Minor fixes to script inputs and running.

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

@@ -7,15 +7,14 @@ class PythonTestScripts {
 """
 import sys
 
+print('12345', '54321')
 # Check if any command-line arguments were provided
-if len(sys.argv) == 1:
+
+for arg in sys.argv:
+    # Print each argument on a separate line
+    print(arg)
     # No arguments were passed, print default coordinates
-    print('12345', '54321')
-else:
-    # Arguments were passed, print an error message to standard error
-    print("Error: Unexpected arguments received.", file=sys.stderr)
-    print('12345', '54321')
-    sys.exit(1)  # Optionally exit with a non-zero status to indicate an error"""
+"""
 
         return getStageCoordinatesTest
     }
@@ -35,10 +34,10 @@ if len(sys.argv) == 3:
         print(f"X: {X}, Y: {Y}")
     except ValueError:
         print("Invalid arguments. Both X and Y must be doubles.", file=sys.stderr)
-        #sys.exit(1)
+        sys.exit(1)
 else:
     print("Expected two arguments, X and Y as doubles", file=sys.stderr)
-    #sys.exit(1)
+    sys.exit(1)
 
 """
         return sendStageCoordinatesTest

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

@@ -1,6 +1,7 @@
 package qupath.ext.qp_scope.utilities
 
 import javafx.application.Platform
+import org.slf4j.Logger
 import org.slf4j.LoggerFactory
 import qupath.lib.gui.QuPathGUI
 import qupath.lib.gui.commands.ProjectCommands
@@ -204,7 +205,7 @@ class UtilityFunctions {
                     return runTestPythonScript(anacondaEnvPath, getStageScriptPath, arguments)
                 }
                 // Construct the command
-                String command = "\"" + pythonExecutable + "\" -u \"" + pythonScriptPath + "\" " + arguments
+                String command = "\"" + pythonExecutable + "\" -u \"" + getStageScriptPath + "\" " + arguments
                 // Execute the command
                 Process process = command.execute()
                 logger.info("Executing command: " + command)
@@ -301,7 +302,10 @@ class UtilityFunctions {
  * @param arguments A list of arguments to pass to the python script.
  * @return The output from the Python script execution, or null in case of an error.
  */
+
     static runTestPythonScript(String anacondaEnvPath, String pythonScriptPath, List arguments) {
+        Logger logger2 = LoggerFactory.getLogger(QuPathGUI.class);
+        logger2.warn("Default script not found, running test script for $pythonScriptPath")
         String pythonScript = "";
         logger.info("calling runtestpythoncommand on $pythonScriptPath")
         // Determine which test script to use based on the file name

src/main/pythonScripts/getStageCoordinates.py

@@ -1,11 +1,15 @@
 import sys
 
+print('12345', '54321')
 # Check if any command-line arguments were provided
-if len(sys.argv) == 2:
+
+for arg in sys.argv:
+    # Print each argument on a separate line
+    print(arg)
     # No arguments were passed, print default coordinates
-    print('12345', '54321')
-else:
-    # Arguments were passed, print an error message to standard error
-    print("Error: Unexpected arguments received.", file=sys.stderr)
-    print('12345', '54321')
-    sys.exit(1)  # Optionally exit with a non-zero status to indicate an error
+
+# else:
+#     # Arguments were passed, print an error message to standard error
+#     print("Error: Unexpected arguments received.", file=sys.stderr)
+#     print('12345', '54321')
+#     sys.exit(1)  # Optionally exit with a non-zero status to indicate an error

src/main/pythonScripts/moveStageToCoordinates.py

@@ -9,7 +9,7 @@
         print(f"X: {X}, Y: {Y}")
     except ValueError:
         print("Invalid arguments. Both X and Y must be doubles.", file=sys.stderr)
-        #sys.exit(1)
+        sys.exit(1)
 else:
     print("Expected two arguments, X and Y as doubles", file=sys.stderr)
-    #sys.exit(1)
+    sys.exit(1)