Diffusion PySONIC (old) (master) History

History
masterb9f08f5eaf675ba6a615bed…

Mar 16 2018

added new lookups except LeechP
b9f08f5eaf67
·tlemaire on Mar 16 2018, 14:11.
Added user input to decide whether to continue batch after assertion error or…
5049e821acd8
·tlemaire on Mar 16 2018, 13:30.
renamed BilayerSonophore.runMech to BilayerSonophore.run, and runMechSingle to…
5b8f09fbd295
·tlemaire on Mar 16 2018, 12:06.
removed unwanted data files from sim directory
cf2459c7182e
·tlemaire on Mar 16 2018, 11:54.
corrected Z bounding for out-of-range deflections
4c475209bac9
·tlemaire on Mar 16 2018, 11:52.

Mar 15 2018

added runMechSingle to simutils and MECH_run script
50e85131e3d9
·tlemaire on Mar 15 2018, 19:23.
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.
generated new lookups for RS and FS neurons with a wider frequency range (20kHz…
4d2d60cc96c5
·tlemaire on Mar 15 2018, 14:28.
renamed INPUT_CHARGE_RANGE to CHARGE_RANGE
e5a0b44e3d54
·tlemaire on Mar 15 2018, 14:02.
added correction of deflection value in eqMech (with warning) if below critical…
d350701db48c
·tlemaire on Mar 15 2018, 14:00.
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.
replaced error raising by a simple warning for out-of-range deflections in…
10fde2422c97
·tlemaire on Mar 15 2018, 11:17.

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.
prepared creation of new lookups
d01c70ab720e
·tlemaire on Mar 13 2018, 17:35.
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.
added neuron name to meta dictionary for ESTIM and ASTIM simulations
0c7107d859aa
·tlemaire on Mar 13 2018, 12:49.
added tcomp to "meta" dictionary.
d2ee8d2274d4
·tlemaire on Mar 13 2018, 12:42.
tested and validated plotting with pandas dataframes.
41e27b5ece2e
·tlemaire on Mar 13 2018, 12:37.
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

adapted batch files for LeechP
34958bd21f55
·tlemaire on Mar 8 2018, 10:02.
adaptive time step lowering for high-PRF protocols in Elec and effective-US…
8d85b3cb30d6
·tlemaire on Mar 8 2018, 09:53.

Mar 7 2018

corrected PRF display issues in command line scripts ESTIM_run and ASTIM_run
6e5878fe0ecf
·tlemaire on Mar 7 2018, 18:52.
updated README and LICENCSE files. added extra BLS lookups. corrected titration…
63c842041ef8
·tlemaire on Mar 7 2018, 15:28.

Mar 2 2018

added pre-commit hook and adapted run_tests.sh command
063d417bd20c
·tlemaire on Mar 2 2018, 18:03.
extended installation instructions in the README file
d12141d0c48b
·tlemaire on Mar 2 2018, 17:57.

Feb 28 2018

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

Jan 18 2018

tried to adapt pre-commit hook after Anaconda re-install to call python with…
bf5a88531d4b
·tlemaire on Jan 18 2018, 17:25.

Jan 16 2018

corrected computation of firing rate in detectSpikes function
7497a2150a6b
·tlemaire on Jan 16 2018, 20:07.

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.

Dec 1 2017

added LeechPressure to channels init. added leechP variables to pltvars. tested…
094fd25223f4
·tlemaire on Dec 1 2017, 09:01.

Nov 29 2017

implemented leechP intracellular pools evolution according to modelDB ref
a270608c8e8c
·tlemaire on Nov 29 2017, 19:28.
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 24 2017

added LeechT lookup
f1fbc6e5b9bb
·tlemaire on Nov 24 2017, 12:32.

Nov 22 2017

added lookup files and template log files to tracking
e5364755a2a5
·tlemaire on Nov 22 2017, 14:38.
added latest dependencies to setup file
69e2945beb69
·tlemaire on Nov 22 2017, 14:26.
corrected code for LeechT neuron, and validated it on electrical stimuli
c9dad3d35684
·tlemaire on Nov 22 2017, 14:01.

