Updates to folder organization and some of the python scripts.

src/main/groovy/qupath/ext/qp_scope/QP_scope.groovy

@@ -61,7 +61,8 @@ class QP_scope implements QuPathExtension {
         def qpScope1 = new MenuItem("Start qp_scope")
         // TODO: tooltip
         qpScope1.setOnAction(e -> {
-            // TODO: check preferences for all necessary entries
+            // TODO: check preferences for all necessary entries, and check for micromanager running+version
+            // search java app with a subprocesses for MicroManager +version number
             QP_scope_GUI.createGUI1()
         })
 

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

@@ -39,7 +39,7 @@ class QP_scope_GUI {
 
     // New text fields for Python environment, script path, and sample label
     static TextField virtualEnvField = new TextField(preferences.environment)
-    static TextField pythonScriptField = new TextField(preferences.installation)
+    static TextField pythonScriptField = new TextField(preferences.pycromanager)
     static TextField projectsFolderField = new TextField(preferences.projects)
     static TextField sampleLabelField = new TextField("First_Test")  // New field for sample label
     // GUI3
@@ -83,6 +83,8 @@ class QP_scope_GUI {
             boolean dataCheck = true
             def annotations = QP.getAnnotationObjects()
             // Check if using annotations
+
+            //TODO REPLACE ALL OF THIS WITH TILING
             if (useAnnotationsCheckBox.isSelected()) {
 
                 // Check if annotations are present

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

@@ -147,24 +147,18 @@ class utilityFunctions {
                 Process process = command.execute();
                 logger.info("Executing command: " + command);
                 logger.info("This should get stage coordinates back")
-                // Construct the command
-                BufferedReader reader = new BufferedReader(new InputStreamReader(process.getInputStream()));
-                String line;
-                String value1
-                String value2
-                while ((line = reader.readLine()) != null) {
-                    // Process the line to retrieve value1 and value2
-                    // For example, if they are printed in a single line separated by space
-                    String[] values = line.split(" ");
-                    value1 = values[0];
-                    value2 = values[1];
-                    // Do something with the values
+                List<String> result = handleProcessOutput(process)
+                if (result != null) {
+                    logger.info("Received coordinates: ${result[0]}, ${result[1]}")
+                    return result
+                } else {
+                    logger.error("Error occurred or no valid output received from the script.")
+                    return null
                 }
-                return [value1, value2]
             } else if (arguments.size() == 2) {
                 // Change the script to 'moveStageToCoordinates.py'
                 File scriptFile = new File(pythonScriptPath);
-                pythonScriptPath = new File(scriptFile.getParent(), "moveStageToCoordinates.py").getCanonicalPath();
+                pythonScriptPath = new File(scriptFile.parent, "moveStageToCoordinates.py").canonicalPath
             }
 
             String args = arguments != null ? arguments.collect { "\"$it\"" }.join(' ') : "";
@@ -176,18 +170,52 @@ class utilityFunctions {
             // Execute the command
             Process process = command.execute();
 
-            process.waitFor();
+            // Redirect the output and error streams to the logger
+            process.consumeProcessOutput(new StringWriter(), new StringWriter())
 
-            // Read and log standard output
-            process.inputStream.eachLine { line -> logger.info(line) };
+            // Wait for the process to complete
+            process.waitFor()
 
