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micro-manager · Dec 11, 2023 · 939c02d · 939c02d
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diff --git a/deprecated-list.html b/deprecated-list.html
@@ -407,27 +407,27 @@ <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="rowColor">
-<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/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:
      <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>,
      <a href="org/micromanager/data/Metadata.html#copyBuilderRemovingUUID--"><code>Metadata.copyBuilderRemovingUUID()</code></a>. This method is equivalent to
      <code>copyBuilderPreservingUUID</code>.</span></div>
 </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/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>
@@ -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
@@ -140,29 +140,29 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 </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">PropertyManager.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyManager.html#emptyPropertyMap--">emptyPropertyMap</a></span>()</code>
-<div class="block">Returns an empty property map.</div>
-</td>
-</tr>
-<tr class="rowColor">
 <td class="colFirst"><code>static <a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
 <td class="colLast"><span class="typeNameLabel">PropertyMaps.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyMaps.html#emptyPropertyMap--">emptyPropertyMap</a></span>()</code>
 <div class="block">Return the empty property map.</div>
 </td>
 </tr>
-<tr class="altColor">
+<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">PropertyManager.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyManager.html#fromJSON-java.lang.String-">fromJSON</a></span>(java.lang.String&nbsp;json)</code>
-<div class="block">Creates a property map from its JSON-serialized form.</div>
+<td class="colLast"><span class="typeNameLabel">PropertyManager.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyManager.html#emptyPropertyMap--">emptyPropertyMap</a></span>()</code>
+<div class="block">Returns an empty property map.</div>
 </td>
 </tr>
-<tr class="rowColor">
+<tr class="altColor">
 <td class="colFirst"><code>static <a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
 <td class="colLast"><span class="typeNameLabel">PropertyMaps.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyMaps.html#fromJSON-java.lang.String-">fromJSON</a></span>(java.lang.String&nbsp;json)</code>
 <div class="block">Create a property map from its JSON-serialized form.</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">PropertyManager.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyManager.html#fromJSON-java.lang.String-">fromJSON</a></span>(java.lang.String&nbsp;json)</code>
+<div class="block">Creates a property map from its JSON-serialized form.</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">PropertyMap.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyMap.html#getPropertyMap-java.lang.String-">getPropertyMap</a></span>(java.lang.String&nbsp;key)</code>
@@ -175,14 +175,14 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
               <a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;aDefault)</code>&nbsp;</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">PropertyManager.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyManager.html#loadJSON-java.io.File-">loadJSON</a></span>(java.io.File&nbsp;file)</code>
+<td class="colFirst"><code>static <a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
+<td class="colLast"><span class="typeNameLabel">PropertyMaps.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyMaps.html#loadJSON-java.io.File-">loadJSON</a></span>(java.io.File&nbsp;file)</code>
 <div class="block">Create a property map from its JSON-serialized form stored in a file.</div>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colFirst"><code>static <a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
-<td class="colLast"><span class="typeNameLabel">PropertyMaps.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyMaps.html#loadJSON-java.io.File-">loadJSON</a></span>(java.io.File&nbsp;file)</code>
+<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">PropertyManager.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyManager.html#loadJSON-java.io.File-">loadJSON</a></span>(java.io.File&nbsp;file)</code>
 <div class="block">Create a property map from its JSON-serialized form stored in a file.</div>
 </td>
 </tr>
@@ -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">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="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">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="altColor">
@@ -431,16 +431,6 @@ <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/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/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/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>
@@ -452,6 +442,16 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 <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>
+</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>
+<div class="block"><span class="deprecatedLabel">Deprecated.</span>&nbsp;</div>
+&nbsp;</td>
+</tr>
 </tbody>
 </table>
 </li>
@@ -468,13 +468,13 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 <tbody>
 <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">AbstractOverlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/AbstractOverlay.html#getConfiguration--">getConfiguration</a></span>()</code>
+<td class="colLast"><span class="typeNameLabel">Overlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/Overlay.html#getConfiguration--">getConfiguration</a></span>()</code>
 <div class="block">Return the user-customizable settings for this overlay.</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">Overlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/Overlay.html#getConfiguration--">getConfiguration</a></span>()</code>
+<td class="colLast"><span class="typeNameLabel">AbstractOverlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/AbstractOverlay.html#getConfiguration--">getConfiguration</a></span>()</code>
 <div class="block">Return the user-customizable settings for this overlay.</div>
 </td>
 </tr>
@@ -489,13 +489,13 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 <tbody>
 <tr class="altColor">
 <td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">AbstractOverlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/AbstractOverlay.html#setConfiguration-org.micromanager.PropertyMap-">setConfiguration</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;config)</code>
+<td class="colLast"><span class="typeNameLabel">Overlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/Overlay.html#setConfiguration-org.micromanager.PropertyMap-">setConfiguration</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;config)</code>
 <div class="block">Configure the overlay with the given parameters.</div>
 </td>
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">Overlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/Overlay.html#setConfiguration-org.micromanager.PropertyMap-">setConfiguration</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;config)</code>
+<td class="colLast"><span class="typeNameLabel">AbstractOverlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/AbstractOverlay.html#setConfiguration-org.micromanager.PropertyMap-">setConfiguration</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;config)</code>
 <div class="block">Configure the overlay with the given parameters.</div>
 </td>
 </tr>