History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
aee2c4e6cb21 | tlemaire | added Lookup.tile and modified SmartLookup.projectDC. modified nbls. | Oct 10 2019 | |||
20f96c135bce | tlemaire | defined Lookup algorihtmic operators. defined OnOffSimulator class. defined… | Oct 7 2019 | |||
d992992a3693 | tlemaire | commented out numdifftools import. updated README.md | Oct 2 2019 | |||
dd102470b272 | tlemaire | added method type in nbls.simulate logging | Sep 18 2019 | |||
6fb96a1716d1 | tlemaire | corrected tirations log file | Sep 18 2019 | |||
69faba51e2c1 | tlemaire | in PWSimulator.compute: added division of offset interval in several slices if… | Sep 17 2019 | |||
133c0ab1ac73 | tlemaire | changed outputdir to keyword argument in queue items in Model.checkOutputDir… | Sep 17 2019 | |||
89e117f6ffaa | tlemaire | add handling of positional and keyword arguments in Batch queues. added… | Sep 17 2019 | |||
8cf15b137151 | tlemaire | abstracted Model.simQueue method (now defined in children classes). changed… | Sep 17 2019 | |||
fd4639a4c602 | tlemaire | parametrised Qm plot range to be neuron-specific. Solved issue with pbar update. | Sep 2 2019 | |||
d2ccd21d9889 | tlemaire | corrected crucial error in nbls.spatialAverage method. corrected Cm0 and Qm0… | Sep 2 2019 | |||
1b3cffe95e7a | tlemaire | added sweeney lookups (ASTIM not working yet). added fixLookup to remove single… | Aug 29 2019 | |||
4f5fb5ee0829 | tlemaire | implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to… | Aug 26 2019 | |||
2278e599a753 | tlemaire | added automatic solution prepending to all simulate methods (to treat initial… | Aug 14 2019 | |||
ec01e1e58099 | tlemaire | fixed error in bls.filecodes | Jul 29 2019 | |||
48fd3e1df816 | tlemaire | test commit. | Jul 26 2019 | |||
8e1403abecb9 | tlemaire | updated README to latest changes. | Jul 24 2019 | |||
a70fc6312da7 | tlemaire | set simFull, simHybrid and simSonic as private nbls methods | Jul 24 2019 | |||
9ba9ca99a89f | tlemaire | corrected error in getSimThresholdAmps (added default fs to 1) | Jul 18 2019 | |||
9e0718eb1a9b | tlemaire | corrected error in Model logNSpikes, checkTitrate and simAndSave methods. | Jul 18 2019 | |||
5aa12c341577 | tlemaire | interoduced derivative function to compute numerical derivatives with various… | Jul 18 2019 | |||
28c94d579a04 | tlemaire | improved QSS fixed points color labeling | Jul 18 2019 | |||
ab25e778e32f | tlemaire | added saddle point classification to QSS analysis. | Jul 17 2019 | |||
17b59c14aa75 | tlemaire | modified TC neuron steadyStates method. | Jul 16 2019 | |||
f768f01cd891 | tlemaire | transformed pneuron qsState and quasiSteadyStates methods to return lambda… | Jul 15 2019 | |||
137ca70ce6a3 | tlemaire | cleaned up nbls | Jul 15 2019 | |||
d50bf6119d40 | tlemaire | started implementing SonicTranslator.parseSteadyStates method. Implemented… | Jul 15 2019 | |||
ffdcb43ba1d8 | tlemaire | improved checkTitrate robustness | Jul 1 2019 | |||
d1a3fbaefd83 | tlemaire | added option to provide simAndSave or simulate to batches. implemented addMeta… | Jul 1 2019 | |||
4937955d0214 | tlemaire | adapted methods of all classes into classmethods and staticmethods when… | Jun 29 2019 | |||
4997a9f88989 | tlemaire | transformed model inputs, checkInputs and simQueue into static methods | Jun 28 2019 | |||
a0db776b7966 | tlemaire | added Model.description method. added nbls.getLookup2D method with correct fs… | Jun 27 2019 | |||
b73594f4d58b | tlemaire | moved lookup to core module. moved getLookup methods to nbls class. | Jun 27 2019 | |||
