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micro-manager · Dec 14, 2024 · a920516 · a920516
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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">
@@ -407,6 +407,16 @@ <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/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/Coords.html#copy--">org.micromanager.data.Coords.copy()</a>
+<div class="block"><span class="deprecationComment">Use <a href="org/micromanager/data/Coords.html#copyBuilder--"><code>copyBuilder</code></a> instead</span></div>
+</td>
+</tr>
+<tr class="altColor">
 <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:
      <a href="org/micromanager/data/Metadata.html#copyBuilderPreservingUUID--"><code>Metadata.copyBuilderPreservingUUID()</code></a>, <a href="org/micromanager/data/Metadata.html#copyBuilderWithNewUUID--"><code>Metadata.copyBuilderWithNewUUID()</code></a>,
@@ -415,24 +425,14 @@ <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>
+<td class="colOne"><a href="org/micromanager/display/DisplaySettings.html#copy--">org.micromanager.display.DisplaySettings.copy()</a></td>
 </tr>
 <tr class="altColor">
-<td class="colOne"><a href="org/micromanager/data/Coords.html#copy--">org.micromanager.data.Coords.copy()</a>
-<div class="block"><span class="deprecationComment">Use <a href="org/micromanager/data/Coords.html#copyBuilder--"><code>copyBuilder</code></a> instead</span></div>
-</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/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>
@@ -538,13 +538,13 @@ <h2 title="Contents">Contents</h2>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colOne"><a href="org/micromanager/display/DataViewer.html#getDatastore--">org.micromanager.display.DataViewer.getDatastore()</a>
-<div class="block"><span class="deprecationComment">use <a href="org/micromanager/display/DataViewer.html#getDataProvider--"><code>DataViewer.getDataProvider()</code></a> instead</span></div>
+<td class="colOne"><a href="org/micromanager/display/AbstractDataViewer.html#getDatastore--">org.micromanager.display.AbstractDataViewer.getDatastore()</a>
+<div class="block"><span class="deprecationComment">user code should call <code>getDataProvider</code></span></div>
 </td>
 </tr>
 <tr class="altColor">
-<td class="colOne"><a href="org/micromanager/display/AbstractDataViewer.html#getDatastore--">org.micromanager.display.AbstractDataViewer.getDatastore()</a>
-<div class="block"><span class="deprecationComment">user code should call <code>getDataProvider</code></span></div>
+<td class="colOne"><a href="org/micromanager/display/DataViewer.html#getDatastore--">org.micromanager.display.DataViewer.getDatastore()</a>
+<div class="block"><span class="deprecationComment">use <a href="org/micromanager/display/DataViewer.html#getDataProvider--"><code>DataViewer.getDataProvider()</code></a> instead</span></div>
 </td>
 </tr>
 <tr class="rowColor">
@@ -916,13 +916,13 @@ <h2 title="Contents">Contents</h2>
 </td>
 </tr>
 <tr class="altColor">
-<td class="colOne"><a href="org/micromanager/display/DataViewer.html#setDisplayedImageTo-org.micromanager.data.Coords-">org.micromanager.display.DataViewer.setDisplayedImageTo(Coords)</a>
-<div class="block"><span class="deprecationComment">use <a href="org/micromanager/display/DataViewer.html#setDisplayPosition-org.micromanager.data.Coords-"><code>DataViewer.setDisplayPosition(Coords)</code></a> instead</span></div>
+<td class="colOne"><a href="org/micromanager/display/AbstractDataViewer.html#setDisplayedImageTo-org.micromanager.data.Coords-">org.micromanager.display.AbstractDataViewer.setDisplayedImageTo(Coords)</a>
+<div class="block"><span class="deprecationComment">user code should call <code>setDisplayPosition</code></span></div>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colOne"><a href="org/micromanager/display/AbstractDataViewer.html#setDisplayedImageTo-org.micromanager.data.Coords-">org.micromanager.display.AbstractDataViewer.setDisplayedImageTo(Coords)</a>
-<div class="block"><span class="deprecationComment">user code should call <code>setDisplayPosition</code></span></div>
+<td class="colOne"><a href="org/micromanager/display/DataViewer.html#setDisplayedImageTo-org.micromanager.data.Coords-">org.micromanager.display.DataViewer.setDisplayedImageTo(Coords)</a>
+<div class="block"><span class="deprecationComment">use <a href="org/micromanager/display/DataViewer.html#setDisplayPosition-org.micromanager.data.Coords-"><code>DataViewer.setDisplayPosition(Coords)</code></a> instead</span></div>
 </td>
 </tr>
 <tr class="altColor">

diff --git a/org/micromanager/class-use/PropertyMap.html b/org/micromanager/class-use/PropertyMap.html
@@ -194,14 +194,14 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 </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">MultiStagePosition.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/MultiStagePosition.html#toPropertyMap--">toPropertyMap</a></span>()</code>
-<div class="block">Returns a propertymap describing this MultiStagePosition.</div>
+<td class="colLast"><span class="typeNameLabel">PositionList.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PositionList.html#toPropertyMap--">toPropertyMap</a></span>()</code>
+<div class="block">Creates a PropertyMap from this PositionList.</div>
 </td>
 </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">PositionList.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PositionList.html#toPropertyMap--">toPropertyMap</a></span>()</code>
-<div class="block">Creates a PropertyMap from this PositionList.</div>
+<td class="colLast"><span class="typeNameLabel">MultiStagePosition.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/MultiStagePosition.html#toPropertyMap--">toPropertyMap</a></span>()</code>
+<div class="block">Returns a propertymap describing this MultiStagePosition.</div>
 </td>
 </tr>
 <tr class="rowColor">
@@ -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>