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Meanfield model #1136
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Meanfield model #1136
Commits on Jul 28, 2021
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add meanfield model to spynnaker
Garandel committedJul 28, 2021 Configuration menu - View commit details
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Commits on Oct 4, 2021
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Merge pull request SpiNNakerManchester#1113 from SpiNNakerManchester/…
…correct_spikearray_waring fixed the check for early spikes
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Commits on Oct 5, 2021
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Merge pull request SpiNNakerManchester#1114 from SpiNNakerManchester/…
…extract_iobuf_during_run remove extract_iobuf_during_run flag
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Fix a whole bunch of minor warnings in the documentation build
There's apparently also a crash, but I can't reproduce that locally
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Merge pull request SpiNNakerManchester#1115 from SpiNNakerManchester/…
…doc-fix Documentation fix
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Merge pull request SpiNNakerManchester#1116 from SpiNNakerManchester/…
…send_sync_repeat allow for mutliple send_sync
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Merge pull request SpiNNakerManchester#1117 from SpiNNakerManchester/…
…doc-fix Trying to fix a crash...
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Commits on Oct 14, 2021
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modified: meanfield/models/meanfield_model_impl.c
add the reel error function
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modified: meanfield/models/meanfield_model_impl.c
change real error function for an erzate
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modified: meanfield/models/meanfield_model_impl.c
write some comments
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Commits on Oct 15, 2021
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modified: meanfield/models/meanfield_model_impl.c
Do an approxiamtion of 2 over sqrt(pi) in order to remove the error due to the sqrtk() function. Start to remove division in the threshold_func().
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remove config-> in the thre_func in order to make a code more clear
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modified: meanfield/models/meanfield_model_impl.c
modified: meanfield/models/meanfield_model_impl.h Set threshold_func() add and remove r_squared() because don't implemented yet. No removing of division yet.
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clean and remove sqrtk indicated when with coms, just to try without …
…optimisation yet
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Commits on Oct 18, 2021
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remove FAKEs (where no divisions) to clean a little bits,
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remove FAKEs (where no divisions) to clean a little bits,
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modified: meanfield/models/meanfield_model_impl.h
modified: ../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../spynnaker/pyNN/models/neuron/implementations/meanfield_impl_standard.py modified: ../../spynnaker/pyNN/models/neuron/neuron_models/config.py modified: ../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_model_eitn.py ADD Vi and put it like state_variables CHANGE muV from state_variables to parameters
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Commits on Oct 19, 2021
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modified: meanfield/models/meanfield_model_impl.c
modified: ../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../spynnaker/pyNN/models/neuron/implementations/meanfield_impl_standard.py modified: ../../spynnaker/pyNN/models/neuron/neuron_models/config.py pbl when add Vi obtain DIBBY0 error but now clue where.
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modified: meanfield/implementations/meanfield_impl_standard.h
modified: meanfield/models/meanfield_model_impl.c modified: meanfield/models/meanfield_model_impl.h modified: ../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../spynnaker/pyNN/models/neuron/implementations/meanfield_impl_standard.py modified: ../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_model_eitn.py try to solved the error DIVBY0 and pass from 10 vars recorded to 5.
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Commits on Oct 21, 2021
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modified: ../../src/meanfield/implementations/meanfield_impl_standard.h
modified: ../../src/meanfield/models/meanfield_model_impl.c modified: ../../../spynnaker/pyNN/models/neuron/implementations/meanfield_impl_standard.py modified: ../../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_model_eitn.py modified: ../../../spynnaker8/extra_models/__init__.py OK problem don't comming from printing data but I guess from creating them. I will change some C code in meanfield_impl_standard.h PBL is like if Ve and g_syn are ok to be create but not Vi and Fout_th for a 5 vars recorded
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modified: ../../src/meanfield/models/meanfield_model_impl.c
Need to add Vi really to tyhe implementation and so to meanfield_model_impl.h and .c and to meanfield_model.h so if need comme back here
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modified: ../../src/meanfield/implementations/meanfield_impl_standard.h
modified: ../../src/meanfield/models/meanfield_model.h modified: ../../src/meanfield/models/meanfield_model_impl.c Ok that working a priori, it's not the most beautiful but it's working Just one comment is : the numbers between Ve and Vi are not treat as the same, don't understadn why??
