDouble(key, fallback)} instead */ @Deprecated - public Double getDouble(Class c, String key, Double fallback); + Double getDouble(Class c, String key, Double fallback); /** @deprecated use {@code getSettings(c).getDoubleList(key, fallback)} instead */ @Deprecated - public Double[] getDoubleArray(Class c, String key, Double[] fallback); + Double[] getDoubleArray(Class c, String key, Double[] fallback); /** @deprecated use {@code getSettings(c).putDouble(key, value)} instead */ @Deprecated - public void setDouble(Class c, String key, Double value); + void setDouble(Class c, String key, Double value); /** @deprecated use {@code getSettings(c).putDoubleList(key, value)} instead */ @Deprecated - public void setDoubleArray(Class c, String key, Double[] value); + void setDoubleArray(Class c, String key, Double[] value); /** @deprecated use {@code getSettings(c).getBoolean(key, fallback)} instead */ @Deprecated - public Boolean getBoolean(Class c, String key, Boolean fallback); + Boolean getBoolean(Class c, String key, Boolean fallback); /** @deprecated use {@code getSettings(c).getBooleanList(key, fallback)} instead */ @Deprecated - public Boolean[] getBooleanArray(Class c, String key, Boolean[] fallback); + Boolean[] getBooleanArray(Class c, String key, Boolean[] fallback); /** @deprecated use {@code getSettings(c).putBoolean(key, value)} instead */ @Deprecated - public void setBoolean(Class c, String key, Boolean value); + void setBoolean(Class c, String key, Boolean value); /** @deprecated use {@code getSettings(c).putBooleanList(key, value)} instead */ @Deprecated - public void setBooleanArray(Class c, String key, Boolean[] value); + void setBooleanArray(Class c, String key, Boolean[] value); } \ No newline at end of file diff --git a/mmstudio/src/main/java/org/micromanager/acquisition/AcquisitionManager.java b/mmstudio/src/main/java/org/micromanager/acquisition/AcquisitionManager.java index 1125d0b919..d68e220b3c 100644 --- a/mmstudio/src/main/java/org/micromanager/acquisition/AcquisitionManager.java +++ b/mmstudio/src/main/java/org/micromanager/acquisition/AcquisitionManager.java @@ -40,13 +40,13 @@ public interface AcquisitionManager { * Provides an empty Sequence Settings Builder * */ - SequenceSettings.Builder getSequenceSettingsBuilder(); + SequenceSettings.Builder sequenceSettingsBuilder(); /** * Provides and empty ChannelSpec Builder * */ - ChannelSpec.Builder getChannelSpecBuilder(); + ChannelSpec.Builder channelSpecBuilder(); /** * Executes Acquisition with settings as in the MDA dialog. diff --git a/mmstudio/src/main/java/org/micromanager/acquisition/SequenceSettings.java b/mmstudio/src/main/java/org/micromanager/acquisition/SequenceSettings.java index 31cd498acb..ef622e9fc8 100644 --- a/mmstudio/src/main/java/org/micromanager/acquisition/SequenceSettings.java +++ b/mmstudio/src/main/java/org/micromanager/acquisition/SequenceSettings.java @@ -383,6 +383,7 @@ public SequenceSettings copy() { * Default constructor needed since we have a copy constructor * @deprecated use Builder instead */ + @Deprecated private SequenceSettings() { } @@ -414,7 +415,7 @@ private SequenceSettings() { /** * Time intervals between the starts of time points in milliseconds */ - public ArrayList customIntervalsMs() { return customIntervalsMs; }; + public ArrayList customIntervalsMs() { return customIntervalsMs; } /** * LIst with channel definitions to be used in the acquisition * @return LIst with channel definitions to be used in the acquisition diff --git a/mmstudio/src/main/java/org/micromanager/acquisition/internal/DefaultAcquisitionManager.java b/mmstudio/src/main/java/org/micromanager/acquisition/internal/DefaultAcquisitionManager.java index 5f8dea5f4d..ca73ca8d9b 100644 --- a/mmstudio/src/main/java/org/micromanager/acquisition/internal/DefaultAcquisitionManager.java +++ b/mmstudio/src/main/java/org/micromanager/acquisition/internal/DefaultAcquisitionManager.java @@ -70,12 +70,12 @@ public DefaultAcquisitionManager(Studio studio, } @Override - public SequenceSettings.Builder getSequenceSettingsBuilder() { + public SequenceSettings.Builder sequenceSettingsBuilder() { return new SequenceSettings.Builder(); } @Override - public ChannelSpec.Builder getChannelSpecBuilder() { + public ChannelSpec.Builder channelSpecBuilder() { return new ChannelSpec.Builder(); } @@ -183,17 +183,10 @@ public SequenceSettings loadSequenceSettings(String path) throws IOException { @Override public void saveSequenceSettings(SequenceSettings settings, String path) throws IOException { File file = new File(path); - FileWriter writer = null; - try { - writer = new FileWriter(file); + try (FileWriter writer = new FileWriter(file)) { writer.write(SequenceSettings.toJSONStream(settings)); writer.close(); } - finally { - if (writer != null) { - writer.close(); - } - } } @Override @@ -251,7 +244,7 @@ public List snap() throws Exception { throw new RuntimeException("No camera configured."); } core.snapImage(); - ArrayList result = new ArrayList(); + ArrayList result = new ArrayList<>(); for (int c = 0; c < core.getNumberOfCameraChannels(); ++c) { TaggedImage tagged = core.getTaggedImage(c); Image temp = new DefaultImage(tagged); diff --git a/mmstudio/src/main/java/org/micromanager/alerts/Alert.java b/mmstudio/src/main/java/org/micromanager/alerts/Alert.java index ebbddcd06f..5ff316bb23 100644 --- a/mmstudio/src/main/java/org/micromanager/alerts/Alert.java +++ b/mmstudio/src/main/java/org/micromanager/alerts/Alert.java @@ -32,10 +32,10 @@ public interface Alert { * been dismissed (either via their dismiss() method or by the user * closing them) are no longer usable. */ - public boolean isUsable(); + boolean isUsable(); /** * Dismiss the Alert, causing it to no longer be visible to the user. */ - public void dismiss(); + void dismiss(); } diff --git a/mmstudio/src/main/java/org/micromanager/alerts/AlertManager.java b/mmstudio/src/main/java/org/micromanager/alerts/AlertManager.java index 332f13ab84..59db97abb6 100644 --- a/mmstudio/src/main/java/org/micromanager/alerts/AlertManager.java +++ b/mmstudio/src/main/java/org/micromanager/alerts/AlertManager.java @@ -49,7 +49,7 @@ public interface AlertManager { * @return Either a newly-created Alert, or the Alert that already existed, * to which this new alert text was added. */ - public Alert postAlert(String title, Class group, String text); + Alert postAlert(String title, Class group, String text); /** * Create a UpdatableAlert. UpdatableAlerts can have their contents changed @@ -61,7 +61,7 @@ public interface AlertManager { * @param text Initial text to display to the user. * @return Newly-created UpdatableAlert */ - public UpdatableAlert postUpdatableAlert(String title, String text); + UpdatableAlert postUpdatableAlert(String title, String text); /** * Create an alert containing the provided special contents. If there is @@ -79,5 +79,5 @@ public interface AlertManager { * @param contents Contents to be inserted into the alert dialog. * @return Newly-created Alert */ - public UpdatableAlert postCustomAlert(String title, JComponent contents); + UpdatableAlert postCustomAlert(String title, JComponent contents); } diff --git a/mmstudio/src/main/java/org/micromanager/alerts/UpdatableAlert.java b/mmstudio/src/main/java/org/micromanager/alerts/UpdatableAlert.java index 05ad156478..d51ed704ea 100644 --- a/mmstudio/src/main/java/org/micromanager/alerts/UpdatableAlert.java +++ b/mmstudio/src/main/java/org/micromanager/alerts/UpdatableAlert.java @@ -41,11 +41,11 @@ public interface UpdatableAlert extends Alert { * directly. * @param text New text of alert. */ - public void setText(String text); + void setText(String text); /** * Returns