Updates to overall scope GUI

Checkbox to use annotations on first round, export json file, and pass location of exported json file to python
uw-loci · Dec 21, 2023 · ede0ffb · ede0ffb
1 parent 6c1e859
commit ede0ffb
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Showing 16 changed files with 211 additions and 63 deletions.
diff --git a/.gradle/7.5.1/checksums/checksums.lock b/.gradle/7.5.1/checksums/checksums.lock
diff --git a/.gradle/7.5.1/checksums/md5-checksums.bin b/.gradle/7.5.1/checksums/md5-checksums.bin
diff --git a/.gradle/7.5.1/checksums/sha1-checksums.bin b/.gradle/7.5.1/checksums/sha1-checksums.bin
diff --git a/.gradle/7.5.1/dependencies-accessors/dependencies-accessors.lock b/.gradle/7.5.1/dependencies-accessors/dependencies-accessors.lock
diff --git a/.gradle/7.5.1/executionHistory/executionHistory.bin b/.gradle/7.5.1/executionHistory/executionHistory.bin
diff --git a/.gradle/7.5.1/executionHistory/executionHistory.lock b/.gradle/7.5.1/executionHistory/executionHistory.lock
diff --git a/.gradle/7.5.1/fileHashes/fileHashes.bin b/.gradle/7.5.1/fileHashes/fileHashes.bin
diff --git a/.gradle/7.5.1/fileHashes/fileHashes.lock b/.gradle/7.5.1/fileHashes/fileHashes.lock
diff --git a/.gradle/7.5.1/fileHashes/resourceHashesCache.bin b/.gradle/7.5.1/fileHashes/resourceHashesCache.bin
diff --git a/.gradle/buildOutputCleanup/buildOutputCleanup.lock b/.gradle/buildOutputCleanup/buildOutputCleanup.lock
diff --git a/.gradle/buildOutputCleanup/outputFiles.bin b/.gradle/buildOutputCleanup/outputFiles.bin
diff --git a/.gradle/file-system.probe b/.gradle/file-system.probe
diff --git a/build.gradle b/build.gradle
@@ -44,7 +44,7 @@ dependencies {
     implementation "io.github.qupath:qupath-extension-bioformats:${qupathVersion}"
     implementation "qupath.ext.basicstitching:BasicStitching:0.1.0"
 
-    //TODO figure out syntax for other plugins
+
     // For logging - the version comes from QuPath's version catalog at
     // https://github.com/qupath/qupath/blob/main/gradle/libs.versions.toml
     // See https://docs.gradle.org/current/userguide/platforms.html

diff --git a/src/main/groovy/qupath/ext/qp_scope/QP_scope.groovy b/src/main/groovy/qupath/ext/qp_scope/QP_scope.groovy
@@ -60,7 +60,7 @@ class QP_scope implements QuPathExtension {
 		fileNameStitching.setOnAction(e -> {
 			//TODO check preferences for all necessary entries
 
-			QP_scope_GUI.createGUI()
+			QP_scope_GUI.createGUI1()
 
 		})
 		menu.getItems() << fileNameStitching

diff --git a/src/main/groovy/qupath/ext/qp_scope/functions/QP_scope_GUI.groovy b/src/main/groovy/qupath/ext/qp_scope/functions/QP_scope_GUI.groovy
diff --git a/src/main/groovy/qupath/ext/qp_scope/utilities/utilityFunctions.groovy b/src/main/groovy/qupath/ext/qp_scope/utilities/utilityFunctions.groovy
@@ -131,17 +131,18 @@ class utilityFunctions {
      * @param x2 The second x-coordinate to be passed to the Python script.
      * @param y2 The second y-coordinate to be passed to the Python script.
      */
-    static void runPythonCommand(String anacondaEnvPath, String pythonScriptPath,String projectsFolderPath, String sampleLabel, String x1, String y1, String x2, String y2) {
+    static void runPythonCommand(String anacondaEnvPath, String pythonScriptPath,String projectsFolderPath, String sampleLabel,String imageType, String x1 = "", String y1 = "", String x2 = "", String y2 = "", annotationJsonFileLocation = null) {
         try {
             def logger = LoggerFactory.getLogger(QuPathGUI.class)
             // Path to the Python executable in the Anaconda environment
             String pythonExecutable = "${anacondaEnvPath}/python.exe";
 
             // Combine coordinates into a single argument
-            String args = "$pythonScriptPath, $projectsFolderPath, $sampleLabel, ${x1},${y1},${x2},${y2}";
+            String args = "$anacondaEnvPath $projectsFolderPath $sampleLabel $imageType $x1 $y1 $x2 $y2 $annotationJsonFileLocation";
             logger.info(args)
             // Construct the command
             String command = "\"${pythonExecutable}\" \"${pythonScriptPath}\" ${args}";
+            logger.info("Check the following command")
             logger.info(command)
             // Execute the command
             Process process = command.execute();
@@ -167,6 +168,6 @@ 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\\python\\py_dummydoc.py", environment: "C:\\Anaconda\\envs\\paquo", projects: "C:\\ImageAnalysis\\slides", firstScanType: "4x_bf_", secondScanType:"20x_bf"]
+        return [installation: "C:\\ImageAnalysis\\python\\pycromanager_step_1.py", environment: "C:\\Anaconda\\envs\\paquo", projects: "C:\\ImageAnalysis\\slides", firstScanType: "4x_bf_", secondScanType:"20x_bf", deleteTiles:"True"]
     }
 }