Fixing some file paths

src/main/groovy/qupath/ext/qp_scope/functions/QP_scope_GUI.groovy

@@ -385,12 +385,13 @@ class QP_scope_GUI {
             }
 
             // Expect the classifier file path to be in a specific location
-            // Extract the directory from pythonScriptPath
-            Path scriptDirectory = Paths.get(pythonScriptPath).getParent();
+            // get the classifier from the groovyScripts folder, which should be "next to" the pythonScripts folder
+            Path groovyScriptDirectory = Paths.get(pythonScriptPath).getParent();
+            groovyScriptDirectory = groovyScriptDirectory.resolveSibling("groovyScripts")
 
             // Combine the directory with the new filename
-            Path jsonFilePath = scriptDirectory.resolve("Tissue-lowres.json");
-            Path exportScriptPath = scriptDirectory.resolve("save4xMacroTiling.groovy")
+            Path jsonFilePath = groovyScriptDirectory.resolve("Tissue-lowres.json");
+            Path exportScriptPath = groovyScriptDirectory.resolve("save4xMacroTiling.groovy")
             // Convert Path back to String and fix slashes to not be escape chars
             String jsonFilePathString = jsonFilePath.toString().replace("\\", "/");
             String exportScriptPathString = exportScriptPath.toString().replace("\\", "/");

src/main/groovy/qupath/ext/qp_scope/utilities/utilityFunctions.groovy

@@ -224,7 +224,7 @@ class utilityFunctions {
         return [installation   : "C:\\ImageAnalysis\\QPExtensionTest\\qp_scope\\src\\main\\pythonScripts/4x_bf_scan_pycromanager.py",
                 environment    : "C:\\Anaconda\\envs\\paquo",
                 projects       : "C:\\ImageAnalysis\\slides",
-                tissueDetection: "C:\\ImageAnalysis\\QPExtensionTest\\qp_scope\\src\\main\\groovyScripts/DetectTissueSize.groovy",
+                tissueDetection: "C:\\ImageAnalysis\\QPExtensionTest\\qp_scope\\src\\main\\groovyScripts/DetectTissue.groovy",
                 firstScanType  : "4x_bf",
                 secondScanType : "20x_bf",
                 tileHandling   : "Zip"] //Zip Delete or anything else is ignored

src/main/groovyScripts/Tissue-lowres.json

@@ -0,0 +1,61 @@
+{
+  "pixel_classifier_type": "OpenCVPixelClassifier",
+  "metadata": {
+    "inputPadding": 0,
+    "inputResolution": {
+      "pixelWidth": {
+        "value": 8.0,
+        "unit": "µm"
+      },
+      "pixelHeight": {
+        "value": 8.0,
+        "unit": "µm"
+      },
+      "zSpacing": {
+        "value": 1.0,
+        "unit": "z-slice"
+      },
+      "timeUnit": "SECONDS",
+      "timepoints": []
+    },
+    "inputWidth": 512,
+    "inputHeight": 512,
+    "inputNumChannels": 3,
+    "outputType": "CLASSIFICATION",
+    "outputChannels": [],
+    "classificationLabels": {
+      "0": {
+        "name": "Tissue",
+        "color": [
+          83,
+          47,
+          31
+        ]
+      }
+    }
+  },
+  "op": {
+    "type": "data.op.channels",
+    "colorTransforms": [
+      {
+        "combineType": "MEAN"
+      }
+    ],
+    "op": {
+      "type": "op.core.sequential",
+      "ops": [
+        {
+          "type": "op.filters.gaussian",
+          "sigmaX": 1.0,
+          "sigmaY": 1.0
+        },
+        {
+          "type": "op.threshold.constant",
+          "thresholds": [
+            230.0
+          ]
+        }
+      ]
+    }
+  }
+}