Hi Troels, I just noticed that you have a footer at the end of your messages. It might be better to turn this off for mailing list messages - it's best that your work number and address is not archived permanently all over the internet.
Regards, Edward On 7 May 2013 14:18, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > Thanks for the lengthy explanation, and I hope that I can honor your effort > in explaining. :-) > > I would be interested to get these things to work in relax, which we most > often use in our lab: > - off-resonance T1rho > - CPMG > -- Fast (Meiboom) > -- slow/intermediate (Richard-Carver) > -- very slow (Tollinger/Kay equation) > > So I will go for the Tollinger, since that is the "easiest" next to the > fast. > > I would need to do the code development at my Windows machine, and > I checked out the relax-disp branch yesterday. > Should I/How do I compile with scons under windows? > Or should I install the pre-compiled Windows binaries, and replace the > files? > > Best > Troels > > Troels Emtekær Linnet > Ved kløvermarken 9, 1.th > 2300 København S > Mobil: +45 60210234 > > > 2013/5/7 Edward d'Auvergne <[email protected]> >> >> Hi again, >> >> Just for reference in the mailing list archives, the sub-thread has >> appeared as a new thread at >> http://thread.gmane.org/gmane.science.nmr.relax.devel/3835. >> >> Regards, >> >> Edward >> >> >> >> >> On 7 May 2013 11:36, Edward d'Auvergne <[email protected]> wrote: >> > Hi Troels, >> > >> > This sub-thread (which will appear at >> > http://thread.gmane.org/gmane.science.nmr.relax.devel/3833) will >> > hopefully be a mini-tutorial covering the development of the >> > relax_disp branch. Before you can be accepted as a relax developer >> > with commit access to the source code repository, you should first >> > submit changes as patches. This takes longer initially, but it allows >> > the other relax developers to see how you code and if you are >> > following the coding conventions as described in the development >> > chapter of the relax manual >> > (http://www.nmr-relax.com/manual/relax_development.html). I can give >> > you feedback as you go as to how to improve the code to fit into >> > relax. We, the relax developers, will after a few patches have a >> > private vote to accept you as a relax developer. This is standard >> > practice in an open source project. The full procedure for becoming a >> > developer is detailed in the 'Committers' section of the manual >> > (http://www.nmr-relax.com/manual/Committers.html). The PDF version of >> > the manual is easier to read >> > (http://download.gna.org/relax/manual/relax.pdf). Patches can be >> > posted to the patch tracker (https://gna.org/patch/?group=relax). >> > >> > relax development begins and ends with the test suite. The idea is >> > that, before any code is present, a relax system test must be created. >> > This allows you to develop the ideas for how the UI should work with >> > the analysis - i.e. which new user functions will need to be created >> > and which ones will need to be expanded. A script is added to >> > test_suite/system_tests/scripts/relax_disp/ and then a test added to >> > test_suite/system_tests/relax_disp.py which executes the script and >> > then checks the data and results. For example see the script >> > 'test_suite/system_tests/scripts/relax_disp/hansen_data.py' and the >> > function test_hansen_cpmg_data_fast_2site() in the file >> > 'test_suite/system_tests/relax_disp.py'. This is obviously not >> > complete as only the script is executed - the results are not yet >> > checked (as we do not know what the result for the optimised model >> > should be yet). This individual test can be executed with the >> > command: >> > >> > $ relax -s Relax_disp.test_hansen_cpmg_data_fast_2site >> > >> > This test, as well as the other Relax_disp tests, were created by >> > Sebastien Morin when he started the development of the relax_disp >> > branch. I have renamed everything since he added it, and will >> > probably do so again soon. It is best to develop for the script UI >> > first - the GUI will later be modified around the graphical versions >> > of the user functions, or directly accessing the back end of the user >> > function. Due to the advanced state of the relax_disp branch, you >> > probably do not need to worry about new user functions. This may be >> > needed if you would like to expand the analysis to new types of data >> > (for example off-resonance R1rho where R1 data need to be measured and >> > used in the analysis, H/D exchange, etc.). >> > >> > The test