Diffusion PySONIC (old) (master) History

R4670/plot
mastereb527762650d902ac89ff6c…

Aug 21 2018

changed package name to PySONIC.
043172721a44
·tlemaire on Aug 21 2018, 16:19.
removed NEURON related code from package (runNEURON method, NMODL folder), used…
2267460a3b52
·tlemaire on Aug 21 2018, 14:29.

Jun 18 2018

minor modifications to plotEffVars, rescale and test_intermolecular_pressure.py
3b9d8b293e8a
·tlemaire on Jun 18 2018, 17:02.

May 25 2018

renamed plotEffCoeffs to plotEffVariables with lots of improvements.
00baa42adf67
·tlemaire on May 25 2018, 22:11.
added script to test intermoleulcar pressure approximation.
7d33ab6ec1f9
·tlemaire on May 25 2018, 15:45.

May 8 2018

added method to find neuron-specific rheobase US amplitudes (findRheobaseAmps)…
383a6cb2fc75
·tlemaire on May 8 2018, 15:19.

May 3 2018

solved minor issue in getPatchesLoc. replaced Rectangle by axvspan instances…
ea14e67aae6f
·tlemaire on May 3 2018, 17:09.

Apr 30 2018

added reinit method to BilayerSonophore class. added ComputeSpikeMetrics…
74c9b13f40bf
·tlemaire on Apr 30 2018, 13:55.

Apr 18 2018

added lookups for IB neuron
3f620b0c56a0
·tlemaire on Apr 18 2018, 18:04.

Apr 17 2018

validated IB neuron gating kinetics for E-STIM
487fd2f0db0a
·tlemaire on Apr 17 2018, 17:11.

Apr 14 2018

removed dependency on colorlover in plotComp
a5aaa17fbd90
·tlemaire on Apr 14 2018, 18:38.

Apr 4 2018

replaced detectSpikes by the more robust findPeaks. added a plot_spikes script…
d5e56c2f9c40
·tlemaire on Apr 4 2018, 17:55.

Mar 30 2018

modified plotComp to take only 1 input variable and added option to plot inset
1ac82339eaf3
·tlemaire on Mar 30 2018, 16:58.

Mar 29 2018

added prominence threshold constant for spike detection. added skeleton for IB…
377594fb12b0
·tlemaire on Mar 29 2018, 18:04.

Mar 21 2018

added extra options to plotComp (custom ticks, black legend with colored plots)
3bee78ffb4bc
·tlemaire on Mar 21 2018, 18:34.

Mar 20 2018

added detailed docstring to detectPeaks
3fabf680de73
·tlemaire on Mar 20 2018, 21:49.

Mar 19 2018

changes to plotComp function allowing to customize linestyles, colors and…
1c8f0234e7e7
·tlemaire on Mar 19 2018, 17:36.

Mar 15 2018

introduced custom defined InputError exceptions (instead of assert statements)…
4ffaa73494ea
·tlemaire on Mar 15 2018, 17:06.

Mar 13 2018

Switched from ode (lsoda) to odeint for classic method to see if it solves…
01238213b788
·tlemaire on Mar 13 2018, 23:22.
implemented neuron-specific charge interval for lookup creation.
1b6d6a579519
·tlemaire on Mar 13 2018, 17:31.

Mar 12 2018

replaced channels by neurons
edd5594d9646
·Theo Lemaire on Mar 12 2018, 20:01.

Mar 7 2018

updated README and LICENCSE files. added extra BLS lookups. corrected titration…
63c842041ef8
·tlemaire on Mar 7 2018, 15:28.

Feb 28 2018

updated titration methods and generated LeechP lookups
89d20f6d2cb6
·tlemaire on Feb 28 2018, 16:53.

Jan 9 2018

corrected LeechP implementation using dynamic Nernst potentials for Sodium and…
c59a8267c97e
·tlemaire on Jan 9 2018, 14:53.

Dec 12 2017

Lots of corrections and improvements to the LeechP model implementation. E-STIM…
33ee63af70aa
·tlemaire on Dec 12 2017, 15:16.

Nov 29 2017

Added sonophore diameter to ASTIM files naming, and changed DF to 2 decimals…
ae51b3bafaec
·tlemaire on Nov 29 2017, 14:59.

Nov 27 2017

validated effective method for LeechT neuron, added that neuron to test_values.
1bb50e8f0025
·tlemaire on Nov 27 2017, 13:18.

Nov 22 2017

corrected code for LeechT neuron, and validated it on electrical stimuli
c9dad3d35684
·tlemaire on Nov 22 2017, 14:01.

Sep 12 2017

added biomech and biophys parameters directly as BilayerSonophore class…
6be1756dda64
·tlemaire on Sep 12 2017, 14:46.

Sep 10 2017

added input pltvars checking to plot functions
c67c8c39a93b
·tlemaire on Sep 10 2017, 19:07.
replaced print statements with logging statements in internal modules
43647159e654
·tlemaire on Sep 10 2017, 17:16.

Sep 2 2017

added standardized plotEffCoeffs function to pltutils
b0a231289d69
·tlemaire on Sep 2 2017, 17:39.

Sep 1 2017

replaced eval statements from plotGatingKinetics & plotRateConstants by getattr…
08165e6a06f3
·tlemaire on Sep 1 2017, 21:30.
removed old plot_RS_rate_constants script
43f0618daa4a
·tlemaire on Sep 1 2017, 21:24.
added standardized plotRateConstants method
4c66e98d971e
·tlemaire on Sep 1 2017, 21:18.
added plotGatingKinetics method to plot the steady-sate and time constant…
3f5921510ae9
·tlemaire on Sep 1 2017, 20:51.
added temporary code to delay last pulse during PW stimuli in runEffective…
32c77b1353fa
·tlemaire on Sep 1 2017, 19:17.
added option to specify labels in plotComp
e2ff032a6759
·tlemaire on Sep 1 2017, 15:55.

Aug 28 2017

renamed LoadParams to load_BLS_params
c61b8e3492f6
·tlemaire on Aug 28 2017, 14:20.
updated test_basic.py with more thorough tests. Added more thorough input…
b50efb81b3cb
·tlemaire on Aug 28 2017, 14:14.

Aug 25 2017

included default plotting scheme inside neuron classes definition. Modified…
06127af4b669
·tlemaire on Aug 25 2017, 18:28.
adapted plotComp to deal with pulsed ESTIM outputs and MECH outputs. corrected…
c30d03edb7cc
·tlemaire on Aug 25 2017, 17:54.
implemented runMechBatch function. adapted plotBatch function to deal with MECH…
0a89dde7f847
·tlemaire on Aug 25 2017, 17:20.
Added pulsed stimuli handling to SolverElec. Implemented moved titration…
3c218a52595b
·tlemaire on Aug 25 2017, 13:06.

Aug 24 2017

debugging of plot functions
3e6f232a2a2e
·tlemaire on Aug 24 2017, 17:59.

Aug 23 2017

created plotting module inside package, with plotComp and plotBatch functions
af10a48546b7
·tlemaire on Aug 23 2017, 15:45.
first commit to c4science
abfba2e921d7
·tlemaire on Aug 23 2017, 14:28.

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R4670/plot
mastereb527762650d902ac89ff6c…