Adds some ways to output training results (#2)

* allows for this extension to be added into the QuPath source for debugging * saves the output of the command runner to a string array * adds logging and logging display possibilities * updates javadoc and readme * updates javadoc
BIOP · Jan 21, 2022 · 8c195c4 · 8c195c4
1 parent cb93155
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diff --git a/README.md b/README.md
@@ -85,9 +85,19 @@ def cellpose = Cellpose2D.builder("cyto") // Can choose "None" if you want to tr
 // 2. Run the cellpose training via command line
 // 3. Recover the model file after training, and copy it to where you defined in the builder, returning the reference to it
 
-def resultModel = cellposeTrainer.train()
+def resultModel = cellpose.train()
+
+// Pick up results to see how the training was performed
+println "Model Saved under "
+println resultModel.getAbsolutePath().toString()
+
+// You can get a ResultsTable of the training. 
+def results = cellpose.getTrainingResults()
+results.show("Training Results")
+
+// Finally you have access to a very simple graph 
+cellpose.showTrainingGraph()
 
-println "Model Saved under "+resultModel
 ```
 
 **Extra training options:**

diff --git a/Scripts/Run-Cellpose.groovy b/Scripts/Run-Cellpose.groovy
diff --git a/Scripts/Train-Cellpose-Model.groovy b/Scripts/Train-Cellpose-Model.groovy
diff --git a/build.gradle b/build.gradle
@@ -2,8 +2,6 @@ plugins {
   id 'java-library'
   // To create a shadow/fat jar, including dependencies
   id 'com.github.johnrengelman.shadow' version '7.0.0'
-  // To manage included native libraries
-  id 'org.bytedeco.gradle-javacpp-platform' version '1.5.6'
 }
 
 repositories {

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 0.2.0 API)</title>
+<title>All Classes (qupath-extension-cellpose 0.3.1 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 Classes (qupath-extension-cellpose 0.2.0 API)";
+            parent.document.title="All Classes (qupath-extension-cellpose 0.3.1 API)";
         }
     }
     catch(err) {

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 0.2.0 API)</title>
+<title>All Classes (qupath-extension-cellpose 0.3.1 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">

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 0.2.0 API)</title>
+<title>All Packages (qupath-extension-cellpose 0.3.1 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 0.2.0 API)";
+            parent.document.title="All Packages (qupath-extension-cellpose 0.3.1 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 0.2.0 API)</title>
+<title>Constant Field Values (qupath-extension-cellpose 0.3.1 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 0.2.0 API)";
+            parent.document.title="Constant Field Values (qupath-extension-cellpose 0.3.1 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 0.2.0 API)</title>
+<title>Deprecated List (qupath-extension-cellpose 0.3.1 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 0.2.0 API)";
+            parent.document.title="Deprecated List (qupath-extension-cellpose 0.3.1 API)";
         }
     }
     catch(err) {

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 0.2.0 API)</title>
+<title>API Help (qupath-extension-cellpose 0.3.1 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 0.2.0 API)";
+            parent.document.title="API Help (qupath-extension-cellpose 0.3.1 API)";
         }
     }
     catch(err) {

diff --git a/docs/index-all.html b/docs/index-all.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc -->
-<title>Index (qupath-extension-cellpose 0.2.0 API)</title>
+<title>Index (qupath-extension-cellpose 0.3.1 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="Index (qupath-extension-cellpose 0.2.0 API)";
+            parent.document.title="Index (qupath-extension-cellpose 0.3.1 API)";
         }
     }
     catch(err) {
@@ -277,10 +277,20 @@ <h2 class="title">G</h2>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/CellposeExtension.html#getName()">getName()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/CellposeExtension.html" title="class in qupath.ext.biop.cellpose">CellposeExtension</a></dt>
 <dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/Cellpose2D.html#getOutputLog()">getOutputLog()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/Cellpose2D.html" title="class in qupath.ext.biop.cellpose">Cellpose2D</a></dt>
+<dd>
+<div class="block">Returns the log from running the cellpose command, with any error messages and status updates of the cellpose process
+ You can use this during training or prediction</div>
+</dd>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/CellposeExtension.html#getQuPathVersion()">getQuPathVersion()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/CellposeExtension.html" title="class in qupath.ext.biop.cellpose">CellposeExtension</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/CellposeExtension.html#getRepository()">getRepository()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/CellposeExtension.html" title="class in qupath.ext.biop.cellpose">CellposeExtension</a></dt>
