Diffusion PySONIC (old) (master) History

R4670/PointNICE
mastercf2846af1eadbbac8afe349…

Mar 30 2018

added better inset handling in plotComp
cf2846af1ead
·tlemaire on Mar 30 2018, 18:09.
modified plotComp to take only 1 input variable and added option to plot inset
1ac82339eaf3
·tlemaire on Mar 30 2018, 16:58.
automatic detection of time vector uniformity in detectPeaksTime
6ec806aa90d6
·tlemaire on Mar 30 2018, 13:02.

Mar 29 2018

renamed matlab utils function more explicitely.
19a21b2ee66b
·tlemaire on Mar 29 2018, 19:00.
added prominence threshold constant for spike detection. added skeleton for IB…
377594fb12b0
·tlemaire on Mar 29 2018, 18:04.

Mar 27 2018

added method to extract compuation times in utils module
c916dd9c8f25
·tlemaire on Mar 27 2018, 14:49.

Mar 22 2018

minor improvements to pltutils module
e59db772ab09
·tlemaire on Mar 22 2018, 01:45.
removed italic for latex style labelling in plotComp
80b620b50b12
·tlemaire on Mar 22 2018, 00:27.
added option to change linestyle of legend handles (dashed -> straight)
d7f0d2a86ee2
·tlemaire on Mar 22 2018, 00:17.

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

corrected TOFF integration error in SolverElec. added PW tests to test_basic.py
dd51b4283191
·tlemaire on Mar 19 2018, 20:03.
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 17 2018

Added new LeechP lookups
ee3a47c57d36
·Theo Lemaire on Mar 17 2018, 19:07.

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 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.
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

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

Mar 7 2018

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

Mar 2 2018

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 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.
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.
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

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.
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

replaced eval statements from plotGatingKinetics & plotRateConstants by getattr…
08165e6a06f3
·tlemaire on Sep 1 2017, 21:30.
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.
updated run functions to deal with zero offset. updated test_graphs
90c71fb8d8e5
·tlemaire on Aug 28 2017, 15:26.
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.

R4670/PointNICEmastercf2846af1eadbbac8afe349…

Mar 30 2018

Mar 29 2018

Mar 27 2018

Mar 22 2018

Mar 21 2018

Mar 20 2018

Mar 19 2018

Mar 18 2018

Mar 17 2018

Mar 16 2018

Mar 15 2018

Mar 14 2018

Mar 13 2018

Mar 12 2018

Mar 8 2018

Mar 7 2018

Mar 2 2018

Feb 28 2018

Jan 16 2018

Jan 9 2018

Dec 12 2017

Dec 1 2017

Nov 29 2017

Nov 27 2017

Nov 24 2017

Nov 22 2017

Sep 12 2017

Sep 10 2017

Sep 6 2017

Sep 4 2017

Sep 3 2017

Sep 2 2017

Sep 1 2017

Aug 30 2017

Aug 29 2017

Aug 28 2017

Aug 25 2017

Aug 24 2017

Aug 23 2017

R4670/PointNICE
mastercf2846af1eadbbac8afe349…