the current text of the alert. * @return Current text of the alert. */ - public String getText(); + String getText(); } diff --git a/mmstudio/src/main/java/org/micromanager/data/DataManager.java b/mmstudio/src/main/java/org/micromanager/data/DataManager.java index 951b44a3c1..633e2fe7f8 100644 --- a/mmstudio/src/main/java/org/micromanager/data/DataManager.java +++ b/mmstudio/src/main/java/org/micromanager/data/DataManager.java @@ -22,25 +22,38 @@ import java.awt.Component; import java.awt.Window; +import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; import java.util.List; import mmcorej.TaggedImage; import mmcorej.org.json.JSONException; import org.micromanager.PropertyMap; +import org.micromanager.PropertyMaps; /** * This class provides general utility functions for working with * Micro-Manager data. You can access it via ScriptInterface's data() method - * (for example, "mm.data().getCoordsBuilder()"). + * (for example, "mm.data().cordsBuilder()"). */ public interface DataManager { + + /** + * Generate a "blank" CoordsBuilder for use in constructing new Coords + * instances. + * + * @return a CoordsBuilder used to construct new Coords instances. + */ + Coords.Builder coordsBuilder(); + /** * Generate a "blank" CoordsBuilder for use in constructing new Coords * instances. * * @return a CoordsBuilder used to construct new Coords instances. + * @deprecated Use {@link #coordsBuilder()} instead */ + @Deprecated Coords.Builder getCoordsBuilder(); /** @@ -57,6 +70,7 @@ public interface DataManager { * underscores. For example, "filter2_pos" is a valid axis, but * "1filter-pos" is not, because it starts with a number, and because it * contains a "-" which is not a legal character. + * * @param def Normalized coordinate definition string. * @return Coords generated based on the definition string. * @throws IllegalArgumentException if the definition string is @@ -321,17 +335,36 @@ Image convertTaggedImage(TaggedImage tagged, Coords coords, * Generate a "blank" MetadataBuilder for use in constructing new * Metadata instances. * @return a MetadataBuilder for creating new Metadata instances. + * @deprecated Use {@link #metadataBuilder()} instead */ + @Deprecated Metadata.Builder getMetadataBuilder(); + /** + * Generate a "blank" MetadataBuilder for use in constructing new + * Metadata instances. + * @return a MetadataBuilder for creating new Metadata instances. + */ + Metadata.Builder metadataBuilder(); + /** * Generate a "blank" SummaryMetadataBuilder for use in constructing new * SummaryMetadata instances. * @return a SummaryMetadataBuilder for creating new SummaryMetadata * instances. + * @deprecated Use {@link #summaryMetadataBuilder()} instead */ + @Deprecated SummaryMetadata.Builder getSummaryMetadataBuilder(); + /** + * Generate a "blank" SummaryMetadataBuilder for use in constructing new + * SummaryMetadata instances. + * @return a SummaryMetadataBuilder for creating new SummaryMetadata + * instances. + */ + SummaryMetadata.Builder summaryMetadataBuilder(); + /** * Generate a "blank" PropertyMap.Builder with all null values. * @return a PropertyMapBuilder for creating new PropertyMap instances. @@ -346,7 +379,7 @@ Image convertTaggedImage(TaggedImage tagged, Coords coords, * @return new PropertyMap based on data in the specified file. * @throws FileNotFoundException if the path does not point to a file. * @throws IOException if there was an error reading the file. - * @deprecated + * @deprecated use {@link PropertyMaps#loadJSON(File)} instead */ @Deprecated PropertyMap loadPropertyMap(String path) throws FileNotFoundException, IOException; diff --git a/mmstudio/src/main/java/org/micromanager/data/Datastore.java b/mmstudio/src/main/java/org/micromanager/data/Datastore.java index f29ced6db4..0eee92211a 100644 --- a/mmstudio/src/main/java/org/micromanager/data/Datastore.java +++ b/mmstudio/src/main/java/org/micromanager/data/Datastore.java @@ -42,7 +42,7 @@ public interface Datastore extends DataProvider { * bus. * * @param image Micro-Manager Image object - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurs * @throws DatastoreFrozenException if the freeze() method has been called. * @throws DatastoreRewriteException if an Image with the same coordinates * already exists in the Datastore. @@ -58,7 +58,7 @@ public interface Datastore extends DataProvider { * bus. This method may only be called once for a given Datastore. * * @param metadata Object representing the summary metadata - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurs * @throws DatastoreFrozenException if the freeze() method has been called. * @throws DatastoreRewriteException if the Datastore already has * SummaryMetadata. @@ -70,22 +70,22 @@ public interface Datastore extends DataProvider { * * @param tag the tag for the annotation * @return true if the annotation exists; false otherwise - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurs */ boolean hasAnnotation(String tag) throws IOException; /** * Get an annotation, creating it if it doesn't exist - * @param tag - * @return - * @throws java.io.IOException + * @param tag tag for the annotation + * @return Annotation for th given tag + * @throws java.io.IOException if an IO error occurs */ Annotation getAnnotation(String tag) throws IOException; /** * Freeze this Datastore so it cannot be further modified. * - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurs */ void freeze() throws IOException; @@ -122,7 +122,8 @@ enum SaveMode { * @param parent Window on top of which to display the dialog prompt; * may be null. * @return true if data was saved; false if user canceled - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurs + * @deprecated Use {@link #save(Component, boolean)} instead */ @Deprecated boolean save(Component parent) throws IOException; @@ -136,7 +137,7 @@ enum SaveMode { * @param blocking if true will return after saving, otherwise will return quickly * and continue saving on another thread * @return Path chosen by user to save the data, null if dialog was canceled - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurs */ String save(Component parent, boolean blocking) throws IOException; @@ -148,7 +149,7 @@ enum SaveMode { * @param mode File format to save to * @param path File path used to save the data * - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurs */ void save(SaveMode mode, String path) throws IOException; @@ -159,13 +160,13 @@ enum SaveMode { * @param path File path used to save the data * @param blocking when true, will block while saving data, otherwise will return * immediately - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurs */ void save(SaveMode mode, String path, boolean blocking) throws IOException; /** * Sets the name of the Datastore. Posts a DatastoreNewNameEvent - * @param name + * @param name new name of the Datastore */ void setName(String name); } \ No newline at end of file diff --git a/mmstudio/src/main/java/org/micromanager/data/RewritableDatastore.java b/mmstudio/src/main/java/org/micromanager/data/RewritableDatastore.java index 00f841940c..cfb1a4e6d2 100644 --- a/mmstudio/src/main/java/org/micromanager/data/RewritableDatastore.java +++ b/mmstudio/src/main/java/org/micromanager/data/RewritableDatastore.java @@ -67,7 +67,7 @@ void setSummaryMetadata(SummaryMetadata metadata) * event bus. Throws an IllegalArgumentException if the provided coordinates * do not correspond to any image in the Datastore. * @param coords Coordinates of the image to remove. - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurred. * @throws IllegalArgumentException if the coords do not match any image. */ void deleteImage(Coords