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micro-manager · Jul 11, 2024 · 0f3aba8 · 0f3aba8
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diff --git a/deprecated-list.html b/deprecated-list.html
@@ -186,13 +186,13 @@ <h2 title="Contents">Contents</h2>
 </td>
 </tr>
 <tr class="altColor">
-<td class="colOne"><a href="org/micromanager/acquisition/ChannelSpec.html#channelGroup">org.micromanager.acquisition.ChannelSpec.channelGroup</a>
-<div class="block"><span class="deprecationComment">Use Builder and getters instead</span></div>
+<td class="colOne"><a href="org/micromanager/acquisition/SequenceSettings.html#channelGroup">org.micromanager.acquisition.SequenceSettings.channelGroup</a>
+<div class="block"><span class="deprecationComment">use Builder and channelGroup() instead</span></div>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colOne"><a href="org/micromanager/acquisition/SequenceSettings.html#channelGroup">org.micromanager.acquisition.SequenceSettings.channelGroup</a>
-<div class="block"><span class="deprecationComment">use Builder and channelGroup() instead</span></div>
+<td class="colOne"><a href="org/micromanager/acquisition/ChannelSpec.html#channelGroup">org.micromanager.acquisition.ChannelSpec.channelGroup</a>
+<div class="block"><span class="deprecationComment">Use Builder and getters instead</span></div>
 </td>
 </tr>
 <tr class="altColor">
@@ -407,11 +407,19 @@ <h2 title="Contents">Contents</h2>
 <td class="colOne"><a href="org/micromanager/PropertyMap.html#copy--">org.micromanager.PropertyMap.copy()</a></td>
 </tr>
 <tr class="altColor">
+<td class="colOne"><a href="org/micromanager/display/DisplaySettings.html#copy--">org.micromanager.display.DisplaySettings.copy()</a></td>
+</tr>
+<tr class="rowColor">
 <td class="colOne"><a href="org/micromanager/acquisition/SequenceSettings.html#copy--">org.micromanager.acquisition.SequenceSettings.copy()</a>
 <div class="block"><span class="deprecationComment">When used correctly, SequenceSettings are immutable.
      If you really need a copy, use copyBuilder().build();</span></div>
 </td>
 </tr>
+<tr class="altColor">
+<td class="colOne"><a href="org/micromanager/data/SummaryMetadata.html#copy--">org.micromanager.data.SummaryMetadata.copy()</a>
+<div class="block"><span class="deprecationComment">- Use SummaryMetadata.Builder.copyBuilder instead</span></div>
+</td>
+</tr>
 <tr class="rowColor">
 <td class="colOne"><a href="org/micromanager/data/Metadata.html#copy--">org.micromanager.data.Metadata.copy()</a>
 <div class="block"><span class="deprecationComment">Use the appropriate of the following:
@@ -426,14 +434,6 @@ <h2 title="Contents">Contents</h2>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colOne"><a href="org/micromanager/data/SummaryMetadata.html#copy--">org.micromanager.data.SummaryMetadata.copy()</a>
-<div class="block"><span class="deprecationComment">- Use SummaryMetadata.Builder.copyBuilder instead</span></div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colOne"><a href="org/micromanager/display/DisplaySettings.html#copy--">org.micromanager.display.DisplaySettings.copy()</a></td>
-</tr>
-<tr class="rowColor">
 <td class="colOne"><a href="org/micromanager/data/DataManager.html#createCoords-java.lang.String-">org.micromanager.data.DataManager.createCoords(String)</a>
 <div class="block"><span class="deprecationComment">use of Strings for Coords is discouraged</span></div>
 </td>
@@ -722,13 +722,13 @@ <h2 title="Contents">Contents</h2>
 <td class="colOne"><a href="org/micromanager/PropertyMap.html#getPropertyMap-java.lang.String-">org.micromanager.PropertyMap.getPropertyMap(String)</a></td>
 </tr>
 <tr class="altColor">
-<td class="colOne"><a href="org/micromanager/data/DataManager.html#getPropertyMapBuilder--">org.micromanager.data.DataManager.getPropertyMapBuilder()</a>
-<div class="block"><span class="deprecationComment">Use PropertyMaps.builder() instead</span></div>
+<td class="colOne"><a href="org/micromanager/display/DisplayManager.html#getPropertyMapBuilder--">org.micromanager.display.DisplayManager.getPropertyMapBuilder()</a>
+<div class="block"><span class="deprecationComment">Use <a href="org/micromanager/PropertyMaps.html#builder--"><code>PropertyMaps.builder()</code></a> instead</span></div>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colOne"><a href="org/micromanager/display/DisplayManager.html#getPropertyMapBuilder--">org.micromanager.display.DisplayManager.getPropertyMapBuilder()</a>
