Diffusion PySONIC (old) (master) History

History
master4937955d02148f66971110a…

Jun 29 2019

adapted methods of all classes into classmethods and staticmethods when…
4937955d0214
·tlemaire on Jun 29 2019, 20:27.

Jun 28 2019

transformed model inputs, checkInputs and simQueue into static methods
4997a9f88989
·tlemaire on Jun 28 2019, 16:15.
created separate test module with TestBase class. renamed test_basic into…
22abb7710105
·tlemaire on Jun 28 2019, 13:51.

Jun 27 2019

re-introduced derivatives as mandatory model method
0fe23305b3ad
·tlemaire on Jun 27 2019, 19:13.
updated README
9ac705d6dbee
·tlemaire on Jun 27 2019, 19:12.
added Model.description method. added nbls.getLookup2D method with correct fs…
a0db776b7966
·tlemaire on Jun 27 2019, 16:10.
moved lookup to core module. moved getLookup methods to nbls class.
b73594f4d58b
·tlemaire on Jun 27 2019, 14:34.
moved effRates vectorization into pneuron.getEffRates method
8f1ea1a16339
·tlemaire on Jun 27 2019, 12:59.
defined TestBase class with smart subset handling (inherited by TestSims)
d909927fd268
·tlemaire on Jun 27 2019, 10:59.
rewrote test_basic into a class
eb0324a5cd27
·tlemaire on Jun 27 2019, 10:47.

Jun 26 2019

changed TimeSeries.getStimPulses to class method
b7e75610c1d2
·tlemaire on Jun 26 2019, 20:03.
added fs (spatially-averaged) as input to nbls model. defined SmartLookup class…
dffee6926b85
·tlemaire on Jun 26 2019, 19:50.
added test at bottom of lookups module
07c34eeed0f7
·tlemaire on Jun 26 2019, 16:50.
added paper url to setup.py
4d047c49f50d
·tlemaire on Jun 26 2019, 13:51.
replaced multiprocessing import by multiprocess import in batches.py to enable…
4ebf9fe64023
·tlemaire on Jun 26 2019, 13:49.
cleaned up model classes. defined mandatory derivatives method for model…
3528fa81b6d1
·tlemaire on Jun 26 2019, 13:38.

Jun 25 2019

improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar…
9965ddc0005d
·tlemaire on Jun 25 2019, 23:21.
corrected README
f83e0e973bd3
·tlemaire on Jun 25 2019, 19:19.
updated README
65a9529c2978
·tlemaire on Jun 25 2019, 18:52.
corrected labeling error in GroupedTimeSeries
8b3f49b0bac4
·tlemaire on Jun 25 2019, 18:26.
removed unnecessary functions from pneuron
acf299185987
·tlemaire on Jun 25 2019, 18:17.
added automatic effRates function definition in pneuron.parse method. removed…
db8cc8e2b5ff
·tlemaire on Jun 25 2019, 17:57.
added precisions about derStates requirements in README
21dda94243b8
·tlemaire on Jun 25 2019, 15:09.
finished implementing pneuron.buildDerEffStates method to automatically create…
4742d6a43494
·tlemaire on Jun 25 2019, 14:59.

Jun 24 2019

defined separate lookup decorator for bls.computePMparams method. updated…
83ff47370d86
·tlemaire on Jun 24 2019, 20:21.

Jun 20 2019

define dLookUp class to perform lookup projections and interpolations
a96a900ad4b4
·tlemaire on Jun 20 2019, 17:35.
added default output directory ("dump"). cleaned up neuron classes.
6c10d4162d71
·tlemaire on Jun 20 2019, 10:09.

Jun 19 2019

refefined derEffstates construction to return a dictionary of function.
fdebb58e8442
·tlemaire on Jun 19 2019, 19:12.
corrected error in subset parsing
1a9277e6bbb4
·tlemaire on Jun 19 2019, 15:46.
added getSteadyStates and getDerStates methods to pneuron to call steadyStates…
f719dddee9f0
·tlemaire on Jun 19 2019, 15:39.
corrected Cinf error in ThalamoCortical neuron
becd2527f268
·tlemaire on Jun 19 2019, 15:19.
redefined derStates and steadyStates as dictionary of lambda functions
98942bac6b56
·tlemaire on Jun 19 2019, 15:16.
cleaned up neuron classes. redefined currents to return functions instead of…
26fe1e08a408
·tlemaire on Jun 19 2019, 11:05.

