History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
143fbd37ca59 | tlemaire | added special case handling to find lookups name | May 27 2021 | |||
40ac2cbf792f | tlemaire | added workaround solution for passive generic lookup name | May 19 2021 | |||
9b83a80b55f5 | tlemaire | started implementing gamma evaluation method | May 17 2021 | |||
6aadfe75ac22 | tlemaire | started working on coupled_nbls module | May 14 2021 | |||
5159d5ca1d87 | tlemaire | improved logging in nbls.computeEffVars | Mar 26 2021 | |||
f23057d86a6e | tlemaire | improved error logging in bls.balancedefQS. | Mar 26 2021 | |||
b4233b34e678 | tlemaire | improved lookup naming system (and renamed all lookups accordingly). | Mar 23 2021 | |||
7d732f9d2c25 | tlemaire | adapted nbls.computeEffVars method to accomodate for Fourier Fourier overtones… | Mar 23 2021 | |||
e7842427f677 | tlemaire | added array-typed charge input (i.e. US-periodic profile) option to… | Mar 23 2021 | |||
e57b064d8f70 | tlemaire | simplified bls.capacitance expresion | Aug 5 2020 | |||
ed71c4613b28 | tlemaire | replaced nbls NEURONS_LOOKUP_DIR by a more general LOOKUP_DIR defined in utils | Aug 4 2020 | |||
9b03fd5152c2 | tlemaire | corrected DrivenNeuronalBilayerSonophore.inputs | May 2 2020 | |||
e1f537dcc076 | tlemaire | corrected error in solve_ivp call. | May 2 2020 | |||
fa9c541d7842 | tlemaire | applied correction to ODESolver.getNsamples to make sure there are at least 2… | May 1 2020 | |||
835803fa8d6b | tlemaire | added progress bar logging to nbls.simFull at INFO level. | Apr 30 2020 | |||
fcb5a387a33e | tlemaire | added input-ouput match pre-check in LogBatch.run method to avoid unnecessary… | Apr 28 2020 | |||
6dedc53ccbc8 | tlemaire | added optional tstart argument to PusledProtocol classes. corrected… | Apr 24 2020 | |||
108548aa8cc8 | tlemaire | added max_nsamples parameter to effective solver to avoid memory allocation… | Apr 18 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 | |||
e62423f9469d | tlemaire | added update interval argument to HybridSolve.solve method. | Apr 17 2020 | |||
69892d75c503 | tlemaire | improved solvers docstrings and clarified their use in model classes. | Apr 16 2020 | |||
d03caf415e89 | tlemaire | removed ambiguity around initialConditions methods to allow correct lookups… | Apr 15 2020 | |||
b77cd9e4eb12 | tlemaire | implemented better solvers (now inside solvers module), including an… | Apr 15 2020 | |||
a8ffc4cf6311 | tlemaire | removed useless error instance catch in utils | Apr 10 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 | |||
9dcd3884ae33 | tlemaire | added TC fs lookup. | Mar 30 2020 | |||
c8a9ea2beb92 | tlemaire | added extra functionalities to Lookup class. continued fiber nodes notebook. | Feb 28 2020 | |||
165caa8bf488 | tlemaire | moved getMeta to utils | Feb 20 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 | |||
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 | |||
062e541857dc | tlemaire | added lookups files in separate lookups folder using LFS. | Feb 3 2020 | |||
9d0666784d2d | tlemaire | Created AcousticSource class to be used for US simulations. | Feb 3 2020 | |||
eec847e65a7a | tlemaire | added sundt fs lookups. adapted RS fs lookups. adapted nbls.getLookup2D method… | Jan 26 2020 | |||
6846298198d4 | tlemaire | added interp_method Lookup attribute to enable choice of lookup interpolation… | Jan 26 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 | |||
a0b6724a45a5 | tlemaire | removed plotVarQSSDynamics function from QSS and plot_QSS | Dec 14 2019 | |||
bac984960467 | tlemaire | corrected nbls fullDerivatives, simFull and simHybrid methods (removed phi… | Dec 4 2019 | |||
f8107574d0a8 | tlemaire | added threshold module with isolated threshold function (now used for all… | Dec 2 2019 | |||
6deb0da8868d | tlemaire | added internal bls.simUntilConvergence method (without decorators) to enable… | Nov 26 2019 | |||
456fa71d226b | tlemaire | added qss_vars and pulse-avg run options to nbls simSonic method. | Nov 20 2019 | |||
36119dd01aec | tlemaire | moved filecode function to utils | Nov 14 2019 | |||
de255e65bccc | tlemaire | Major update: | Nov 14 2019 | |||
4a5626da478c | tlemaire | improved filecodes generation from meta dictionary in Model.filecode | Nov 13 2019 | |||
bc1800471252 | tlemaire | created Timeprotocol and PulsedProtocol classes, now used in pneuron, nbls and… | Nov 13 2019 | |||
a2c1e3e2eb02 | tlemaire | modified nbls.QSSderivatives and nbls.__simQSS to work with any specified… | Nov 6 2019 | |||
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 |
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