scripts to export annotations as rois and create masks from them

.gitignore

@@ -1 +1,4 @@
 *.class
+# User-specific stuff
+**/.idea/**
+

volker/toolsets/tree_ring_segmentation/groovy/export_rois.groovy

@@ -0,0 +1,18 @@
+import ij.plugin.frame.RoiManager
+
+
+def imageData = getCurrentImageData()
+def name = GeneralTools.getNameWithoutExtension(imageData.getServer().getMetadata().getName())
+def path = buildFilePath(PROJECT_BASE_DIR, name + ".zip")
+
+def annotations = getAnnotationObjects()
+def roiMan = new RoiManager(false)
+double x = 0
+double y = 0
+double downsample = 1 // Increase if you want to export to work at a lower resolution
+annotations.each {
+  def roi = IJTools.convertToIJRoi(it.getROI(), x, y, downsample)
+  roiMan.addRoi(roi)
+}
+roiMan.runCommand("Save", path)
+roiMan.runCommand("Reset")

volker/toolsets/tree_ring_segmentation/mri_tree_ring_tools.ijm

@@ -21,7 +21,7 @@ macro "extract masks Action Tool - C000T4b12e" {
 
 
 macro "batch extract masks Action Tool - C000T4b12b" {
-    batchExtractMasks();
+    batchExtractMasksFromZip();
 }
 
 
@@ -40,7 +40,7 @@ function extractMasks() {
     }
 }
 
-
+// Unused
 function batchExtractMasks() {
     folder = getDir("Select the input folder!");
     if (!File.exists(folder + "masks/")) {
@@ -59,6 +59,41 @@ function batchExtractMasks() {
     }
 }
 
+function batchExtractMasksFromZip() {
+    folder = getDir("Select the input folder!");
+    if (!File.exists(folder + "masks/")) {
+        File.makeDirectory(folder + "masks/");
+    }
+    files = getFileList(folder);
+    zipFiles = filterFilesByExtension(files, "zip");
+    for (i=0; i<zipFiles.length; i++) {
+        zipFile = zipFiles[i];
+        image = replace(zipFile, ".zip", ".tif");
+        open(folder + image);
+        Overlay.remove()
+        roiManager("open", folder + zipFile);
+        run("From ROI Manager");
+        roiManager("reset");
+        extractMasks();
+        save(folder + "masks/" + image);
+        close("*");
+    }
+}
+
+
+function filterFilesByExtension(files, ext) {
+    results = newArray(0);    
+    for (i=0; i<files.length; i++) {
+        file = files[i];
+        if (!endsWith(file, "." + ext)) {
+            continue;
+        }
+        results = Array.concat(results, file);
+    }
+    return results;
+}
+
+
 function showOptionsForCommand(command) {
     call("ij.Prefs.set", "mri.options.only", "true");
     run(command);