Diffusion PySONIC (old) (master) History

R4670/PointNICE/solvers/SolverUS.py
master8e3d2db927b59381a6b00a2…

Jul 18 2018

grouped mod files in single directory. defined stimonoff procedure in separate…
8e3d2db927b5
·tlemaire on Jul 18 2018, 15:44.

Jul 17 2018

corrected TC mod file (needs smaller time step to be fully accurate).
09ead26fe237
·tlemaire on Jul 17 2018, 16:29.

Jul 13 2018

separated mod files. corrected variables outputing in runNEURON. corrected Vm…
eaed73930e7c
·tlemaire on Jul 13 2018, 14:59.

Jul 6 2018

improved runNEURON method. added LTS mechanism.
cca23e04187b
·tlemaire on Jul 6 2018, 17:44.

Jul 5 2018

added runNEURON method to run US simulation with NEURON (to be ctd).
5011ac8891a5
·tlemaire on Jul 5 2018, 23:50.

May 22 2018

minor modifications to plotActivationMap function, added plotTraces function…
e238a7caa389
·tlemaire on May 22 2018, 16:36.

May 8 2018

added method to find neuron-specific rheobase US amplitudes (findRheobaseAmps)…
383a6cb2fc75
·tlemaire on May 8 2018, 15:19.
divided 3D -> 1D lookups projection into 2 distinct steps (defined…
a148e58c0951
·tlemaire on May 8 2018, 10:40.

May 2 2018

replaced numpy.vectorize by explicit definition of vectorized BLS methods.
419fdbc72f8c
·tlemaire on May 2 2018, 21:15.
vectorized relevant functions of the BilayerSonophore class
f7bc3b340b2d
·tlemaire on May 2 2018, 15:40.

Apr 24 2018

added PmCompMethod as a parameter for all relevant methods of the…
5e84496cf5e0
·tlemaire on Apr 24 2018, 19:06.

Apr 17 2018

corrected return error in findPeaks. added new algorithmic constant: minimal…
e2763f9ad093
·tlemaire on Apr 17 2018, 11:45.

Mar 29 2018

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

Mar 19 2018

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

Mar 18 2018

corrected initial conditions error in pulsed protocols integration of…
900de6e3aa75
·Theo Lemaire on Mar 18 2018, 19:58.
removed erroneous use of y_pulse_off in runClassic method
708bc9223628
·Theo Lemaire on Mar 18 2018, 11:47.

Mar 16 2018

programmed classic method progress bar to show up both on DEBUG and INFO levels
c6b29afe2de9
·tlemaire on Mar 16 2018, 17:31.
corrected createLookup runMech error by calling super.run method
4b7e412bb8d6
·tlemaire on Mar 16 2018, 14:32.
Added user input to decide whether to continue batch after assertion error or…
5049e821acd8
·tlemaire on Mar 16 2018, 13:30.

Mar 15 2018

added user input to decide whether lookup file should be overwritten in case of…
69a4e42fa766
·tlemaire on Mar 15 2018, 17:45.
introduced custom defined InputError exceptions (instead of assert statements)…
4ffaa73494ea
·tlemaire on Mar 15 2018, 17:06.
addded time-step-dependent output arrays downsampling in classic simulations to…
9df57ec1684b
·tlemaire on Mar 15 2018, 12:00.
temporarily removed checking for prior lookup file existence upon new lookup…
d8a1246ad44e
·tlemaire on Mar 15 2018, 11:20.

Mar 14 2018

general optimization of integration methods (elec, mech and US classic) using…
b65f7bad637c
·tlemaire on Mar 14 2018, 19:30.

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.
changed "ch_mech" by "neuron"
acab28778569
·tlemaire on Mar 13 2018, 14:33.
replaced DF by DC, and added pandas dataframes to store and retrieve simulation…
1edd575f6465
·Theo Lemaire on Mar 13 2018, 01:14.

Mar 12 2018

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

Mar 8 2018

adaptive time step lowering for high-PRF protocols in Elec and effective-US…
8d85b3cb30d6
·tlemaire on Mar 8 2018, 09:53.

Feb 28 2018

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

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

replaced print statements with logging statements in internal modules
43647159e654
·tlemaire on Sep 10 2017, 17:16.

Sep 6 2017

replaced getopt with argparse in test scripts
ffed8b864bbf
·tlemaire on Sep 6 2017, 17:10.
replaced printPct by progressbar
7fff2117cd10
·tlemaire on Sep 6 2017, 14:34.

Sep 3 2017

updated test_values
f51d67fdf64a
·tlemaire on Sep 3 2017, 17:23.
added profiling option for each method inside test_basic.py, using cProfile and…
92e2cd326a4e
·tlemaire on Sep 3 2017, 16:53.

Sep 2 2017

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

Sep 1 2017

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 30 2017

debugged and validated new runEffective method: interpolation datasets at…
cf8e6794b04c
·tlemaire on Aug 30 2017, 15:46.

Aug 29 2017

added 2nd version of runEffective where 3D (f, A, Q) interpolation datasets are…
7da392ae7e7a
·tlemaire on Aug 29 2017, 18:17.
modified data validation on Adrive for MECH and ASTIM simulations (strictly…
071e81993e19
·tlemaire on Aug 29 2017, 16:27.
modified createLookup method to create, for each coefficient, a 3D array of…
0f69714e39ec
·tlemaire on Aug 29 2017, 16:14.

Aug 28 2017

optimized effective method: 2D (amp, charge) coefficients interpolators are…
1ea422ad10eb
·tlemaire on Aug 28 2017, 18:02.
updated run functions to deal with zero offset. updated test_graphs
90c71fb8d8e5
·tlemaire on Aug 28 2017, 15:26.
updated test_basic.py with more thorough tests. Added more thorough input…
b50efb81b3cb
·tlemaire on Aug 28 2017, 14:14.

Aug 25 2017

Added pulsed stimuli handling to SolverElec. Implemented moved titration…
3c218a52595b
·tlemaire on Aug 25 2017, 13:06.

Aug 23 2017

moved some utils functions into simutils & pltutils modules
4f9a8fd2aed4
·tlemaire on Aug 23 2017, 16:28.
first commit to c4science
abfba2e921d7
·tlemaire on Aug 23 2017, 14:28.