Jun 18 2019

started implementation of buildDerEffStates to contruct the derEffStates…
40b5a09c46c2
·tlemaire on Jun 18 2019, 23:14.
replaced obscur states list by explicit dictionary in all currents methods
7b2aee9851af
·tlemaire on Jun 18 2019, 18:21.
replaced obscur states list by explicit states dictionary in derStates and…
00f57af96cfb
·tlemaire on Jun 18 2019, 16:04.

Jun 17 2019

added custom parsing to paper figure scripts
d4798d527ccc
·tlemaire on Jun 17 2019, 22:08.
corrected y, t order error in nbls.fullDerivatives. added custom parsing in…
66eaf2f41fba
·tlemaire on Jun 17 2019, 21:43.
added custom parsing to plot_gating_kinetics.py
a03eb1b35b77
·tlemaire on Jun 17 2019, 21:19.
added custom parsing to plot_effective_variables.py
3b86ec877351
·tlemaire on Jun 17 2019, 21:13.
adde prettify option to timeseries plots
1465c48312a6
·tlemaire on Jun 17 2019, 20:43.
defined PlotParser and TimeSeriesParser classes
e3f3982b8981
·tlemaire on Jun 17 2019, 18:52.
added colormap functionality to PhaseDiagram
9e96cf6ee947
·tlemaire on Jun 17 2019, 18:29.
replaced plotPhaseDiagram by PhaseDiagram class inheriting from ComparativePlot…
e01fa72e6143
·tlemaire on Jun 17 2019, 17:55.
moved nmodl generator to ExSONIC package
0efc60073f8b
·tlemaire on Jun 17 2019, 10:58.
added custom parsing to generate_mod_file.py
9556faead02c
·tlemaire on Jun 17 2019, 10:52.
solved issue with ActivationMap Ascale
4ce5e074ca4c
·tlemaire on Jun 17 2019, 10:24.
replaced no_offset by tbounds in plotting options. added custom parsing to…
75f6032d2f63
·tlemaire on Jun 17 2019, 09:34.

Jun 16 2019

removed plotFRProfile from init file
cf146fbc835e
·tlemaire on Jun 16 2019, 22:52.
finished implmenting Firing Rate as plot variable (now replacing plotFRProfile).
63faa327c865
·tlemaire on Jun 16 2019, 22:47.
added consistent time bounding to plotters
1329e50433cd
·tlemaire on Jun 16 2019, 20:42.
added firing rate to plot variables
b461503582fb
·tlemaire on Jun 16 2019, 13:05.

Jun 15 2019

added colormap functionality to CompPlot, with lin or log scale.
012f2603c5d7
·tlemaire on Jun 15 2019, 19:15.
added simkey to meta dictionary. added automatic parsing and labeling of…
c14fa0da1fd7
·tlemaire on Jun 15 2019, 18:32.

Jun 14 2019

added spike details plotting options to TimeSeriesPlot
fb7c07fee5cb
·tlemaire on Jun 14 2019, 16:06.
added frequency and mark_spikes option to both CompPlot and SchemePlot classes
bdf8ef51d3db
·tlemaire on Jun 14 2019, 11:53.
added outputdir option to simQueue methods. added automatic parsing to Parser…
de8bdbc4fee0
·tlemaire on Jun 14 2019, 11:34.

Jun 13 2019

updated constants
b0f51febd195
·tlemaire on Jun 13 2019, 23:54.
removed extra line in EStimParser
bd54da55cc7c
·tlemaire on Jun 13 2019, 15:24.
removed extra line in run_lookups.py
da542f2db42b
·tlemaire on Jun 13 2019, 15:24.
adapted MechSimParser for use in run_lookups.py
af7294977045
·tlemaire on Jun 13 2019, 15:22.
updated README with more information on repo content
94fbf591d2b0
·tlemaire on Jun 13 2019, 04:13.
updated README with future developments and license information
502b8d45d5bf
·tlemaire on Jun 13 2019, 03:36.
updated README headers
812cb5c1cb3a
·tlemaire on Jun 13 2019, 03:18.

Jun 12 2019

updated all file headers
b42a0de93240
·tlemaire on Jun 12 2019, 23:15.
adapted README recipe to cleaned up neuron classes
0ab79b08684a
·tlemaire on Jun 12 2019, 17:16.
cleaned-up all neuron classes
cc309fa78cd9
·tlemaire on Jun 12 2019, 16:35.
replaced "neuron" by "pneuron" for all PointNeuron instances
6e017b421f3e
·tlemaire on Jun 12 2019, 12:58.