Sep 12 2017

debugged double printing issue of logging statements
6249b5298f4c
·tlemaire on Sep 12 2017, 18:56.
emphasized code in README
3cb02a5f8d12
·tlemaire on Sep 12 2017, 18:06.
modified README file to include installation and usage info
d67a94aa1050
·tlemaire on Sep 12 2017, 17:57.
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.
added color to logging statements
189a078bf8d2
·tlemaire on Sep 10 2017, 18:46.
improved error handling
6cd8d175ad7b
·tlemaire on Sep 10 2017, 17:53.
replaced print statements with logging statements in internal modules
43647159e654
·tlemaire on Sep 10 2017, 17:16.

Sep 6 2017

added ESTIM_run script. added plot command line option to ASTIM_run and…
34e47b5286e0
·tlemaire on Sep 6 2017, 17:58.
replaced getopt with argparse in test scripts
ffed8b864bbf
·tlemaire on Sep 6 2017, 17:10.
added ASTIM_run script to run single ASTIM simulation from command line
15cf962d7fc7
·tlemaire on Sep 6 2017, 16:31.
replaced neurons object lists by neurons name list in batch functions input
14d95d317eeb
·tlemaire on Sep 6 2017, 16:14.
introduced default arguments in batch functions for bls_params and geom
151337217cab
·tlemaire on Sep 6 2017, 15:03.
replaced printPct by progressbar
7fff2117cd10
·tlemaire on Sep 6 2017, 14:34.
separated checkBatchLog function into setBatchDir and checkBatchLog functions
63f20548155d
·tlemaire on Sep 6 2017, 13:42.

Sep 4 2017

added runEStim and runAStim functions. added locker to xlslog
8680bc7dccaf
·tlemaire on Sep 4 2017, 17:00.

Sep 3 2017

added smart loading of derived parameters from lookup file at BLS initiation
6688904b2a82
·tlemaire on Sep 3 2017, 19:15.
test pre-commit hook
9015dddabee1
·tlemaire on Sep 3 2017, 18:01.
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

separated test into test_basic (initiating solvers and running simple…
f875411afd08
·tlemaire on Sep 2 2017, 18:44.
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 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.
added getNeuronsDict function to utils
c5cad185b222
·tlemaire on Aug 29 2017, 15:38.

Aug 28 2017

optimized effective method: 2D (amp, charge) coefficients interpolators are…
1ea422ad10eb
·tlemaire on Aug 28 2017, 18:02.
corrected setup.py
a2f5d17c8bff
·tlemaire on Aug 28 2017, 16:16.
updated run functions to deal with zero offset. updated test_graphs
90c71fb8d8e5
·tlemaire on Aug 28 2017, 15:26.
updated test_graphs.py
3120330fdccd
·tlemaire on Aug 28 2017, 14:40.
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 titrateEStim and titrateEStimBatch functions
c9053e689690
·tlemaire on Aug 25 2017, 14:59.
Added pulsed stimuli handling to SolverElec. Implemented moved titration…
3c218a52595b
·tlemaire on Aug 25 2017, 13:06.

Aug 24 2017

added smart labels to plotComp, smart title to plotBatch
788e6d1c95b2
·tlemaire on Aug 24 2017, 18:48.
added LeechT variables to workflow
b139db9e82d1
·tlemaire on Aug 24 2017, 18:17.
debugging of plot functions
3e6f232a2a2e
·tlemaire on Aug 24 2017, 17:59.
introduced standardized workflow for both E-STIM and A-STIM simulations and…
2c7de2047898
·tlemaire on Aug 24 2017, 17:49.

Aug 23 2017

moved some utils functions into simutils & pltutils modules
4f9a8fd2aed4
·tlemaire on Aug 23 2017, 16:28.
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.