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Commits on Oct 22, 2021
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modified: src/meanfield/implementations/meanfield_impl_standard.h
modified: src/meanfield/models/meanfield_model.h modified: src/meanfield/models/meanfield_model_impl.c a priori that's work for Ve, Vi and Fout_th ->will add an other TF() and so an other threshold_function() in order to have a MF
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modified: ../../src/meanfield/models/meanfield_model_impl.c
before add config Vi
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Commits on Oct 25, 2021
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modified: config.h modified: meanfield_model.h modified: meanfield_model_impl.c Add in the c code the inhibitory contribution of the MF and so the differenciation btw Exc and Inh. Names of some variables and params will be change in order to don't induce misunderstanding.
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Commits on Oct 26, 2021
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modified: ../meanfield_build.mk
modified: Makefile modified: ../../../src/meanfield/implementations/meanfield_impl_standard.h renamed: ../../../src/meanfield/models/Vthre_params.h -> ../../../src/meanfield/models/P_fit_polynomial.h modified: ../../../src/meanfield/models/meanfield_model.h modified: ../../../src/meanfield/models/meanfield_model_impl.c modified: ../../../../spynnaker/pyNN/models/neuron/abstract_pynn_meanfield_model_standard.py modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py Add the other transfert function for inhibitors in C code, -> take parameters from config.h to an other Opaque structure P_fit_polynomial.h that's compile
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modified: ../meanfield_build.mk
modified: Makefile modified: ../../../src/meanfield/implementations/meanfield_impl_standard.h modified: ../../../src/meanfield/models/meanfield_model.h modified: ../../../src/meanfield/models/meanfield_model_impl.c renamed: ../../../src/meanfield/models/config.h -> ../../../src/meanfield/models/params_from_network.h renames config.h to params_from_network.h in order to be more precise in the correspondance btw code and litterature. change names of types, arrays and structure. compilation is ok
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modified: ../../../src/meanfield/models/meanfield_model.h
modified: ../../../src/meanfield/models/params_from_network.h was changeing mathsbox.h for estimate_err_func.h but go back bcs I don't know if I will implement other function inside mathsbox and not just error function
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modified: ../../../src/meanfield/models/meanfield_model.h
wasn't go back totaly
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modified: abstract_pynn_meanfield_model_standard.py
modified: builds/meanfield_base.py modified: implementations/meanfield_impl_standard.py renamed: neuron_models/config.py -> neuron_models/params_from_network.py change name config.py for params_from_network.py and so in files
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modified: abstract_pynn_meanfield_model_standard.py
modified: builds/meanfield_base.py new file: neuron_models/p_fit_polynomial.py modified: neuron_models/params_from_network.py add an other struct file to implemente params from fit of single neuron for Vthre polynome
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Commits on Oct 27, 2021
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modified: ../../../src/meanfield/implementations/meanfield_impl_stan…
…dard.h modified: ../../../src/meanfield/models/params_from_network.h modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../../../spynnaker/pyNN/models/neuron/implementations/meanfield_impl_standard.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/__init__.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/p_fit_polynomial.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/params_from_network.py A priori meanfield_model_cond.dict says that I'm out of DTCM. That's why I get the error: "Population meanfield_model_cond does not have parameter p0" Go back to the past commit without inh implemented, just to see.