coords) throws IOException; @@ -84,7 +84,7 @@ void setSummaryMetadata(SummaryMetadata metadata) * This method may potentially remove no images. * @param coords Potentially-underspecified coordinates of the image(s) to * remove. - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurred. */ void deleteImagesMatching(Coords coords) throws IOException; @@ -92,7 +92,7 @@ void setSummaryMetadata(SummaryMetadata metadata) * Delete all images from the Datastore. An ImageDeletedEvent will be * published on the Datastore's event bus for each image, as will a * DatastoreClearedEvent. - * @throws java.io.IOException + * @throws java.io.IOException if an IO error occurred. */ void deleteAllImages() throws IOException; } diff --git a/mmstudio/src/main/java/org/micromanager/data/internal/DefaultDataManager.java b/mmstudio/src/main/java/org/micromanager/data/internal/DefaultDataManager.java index c03d5756a4..6aabaeaea7 100644 --- a/mmstudio/src/main/java/org/micromanager/data/internal/DefaultDataManager.java +++ b/mmstudio/src/main/java/org/micromanager/data/internal/DefaultDataManager.java @@ -20,14 +20,6 @@ package org.micromanager.data.internal; -import java.awt.Component; -import java.awt.Window; -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.List; -import javax.swing.JOptionPane; -import javax.swing.ProgressMonitor; import mmcorej.TaggedImage; import mmcorej.org.json.JSONException; import org.micromanager.PropertyMap; @@ -38,7 +30,6 @@ import org.micromanager.data.Image; import org.micromanager.data.ImageJConverter; import org.micromanager.data.Metadata; -import org.micromanager.data.NewPipelineEvent; import org.micromanager.data.Pipeline; import org.micromanager.data.Processor; import org.micromanager.data.ProcessorConfigurator; @@ -55,6 +46,15 @@ import org.micromanager.internal.utils.JavaUtils; import org.micromanager.internal.utils.ReportingUtils; +import javax.swing.JOptionPane; +import javax.swing.ProgressMonitor; +import java.awt.Component; +import java.awt.Window; +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; + /** * This implementation of the DataManager interface provides general utility * access to Micro-Manager's data objects. @@ -72,10 +72,15 @@ public DefaultDataManager(MMStudio studio) { ijConverter_ = new DefaultImageJConverter(studio); } + @Override + public Coords.Builder coordsBuilder() { + return new DefaultCoords.Builder(); + } + @Override @Deprecated public Coords.Builder getCoordsBuilder() { - return new DefaultCoords.Builder(); + return coordsBuilder(); } @Override @@ -305,12 +310,24 @@ public Image convertTaggedImage(TaggedImage tagged, Coords coords, } @Override + @Deprecated public Metadata.Builder getMetadataBuilder() { + return metadataBuilder(); + } + + @Override + public Metadata.Builder metadataBuilder() { return new DefaultMetadata.Builder(); } @Override + @Deprecated public SummaryMetadata.Builder getSummaryMetadataBuilder() { + return summaryMetadataBuilder(); + } + + @Override + public SummaryMetadata.Builder summaryMetadataBuilder() { return new DefaultSummaryMetadata.Builder(); } diff --git a/mmstudio/src/main/java/org/micromanager/display/ChannelDisplaySettings.java b/mmstudio/src/main/java/org/micromanager/display/ChannelDisplaySettings.java index efc2cad532..9bbaa1d437 100644 --- a/mmstudio/src/main/java/org/micromanager/display/ChannelDisplaySettings.java +++ b/mmstudio/src/main/java/org/micromanager/display/ChannelDisplaySettings.java @@ -12,7 +12,7 @@ * @author mark */ public interface ChannelDisplaySettings { - public interface Builder { + interface Builder { Builder color(Color color); Builder colorWhite(); Builder colorColorBlindFriendly(int number); diff --git a/mmstudio/src/main/java/org/micromanager/internal/DefaultPropertyManager.java b/mmstudio/src/main/java/org/micromanager/internal/DefaultPropertyManager.java