dffee6926b85 | tlemaire | added fs (spatially-averaged) as input to nbls model. defined SmartLookup class… | Jun 26 2019 | |||
3528fa81b6d1 | tlemaire | cleaned up model classes. defined mandatory derivatives method for model… | Jun 26 2019 | |||
9965ddc0005d | tlemaire | improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar… | Jun 25 2019 | |||
acf299185987 | tlemaire | removed unnecessary functions from pneuron | Jun 25 2019 | |||
db8cc8e2b5ff | tlemaire | added automatic effRates function definition in pneuron.parse method. removed… | Jun 25 2019 | |||
4742d6a43494 | tlemaire | finished implementing pneuron.buildDerEffStates method to automatically create… | Jun 25 2019 | |||
83ff47370d86 | tlemaire | defined separate lookup decorator for bls.computePMparams method. updated… | Jun 24 2019 | |||
a96a900ad4b4 | tlemaire | define dLookUp class to perform lookup projections and interpolations | Jun 20 2019 | |||
6c10d4162d71 | tlemaire | added default output directory ("dump"). cleaned up neuron classes. | Jun 20 2019 | |||
fdebb58e8442 | tlemaire | refefined derEffstates construction to return a dictionary of function. | Jun 19 2019 | |||
f719dddee9f0 | tlemaire | added getSteadyStates and getDerStates methods to pneuron to call steadyStates… | Jun 19 2019 | |||
26fe1e08a408 | tlemaire | cleaned up neuron classes. redefined currents to return functions instead of… | Jun 19 2019 | |||
40b5a09c46c2 | tlemaire | started implementation of buildDerEffStates to contruct the derEffStates… | Jun 18 2019 | |||
7b2aee9851af | tlemaire | replaced obscur states list by explicit dictionary in all currents methods | Jun 18 2019 | |||
00f57af96cfb | tlemaire | replaced obscur states list by explicit states dictionary in derStates and… | Jun 18 2019 | |||
66eaf2f41fba | tlemaire | corrected y, t order error in nbls.fullDerivatives. added custom parsing in… | Jun 17 2019 | |||
c14fa0da1fd7 | tlemaire | added simkey to meta dictionary. added automatic parsing and labeling of… | Jun 15 2019 | |||
de8bdbc4fee0 | tlemaire | added outputdir option to simQueue methods. added automatic parsing to Parser… | Jun 14 2019 | |||
b0f51febd195 | tlemaire | updated constants | Jun 13 2019 | |||
b42a0de93240 | tlemaire | updated all file headers | Jun 12 2019 | |||
cc309fa78cd9 | tlemaire | cleaned-up all neuron classes | Jun 12 2019 | |||
6e017b421f3e | tlemaire | replaced "neuron" by "pneuron" for all PointNeuron instances | Jun 12 2019 | |||
1354c6f9d2e9 | tlemaire | switched back to old evaluateStability version | Jun 10 2019 | |||
dd32fc0479b4 | tlemaire | first attempt at replacing custom integration in nbls.evaluateStability by call… | Jun 10 2019 | |||
84c54a491722 | tlemaire | removed STN temporary fix in nbls.titrate | Jun 9 2019 | |||
b88c300e48f0 | tlemaire | added first-call check that condition changes within the interval to… | Jun 9 2019 | |||
c7f94b320ba7 | tlemaire | set t first in all derivatives function | Jun 9 2019 | |||
b46a8cd85a73 | tlemaire | removed ng and Z explicit computation in runSONIC (replaced by nan arrays) | Jun 9 2019 | |||
5eed591ede6e | tlemaire | corrected errors in nbls interpEFFVariable and runSONIC methods | Jun 9 2019 | |||
863bdf8330f4 | tlemaire | added nbls isStableQSS and titrateQSS methods. finished plotQSSThresholdCurve | Jun 9 2019 | |||
86564c193a65 | tlemaire | added multiprocessing for runAndGetStab function | Jun 7 2019 | |||
1f1e59762ea3 | tlemaire | added custom parsers to plot_timeseries and plot_QSS | Jun 7 2019 | |||
0984b86caa8f | tlemaire | moved lookups utilities into separate lookups module (in neurons folder) | Jun 6 2019 | |||
3556a765fe5c | tlemaire | created ActivationMap class | Jun 6 2019 | |||