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modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_…
…base.py modified: ../../../../spynnaker/pyNN/models/neuron/implementations/meanfield_impl_standard.py renamed: ../../../../spynnaker/pyNN/models/neuron/neuron_models/p_fit_polynomial.py -> ../../../../spynnaker/pyNN/models/neuron/neuron_models/P_fit_polynomial_exc.py new file: ../../../../spynnaker/pyNN/models/neuron/neuron_models/P_fit_polynomial_inh.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/__init__.py CHECK POINT That's compile and work in virtual mode for c and python. ERROR : DIVBY0 when reel mode
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Commits on Oct 28, 2021
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modified: ../../../src/meanfield/models/meanfield_model_impl.c
modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py DIVBY0 error is solved, due to put state var in local but don't go back to struct so all the time 0. RESUME : - TF for exc and inh with - some name changed in the files and in variables WILL: - Change MeanfieldModelEitn in python - add adaptation W ODE - change Fout_th for W in output
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modified: ../builds/meanfield_base.py
modified: __init__.py renamed: meanfield_model_eitn.py -> meanfield_of_adex_network.py Change the name from meanfield_model_eitn.py to meanfield_of_adex_network.py
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modified: ../../../src/meanfield/implementations/meanfield_impl_stan…
…dard.h modified: ../../../src/meanfield/models/meanfield_model_impl.c modified: ../../../src/meanfield/models/meanfield_model_impl.h modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../../../spynnaker/pyNN/models/neuron/implementations/meanfield_impl_standard.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_of_adex_network.py Add the structure for adaptation W, that's work but give non-sense results. Need to add a start value and the real ODE.
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Commits on Oct 29, 2021
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modified: ../../../src/meanfield/models/meanfield_model_impl.c
modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_of_adex_network.py Correct some error but have an error when calculating EDO with RK2_midpoint. maybe "error" come from recorder.py and constant.py will do some test so if need come back here
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Commits on Nov 2, 2021
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modified: ../../../src/meanfield/models/meanfield_model_impl.c
modified: ../../../src/meanfield/models/meanfield_model_impl.h modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../../../spynnaker/pyNN/models/neuron/implementations/meanfield_impl_standard.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_of_adex_network.py modified: ../../../../spynnaker/pyNN/models/recorder.py modified: ../../../../spynnaker/pyNN/utilities/constants.py do some modification aparently without effect of recorder and constant in rder to integrate Ve, Vi and W. Will modify meanfield_t because Vthre left in it but not anymore in meanfield_t and so modif meanfield_f_adex_network.py
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modified: ../../../src/meanfield/models/meanfield_model_impl.h
modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_of_adex_network.py remove nbr from meanfielf_t and to meanfield_of_adex_network.py
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Commits on Nov 3, 2021
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modified: ../../../src/meanfield/models/meanfield_model_impl.c
modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_of_adex_network.py No clue of why w return uint32 DataType and not S1615. Will try in switching Vi and w
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Commits on Nov 4, 2021
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modified: ../../../src/meanfield/implementations/meanfield_impl_stan…
…dard.h modified: ../../../src/meanfield/models/meanfield_model.h modified: ../../../src/meanfield/models/meanfield_model_impl.c modified: ../../../../spynnaker/pyNN/models/neuron/neuron_models/meanfield_of_adex_network.py SAVE POINT now that's fonctionnaly work. NEED to optimise or doing real ode solver and error_function
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modified: ../../../src/meanfield/models/mathsbox.h
modified: ../../../src/meanfield/models/meanfield_model_impl.c modified error_function with midpoint methode for integration. will do pregressively trapezoidale and Simpson if possible in ITCM BUT try to have an homogeneous patern i.e. EULER and Midpoint integrale for error function.
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Commits on Nov 5, 2021
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modified: ../../../src/meanfield/models/meanfield_model_impl.c
modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py Did some cleanning, correction and rewriting of euler, RK2, mu_Ge and modif TvN= Tv only because of the original paper. Need to ask for that!! Modif T_inv in value. need to find a way to plot but plt.show don't work on the terminal.
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Commits on Nov 19, 2021
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modified: ../../../src/meanfield/models/mathsbox.h
modified: ../../../src/meanfield/models/meanfield_model_impl.c modified: ../../../../spynnaker/pyNN/models/neuron/builds/meanfield_base.py Do some clarification and try some method to remove the 'overflowed ITCM' message because of sqrtk sqrt function is not activated, so sV is on the square value. Need to find a solution for sqrt without overflowed ITCM
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Commits on Nov 25, 2021
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Merge branch 'master' into meanfield_model
too much changes, so will have too much conflict to fixe so merge with -s ours
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Merge branch 'meanfield_model' of https://github.com/garandel/meanfie…
…ld_model into meanfield_model try to merge origin_MF with this local branch with -s ours option in order to remove conflict
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