-<div class="block"><span class="deprecationComment">Use <a href="org/micromanager/PropertyMaps.html#builder--"><code>PropertyMaps.builder()</code></a> instead</span></div>
+<td class="colOne"><a href="org/micromanager/data/DataManager.html#getPropertyMapBuilder--">org.micromanager.data.DataManager.getPropertyMapBuilder()</a>
+<div class="block"><span class="deprecationComment">Use PropertyMaps.builder() instead</span></div>
 </td>
 </tr>
 <tr class="altColor">

diff --git a/org/micromanager/class-use/PropertyMap.html b/org/micromanager/class-use/PropertyMap.html
@@ -356,14 +356,14 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 </tr>
 <tr class="altColor">
 <td class="colFirst"><code><a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Metadata.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/Metadata.html#getUserData--">getUserData</a></span>()</code>
-<div class="block">Arbitrary additional metadata added by third-party code.</div>
+<td class="colLast"><span class="typeNameLabel">SummaryMetadata.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/SummaryMetadata.html#getUserData--">getUserData</a></span>()</code>
+<div class="block">Any general-purpose user meta data.</div>
 </td>
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code><a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
-<td class="colLast"><span class="typeNameLabel">SummaryMetadata.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/SummaryMetadata.html#getUserData--">getUserData</a></span>()</code>
-<div class="block">Any general-purpose user meta data.</div>
+<td class="colLast"><span class="typeNameLabel">Metadata.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/Metadata.html#getUserData--">getUserData</a></span>()</code>
+<div class="block">Arbitrary additional metadata added by third-party code.</div>
 </td>
 </tr>
 <tr class="altColor">
@@ -431,24 +431,24 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colFirst"><code><a href="../../../org/micromanager/data/Metadata.Builder.html" title="interface in org.micromanager.data">Metadata.Builder</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Metadata.Builder.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/Metadata.Builder.html#userData-org.micromanager.PropertyMap-">userData</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;userData)</code>
-<div class="block">Add user-defined data.</div>
-</td>
+<td class="colFirst"><code><a href="../../../org/micromanager/data/SummaryMetadata.Builder.html" title="interface in org.micromanager.data">SummaryMetadata.Builder</a></code></td>
+<td class="colLast"><span class="typeNameLabel">SummaryMetadata.Builder.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/SummaryMetadata.Builder.html#userData-org.micromanager.PropertyMap-">userData</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;userData)</code>&nbsp;</td>
 </tr>
 <tr class="altColor">
-<td class="colFirst"><code><a href="../../../org/micromanager/data/Metadata.MetadataBuilder.html" title="interface in org.micromanager.data">Metadata.MetadataBuilder</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Metadata.MetadataBuilder.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/Metadata.MetadataBuilder.html#userData-org.micromanager.PropertyMap-">userData</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;userData)</code>
+<td class="colFirst"><code><a href="../../../org/micromanager/data/SummaryMetadata.SummaryMetadataBuilder.html" title="interface in org.micromanager.data">SummaryMetadata.SummaryMetadataBuilder</a></code></td>
+<td class="colLast"><span class="typeNameLabel">SummaryMetadata.SummaryMetadataBuilder.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/SummaryMetadata.SummaryMetadataBuilder.html#userData-org.micromanager.PropertyMap-">userData</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;userData)</code>
 <div class="block"><span class="deprecatedLabel">Deprecated.</span>&nbsp;</div>
 &nbsp;</td>
 </tr>
 <tr class="rowColor">
-<td class="colFirst"><code><a href="../../../org/micromanager/data/SummaryMetadata.Builder.html" title="interface in org.micromanager.data">SummaryMetadata.Builder</a></code></td>
