Conda returns

build.gradle

@@ -25,7 +25,7 @@ ext.qupathVersion = gradle.ext.qupathVersion
 
 description = 'QuPath extension to use Cellpose'
 
-version = "0.9.3"
+version = "0.9.4-SNAPSHOT"
 
 dependencies {
     implementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"

src/main/java/qupath/ext/biop/cellpose/CellposeBuilder.java

@@ -67,7 +67,7 @@ public class CellposeBuilder {
     // Cellpose Related Options
     private String modelNameOrPath;
     // Cellpose Training options
-    private File modelDirectory = null;
+    private transient File modelDirectory = null;
     // QuPath Object handling options
     private ColorTransform[] channels = new ColorTransform[0];
     private Double cellExpansion = Double.NaN;
@@ -89,13 +89,14 @@ public class CellposeBuilder {
     private TileOpCreator globalPreprocessing;
     private int nThreads = -1;
 
-    private File tempDirectory = null;
-    private File groundTruthDirectory = null;
+    private transient File tempDirectory = null;
+    private transient File groundTruthDirectory = null;
 
     private ImageOp extendChannelOp = null;
 
     private boolean doReadResultsAsynchronously = false;
     private boolean useGPU = true;
+    private String outputModelName;
 
     /**
      * can create a cellpose builder from a serialized JSON version of this builder.
@@ -581,7 +582,7 @@ public CellposeBuilder addParameter(String flagName) {
      * @return this builder
      */
     public CellposeBuilder useOmnipose() {
-        if (cellposeSetup.getOmniposePytonPath() == "")
+        if (cellposeSetup.getOmniposePythonPath() == "")
             logger.warn("Omnipose environment path not set. Using cellpose path instead.");
         addParameter("omni");
         return this;
@@ -759,7 +760,7 @@ public CellposeBuilder normalizePercentilesGlobal(double percentileMin, double p
         // Deactivate cellpose normalization
         this.noCellposeNormalization();
 
-        // Add this operation the the preprocessing
+        // Add this operation to the preprocessing
         return this.preprocess(normOp);
     }
 
@@ -772,6 +773,10 @@ public CellposeBuilder noCellposeNormalization() {
         return this.addParameter("no_norm");
     }
 
+    public CellposeBuilder setOutputModelName(String outputName) {
+        this.outputModelName = outputName;
+        return this;
+    }
     /**
      * Create a {@link Cellpose2D}, all ready for detection.
      *
@@ -812,13 +817,10 @@ public Cellpose2D build() {
 
         if (this.modelDirectory == null) {
             this.modelDirectory = new File(quPathProjectDir, "models");
+            this.modelDirectory.mkdirs();
         }
 
-        // Define training and validation directories inside the QuPath Project
-        File trainDirectory = new File(groundTruthDirectory, "train");
-        File valDirectory = new File(groundTruthDirectory, "test");
-
-
+        cellpose.outputModelName = outputModelName;
         cellpose.modelDirectory = modelDirectory;
         cellpose.groundTruthDirectory = groundTruthDirectory;
         cellpose.tempDirectory = tempDirectory;
@@ -851,6 +853,7 @@ public Cellpose2D build() {
         cellpose.constrainToParent = constrainToParent;
         cellpose.creatorFun = creatorFun;
         cellpose.globalPathClass = globalPathClass;
+        cellpose.outputModelName = outputModelName;
 
         cellpose.compartments = new LinkedHashSet<>(compartments);
 
@@ -869,9 +872,9 @@ public Cellpose2D build() {
                     cellpose.overlap = 30 * 2;
                     logger.info("Tile overlap was not set and diameter was set to {}. Will default to {} pixels overlap. Use `.setOverlap( int )` to modify overlap", diameter, cellpose.overlap);
                 } else {
+                    cellpose.overlap = (int) (diameter * 2);
+                    logger.info("Tile overlap was not set, but diameter exists. Using provided diameter {} x 2: {} pixels overlap", diameter, cellpose.overlap);
                 }
-                cellpose.overlap = (int) (diameter * 2);
-                logger.info("Tile overlap was not set, but diameter exists. Using provided diameter {} x 2: {} pixels overlap", diameter, cellpose.overlap);
             } else { // Nothing was set, let's get lucky
                 cellpose.overlap = 30 * 2;
                 logger.info("Neither diameter nor overlap provided. Overlap defaulting to {} pixels. Use `.setOverlap( int )` to modify overlap", cellpose.overlap);

src/main/java/qupath/ext/biop/cellpose/CellposeExtension.java

@@ -67,15 +67,19 @@ public void installExtension(QuPathGUI qupath) {
         // Create the options we need
         StringProperty cellposePath = PathPrefs.createPersistentPreference("cellposePythonPath", "");
         StringProperty omniposePath = PathPrefs.createPersistentPreference("omniposePythonPath", "");
+        StringProperty condaPath = PathPrefs.createPersistentPreference("condaPath", "");
 
 
         //Set options to current values
-        options.setCellposePytonPath(cellposePath.get());
-        options.setOmniposePytonPath(omniposePath.get());
+        options.setCellposePythonPath(cellposePath.get());
+        options.setOmniposePythonPath(omniposePath.get());
+        options.setCondaPath(condaPath.get());
 