new file mode 100644 index 0000000000..d0b1a96219 --- /dev/null +++ b/mmstudio/src/main/java/org/micromanager/internal/DefaultPropertyManager.java @@ -0,0 +1,63 @@ +package org.micromanager.internal; + +import org.micromanager.PropertyManager; +import org.micromanager.PropertyMap; +import org.micromanager.PropertyMaps; +import org.micromanager.internal.propertymap.DefaultPropertyMap; + +import java.io.File; +import java.io.IOException; + + +public class DefaultPropertyManager implements PropertyManager { + /** + * Provides an easy way for a script to obtain a PropertyMap Builder + * + * @return PropertyMap Builder + */ + @Override + public PropertyMap.Builder propertyMapBuilder() { + return DefaultPropertyMap.builder(); + } + + /** + * Returns an empty property map. + * + * @return empty property map + */ + @Override + public PropertyMap emptyPropertyMap() { + return PropertyMaps.emptyPropertyMap(); + } + + /** + * Creates a property map from its JSON-serialized form. + * JSON format is described in {@link org.micromanager.internal.propertymap.PropertyMapJSONSerializer} + * @param json json formatted String to be converted into a PropertyMap + * @return PropertyMap result from conversion + * @throws IOException if {@code json} is invalid JSON or if it does not + * represent a valid property map + */ + @Override + public PropertyMap fromJSON(String json) throws IOException { + return PropertyMaps.fromJSON(json); + } + + /** + * Create a property map from its JSON-serialized form stored in a file. + * + * JSON format is described in {@link org.micromanager.internal.propertymap.PropertyMapJSONSerializer} + * @param file File containing JSON serialized Properties. + * @return PropertyMap resulting from conversion fo JSON in file. + * @throws IOException if there was a problem reading {@code file} or if the + * file contained invalid JSON or if the JSON did not represent a valid + * property map + * @throws java.io.FileNotFoundException this subclass of {@code IOException} + * is thrown if {@code file} does not exist + */ + @Override + public PropertyMap loadJSON(File file) throws IOException { + return PropertyMaps.loadJSON(file); + } + +} \ No newline at end of file diff --git a/mmstudio/src/main/java/org/micromanager/internal/MMStudio.java b/mmstudio/src/main/java/org/micromanager/internal/MMStudio.java index b70a607193..fd795e3278 100644 --- a/mmstudio/src/main/java/org/micromanager/internal/MMStudio.java +++ b/mmstudio/src/main/java/org/micromanager/internal/MMStudio.java @@ -33,6 +33,7 @@ import org.micromanager.LogManager; import org.micromanager.PluginManager; import org.micromanager.PositionListManager; +import org.micromanager.PropertyManager; import org.micromanager.ScriptController; import org.micromanager.ShutterManager; import org.micromanager.Studio; @@ -135,6 +136,7 @@ public final class MMStudio implements Studio { private UiMovesStageManager uiMovesStageManager_; private DefaultApplication defaultApplication_; private DefaultCompatibilityInterface compatibility_; + private PropertyManager propertyManager_; // Local Classes private final MMSettings settings_ = new MMSettings(); @@ -296,6 +298,8 @@ public MMStudio(boolean startAsImageJPlugin, String profileNameAutoStart) { posListManager_ = new DefaultPositionListManager(this); acqEngine_.setPositionList(posListManager_.getPositionList()); + propertyManager_ = new DefaultPropertyManager(); + initializeLogging(core_); // Tell Core to start logging events().registerForEvents(this); // We need to be subscribed to the global event bus for plugin loading @@ -1089,6 +1093,18 @@ public AlertManager getAlertManager() { return alerts(); } + @Override + public PropertyManager getPropertyManager() { + return propertyManager_; + } + + @Override + public PropertyManager properties() { + return