Hi, As you are setting this up, if you have any simple suggestions for improving the MS Windows development platform webpage (http://www.nmr-relax.com/windows_devel.html), for example updating the MSVC instructions or adding information about using pyscripter and Ipython alongside the VIM instructions (http://www.nmr-relax.com/windows_devel.html#vim), this would be much appreciated. If you are interested, you can obtain a copy of the relax website with the command:
$ svn co https://svn.gna.org/svn/relax/website I wrote these instructions back in about 2006, so this HTML page is probably quite out of date now. Cheers, Edward On 7 May 2013 20:22, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > I use pyscripter and Ipython for coding, but def. not vim. > I am aware of Python PEP style guide, and the indention thing. > Trying to remember to comply to the rules of style. :-) > > I would need to program at home, since I cannot spend effort when I am the > lab. > > Still having troubles with scons. Tried following this: > http://www.nmr-relax.com/windows_devel.html > I installed scons 2.3 for windows > And Visual Studio Express 2012 > > I don't understand this: > 'cl' is not recognized as an internal or external command, operable program > or batch file. > I can call cl from command line, so... > > Have you seen this before? > > ----------------------------------------- > C:\Python27\github\relax_disp>"C:\Program Files (x86)\Microsoft Visual > Studio 11 > .0\VC\vcvarsall" > > C:\Python27\github\relax_disp>scons > scons: Reading SConscript files ... > scons: done reading SConscript files. > scons: Building targets ... > > ########################### > # Compiling the C modules # > ########################### > > Building the relaxation curve fitting module > 'target_functions\\relax_fit.pyd' > > cl /Fotarget_functions\c_chi2.obj /c target_functions\c_chi2.c /nologo > /I"C:\Pyt > hon27\Scripts\..\include" > 'cl' is not recognized as an internal or external command, > operable program or batch file. > scons: *** [target_functions\c_chi2.obj] Error 1 > scons: building terminated because of errors. > > C:\Python27\github\relax_disp>cl > Microsoft (R) C/C++ Optimizing Compiler Version 17.00.50727.1 for x86 > Copyright (C) Microsoft Corporation. All rights reserved. > > usage: cl [ option... ] filename... [ /link linkoption... ] > > > > Troels Emtekær Linnet > > > 2013/5/7 Edward d'Auvergne <[email protected]> >> >> 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
