Qp v0.4.0 update (#18)

* gradle config update * updates JavaDoc
BIOP · Dec 15, 2022 · dc1a727 · dc1a727
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diff --git a/README.md b/README.md
@@ -282,17 +282,6 @@ The output will be under `build/libs`.
 
 # Notes and debugging
 
-## Normalization
-
-Like the StarDist extension, we provide a normalization option `normalizePercentiles`.
-However, the QuPath Stardist Extension that keeps the normalized image in 32-bit with no clipping.
-In turn, because Cellpose does its own normalization, there was no effect from using the normalization. 
-However, the QuPath Cellpose Extension adds a clipping of values below 0.0 and above 1.0 to the normalization.
-
-> Note however that QuPath normalizes channels jointly rather than independently, so you might get some odd results
-
- [Cellpose has implemented turning off their normalization, but it is not yet part of the current cellpose release](https://github.com/MouseLand/cellpose/issues).
-
 ## Preprocessing your data, extracting Color Deconvolution stains
 
 It has been useful to preprocess data to extract color-deconvolved channels feeding these to Cellpose, for example. This is where the `preprocess()` method is useful. 

diff --git a/build.gradle b/build.gradle
@@ -85,6 +85,11 @@ if (!strictJavadoc) {
     }
 }
 
+javadoc {
+    options.addBooleanOption('html5', true)
+    destinationDir = new File(project.rootDir,"docs")
+}
+
 /*
  * Avoid 'Entry .gitkeep is a duplicate but no duplicate handling strategy has been set.'
  * when using withSourcesJar()