-<td class="colLast"><span class="typeNameLabel">SummaryMetadata.Builder.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/SummaryMetadata.Builder.html#userData-org.micromanager.PropertyMap-">userData</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;userData)</code>&nbsp;</td>
+<td class="colFirst"><code><a href="../../../org/micromanager/data/Metadata.Builder.html" title="interface in org.micromanager.data">Metadata.Builder</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Metadata.Builder.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/Metadata.Builder.html#userData-org.micromanager.PropertyMap-">userData</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;userData)</code>
+<div class="block">Add user-defined data.</div>
+</td>
 </tr>
 <tr class="altColor">
-<td class="colFirst"><code><a href="../../../org/micromanager/data/SummaryMetadata.SummaryMetadataBuilder.html" title="interface in org.micromanager.data">SummaryMetadata.SummaryMetadataBuilder</a></code></td>
-<td class="colLast"><span class="typeNameLabel">SummaryMetadata.SummaryMetadataBuilder.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/SummaryMetadata.SummaryMetadataBuilder.html#userData-org.micromanager.PropertyMap-">userData</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;userData)</code>
+<td class="colFirst"><code><a href="../../../org/micromanager/data/Metadata.MetadataBuilder.html" title="interface in org.micromanager.data">Metadata.MetadataBuilder</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Metadata.MetadataBuilder.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/data/Metadata.MetadataBuilder.html#userData-org.micromanager.PropertyMap-">userData</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;userData)</code>
 <div class="block"><span class="deprecatedLabel">Deprecated.</span>&nbsp;</div>
 &nbsp;</td>
 </tr>

diff --git a/org/micromanager/data/class-use/Coords.html b/org/micromanager/data/class-use/Coords.html
@@ -252,14 +252,14 @@ <h3>Uses of <a href="../../../../org/micromanager/data/Coords.html" title="inter
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">RewritableDatastore.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/RewritableDatastore.html#deleteImage-org.micromanager.data.Coords-">deleteImage</a></span>(<a href="../../../../org/micromanager/data/Coords.html" title="interface in org.micromanager.data">Coords</a>&nbsp;coords)</code>
-<div class="block">Delete an image from the Datastore.</div>
+<td class="colLast"><span class="typeNameLabel">RewritableStorage.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/RewritableStorage.html#deleteImage-org.micromanager.data.Coords-">deleteImage</a></span>(<a href="../../../../org/micromanager/data/Coords.html" title="interface in org.micromanager.data">Coords</a>&nbsp;coords)</code>
+<div class="block">Delete an image from the Storage.</div>
 </td>
 </tr>
 <tr class="altColor">
 <td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">RewritableStorage.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/RewritableStorage.html#deleteImage-org.micromanager.data.Coords-">deleteImage</a></span>(<a href="../../../../org/micromanager/data/Coords.html" title="interface in org.micromanager.data">Coords</a>&nbsp;coords)</code>
-<div class="block">Delete an image from the Storage.</div>
+<td class="colLast"><span class="typeNameLabel">RewritableDatastore.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/RewritableDatastore.html#deleteImage-org.micromanager.data.Coords-">deleteImage</a></span>(<a href="../../../../org/micromanager/data/Coords.html" title="interface in org.micromanager.data">Coords</a>&nbsp;coords)</code>
+<div class="block">Delete an image from the Datastore.</div>
 </td>
 </tr>
 <tr class="rowColor">
@@ -390,14 +390,14 @@ <h3>Uses of <a href="../../../../org/micromanager/data/Coords.html" title="inter
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code><a href="../../../../org/micromanager/data/Coords.html" title="interface in org.micromanager.data">Coords</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DataViewer.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/display/DataViewer.html#getDisplayPosition--">getDisplayPosition</a></span>()</code>
-<div class="block">Get the coordinates for the currently displayed images.</div>