Jun 11 2019

corrected README
bc6f2d49e7db
·tlemaire on Jun 11 2019, 17:33.
corrected numbering errors in README
ea20cb84a617
·tlemaire on Jun 11 2019, 16:59.
added neuron templyte class. added procedure to follow to add new neuron types…
0028dbdfe69f
·tlemaire on Jun 11 2019, 16:56.

Jun 10 2019

added plotting of real QS SFPs and UFPs in plotQSSdynamics and plotQSSVarVsQm…
3accccc91cbe
·tlemaire on Jun 10 2019, 22:27.
minor change to getCycleProfiles
ed095e030274
·tlemaire on Jun 10 2019, 21:56.
moved example script in README and updated rest of the text.
9c883a796eff
·tlemaire on Jun 10 2019, 21:45.
added functionality to load data directly from sim results in TimeSeriesPlot…
2f0254ea5b53
·tlemaire on Jun 10 2019, 20:52.
switched back to old evaluateStability version
1354c6f9d2e9
·tlemaire on Jun 10 2019, 16:34.
first attempt at replacing custom integration in nbls.evaluateStability by call…
dd32fc0479b4
·tlemaire on Jun 10 2019, 00:06.

Jun 9 2019

removed STN temporary fix in nbls.titrate
84c54a491722
·tlemaire on Jun 9 2019, 23:00.
added first-call check that condition changes within the interval to…
b88c300e48f0
·tlemaire on Jun 9 2019, 22:48.
added file locking to cache functions
db58a9d4e8b7
·tlemaire on Jun 9 2019, 21:55.
added solve_ivp optional use to Simulator.integrate method
2e0f97a8baaf
·tlemaire on Jun 9 2019, 21:36.
set t first in all derivatives function
c7f94b320ba7
·tlemaire on Jun 9 2019, 21:16.
removed ng and Z explicit computation in runSONIC (replaced by nan arrays)
b46a8cd85a73
·tlemaire on Jun 9 2019, 20:47.
corrected errors in nbls interpEFFVariable and runSONIC methods
5eed591ede6e
·tlemaire on Jun 9 2019, 20:10.
added nbls isStableQSS and titrateQSS methods. finished plotQSSThresholdCurve
863bdf8330f4
·tlemaire on Jun 9 2019, 19:51.

Jun 7 2019

added getSimThresholdAmps and plotQSSThresholdCurve functions to QSS module…
26fdc0bbfe8d
·tlemaire on Jun 7 2019, 18:28.
added multiprocessing for runAndGetStab function
86564c193a65
·tlemaire on Jun 7 2019, 16:41.
added custom parsers to plot_timeseries and plot_QSS
1f1e59762ea3
·tlemaire on Jun 7 2019, 15:56.

Jun 6 2019

moved getLowIntensitiesSTN to STN class
50103226d72b
·tlemaire on Jun 6 2019, 21:30.
moved lookups utilities into separate lookups module (in neurons folder)
0984b86caa8f
·tlemaire on Jun 6 2019, 21:25.
created ActivationMap class
3556a765fe5c
·tlemaire on Jun 6 2019, 21:04.
added getModel and getPointNeuron functions. removed deprecated scripts.
1c9c63d4ba6a
·tlemaire on Jun 6 2019, 18:29.

Jun 4 2019

minodr edits
01bf73a48e1a
·Theo Lemaire on Jun 4 2019, 17:21.

Jun 3 2019

added caching of QSS analysis results
bc5a29bc6c9a
·Theo Lemaire on Jun 3 2019, 20:23.
corrected plot_QSS inputdir error
6cbf141d9754
·Theo Lemaire on Jun 3 2019, 17:02.
added custom parser to plot_QSS_IQ.py
1295ce41f2c3
·Theo Lemaire on Jun 3 2019, 15:58.
added parsers module, now used in sim scripts for more consistency.
f75ca2e6e294
·Theo Lemaire on Jun 3 2019, 15:11.

Jun 2 2019

removed unnecessary script
b21bb388bb20
·Theo Lemaire on Jun 2 2019, 22:42.
simplified run scripts
fdc484dcbe00
·Theo Lemaire on Jun 2 2019, 22:15.
changed marker styles for QSS plots
49e81c5ace12
·Theo Lemaire on Jun 2 2019, 17:55.