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 > >> >> > > > > >
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