diff --git a/docs/allclasses-index.html b/docs/allclasses-index.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc -->
-<title>All Classes (qupath-extension-cellpose 0.5.1 API)</title>
+<title>All Classes (qupath-extension-cellpose 0.6.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <link rel="stylesheet" type="text/css" href="jquery/jquery-ui.css" title="Style">
@@ -20,14 +20,14 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="All Classes (qupath-extension-cellpose 0.5.1 API)";
+            parent.document.title="All Classes (qupath-extension-cellpose 0.6.0 API)";
         }
     }
     catch(err) {
     }
 //-->
-var data = {"i0":2,"i1":2,"i2":2,"i3":2,"i4":4,"i5":2,"i6":4};
-var tabs = {65535:["t0","All Classes"],2:["t2","Class Summary"],4:["t3","Enum Summary"]};
+var data = {"i0":2,"i1":2,"i2":2,"i3":2,"i4":2,"i5":2,"i6":2,"i7":1,"i8":2,"i9":2,"i10":4};
+var tabs = {65535:["t0","All Classes"],1:["t1","Interface Summary"],2:["t2","Class Summary"],4:["t3","Enum Summary"]};
 var altColor = "altColor";
 var rowColor = "rowColor";
 var tableTab = "tableTab";
@@ -104,7 +104,7 @@ <h1 title="All&amp;nbsp;Classes" class="title">All&nbsp;Classes</h1>
 <ul class="blockList">
 <li class="blockList">
 <table class="typeSummary">
-<caption><span id="t0" class="activeTableTab"><span>All Classes</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Class Summary</a></span><span class="tabEnd">&nbsp;</span></span><span id="t3" class="tableTab"><span><a href="javascript:show(4);">Enum Summary</a></span><span class="tabEnd">&nbsp;</span></span></caption>
+<caption><span id="t0" class="activeTableTab"><span>All Classes</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Interface Summary</a></span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Class Summary</a></span><span class="tabEnd">&nbsp;</span></span><span id="t3" class="tableTab"><span><a href="javascript:show(4);">Enum Summary</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 <tr>
 <th class="colFirst" scope="col">Class</th>
 <th class="colLast" scope="col">Description</th>
@@ -118,7 +118,7 @@ <h1 title="All&amp;nbsp;Classes" class="title">All&nbsp;Classes</h1>
 <tr id="i1" class="rowColor">
 <td class="colFirst"><a href="qupath/ext/biop/cellpose/CellposeBuilder.html" title="class in qupath.ext.biop.cellpose">CellposeBuilder</a></td>
 <th class="colLast" scope="row">
-<div class="block">This class will contain all parameters that are usable by cellpose</div>
+<div class="block">Cell detection based on the following method:</div>
 </th>
 </tr>
 <tr id="i2" class="altColor">
@@ -132,16 +132,45 @@ <h1 title="All&amp;nbsp;Classes" class="title">All&nbsp;Classes</h1>
 <th class="colLast" scope="row">&nbsp;</th>
 </tr>
 <tr id="i4" class="altColor">
-<td class="colFirst"><a href="qupath/ext/biop/cellpose/CellposeSetup.CellposeVersion.html" title="enum in qupath.ext.biop.cellpose">CellposeSetup.CellposeVersion</a></td>
-<th class="colLast" scope="row">&nbsp;</th>
+<td class="colFirst"><a href="qupath/ext/biop/cellpose/OpCreators.html" title="class in qupath.ext.biop.cellpose">OpCreators</a></td>
+<th class="colLast" scope="row">
+<div class="block">Helper class for creating new ImageOps based upon other image properties.</div>
+</th>
 </tr>
 <tr id="i5" class="rowColor">
+<td class="colFirst"><a href="qupath/ext/biop/cellpose/OpCreators.ImageNormalizationBuilder.html" title="class in qupath.ext.biop.cellpose">OpCreators.ImageNormalizationBuilder</a></td>
+<th class="colLast" scope="row">
+<div class="block">Builder for a <a href="qupath/ext/biop/cellpose/OpCreators.TileOpCreator.html" title="interface in qupath.ext.biop.cellpose"><code>OpCreators.TileOpCreator</code></a> that can be used for image preprocessing 
+ using min/max percentiles or zero-mean-unit-variance normalization.</div>
+</th>
+</tr>
+<tr id="i6" class="altColor">
+<td class="colFirst"><a href="qupath/ext/biop/cellpose/OpCreators.PercentileTileOpCreator.html" title="class in qupath.ext.biop.cellpose">OpCreators.PercentileTileOpCreator</a></td>
+<th class="colLast" scope="row">
+<div class="block">Tile op creator that computes offset and scale values across the full image 
+ to normalize using min and max percentiles.</div>
+</th>
+</tr>
+<tr id="i7" class="rowColor">
+<td class="colFirst"><a href="qupath/ext/biop/cellpose/OpCreators.TileOpCreator.html" title="interface in qupath.ext.biop.cellpose">OpCreators.TileOpCreator</a></td>
+<th class="colLast" scope="row">
+<div class="block">Helper class for creating (tile-based) ImageOps with parameters that are derived from an entire image or ROI.</div>
+</th>
+</tr>
+<tr id="i8" class="altColor">
+<td class="colFirst"><a href="qupath/ext/biop/cellpose/OpCreators.ZeroMeanVarianceTileOpCreator.html" title="class in qupath.ext.biop.cellpose">OpCreators.ZeroMeanVarianceTileOpCreator</a></td>
+<th class="colLast" scope="row">
+<div class="block">Tile op creator that computes offset and scale values across the full image 
+ to normalize to zero mean and unit variance.</div>
+</th>
+</tr>
+<tr id="i9" class="rowColor">
 <td class="colFirst"><a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.html" title="class in qupath.ext.biop.cmd">VirtualEnvironmentRunner</a></td>
 <th class="colLast" scope="row">
 <div class="block">A wrapper to run python virtualenvs, that tries to figure out the commands to run based on the environment type</div>
 </th>
 </tr>
-<tr id="i6" class="altColor">
+<tr id="i10" class="altColor">
 <td class="colFirst"><a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.EnvType.html" title="enum in qupath.ext.biop.cmd">VirtualEnvironmentRunner.EnvType</a></td>
 <th class="colLast" scope="row">
 <div class="block">This enum helps us figure out the type of virtualenv.</div>

diff --git a/docs/allclasses.html b/docs/allclasses.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc -->
-<title>All Classes (qupath-extension-cellpose 0.5.1 API)</title>
+<title>All Classes (qupath-extension-cellpose 0.6.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <link rel="stylesheet" type="text/css" href="jquery/jquery-ui.css" title="Style">
@@ -24,7 +24,11 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="qupath/ext/biop/cellpose/CellposeBuilder.html" title="class in qupath.ext.biop.cellpose">CellposeBuilder</a></li>
 <li><a href="qupath/ext/biop/cellpose/CellposeExtension.html" title="class in qupath.ext.biop.cellpose">CellposeExtension</a></li>
 <li><a href="qupath/ext/biop/cellpose/CellposeSetup.html" title="class in qupath.ext.biop.cellpose">CellposeSetup</a></li>
-<li><a href="qupath/ext/biop/cellpose/CellposeSetup.CellposeVersion.html" title="enum in qupath.ext.biop.cellpose">CellposeSetup.CellposeVersion</a></li>
+<li><a href="qupath/ext/biop/cellpose/OpCreators.html" title="class in qupath.ext.biop.cellpose">OpCreators</a></li>
+<li><a href="qupath/ext/biop/cellpose/OpCreators.ImageNormalizationBuilder.html" title="class in qupath.ext.biop.cellpose">OpCreators.ImageNormalizationBuilder</a></li>
+<li><a href="qupath/ext/biop/cellpose/OpCreators.PercentileTileOpCreator.html" title="class in qupath.ext.biop.cellpose">OpCreators.PercentileTileOpCreator</a></li>
+<li><a href="qupath/ext/biop/cellpose/OpCreators.TileOpCreator.html" title="interface in qupath.ext.biop.cellpose"><span class="interfaceName">OpCreators.TileOpCreator</span></a></li>
+<li><a href="qupath/ext/biop/cellpose/OpCreators.ZeroMeanVarianceTileOpCreator.html" title="class in qupath.ext.biop.cellpose">OpCreators.ZeroMeanVarianceTileOpCreator</a></li>
 <li><a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.html" title="class in qupath.ext.biop.cmd">VirtualEnvironmentRunner</a></li>
 <li><a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.EnvType.html" title="enum in qupath.ext.biop.cmd">VirtualEnvironmentRunner.EnvType</a></li>
 </ul>