suite is one area which can be expanded to handle the >> > different CPMG models. The testing is currently not very extensive. >> > For example before a new dispersion model is added to relax, it would >> > be good if synthetic data were to be created in an external program (a >> > Python script, Matlab, Mathematica, Maxima, etc.). It is very >> > important that relax is not used to create the data. Synthetic data >> > is very important for making sure that relax obtains the correct >> > result, as you know what the result should be. With measured data you >> > can never really know what the true result is - this is the entire >> > point of the mathematical field of modelling (this field makes that of >> > NMR look very, very small). Synthetic data is also useful for double >> > checking results against other relaxation dispersion software (for >> > reference: NESSY - http://home.gna.org/nessy/; CPMGFit - >> > http://www.palmer.hs.columbia.edu/software/cpmgfit.html; ShereKhan - >> > http://sherekhan.bionmr.org/; CATIA - >> > http://www.biochem.ucl.ac.uk/hansen/catia/). Data could also be taken >> > from Art Palmer's CPMGFit manual >> > (http://www.palmer.hs.columbia.edu/software/cpmgfit_manual.html). >> > This would need to be converted into peak intensities in a peak list >> > file, but that is easy enough by simply picking random I0 values for >> > the exponential curves. The data could be passed quickly through each >> > of the models of the CPMGFit program and results noted. Then the >> > results would be added to the checks of different relax system tests. >> > >> > Each different data set used in the testing process should be located >> > in its own directory in test_suite/shared_data/dispersion/. That >> > directory can include the data and all scripts used to generate the >> > data and, for reference, it can also contain subdirectories for >> > holding the input and output for different programs (as long as the >> > files are not too big). >> > >> > The current state of the branch is that all of the user functions are >> > pretty close to complete. The user function consists of a front end >> > definition in user_functions/, and a backend either in pipe_control/ >> > or specific_analyses/. The relaxation dispersion target function >> > setup for optimisation is close to complete. You can see this in the >> > minimise() method of the specific_analyses/relax_disp/__init__.py >> > file, and then the __init__() method of the class in >> > target_functions/relax_disp.py. As you will see in the model_loop() >> > method of the specific_analyses/relax_disp/__init__.py code, >> > clustering of spin systems is already part of this design - everything >> > handles a group of spins assuming the same parameter values. One >> > missing feature that I might work on soon is the handling of missing >> > input data, as this affects my current work. This is a problem >> > currently caught by the >> > test_suite/shared_data/dispersion/Hansen/relax_disp.py script, as >> > residue :71 is missing data at one field strength. But once the >> > dispersion tests have been expanded, this can be tested properly by >> > deleting data for single points on the exponential curves, deleting >> > entire exponential curves (or dispersion points for the two-point >> > analysis type), or all data from a single spectrometer field strength >> > for a single spin. >> > >> > So I would suggest that you pick one of the dispersion models you are >> > interested in and try to implement that. I am working on the Luz and >> > Meiboom, 1963 model, but all of the other models are safe to work on. >> > Just say which you are interested in so that we don't both change the >> > same code. The system test data would come first. The formula can be >> > taken, a set of parameters for 2-3 spins chosen, and a simple script >> > written to generate the R2eff data, importantly at multiple magnetic >> > field strengths. That data can then be converted into a generic peak >> > list for different time periods on a basic 2-parameter exponential >> > curve. See the 'File formats' section of the >> > spectrum.read_intensities user function docstring, for example by >> > typing help(spectrum.read_intensities) in the prompt UI. In the same >> > script the creation of input files for other programs could be added, >> > possibly at a later stage, and the data quickly run through CPMGFit, >> > for example, for a sanity check. >> > >> > If you do test the other programs, you may encounter a severe bug in >> > one of their models. No software is bug free. In such a case, we >> > should communicate with the authors in private and they can decide >> > what to do. You can see that I did this with Art Palmer's Modelfree >> > program at >> > http://biochemistry.hs.columbia.edu/labs/palmer/software/modelfree.html. >> > Versions 4.16 and 4.20 consist of patches that I send to Art to fix >> > compilation issues and other bugs (I pointed out the grid search >> > problem due to the singular matrix failure of the Levenberg-Marquardt >> > algorithm and Art made that change himself). >> > >> > Once some data has been created and files attached to the patch >> > tracker (https://gna.org/patch/?group=relax), then the relax script >> > can be written and added to >> > test_suite/system_tests/scripts/relax_disp/. The best way would >> > probably be for one of the current scripts to be copied (by me to >> > start with) in the repository and then you make small changes to it >> > and send the patches created with: >> > >> > $ svn diff > patch >> > >> > Then the script execution and data and parameter checking code can be >> > added to test_suite/system_tests/relax_disp.py - again you can look at >> > the other methods in that file and create a new one by copying how an >> > old method operates. In that system test you would check that the >> > original parameters have been found. >> > >> > At this stage, the test should run fine up to the grid_search user >> > function, and then fail (or possibly at the relax_disp.select_model >> > user function call in the script depending on whether you use the >> > auto-analysis code in auto_analyses.relax_disp or not). This is the >> > point where the model can be implemented. Then you would take the >> > following steps: >> > >> > - Add a description of the new model with the equation and reference >> > to the user_functions.relax_disp module. >> > >> > - Add the model and its parameters to the _select_model() method of >> > the specific_analyses/relax_disp/__init__.py file. >> > >> > - Add any new parameter definitions to the top of the >> > specific_analyses/relax_disp/__init__.py file in the __init__() method >> > as needed. If new parameters are needed, then there are various >> > places in the specific_analyses.relax_disp package where support will >> > be needed, mainly in the specific_analyses.relax_disp.parameters >> > module. >> > >> > - Create a new module in the lib.dispersion package for the model >> > function. This module will eventually hold the model function, the >> > gradient (each partial derivative with respect to each parameter would >> > be in a different function), and the Hessian (the matrix of second >> > partial derivatives). Having the gradient and Hessian will allow for >> > the more powerful optimisation algorithms to be used. >> > >> > - Add a new method to target_functions/relax_disp.py which uses the >> > new code in lib.dispersion to calculate R2eff values, combine this >> > with the chi2 function, and return the chi-squared value (see the >> > current func_LM63() method for how to do this). >> > >> > - Finally, see if the system test passes. If not, then it is time to >> > debug. >> > >> > During these steps, the unit test part of the test suite can be used >> > to make sure that individual functions and methods behave correctly. >> > This is useful as users will always find a way to break your code. >> > Once the system test passes, then you will know that the >> > implementation is complete and fully functional. >> > >> > >> > If your interest is in the numerical integration of the >> > Bloch-McConnell equations, then the procedure might be slightly >> > different. We would have to discuss this in more detail, with paper >> > references and the necessary equations. But I think that all of this >> > can be handled in a module of the lib.dispersion package, and the rest >> > of the above detailed procedure would be the same. I hope this post >> > wasn't too long for you! >> > >> > Regards, >> > >> > Edward >> > >> > >> > >> > >> > On 6 May 2013 21:14, Troels Emtekær Linnet <[email protected]> wrote: >> >> Hi Edward. >> >> >> >> When you have completed your ideas of change to the >> >> disp branch, could you send me a notits? >> >> >> >> And maybe a script file, how to launch the code? >> >> >> >> Then I could try to figure out where I should extend new code. >> >> >> >> Best >> >> Troels >> >> >> >> >> >> _______________________________________________ >> >> 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 >> >> > > _______________________________________________ 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