-            // Read and log standard error
-            process.errorStream.eachLine { line -> logger.error(line) };
+            // Log the output and error (or use it as needed)
+            logger.info(process.text) // This logs the standard output
+            logger.error(process.err.text) // This logs the standard error
             return null
         } catch (Exception e) {
             e.printStackTrace();
         }
     }
+    static List<String> handleProcessOutput(Process process) {
+        BufferedReader outputReader = new BufferedReader(new InputStreamReader(process.getInputStream()));
+        BufferedReader errorReader = new BufferedReader(new InputStreamReader(process.getErrorStream()));
+
+        String line;
+        List<String> outputLines = []
+        List<String> errorLines = []
+        String value1 = null
+        String value2 = null
+
+        while ((line = outputReader.readLine()) != null) {
+            outputLines.add(line)
+            // Assuming coordinates are on the first line
+            if (outputLines.size() == 1) {
+                String[] values = line.split(" ");
+                value1 = values[0];
+                value2 = values[1];
+            }
+        }
+
+        while ((line = errorReader.readLine()) != null) {
+            errorLines.add(line)
+        }
+
+        // Check for errors or invalid output
+        if (!errorLines.isEmpty() || value1 == null || value2 == null) {
+            return null;
+        }
+
+        return [value1, value2];
+    }
+
 //    static void runPythonCommand(String anacondaEnvPath, String pythonScriptPath, List arguments) {
 //        try {
 //            def logger = LoggerFactory.getLogger(QuPathGUI.class)
@@ -221,10 +249,10 @@ class utilityFunctions {
         //If preferences are null or missing, throw an error and close
         //Open to discussion whether scan types should be included here or typed every time, or some other option
         //TODO fix the installation to be a folder with an expected .py file target? Or keep as .py file target?
-        return [installation   : "C:\\ImageAnalysis\\QPExtensionTest\\qp_scope\\src\\main\\pythonScripts/4x_bf_scan_pycromanager.py",
+        return [ pycromanager   : "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/DetectTissue.groovy",
+                projects       : "C:\\ImageAnalysis\\QPExtensionTest\\data\\slides",
+                tissueDetection: "DetectTissue.groovy",
                 firstScanType  : "4x_bf",
                 secondScanType : "20x_bf",
                 tileHandling   : "Zip"] //Zip Delete or anything else is ignored
@@ -505,6 +533,10 @@ class utilityFunctions {
     //Convert the QuPath pixel based coordinates for a location into the MicroManager micron based stage coordinates
     static List<Double> QPtoMicroscopeCoordinates(List<Double> qpCoordinates, Double imagePixelSize, Object transformation) {
         //TODO figure out conversion
+        def xUpperLeft = qpCoordinates[0]*imagePixelSize
+        def yUpperLeft = qpCoordinates[1]*imagePixelSize
+
+
         def mmCoordinates = qpCoordinates
         return mmCoordinates
     }

src/main/pythonScripts/4x_bf_scan_pycromanager.py

@@ -3,138 +3,111 @@
 import shutil
 import glob
 
-# Function to log messages
-def log_message(message):
-    with open('D:/log.txt', 'a') as log_file:
-        print(message, file=log_file, flush=True)
-
 def copy_tif_files(projectsFolderPath, sampleLabel, imageType):
 
     if "4x" in imageType:
-        TILES_LOCATION = 'C:/ImageAnalysis/Brightfield demo/Tiles/BurnTest2-4x-bf'
+        TILES_LOCATION = 'C:/ImageAnalysis/QPExtensionTest/data/sample_tiles/some_4x_data'
     else:
-        TILES_LOCATION = 'C:/ImageAnalysis/Brightfield demo/Tiles/PDAC.3.A_Unstained-20x--C-7'
+        TILES_LOCATION = 'C:/ImageAnalysis/QPExtensionTest/data/sample_tiles/some_20x_data'
 
-    log_message(f"Copying .tif files from {TILES_LOCATION} to {projectsFolderPath}/{sampleLabel}")
+    print(f"Copying .tif files from {TILES_LOCATION} to {projectsFolderPath}/{sampleLabel}")
 
     dest_dir = os.path.join(projectsFolderPath, sampleLabel, imageType)
-    log_message(f"Destination directory: {dest_dir}")
+    print(f"Destination directory: {dest_dir}")
     if not os.path.exists(dest_dir):
-        log_message("Destination directory does not exist, creating it.")
+        print("Destination directory does not exist, creating it.")
         os.makedirs(dest_dir)
 
     tif_files = []
     for extension in ['*.tif', '*.tiff', '*.txt']:
         tif_files.extend(glob.glob(os.path.join(TILES_LOCATION, extension)))
 
