I would like to understand better the lines corresponding to the View registration in the .xml files from the Big Data Viewer, as I would need them for the mamut2r package I am currently developping and which aim is to provide tools to import MaMuT .xml files in R (see https://github.com/marionlouveaux/mamut2r for more info).
I am currently working on the dataset provided in the “Get started” page of the MaMuT Fiji plugin (dataset here: http://bds.mpi-cbg.de/mamut-example/ and MaMuT manual here https://imagej.net/Getting_started_with_MaMuT).
In the ViewRegistration nodes of the MaMuT_Parhyale_demo.xml, I see two affine transforms per timepoint and setup stored as vectors (one named calibration and the second one Fast 3d geometric hashing…).
(1) In the affine transform vectors, which indices correspond to the translation, the scales, the skews and the angles? I need to know that in order to build the 4x4 matrix from its constituent using the buildAffine() function from the RNiftyReg package.
(2) I guess that I need to compute the composition of the affine transforms when there is two or more of them. If I got it right from what I read online, the order of the composition matter. Here the order would be calibration*Fast 3d geometric hashing, is that right?
(3) Can I assume that the structure of other .xml coming from the BigDataViewer will be similar, e.g. one or several affine transforms stored for each timepoint and setup in the nodes?
Many thanks in advance