+<td class="colLast"><span class="typeNameLabel">DisplayPositionChangedEvent.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/display/DisplayPositionChangedEvent.html#getDisplayPosition--">getDisplayPosition</a></span>()</code>
+<div class="block">returns the new display position.</div>
 </td>
 </tr>
 <tr class="altColor">
 <td class="colFirst"><code><a href="../../../../org/micromanager/data/Coords.html" title="interface in org.micromanager.data">Coords</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DisplayPositionChangedEvent.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/display/DisplayPositionChangedEvent.html#getDisplayPosition--">getDisplayPosition</a></span>()</code>
-<div class="block">returns the new display position.</div>
+<td class="colLast"><span class="typeNameLabel">DataViewer.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/display/DataViewer.html#getDisplayPosition--">getDisplayPosition</a></span>()</code>
+<div class="block">Get the coordinates for the currently displayed images.</div>
 </td>
 </tr>
 <tr class="rowColor">

diff --git a/org/micromanager/data/class-use/Datastore.html b/org/micromanager/data/class-use/Datastore.html
@@ -268,28 +268,28 @@ <h3>Uses of <a href="../../../../org/micromanager/data/Datastore.html" title="in
 </tr>
 <tr class="altColor">
 <td class="colFirst"><code><a href="../../../../org/micromanager/data/Datastore.html" title="interface in org.micromanager.data">Datastore</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Annotation.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/Annotation.html#getDatastore--">getDatastore</a></span>()</code>
-<div class="block">Return the datastore to which this annotation is associated.</div>
+<td class="colLast"><span class="typeNameLabel">ImageOverwrittenEvent.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/ImageOverwrittenEvent.html#getDatastore--">getDatastore</a></span>()</code>
+<div class="block">Provides the Datastore this image was added to; potentially useful for
+ code that listens to events from multiple Datastores.</div>
 </td>
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code><a href="../../../../org/micromanager/data/Datastore.html" title="interface in org.micromanager.data">Datastore</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ImageOverwrittenEvent.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/ImageOverwrittenEvent.html#getDatastore--">getDatastore</a></span>()</code>
+<td class="colLast"><span class="typeNameLabel">ImageDeletedEvent.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/ImageDeletedEvent.html#getDatastore--">getDatastore</a></span>()</code>
 <div class="block">Provides the Datastore this image was added to; potentially useful for
  code that listens to events from multiple Datastores.</div>
 </td>
 </tr>
 <tr class="altColor">
 <td class="colFirst"><code><a href="../../../../org/micromanager/data/Datastore.html" title="interface in org.micromanager.data">Datastore</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DatastoreClosingEvent.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/DatastoreClosingEvent.html#getDatastore--">getDatastore</a></span>()</code>
-<div class="block">Returns the Datastore that is closing.</div>
+<td class="colLast"><span class="typeNameLabel">Annotation.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/Annotation.html#getDatastore--">getDatastore</a></span>()</code>
+<div class="block">Return the datastore to which this annotation is associated.</div>
 </td>
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code><a href="../../../../org/micromanager/data/Datastore.html" title="interface in org.micromanager.data">Datastore</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ImageDeletedEvent.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/ImageDeletedEvent.html#getDatastore--">getDatastore</a></span>()</code>
-<div class="block">Provides the Datastore this image was added to; potentially useful for
- code that listens to events from multiple Datastores.</div>
+<td class="colLast"><span class="typeNameLabel">DatastoreClosingEvent.</span><code><span class="memberNameLink"><a href="../../../../org/micromanager/data/DatastoreClosingEvent.html#getDatastore--">getDatastore</a></span>()</code>
+<div class="block">Returns the Datastore that is closing.</div>
 </td>
 </tr>
 <tr class="altColor">