From d16b539cce6787dda02ad00127498dcc5807ca0c Mon Sep 17 00:00:00 2001
From: Olivier Burri <olivier.burri@epfl.ch>
Date: Thu, 10 Feb 2022 16:23:52 +0100
Subject: [PATCH] Impoved support for logging when training cellpose (#6)

* adds support for cellpose 1.0

* Bump cellpose version
---
 build.gradle                                                 | 2 +-
 src/main/java/qupath/ext/biop/cellpose/Cellpose2D.java       | 5 +++--
 .../java/qupath/ext/biop/cellpose/CellposeExtension.java     | 2 +-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/build.gradle b/build.gradle
index 96ea5e6..0151c41 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,7 +24,7 @@ ext.moduleName = 'qupath.extension.cellpose'
 
 description = 'QuPath extension to use Cellpose'
 
-version = "0.3.2"
+version = "0.3.3"
 
 dependencies {
     def qupathVersion = "0.3.2" // For now
diff --git a/src/main/java/qupath/ext/biop/cellpose/Cellpose2D.java b/src/main/java/qupath/ext/biop/cellpose/Cellpose2D.java
index 9430ce5..78a0ec8 100644
--- a/src/main/java/qupath/ext/biop/cellpose/Cellpose2D.java
+++ b/src/main/java/qupath/ext/biop/cellpose/Cellpose2D.java
@@ -583,8 +583,6 @@ public File train() {
      */
     private void runCellposeTraining() throws IOException, InterruptedException {
 
-        //python -m cellpose --train --dir ~/images_cyto/train/ --test_dir ~/images_cyto/test/ --pretrained_model cyto --chan 2 --chan2 1
-
         // Create command to run
         VirtualEnvironmentRunner veRunner = new VirtualEnvironmentRunner(cellposeSetup.getEnvironmentNameOrPath(), cellposeSetup.getEnvironmentType(), this.getClass().getSimpleName() + "-train");
 
@@ -635,6 +633,9 @@ private void runCellposeTraining() throws IOException, InterruptedException {
 
         if (useGPU) cellposeArguments.add("--use_gpu");
 
+        if (cellposeSetup.getVersion().equals(CellposeSetup.CellposeVersion.CELLPOSE_1))
+            cellposeArguments.add("--verbose");
+
         veRunner.setArguments(cellposeArguments);
 
         // Finally, we can run Cellpose
diff --git a/src/main/java/qupath/ext/biop/cellpose/CellposeExtension.java b/src/main/java/qupath/ext/biop/cellpose/CellposeExtension.java
index 3373ac0..10a0dcb 100644
--- a/src/main/java/qupath/ext/biop/cellpose/CellposeExtension.java
+++ b/src/main/java/qupath/ext/biop/cellpose/CellposeExtension.java
@@ -86,6 +86,6 @@ public Version getQuPathVersion() {
 
     @Override
     public Version getVersion() {
-        return Version.parse("0.3.2");
+        return Version.parse("0.3.3");
     }
 }
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