I’ve got some trouble using bUnwarpJ in a macro.
I did all the steps by hand and it worked just fine, but when I try to run the recorded macro, it doesn’t load the landmarks into the images before running the data, and therefore doesn’t do the transformation needed. This is the macro boiled down to these steps:
open("/path/template.tif"); open("/path/fiducialavgI-1.tif"); //run("Brightness/Contrast..."); setMinAndMax(0, 1); run("bUnwarpJ", "load=/u/npeters/Downloads/fiducial_landmarks/landmarks_camera_I.txt source_image=template.tif target_image=fiducialavgI-1.tif registration=Accurate image_subsample_factor=0 initial_deformation=Coarse final_deformation=[Very Fine] divergence_weight=0 curl_weight=0 landmark_weight=1 image_weight=0 consistency_weight=10 stop_threshold=0.01 verbose");
“load=…” is where it’s supposed to load the landmarks.
The landmark.txt is of the following format and works, as I mentioned, just fine when I load it manually.
Index xSource ySource xTarget yTarget 0 67 85 74 88 ...
My best guess is that the macro recorder leaves out a step? Really looking forward to any kind of help.