adds support for cellpose 1.0 (#4)

BIOP · Jan 31, 2022 · 5f1e6c3 · 5f1e6c3
1 parent 8c195c4
commit 5f1e6c3
Show file tree

Hide file tree

Showing 4 changed files with 13 additions and 7 deletions.
diff --git a/build.gradle b/build.gradle
@@ -24,10 +24,10 @@ ext.moduleName = 'qupath.extension.cellpose'
 
 description = 'QuPath extension to use Cellpose'
 
-version = "0.3.1"
+version = "0.3.2"
 
 dependencies {
-    def qupathVersion = "0.3.0" // For now
+    def qupathVersion = "0.3.2" // For now
 
     shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
     shadow "org.slf4j:slf4j-api:1.7.30"

diff --git a/src/main/java/qupath/ext/biop/cellpose/Cellpose2D.java b/src/main/java/qupath/ext/biop/cellpose/Cellpose2D.java
@@ -522,10 +522,11 @@ private void runCellpose() throws IOException, InterruptedException {
         }
 
         if (!maskThreshold.isNaN()) {
-            if (cellposeSetup.getVersion().equals(CellposeSetup.CellposeVersion.OMNIPOSE))
+            if (!cellposeSetup.getVersion().equals(CellposeSetup.CellposeVersion.CELLPOSE))
                 cellposeArguments.add("--mask_threshold");
             else cellposeArguments.add("--cellprob_threshold");
 
+
             cellposeArguments.add("" + maskThreshold);
         }
 
@@ -539,10 +540,14 @@ private void runCellpose() throws IOException, InterruptedException {
 
         cellposeArguments.add("--no_npy");
 
-        cellposeArguments.add("--resample");
+        if (!cellposeSetup.getVersion().equals(CellposeSetup.CellposeVersion.CELLPOSE_1))
+            cellposeArguments.add("--resample");
 
         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
@@ -41,7 +41,7 @@ public void installExtension(QuPathGUI qupath) {
 
         // Create the options we need
         ObjectProperty<EnvType> envType = PathPrefs.createPersistentPreference("cellposeEnvType", EnvType.CONDA, EnvType.class);
-        ObjectProperty<CellposeVersion> version = PathPrefs.createPersistentPreference("cellposeVersion",CellposeVersion.CELLPOSE, CellposeVersion.class);
+        ObjectProperty<CellposeVersion> version = PathPrefs.createPersistentPreference("cellposeVersion",CellposeVersion.CELLPOSE_1, CellposeVersion.class);
         StringProperty envPath = PathPrefs.createPersistentPreference("cellposeEnvPath", "");
 
         //Set options to current values
@@ -86,6 +86,6 @@ public Version getQuPathVersion() {
 
     @Override
     public Version getVersion() {
-        return Version.parse("0.3.1");
+        return Version.parse("0.3.2");
     }
 }
diff --git a/src/main/java/qupath/ext/biop/cellpose/CellposeSetup.java b/src/main/java/qupath/ext/biop/cellpose/CellposeSetup.java
@@ -8,7 +8,8 @@ public class CellposeSetup {
     private CellposeVersion version;
     public enum CellposeVersion {
         CELLPOSE("Cellpose before v0.7.0"),
-        OMNIPOSE("Omnipose after v0.7.2");
+        OMNIPOSE("Omnipose after v0.7.2"),
+        CELLPOSE_1("Cellpose Version 1.0");
 
         private final String description;