History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
3dd0e7ca4b5c | tlemaire | added pneuron.is_passive property and getDefaultPassiveNeuron function | May 28 2021 | |||
47f7640b7bcb | tlemaire | added factor to Qnorm pltvar. | May 27 2021 | |||
28b9ed25d674 | tlemaire | added transition handling in computeTimeStep. | Mar 2 2021 | |||
bb9f2c79c74a | tlemaire | latest changes for morphoSONIC paper | Sep 15 2020 | |||
e57b064d8f70 | tlemaire | simplified bls.capacitance expresion | Aug 5 2020 | |||
d5c62320c0e3 | tlemaire | added expandRange docstring | Aug 4 2020 | |||
aaeaaeac3732 | tlemaire | removed call to unstable iax in pltvars['iax'] definition | Jul 22 2020 | |||
0d4af61c20f7 | tlemaire | corrected PointNeuron dQdt method (now calculating charge derviative by finite… | Jul 22 2020 | |||
42a3be29b47b | tlemaire | introduced default celsius (36°C) as a PointNeuron property shared by all… | Jul 21 2020 | |||
4884f5695b3e | tlemaire | added HH point neuron | Jul 21 2020 | |||
c9894bdbd61c | tlemaire | removed SilentMRGNode class (now generated on-the-fly in analysis notebook) | Jul 15 2020 | |||
095a41517e86 | tlemaire | added pneuron.tau_pas property | Jul 3 2020 | |||
0d1777407add | tlemaire | corrected drives and protocols inputs. | Apr 18 2020 | |||
241946f34fa2 | tlemaire | simplified drives and protocols | Apr 17 2020 | |||
6895a19a147f | tlemaire | implemented simQueueBurst method in pneuron and nbls classes. | Apr 17 2020 | |||
e3ca275ebe0f | tlemaire | harmonized repr, desc and filecodes methods across protocols. | Apr 17 2020 | |||
69892d75c503 | tlemaire | improved solvers docstrings and clarified their use in model classes. | Apr 16 2020 | |||
b77cd9e4eb12 | tlemaire | implemented better solvers (now inside solvers module), including an… | Apr 15 2020 | |||
f8511250c9b8 | tlemaire | corrected LogBatch class to enable correct use with mpi. | Apr 13 2020 | |||
cc5348bc40ca | tlemaire | added __eq__ methods to pneuron and nbls classes | Apr 3 2020 | |||
9239911c1f35 | tlemaire | added ASTIM_REL_CONV_THR to constants file. | Mar 31 2020 | |||
7f8a3be5ceb4 | tlemaire | changed meta property of model classes to return solely model information. | Feb 20 2020 | |||
68961385d17e | tlemaire | added copy method to all model classes. added TI US notebook. updated… | Feb 11 2020 | |||
892f924d6e9e | tlemaire | renamed ElectricDrive A to I | Feb 5 2020 | |||
073e28b388f6 | tlemaire | added xkey property to XDrive class and Arange property to pneuron and nbls… | Feb 3 2020 | |||
27d8aafffa88 | tlemaire | Created Drive objects inheritance scheme (now used in all model classes). | Feb 3 2020 | |||
dba63f835a31 | tlemaire | corrected docstring errors in pneuron Cm0 and Qm0 | Feb 3 2020 | |||
9d0666784d2d | tlemaire | Created AcousticSource class to be used for US simulations. | Feb 3 2020 | |||
c995e8999df7 | tlemaire | Modified Lookup class (new properties, corrected methods). | Jan 26 2020 | |||
38dc94d61fe7 | tlemaire | added DQ_LOOKUP constant (used in run_lookups.py) | Jan 26 2020 | |||
8478fde7a5d4 | tlemaire | Automated getModel using automatically generated dictionary of models with… | Jan 14 2020 | |||
d0b57c5e137d | tlemaire | re-ran and completed STN notebook | Dec 6 2019 | |||
f8107574d0a8 | tlemaire | added threshold module with isolated threshold function (now used for all… | Dec 2 2019 | |||
b46ab57b16d3 | tlemaire | corrected borg-graham formalism methods | Nov 22 2019 | |||
6197f85f0709 | tlemaire | corrected Astim factor error in pneuron desc. added extra parsing methods | Nov 20 2019 | |||
36119dd01aec | tlemaire | moved filecode function to utils | Nov 14 2019 | |||
de255e65bccc | tlemaire | Major update: | Nov 14 2019 | |||
bc1800471252 | tlemaire | created Timeprotocol and PulsedProtocol classes, now used in pneuron, nbls and… | Nov 13 2019 | |||
f1d2ab4cfb4b | tlemaire | added PointNeuron alphaBorgGaham and betaBorgGraham methods, now used for sundt… | Nov 7 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 | |||
d65e74f5c30c | tlemaire | implemmented inheritance scheme for PointNeuron.chooseTimeStep method | Sep 11 2019 | |||
bd840351d13f | tlemaire | corrected SweeneyNode alpham equation according to Basser and Roth, 1991. | Sep 10 2019 | |||
614c56792d61 | tlemaire | expanded charge range for pneuron.getLookup | Sep 4 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 | |||
4f5fb5ee0829 | tlemaire | implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to… | Aug 26 2019 | |||
db880034dc26 | tlemaire | harmonized peaks/spikes detection process across the package. | Aug 22 2019 | |||
3146cab6bade | tlemaire | added iCap to plot variables. added colormap option for comparative plots even… | Aug 15 2019 | |||
2278e599a753 | tlemaire | added automatic solution prepending to all simulate methods (to treat initial… | Aug 14 2019 | |||
366c7e528105 | tlemaire | added VoltageClamp class with associated script and parser | Aug 14 2019 | |||
dc37f0afbd17 | tlemaire | removed all static quasiSteadyStates definition in neuron classes. | Jul 17 2019 | |||
f113d822d4fb | tlemaire | added findModifiedEq function to utils, using brentq to find a new equilibrium… | 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 | |||
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 | |||
8f1ea1a16339 | tlemaire | moved effRates vectorization into pneuron.getEffRates method | Jun 27 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 | |||
8b3f49b0bac4 | tlemaire | corrected labeling error in GroupedTimeSeries | 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 | |||
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 | |||
98942bac6b56 | tlemaire | redefined derStates and steadyStates as dictionary of lambda functions | Jun 19 2019 | |||
26fe1e08a408 | tlemaire | cleaned up neuron classes. redefined currents to return functions instead of… | Jun 19 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 | |||
63faa327c865 | tlemaire | finished implmenting Firing Rate as plot variable (now replacing plotFRProfile). | Jun 16 2019 | |||
b461503582fb | tlemaire | added firing rate to plot variables | Jun 16 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 | |||
0028dbdfe69f | tlemaire | added neuron templyte class. added procedure to follow to add new neuron types… | Jun 11 2019 | |||
c7f94b320ba7 | tlemaire | set t first in all derivatives function | 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 | |||
1c9c63d4ba6a | tlemaire | added getModel and getPointNeuron functions. removed deprecated scripts. | Jun 6 2019 | |||
6cbf141d9754 | Theo Lemaire | corrected plot_QSS inputdir error | Jun 3 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 | |||
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 | |||
e08e8c736efa | Theo Lemaire | replaced progressbar2 by tqdm | May 29 2019 |
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