-    log_message(f"Number of .tif files found: {len(tif_files)}")
+    print(f"Number of .tif files found: {len(tif_files)}")
     if not tif_files:
-        log_message(f"No .tif files found in {TILES_LOCATION}")
+        print(f"No .tif files found in {TILES_LOCATION}")
         return False
 
     for file in tif_files:
         try:
-            log_message(file)
+            print(file)
             shutil.copy(file, dest_dir)
         except Exception as e:
             print(f"Error copying file {file}: {e}")
 
-
     return True
 
-log_message("Python script started.")
+print("Python script started.")
 projectsFolderPath = sys.argv[2]
-log_message(f"Projects Folder Path: {projectsFolderPath}")
+print(f"Projects Folder Path: {projectsFolderPath}")
 sampleLabel = sys.argv[3]
-log_message(f"Sample Label: {sampleLabel}")
+print(f"Sample Label: {sampleLabel}")
 imageType = sys.argv[4]
-log_message(f"Image Type: {imageType}")
+print(f"Image Type: {imageType}")
 
 success = copy_tif_files(projectsFolderPath, sampleLabel, imageType)
 
 if not success:
-    log_message("File copying did not complete successfully.")
+    print("File copying did not complete successfully.")
 else:
-    log_message("File copying completed successfully.")
+    print("File copying completed successfully.")
 
 
 # import os
 # import sys
 # import shutil
 # import glob
 
-# # Redirecting print statements to a log file
-# sys.stdout = open('logpython.txt', 'w')
-# print(os.getcwd())
+# # Function to log messages
+# def log_message(message):
+#     with open('D:/log.txt', 'a') as log_file:
+#         print(message, file=log_file, flush=True)
+
 # def copy_tif_files(projectsFolderPath, sampleLabel, imageType):
 
 #     if "4x" in imageType:
-#         TILES_LOCATION = 'C:/ImageAnalysis/Brightfield demo/Tiles/BurnTest2-4x-bf'  # Replace with the absolute path
+#         TILES_LOCATION = 'C:/ImageAnalysis/QPExtensionTest/data/sample_tiles/some_4x_data'
 #     else:
-#         TILES_LOCATION = 'C:/ImageAnalysis/Brightfield demo/Tiles/PDAC_MetroHealth_N352L42-20x--null'
-
+#         TILES_LOCATION = 'C:/ImageAnalysis/QPExtensionTest/data/sample_tiles/some_20x_data'
 
-#     print(f"Copying .tif files from {TILES_LOCATION} to {projectsFolderPath}/{sampleLabel}")
+#     log_message(f"Copying .tif files from {TILES_LOCATION} to {projectsFolderPath}/{sampleLabel}")
 
-#     dest_dir = os.path.join(projectsFolderPath, sampleLabel, f"{imageType}{sampleLabel}")
-#     print(f"Destination directory: {dest_dir}")
+#     dest_dir = os.path.join(projectsFolderPath, sampleLabel, imageType)
+#     log_message(f"Destination directory: {dest_dir}")
 #     if not os.path.exists(dest_dir):
-#         print("Destination directory does not exist, creating it.")
+#         log_message("Destination directory does not exist, creating it.")
 #         os.makedirs(dest_dir)
 
-#     # Find all .tif files
 #     tif_files = []
 #     for extension in ['*.tif', '*.tiff', '*.txt']:
 #         tif_files.extend(glob.glob(os.path.join(TILES_LOCATION, extension)))
 
-#     print(f"Number of .tif files found: {len(tif_files)}")
-#     #print(f"Files: {tif_files}")
-#     # Check if any.tif files were found
+#     log_message(f"Number of .tif files found: {len(tif_files)}")
 #     if not tif_files:
-#         print(f"No .tif files found in {TILES_LOCATION}")
+#         log_message(f"No .tif files found in {TILES_LOCATION}")
 #         return False
-#     #Copy each .tif file
-#     #shutil.copy(tif_files[0], dest_dir)
-#     # print(f"Copying last file: {tif_files[-1]}")
-#     # shutil.copy(tif_files[-1], dest_dir)
-
-#     # for file in tif_files[:42]:
-#     #     print(f"Copying file: {file}")
-#     #     shutil.copy(file, dest_dir)
 