         // Listen for property changes
-        cellposePath.addListener((v, o, n) -> options.setCellposePytonPath(n));
-        omniposePath.addListener((v, o, n) -> options.setOmniposePytonPath(n));
+        cellposePath.addListener((v, o, n) -> options.setCellposePythonPath(n));
+        omniposePath.addListener((v, o, n) -> options.setOmniposePythonPath(n));
+        condaPath.addListener((v, o, n) -> options.setCondaPath(n));
+
 
         PropertySheet.Item cellposePathItem = new PropertyItemBuilder<>(cellposePath, String.class)
                 .propertyType(PropertyItemBuilder.PropertyType.GENERAL)
@@ -91,8 +95,15 @@ public void installExtension(QuPathGUI qupath) {
                 .description("Enter the full path to your omnipose environment, including 'python.exe'")
                 .build();
 
+        PropertySheet.Item condaPathItem = new PropertyItemBuilder<>(condaPath, String.class)
+                .propertyType(PropertyItemBuilder.PropertyType.GENERAL)
+                .name("'Conda' script location (optional)")
+                .category("Cellpose/Omnipose")
+                .description("The full path to you conda/mamba command, in case you want the extension to use the 'conda activate' command.\ne.g 'C:\\ProgramData\\Miniconda3\\condabin\\mamba.bat'")
+                .build();
+
         // Add Permanent Preferences and Populate Preferences
-        QuPathGUI.getInstance().getPreferencePane().getPropertySheet().getItems().addAll(cellposePathItem, omniposePathItem);
+        QuPathGUI.getInstance().getPreferencePane().getPropertySheet().getItems().addAll(cellposePathItem, omniposePathItem, condaPathItem);
 
     }
 

src/main/java/qupath/ext/biop/cellpose/CellposeSetup.java

@@ -1,29 +1,33 @@
 package qupath.ext.biop.cellpose;
 
-import qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType;
-
 public class CellposeSetup {
     private static final CellposeSetup instance = new CellposeSetup();
     private String cellposePythonPath = null;
     private String omniposePythonPath = null;
 
+    private String condaPath = null;
+
     public static CellposeSetup getInstance() {
         return instance;
     }
 
-    public String getCellposePytonPath() {
+    public String getCellposePythonPath() {
         return cellposePythonPath;
     }
 
-    public void setCellposePytonPath(String path) {
+    public void setCellposePythonPath(String path) {
         this.cellposePythonPath = path;
     }
 
-    public String getOmniposePytonPath() {
+    public String getOmniposePythonPath() {
         return omniposePythonPath;
     }
 
-    public void setOmniposePytonPath(String path) {
+    public void setOmniposePythonPath(String path) {
         this.omniposePythonPath = path;
     }
+
+    public void setCondaPath(String condaPath) { this.condaPath = condaPath; }
+
+    public String getCondaPath() { return condaPath; }
 }

src/main/java/qupath/ext/biop/cmd/VirtualEnvironmentRunner.java

@@ -26,6 +26,9 @@
 public class VirtualEnvironmentRunner {
     private final static Logger logger = LoggerFactory.getLogger(VirtualEnvironmentRunner.class);
     private final EnvType envType;
+
+    private final String condaPath;
+
     private WatchService watchService;
     private String name;
     private String pythonPath;
@@ -61,9 +64,14 @@ public String toString() {
     }
 
     public VirtualEnvironmentRunner(String environmentNameOrPath, EnvType type, String name) {
+        this(environmentNameOrPath, type, null, name );
+    }
+
+    public VirtualEnvironmentRunner(String environmentNameOrPath, EnvType type, String condaPath, String name) {
         this.pythonPath = environmentNameOrPath;
         this.envType = type;
         this.name = name;
+        this.condaPath = condaPath;
         if (envType.equals(EnvType.OTHER))
             logger.error("Environment is unknown, please set the environment type to something different than 'Other'");
     }
@@ -79,18 +87,25 @@ private List<String> getActivationCommand() {
 
         Platform platform = Platform.getCurrent();
         List<String> cmd = new ArrayList<>();
+        String condaCommand = this.condaPath;
 
         switch (envType) {
             case CONDA:
                 switch (platform) {
                     case WINDOWS:
+                        if( condaCommand == null ) {
+                            condaCommand = "conda.bat";
+                        }
                         // Adjust path to the folder with the env name based on the python location. On Windows it's at the root of the environment
-                        cmd.addAll(Arrays.asList("CALL", "conda.bat", "activate", new File(pythonPath).getParent(), "&", "python"));
+                        cmd.addAll(Arrays.asList("CALL", condaCommand, "activate", new File(pythonPath).getParent(), "&", "python"));
                         break;
                     case UNIX:
                     case OSX:
+                        if( condaCommand == null ) {
+                            condaCommand = "conda";
+                        }
                         // Adjust path to the folder with the env name based on the python location. In Linux/MacOS it's in the 'bin' sub folder
-                        cmd.addAll(Arrays.asList("conda", "activate", new File(pythonPath).getParentFile().getParent(), ";", "python"));
+                        cmd.addAll(Arrays.asList(condaCommand, "activate", new File(pythonPath).getParentFile().getParent(), ";", "python"));
                         break;
                 }
                 break;