diff --git a/docs/allpackages-index.html b/docs/allpackages-index.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc -->
-<title>All Packages (qupath-extension-cellpose 0.5.1 API)</title>
+<title>All Packages (qupath-extension-cellpose 0.6.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <link rel="stylesheet" type="text/css" href="jquery/jquery-ui.css" title="Style">
@@ -20,7 +20,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="All Packages (qupath-extension-cellpose 0.5.1 API)";
+            parent.document.title="All Packages (qupath-extension-cellpose 0.6.0 API)";
         }
     }
     catch(err) {

diff --git a/docs/constant-values.html b/docs/constant-values.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc -->
-<title>Constant Field Values (qupath-extension-cellpose 0.5.1 API)</title>
+<title>Constant Field Values (qupath-extension-cellpose 0.6.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <link rel="stylesheet" type="text/css" href="jquery/jquery-ui.css" title="Style">
@@ -20,7 +20,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Constant Field Values (qupath-extension-cellpose 0.5.1 API)";
+            parent.document.title="Constant Field Values (qupath-extension-cellpose 0.6.0 API)";
         }
     }
     catch(err) {

diff --git a/docs/deprecated-list.html b/docs/deprecated-list.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc -->
-<title>Deprecated List (qupath-extension-cellpose 0.5.1 API)</title>
+<title>Deprecated List (qupath-extension-cellpose 0.6.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <link rel="stylesheet" type="text/css" href="jquery/jquery-ui.css" title="Style">
@@ -20,7 +20,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Deprecated List (qupath-extension-cellpose 0.5.1 API)";
+            parent.document.title="Deprecated List (qupath-extension-cellpose 0.6.0 API)";
         }
     }
     catch(err) {
@@ -94,6 +94,32 @@
 <div class="header">
 <h1 title="Deprecated API" class="title">Deprecated API</h1>
 <h2 title="Contents">Contents</h2>
+<ul>
+<li><a href="#method">Methods</a></li>
+</ul>
+</div>
+<div class="contentContainer"><a id="method">
+<!--   -->
+</a>
+<ul class="blockList">
+<li class="blockList">
+<table class="deprecatedSummary">
+<caption><span>Methods</span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Method</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<th class="colDeprecatedItemName" scope="row"><a href="qupath/ext/biop/cellpose/CellposeBuilder.html#maskThreshold(java.lang.Double)">qupath.ext.biop.cellpose.CellposeBuilder.maskThreshold&#8203;(Double)</a></th>
+<td class="colLast">
+<div class="deprecationComment">use <a href="qupath/ext/biop/cellpose/CellposeBuilder.html#cellprobThreshold(java.lang.Double)"><code>CellposeBuilder.cellprobThreshold(Double)</code></a></div>
+</td>
+</tr>
+</tbody>
+</table>
+</li>
+</ul>
 </div>
 </main>
 <footer role="contentinfo">

diff --git a/docs/help-doc.html b/docs/help-doc.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc -->
-<title>API Help (qupath-extension-cellpose 0.5.1 API)</title>
+<title>API Help (qupath-extension-cellpose 0.6.0 API)</title>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <link rel="stylesheet" type="text/css" href="jquery/jquery-ui.css" title="Style">
@@ -20,7 +20,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="API Help (qupath-extension-cellpose 0.5.1 API)";
+            parent.document.title="API Help (qupath-extension-cellpose 0.6.0 API)";
         }
     }
     catch(err) {