1c9c63d4ba6a | tlemaire | added getModel and getPointNeuron functions. removed deprecated scripts. | Jun 6 2019 | |||
874f4649ec44 | Theo Lemaire | corrected QSS module to work correctly with "load" option. | Jun 2 2019 | |||
88811f7a8aa5 | Theo Lemaire | major cleanup of all core classes. | Jun 2 2019 | |||
c49110f6c3cf | Theo Lemaire | added isAsymptoticallyStable method to PeriodicSolver | Jun 1 2019 | |||
7c909ad7dbbd | Theo Lemaire | added convfunc attribute to PeriodicSimulator class | Jun 1 2019 | |||
e0aa4041f3b8 | Theo Lemaire | added caching to nbls.titrate method | Jun 1 2019 | |||
10d2b5bb498e | Theo Lemaire | redefined titration procedures with binarySearch method. now single runAndSave… | Jun 1 2019 | |||
de01bc8b1676 | Theo Lemaire | moved batches to core module | May 31 2019 | |||
25d498c21187 | Theo Lemaire | implemented abstract Model class to be inherit by bls, pneuron and nbls | May 31 2019 | |||
4dd95ba1d83c | Theo Lemaire | added toffset to args list of pneuron and nbls filecode methods | May 31 2019 | |||
6cb5dac16172 | Theo Lemaire | moved createAStimQueue and createEStimQueue to their respective classes | May 31 2019 | |||
aae3bfea421b | Theo Lemaire | moved "amp" parameter back to appropriate in args list of runAndSave functions | May 31 2019 | |||
42ef7cb1063a | Theo Lemaire | added "meta" method to core classes | May 31 2019 | |||
af6f9a02ed42 | Theo Lemaire | reformatted simulate methods of bls, pneuron and nbls classes to return output… | May 31 2019 | |||
19a9b2f737fd | Theo Lemaire | cleaned up simulators classes | May 31 2019 | |||
17f1482bc336 | Theo Lemaire | added docstring to simulators classes | May 30 2019 | |||
e08e8c736efa | Theo Lemaire | replaced progressbar2 by tqdm | May 29 2019 | |||
440f5459adf4 | Theo Lemaire | added HybridSimulator used for nbls.runHybrid | May 29 2019 | |||
370f27746bca | Theo Lemaire | added use of PWSimulator in pneuron | May 29 2019 | |||
4ba3212edf92 | Theo Lemaire | added simulators classes to take care of simulations | May 29 2019 | |||
1391db99409d | Theo Lemaire | added intermediate "run" method that return output data and metadata | May 27 2019 | |||
21d010292ddf | Theo Lemaire | added return_val option to isExcited and isSilenced | May 27 2019 | |||
c23526a0ca16 | Theo Lemaire | added logNSpikes function to pneuron class. | May 27 2019 | |||
13e29c29bbb1 | Theo Lemaire | haromized amplitude and plot_scheme parsing across simulation scripts | May 27 2019 | |||
71a2cddb684e | Theo Lemaire | replaced filecode functions by class methods | May 27 2019 | |||
678bec02c372 | Theo Lemaire | added "PI" type control of convergence in nbls.evaluateStability method | May 23 2019 | |||
1a5f9b3c215b | Theo Lemaire | implemented neuron-dependent titration to find specific thresholds (excitation… | May 22 2019 | |||
0ee058e8778d | Theo Lemaire | added max integration duration to stability analysis to avoid infinite loops in… | May 22 2019 | |||
3addfe632329 | Theo Lemaire | implemented quasiSteadyStateFixedPoints as part of nbls class. Added… | May 22 2019 | |||
2024b001441b | Theo Lemaire | implemented nbls.quasiSteadStateiNet method, used to compute Q-SFPs iteratively… | May 22 2019 | |||
8a17ab2f8c11 | Theo Lemaire | implemented specific nbls evaluateStability method to evaluate FP stability by… | May 21 2019 | |||
3ad8ad914eec | Theo Lemaire | replaced linear interpolation of QSS at Q-SFPs (inaccurate) by full… | May 16 2019 | |||
3f4135902bdc | Theo Lemaire | added np.nan bounding to all np.interp uses in the code. implemented… | May 16 2019 |
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