 <dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/Cellpose2D.html#getTrainingResults()">getTrainingResults()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/Cellpose2D.html" title="class in qupath.ext.biop.cellpose">Cellpose2D</a></dt>
+<dd>
+<div class="block">Returns a parsed version of the cellpose log as a ResultsTable with columns
+ Epoch, Time, Loss, Loss Test and LR</div>
+</dd>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/CellposeExtension.html#getVersion()">getVersion()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/CellposeExtension.html" title="class in qupath.ext.biop.cellpose">CellposeExtension</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/CellposeSetup.html#getVersion()">getVersion()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/CellposeSetup.html" title="class in qupath.ext.biop.cellpose">CellposeSetup</a></dt>
@@ -451,6 +461,10 @@ <h2 class="title">S</h2>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/CellposeSetup.html#setVersion(qupath.ext.biop.cellpose.CellposeSetup.CellposeVersion)">setVersion(CellposeSetup.CellposeVersion)</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/CellposeSetup.html" title="class in qupath.ext.biop.cellpose">CellposeSetup</a></dt>
 <dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/Cellpose2D.html#showTrainingGraph()">showTrainingGraph()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/Cellpose2D.html" title="class in qupath.ext.biop.cellpose">Cellpose2D</a></dt>
+<dd>
+<div class="block">Displays a JavaFX graph as a dialog so you can inspect the Losses per epoch</div>
+</dd>
 </dl>
 <a id="I:T">
 <!--   -->
@@ -474,7 +488,10 @@ <h2 class="title">T</h2>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.EnvType.html#toString()">toString()</a></span> - Method in enum qupath.ext.biop.cmd.<a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.EnvType.html" title="enum in qupath.ext.biop.cmd">VirtualEnvironmentRunner.EnvType</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/Cellpose2D.html#train()">train()</a></span> - Method in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/Cellpose2D.html" title="class in qupath.ext.biop.cellpose">Cellpose2D</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Executes the cellpose training by
+ 1.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="qupath/ext/biop/cellpose/Cellpose2D.html#trainDirectory">trainDirectory</a></span> - Variable in class qupath.ext.biop.cellpose.<a href="qupath/ext/biop/cellpose/Cellpose2D.html" title="class in qupath.ext.biop.cellpose">Cellpose2D</a></dt>
 <dd>&nbsp;</dd>
 </dl>
@@ -527,7 +544,7 @@ <h2 class="title">V</h2>
 <dd>
 <div class="block">A wrapper to run python virtualenvs, that tries to figure out the commands to run based on the environment type</div>
 </dd>
-<dt><span class="memberNameLink"><a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.html#%3Cinit%3E(java.lang.String,qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType)">VirtualEnvironmentRunner(String, VirtualEnvironmentRunner.EnvType)</a></span> - Constructor for class qupath.ext.biop.cmd.<a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.html" title="class in qupath.ext.biop.cmd">VirtualEnvironmentRunner</a></dt>
+<dt><span class="memberNameLink"><a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.html#%3Cinit%3E(java.lang.String,qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType,java.lang.String)">VirtualEnvironmentRunner(String, VirtualEnvironmentRunner.EnvType, String)</a></span> - Constructor for class qupath.ext.biop.cmd.<a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.html" title="class in qupath.ext.biop.cmd">VirtualEnvironmentRunner</a></dt>
 <dd>&nbsp;</dd>
 <dt><a href="qupath/ext/biop/cmd/VirtualEnvironmentRunner.EnvType.html" title="enum in qupath.ext.biop.cmd"><span class="typeNameLink">VirtualEnvironmentRunner.EnvType</span></a> - Enum in <a href="qupath/ext/biop/cmd/package-summary.html">qupath.ext.biop.cmd</a></dt>
 <dd>

diff --git a/docs/index.html b/docs/index.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc -->
-<title>Overview (qupath-extension-cellpose 0.2.0 API)</title>
+<title>Overview (qupath-extension-cellpose 0.3.1 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="Overview (qupath-extension-cellpose 0.2.0 API)";
+            parent.document.title="Overview (qupath-extension-cellpose 0.3.1 API)";
         }
     }
     catch(err) {
@@ -91,7 +91,7 @@
 </nav>
 </header>
 <div class="header">
-<h1 class="title">qupath-extension-cellpose 0.2.0 API</h1>
+<h1 class="title">qupath-extension-cellpose 0.3.1 API</h1>
 </div>
 <main role="main">
 <div class="contentContainer">