propertyManager_; + } + + + public UiMovesStageManager getUiMovesStageManager () { return uiMovesStageManager_; } diff --git a/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/AcquisitionPanel.java b/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/AcquisitionPanel.java index 44105e10b0..e38dfe85fd 100644 --- a/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/AcquisitionPanel.java +++ b/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/AcquisitionPanel.java @@ -2463,7 +2463,7 @@ private boolean runAcquisitionPrivate(boolean testAcq, Devices.Sides testAcqSide if (acqNum > 0) { name += "_" + acqNum; } - SummaryMetadata.Builder smb = gui_.data().getSummaryMetadataBuilder(); + SummaryMetadata.Builder smb = gui_.data().summaryMetadataBuilder(); smb = smb.channelNames(channelNames_). channelGroup(multiChannelPanel_.getChannelGroup()). zStepUm((double) acqSettings.stepSizeUm). @@ -3166,7 +3166,7 @@ private void setRootDirectory(JTextField rootField) { * @param position - position at which to insert image * @param ms - Time stamp to be added to the image metadata * @param taggedImg - image + metadata to be added - * @throws org.json.JSONException + * @throws mmcorej.org.json.JSONException * @throws org.micromanager.data.DatastoreFrozenException * @throws org.micromanager.data.DatastoreRewriteException */ diff --git a/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/utils/AutofocusUtils.java b/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/utils/AutofocusUtils.java index 43de27e2ef..63812f4fc4 100644 --- a/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/utils/AutofocusUtils.java +++ b/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/utils/AutofocusUtils.java @@ -346,7 +346,7 @@ protected FocusResult doInBackground() throws Exception { DisplaySettings.Builder dsb = ourWindow_.getDisplaySettings().copyBuilder(); ourWindow_.setDisplaySettings(dsb.colorModeGrayscale(). build()); - SummaryMetadata.Builder smb = gui_.data().getSummaryMetadataBuilder(); + SummaryMetadata.Builder smb = gui_.data().summaryMetadataBuilder(); Coords dim = Coordinates.builder().z(nrImages). channel(1).stagePosition(1).t(1).build(); store.setSummaryMetadata(smb.intendedDimensions(dim).build()); diff --git a/plugins/ImageFlipper/src/main/java/org/micromanager/imageflipper/FlipperConfigurator.java b/plugins/ImageFlipper/src/main/java/org/micromanager/imageflipper/FlipperConfigurator.java index 945baa5009..b9be5c5494 100644 --- a/plugins/ImageFlipper/src/main/java/org/micromanager/imageflipper/FlipperConfigurator.java +++ b/plugins/ImageFlipper/src/main/java/org/micromanager/imageflipper/FlipperConfigurator.java @@ -297,7 +297,7 @@ private void processExample() { Image testImage = studio_.data().ij().createImage(proc, Coordinates.builder().build(), - studio_.data().getMetadataBuilder().build()); + studio_.data().metadataBuilder().build()); testImage = FlipperProcessor.transformImage(studio_, testImage, getMirror(), getRotate()); exampleImageTarget_.setIcon( diff --git a/plugins/PTCTools/src/main/java/org/micromanager/ptctools/PtcToolsExecutor.java b/plugins/PTCTools/src/main/java/org/micromanager/ptctools/PtcToolsExecutor.java index 4245bc478e..fc74e5f4e5 100644 --- a/plugins/PTCTools/src/main/java/org/micromanager/ptctools/PtcToolsExecutor.java +++ b/plugins/PTCTools/src/main/java/org/micromanager/ptctools/PtcToolsExecutor.java @@ -118,7 +118,7 @@ public void doSequence(JLabel resultLabel) { // temporary store to hold images while calculating mean and stdDev Datastore store = studio_.data().createRAMDatastore(); - final SummaryMetadata.Builder smb = studio_.data().getSummaryMetadataBuilder(); + final SummaryMetadata.Builder smb = studio_.data().summaryMetadataBuilder(); final Coords.Builder cb = Coordinates.builder(); Coords coords = cb.c(1).p(1). t(nrFrames).z(1).build();