Hi Troels, Could you rename this to the error_analysis.covariance_matrix user function? I.e. as I mentioned in http://thread.gmane.org/gmane.science.nmr.relax.scm/23526/focus=7096. There is nothing about this new user function that is specific to the relaxation curve-fitting analysis type. If the covariance matrix error estimation technique is extended to the other analysis types - reduced spectral density mapping, model-free analysis, frame order analysis, N-state model - then this function will have to be duplicated each time. I am actually considering using it for the frame order analysis where the optimisation of one model (from ~10) takes days or weeks to complete.
Also, you should develop such features in branches rather than the trunk. The trunk is supposed to be stable so that I can make new bug fix releases quickly, if users require it. The recent changes have broken the GUI tests and the software verification tests. Cheers, Edward On 12 September 2014 11:25, <[email protected]> wrote: > Author: tlinnet > Date: Fri Sep 12 11:25:56 2014 > New Revision: 25776 > > URL: http://svn.gna.org/viewcvs/relax?rev=25776&view=rev > Log: > Implemented userfunction 'relax_fit.rx_err_estimate' in relax_fit to estimate > rx and i0 errors from the Jacobian Co-variance matrix. > > Modified: > trunk/user_functions/relax_fit.py > > Modified: trunk/user_functions/relax_fit.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/user_functions/relax_fit.py?rev=25776&r1=25775&r2=25776&view=diff > ============================================================================== > --- trunk/user_functions/relax_fit.py (original) > +++ trunk/user_functions/relax_fit.py Fri Sep 12 11:25:56 2014 > @@ -22,9 +22,14 @@ > # Module docstring. > """The relax_fit user function definitions.""" > > +# Python module imports. > +from os import sep > + > # relax module imports. > +from graphics import ANALYSIS_IMAGE_PATH > from pipe_control import spectrum > from specific_analyses.relax_fit.uf import relax_time, select_model > +from specific_analyses.relax_fit.estimate_rx_err import estimate_rx_err > from user_functions.data import Uf_info; uf_info = Uf_info() > from user_functions.objects import Desc_container > > @@ -65,6 +70,50 @@ > uf.wizard_size = (700, 500) > > > +# The relax_fit.rx_err_estimate user function. > +uf = uf_info.add_uf('relax_fit.rx_err_estimate') > +uf.title = "Estimate Rx errors by the Jacobian matrix." > +uf.title_short = "Estimate Rx errors." > +uf.add_keyarg( > + name = "spin_id", > + py_type = "str", > + arg_type = "spin ID", > + desc_short = "spin ID to restrict value setting to", > + desc = "The spin ID string to restrict value setting to.", > + can_be_none = True > +) > +uf.add_keyarg( > + name = "epsrel", > + py_type = "float", > + default = 0.0, > + desc_short = "parameter to remove linear-dependent columns.", > + desc = "The parameter to remove linear-dependent columns when J is rank > deficient.", > + can_be_none = False > +) > +uf.add_keyarg( > + name = "verbosity", > + default = 1, > + py_type = "int", > + desc_short = "amount of information to print.", > + desc = "The higher the value, the greater the verbosity.", > + can_be_none = False > +) > +# Description. > +uf.desc.append(Desc_container()) > +uf.desc[-1].add_paragraph("This is a new experimental feature from version > 3.3.") > +uf.desc[-1].add_paragraph("This will estimate Rx errors by using the > exponential decay Jacobian matrix 'J' to compute the covariance matrix of the > best-fit parameters.") > +uf.desc[-1].add_paragraph("This can be used to for comparison to Monte-Carlo > simulations.") > +uf.desc[-1].add_paragraph("This method is inspired from the GNU Scientific > Library (GSL).") > +uf.desc[-1].add_paragraph("The covariance matrix is given by: covar = Qxx = > (J^T.W.J)^-1, where the weight matrix W is constructed by the multiplication > of an Identity matrix I and a weight array w. The weight array is > 1/errors^2, which then gives W = I.w = I x 1/errors^2.") > +uf.desc[-1].add_paragraph("Qxx is computed by QR decomposition, J^T.W.J=QR, > Qxx=R^-1. Q^T. The columns of R which satisfy: |R_{kk}| <= epsrel |R_{11}| > are considered linearly-dependent and are excluded from the covariance matrix > (the corresponding rows and columns of the covariance matrix are set to > zero).") > +uf.desc[-1].add_paragraph("The parameter 'epsrel' is used to remove > linear-dependent columns when J is rank deficient.") > +uf.backend = estimate_rx_err > +uf.menu_text = "&rx_err_estimate" > +uf.gui_icon = "relax.relax_fit" > +uf.wizard_size = (800, 800) > +uf.wizard_image = ANALYSIS_IMAGE_PATH + sep + 'blank_150x150.png' > + > + > # The relax_fit.select_model user function. > uf = uf_info.add_uf('relax_fit.select_model') > uf.title = "Select the relaxation curve type." > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits 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-commits _______________________________________________ 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
