// Registration
//run("Memory & Threads...", "maximum=6951 parallel=1");

print ("-> images opening...");
im_target="./temp/bUnwarpJ/Rat_Kidney_HE.jpg"
im_source="./temp/bUnwarpJ/Rat_Kidney_PanCytokeratin.jpg"
output="./temp/bUnwarpJ/"
open(im_target);
open(im_source);

print ("-> start registration...");
run("bUnwarpJ",
    "source_image=Rat_Kidney_PanCytokeratin.jpg target_image=Rat_Kidney_HE.jpg "
    + " registration=Fast image_subsample_factor=1 initial_deformation=[Very Coarse] final_deformation=Fine divergence_weight=0.0 curl_weight=0.0 landmark_weight=0.0 image_weight=1 consistency_weight=10 stop_threshold=0.001 verbose save_transformations "
    + " save_direct_transformation="+output+"direct_transform.txt "
    + " save_inverse_transformation="+output+"invers_transform.txt");
print ("-> registration finished");

run("Close All");

// Transform image
call("bunwarpj.bUnwarpJ_.elasticTransformImageMacro",
     im_target, im_source, output+"direct_transform.txt", output+"Rat_Kidney_PanCytokeratin_warped.jpg");
// resave image while bunwarpj macro have an issue
open(output+"Rat_Kidney_PanCytokeratin.jpg");
saveAs("PNG", output+"Rat_Kidney_PanCytokeratin.jpg");

run("Close All");

// Convert transformation
call("bunwarpj.bUnwarpJ_.convertToRawTransformationMacro",
     im_target, im_source, output+"invers_transform.txt", output+"transform_raw.txt");
print ("-> DONE");

//run("Quit");
//exit();


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