 #     for file in tif_files:
 #         try:
-#             print(f"Copying file: {file}")
+#             log_message(file)
 #             shutil.copy(file, dest_dir)
 #         except Exception as e:
 #             print(f"Error copying file {file}: {e}")
 
-#     # print("Copy operation completed.")
 #     return True
 
-
-# # if len(sys.argv) != 9:
-# #     print("Incorrect arguments for function: python script.py <projectsFolderPath> <sampleLabel> <imageType> <x1> <y1> <x2> <y2>")
-# #     print(len(sys.argv))
-# #     return
-# print("Python script started.")
+# log_message("Python script started.")
 # projectsFolderPath = sys.argv[2]
-# print(f"Projects Folder Path: {projectsFolderPath}")
+# log_message(f"Projects Folder Path: {projectsFolderPath}")
 # sampleLabel = sys.argv[3]
-# print(f"Sample Label: {sampleLabel}")
+# log_message(f"Sample Label: {sampleLabel}")
 # imageType = sys.argv[4]
-# print(f"Image Type: {imageType}")
-# # x1, y1, x2, y2 are received but not used in this script. They can be used if needed.
-
-# #jsonFileLocation = sys.arv[9]
-# #WOULD NEED FUNCTION HERE TO TRANSLATE COORDINATES TO STAGE COORDINATES
+# log_message(f"Image Type: {imageType}")
 
 # success = copy_tif_files(projectsFolderPath, sampleLabel, imageType)
 
 # if not success:
-#     print("File copying did not complete successfully.")
+#     log_message("File copying did not complete successfully.")
 # else:
-#     print("File copying completed successfully.")
+#     log_message("File copying completed successfully.")
+
 
-# # Close the log file
-# sys.stdout.close()

src/main/pythonScripts/getStageCoordinates.py

@@ -1,17 +1,10 @@
 import sys
 
-# Function to log messages
-def log_message(message):
-    with open('D:/log.txt', 'a') as log_file:
-        print(message, file=log_file, flush=True)
-
-log_message("Python script started.")
-
-# Check if the first command-line argument is None
-if len(sys.argv) >= 2:
-    first_argument = sys.argv[1]
-    if first_argument is None:
-        log_message("The first argument is None.")
+# Check if any command-line arguments were provided
+if len(sys.argv) == 1:
+    # No arguments were passed, print default coordinates
+    print('12345', '54321')
 else:
-    log_message("No arguments were provided.")
-print('12345', '54321')
+    # Arguments were passed, print an error message to standard error
+    print("Error: Unexpected arguments received.", file=sys.stderr)
+    sys.exit(1)  # Optionally exit with a non-zero status to indicate an error

src/main/pythonScripts/moveStageToCoordinates.py

@@ -1,20 +1,15 @@
 import sys
 
-# Function to log messages
-def log_message(message):
-    with open('D:/log.txt', 'a') as log_file:
-        print(message, file=log_file, flush=True)
-
-log_message("Python script started.")
-
 # Check if there are exactly two command-line arguments
 if len(sys.argv) == 3:
     try:
         # Parse the two arguments as doubles (X and Y)
         X = float(sys.argv[1])
         Y = float(sys.argv[2])
-        log_message(f"X: {X}, Y: {Y}")
+        print(f"X: {X}, Y: {Y}")
     except ValueError:
-        log_message("Invalid arguments. Both X and Y must be doubles.")
+        print("Invalid arguments. Both X and Y must be doubles.", file=sys.stderr)
+        sys.exit(1)
 else:
-    log_message("Usage: python script.py <X> <Y>")
+    print("Expected two arguments, X and Y as doubles", file=sys.stderr)
+    sys.exit(1)