--- a
+++ b/Alignment - StoreMatrix automatic.groovy
@@ -0,0 +1,52 @@
+// From https://forum.image.sc/t/qupath-multiple-image-alignment-and-object-transfer/35521
+//0.2.0m9
+//Script writes out a file with the name of the current image, and the Affine Transformation in effect in the current viewer.
+//Can get confused if there is more than one overlay active at once.
+//Current image should be the destination image
+// Michael Nelson 03/2020
+import static qupath.lib.gui.scripting.QPEx.*
+import qupath.ext.align.gui.ImageServerOverlay
+/*
+Usage:
+- Open reference image in viewer
+- Open the `Interactive Image Alignment` overlay, align an image
+- While the overlay is still open, set `name` to the name of the current moving image, and run script
+ */
+
+//def name = getProjectEntry().getImageName()
+////////////////////
+
+def name='D1_PIMO' //specify name of moving (transform) image, as listed in the project
+
+////////////////////
+path = buildFilePath(PROJECT_BASE_DIR, 'Affine')
+mkdirs(path)
+path = buildFilePath(PROJECT_BASE_DIR, 'Affine', name)
+
+
+
+
+def overlay = getCurrentViewer().getCustomOverlayLayers().find {it instanceof ImageServerOverlay}
+
+affine = overlay.getAffine()
+
+print affine
+afString = affine.toString()
+afString = afString.minus('Affine [').minus(']').trim().split('\n')
+cleanAffine =[]
+afString.each{
+    temp = it.split(',')
+    temp.each{cleanAffine << Double.parseDouble(it)}
+}
+
+def matrix = []
+affineList = [0,1,3,4,5,7]
+for (i=0;i<12; i++){
+if (affineList.contains(i))
+    matrix << cleanAffine[i]
+}
+
+new File(path).withObjectOutputStream {
+    it.writeObject(matrix)
+}
+print 'Done!'
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