- added qupath script to rename and reclassify annotations

- renamed a script to make it more explicit

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cuisto"
-version = "2025.01.07"
+version = "2025.01.7"
 authors = [{ name = "Guillaume Le Goc", email = "[email protected]" }]
 description = "Quantification of objects in histological slices"
 readme = "README.md"

scripts/qupath-utils/tools/renameAndReclassifyAnnotations.groovy

@@ -0,0 +1,36 @@
+/**
+ * renameAndReclassifyAnnotations.groovy
+ *
+ * Set the name and classification of existing annotations based
+ * on their actual name and classification.
+ * Assumes the classification AND name is in the form "Name Hemisphere",
+ * and does not contain blank spaces other than the one separating
+ * the region name and the hemisphere.
+ * Hemispheres can be renamed.
+ * Note that this processes all existing annotations, so proceed with
+ * caution.
+ */
+
+// Parameters
+// Hesmishere names : [existing: new]
+def hemispheresMap = ["Ipsi": "Left", "Contra": "Right"]
+
+// Get all annotations objects
+def annotations = getAnnotationObjects()
+
+// Set classification based on the name
+for (annotation in annotations) {
+    // split name on blank space
+    oldNameParts = annotation.getName().split()
+    // get region name which is the first part
+    regionName = oldNameParts[0]
+    // get hemisphere name which is the second part
+    // and convert it to the new name
+    hemisphereName = hemispheresMap[oldNameParts[1]]
+    // build the new name as hemisphere: region
+    newClassification = hemisphereName + ": " + regionName
+    // set the new classification
+    annotation.setPathClass(getPathClass(newClassification))
+    // set the name to the region name only
+    annotation.setName(regionName)
+}

scripts/qupath-utils/tools/setNameAsClassification.groovy

@@ -0,0 +1,10 @@
+/**
+ * setNameAsClassification.groovy
+ *
+ * Set all annotations' names to their derived classification.
+ * Useful to rename the annotations with the region name in the
+ * case where the classification is in the form "Left: Region name".
+ */
+
+getAnnotationObjects().findAll {
+    it.setName(it.getClassifications()[-1])}