Hi, See below:
> The problem is, that if you make multiply with [300], to a numpy > array, it will expand the last axis. > > Reshaping that into a usable form is the problem. > > I spent many many many hours, to get to this: > # Reshape dw to per experiment and nr spins. Or for R20A per > experiment, spin and frequency. > [300] -> [1, 300] : [300] -> [1, 100, 3] > > # Expand axis > [1, 300] -> [1, 300, 1, 1, 1] : [1, 100, 3]-> [1, 100, 3, 1, 1] > > # Then tile to dimensions > [1, 300, 1, 1, 1] -> [1, 300, 3, 1, 22] : [1, 100, 3, 1, 22] > > This is a very logic build up of the shapes. > The add or multiply would multiply to the last axis. > > The only thing I could do, was to create newaxis. > And then tile up! > > --------- Example code to play with. > import numpy as np > s = [1, 100, 3, 1, 22] > print "dw" > dw = np.asarray(range(100)) > print dw.shape > dw1 = dw.reshape( (s[0], s[1]) ) > print dw1.shape > dw2 = dw1[:,:,None,None,None] > print dw2.shape > dw3 = np.tile(dw2, (1, 1, s[2], s[3], s[4])) > print dw3.shape > > print "r20" > r = np.asarray(range(300)) > print r.shape > r1 = r.reshape( (s[0], s[1], s[2]) ) > print r1.shape > r2 = r1[:,:,:,None,None] > print r2.shape > r3 = np.tile(r2, (1, 1, 1, s[3], s[4])) > print r3.shape > ------------------- > > > With this, I think I am done! With the code example I gave (http://thread.gmane.org/gmane.science.nmr.relax.devel/6135/focus=6154), all of this logic can be replaced. I hope the example is enough for both dw and R20 structure creation. Despite reintroducing a loop - note that the loop does not involve calls to the lib.dispersion functions so it does not have anywhere near the same cost as the loops you eliminated - this solution will speed things up by avoiding automatic Python data structure creation and deletion. > I really would like to wrap this up and continue with my own stuff. > So, what needs to be done, before you can accept this? > > I will: > Expand to other CPMG models, which are analytical > Include R1rho. That should be rather easy now with your infrastructure. I would recommend the dw and R20 speed ups first, as that will make the target functions far simpler and quicker to upgrade to the new design. > I cannot do for numerical, do to the looping. To keep the API clean, the looping needs to be shifted to be inside the lib.dispersion functions. That should be easy enough. > Should I add unit tests for each? You probably saw how useful the unit tests were when you were making the changes to the 'disp_spin_speed' branch. Feel free to add tests as you wish. I don't think we have universal coverage of all models yet, though I could be wrong with that. Additional points would be to clean up the code and comments (for example there are quite a few '##' that should be '#', and a few trivial whitespace issues). Then I can check it and give feedback for anything else that needs to be done. I can then merge the branch back to trunk and release it with a new version of relax. Cheers! Edward _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
