Osprey without GUI

Dear experts,

I’m trying to run Osprey on our HPC, which doesn’t support the GUI Layout Toolbox or Widgets Toolbox. I’ve gotten Osprey to run through to completion and it outputs quantified results; however, I’m not sure if there’s a way to extract the visuals normally produced by the Osprey GUI (e.g., spectrum display and fit plot) for QC purposes.

My code currently looks like this:

[MRSCont] = OspreyJob('OspreyJob.m');
[MRSCont] = OspreyLoad(MRSCont);
[MRSCont] = OspreyProcess(MRSCont);
[MRSCont] = OspreyCoreg(MRSCont);
[MRSCont] = OspreySeg(MRSCont);
[MRSCont] = OspreyFit(MRSCont);
[MRSCont] = OspreyQuantify(MRSCont);

I’m happy to provide any further information necessary.



Hi Mark,

Thanks for getting in touch, and for providing this really critical feedback. I think we can certainly make some progress in terms of the reporting (potentially generating HTML outputs for each dataset, or something like that).

For the time being, the functions you can use are in the plot folder of the Osprey repository, and are called osp_plotLoad, osp_plotProcess, osp_plotFit, osp_plotCoreg, osp_plotSegment, osp_plotMeanSpec and osp_plotOverviewSpec. They all take the MRSCont container as first input argument; some then want the running number of the dataset you want to display, while others require you to select the (sub-)spectrum you want to display (e.g. 'A', 'diff1' or 'ref').

Let us know if that helps for the time being (and if not, what you would envision an ideal outcome to look like!).