Diffusion Nanopore Tools (master) History

History
master58aa4022814834d9ee4de96…

Apr 2 2019

Added lines for plotting on Mac OS X
58aa40228148
·thakur on Apr 2 2019, 17:37.
Fixed stubborn window by adding root withdraw in the end.
3b5805684ada
·thakur on Apr 2 2019, 14:38.

Apr 1 2019

Michaels code modified to import Jochems code. Gives translocation statistics…
a0aa7f4218f0
·thakur on Apr 1 2019, 19:01.

Mar 22 2019

Changed classes such that Currentdrop is always mean
1a44d300663d
·deen on Mar 22 2019, 17:33.
import Range1D
47a96ece775c
·deen on Mar 22 2019, 16:54.
Merge branch 'master' of ssh://c4science.ch/source/Nanopore-tools
94b4da545ead
·deen on Mar 22 2019, 16:48.
xlim and ylim on figure
bac909099f2c
·deen on Mar 22 2019, 16:48.
Removed import EventPlots, was unused
524548c68787
·deen on Mar 22 2019, 16:02.
added limits to the function
60231057e4c9
·deen on Mar 22 2019, 15:35.

Mar 13 2019

Merge remote-tracking branch 'origin/master'
c15fa882f3b4
·Axopatch on Mar 13 2019, 18:20.
Fixed capital letter
f965f55c4d5c
·Axopatch on Mar 13 2019, 18:19.
bugfix
b312fafccb7f
·deen on Mar 13 2019, 17:54.
added GetEventTypes
3d74c7680482
·Axopatch on Mar 13 2019, 17:41.
Open multiple files
930e44a351de
·Axopatch on Mar 13 2019, 17:22.
Merge remote-tracking branch 'origin/master'
c4a4ce134a66
·Axopatch on Mar 13 2019, 13:29.

Feb 28 2019

Added Drndic pore estimation.
c365cbf76e0b
·Microtubulus <michael.graf> on Feb 28 2019, 16:40.

Feb 25 2019

Slight modification
819291dbdcac
·Axopatch on Feb 25 2019, 12:46.

Feb 19 2019

Added WaveletDenoising function based on DOI: 10.1021/acs.nanolett.8b0438
23bbd39cbe27
·schneuwly on Feb 19 2019, 11:14.

Jan 28 2019

Merge remote-tracking branch 'origin/master'
32cc2a9272f4
·Axopatch on Jan 28 2019, 16:09.
for PSDs
d37dbe352a43
·Axopatch on Jan 28 2019, 16:08.

Jan 27 2019

more docstrings
321317e9b140
·schneuwly on Jan 27 2019, 22:36.

Jan 24 2019

added docstrings to document some functions
978ab3ff6e83
·schneuwly on Jan 24 2019, 00:20.

Jan 16 2019

Simplified version of GTau plot using Bokeh
475f5761a285
·deen on Jan 16 2019, 10:35.

Jan 14 2019

Added PSF plotting function
ac035c18794d
·deen on Jan 14 2019, 17:17.

Dec 12 2018

Fix plotting of data. Use Math.abs (capital letter for javascript!). Also shows…
4992f8975ef8
·deen on Dec 12 2018, 20:37.
absolute value of tick
2ba93daf2eed
·Axopatch on Dec 12 2018, 15:46.
Fixed deprecated function in pandas.
c710ce839009
·Axopatch on Dec 12 2018, 13:54.

Dec 11 2018

added option to fit IV with exponential
1fbb9b0533a3
·Axopatch on Dec 11 2018, 14:50.
Added function GetParameters() to see default parameters Changed…
c6b661d2d480
·Axopatch on Dec 11 2018, 10:08.

Dec 10 2018

Merge remote-tracking branch 'origin/master'
0e9cb3c37ced
·Axopatch on Dec 10 2018, 16:34.
Clear matplotGui
0b82d48a1d63
·Axopatch on Dec 10 2018, 16:34.
Import Functions in LoadData
9530fc72ff2c
·deen on Dec 10 2018, 09:50.

Dec 6 2018

added back plotgui.py
3e9d528dfa0a
·deen on Dec 6 2018, 14:08.

Dec 5 2018

Added LoadVariable function
e916c0949892
·deen on Dec 5 2018, 19:09.
Removed cutting of FullTrace
4e1051e88fcb
·deen on Dec 5 2018, 18:47.
Implemented plotting in Bokeh
42aa378d194c
·deen on Dec 5 2018, 15:00.
Added Plotting function for simple trace plot
ce6047fe7825
·deen on Dec 5 2018, 13:14.
Optimized imports, restructured code a bit
f6493234bb87
·deen on Dec 5 2018, 10:59.
Moved Loading data functions to new script, for easier access. Moved unused…
f6dac0696a44
·deen on Dec 5 2018, 10:47.
Cleaning up of git
c174859d5b62
·deen on Dec 5 2018, 10:28.
Added check for length to not show error message if missing data
d20e559ae01d
·deen on Dec 5 2018, 10:14.

Dec 4 2018

Merge remote-tracking branch 'origin/master'
acffb6d8ec58
·deen on Dec 4 2018, 16:26.
changed check to not 0
ecfb78678b73
·deen on Dec 4 2018, 16:25.

Nov 29 2018

Merge branch 'master' of https://c4science.ch/diffusion/5484/nanopore-tools
65e4816bf5ea
·Microtubulus <michael.graf> on Nov 29 2018, 15:32.
Merge branch 'master' of https://c4science.ch/diffusion/5484/nanopore-tools
fbf8f3beb1e9
·Microtubulus <michael.graf> on Nov 29 2018, 15:31.
Added log scale function
2bb51f0f8cee
·thakur / Axopatch on Nov 29 2018, 11:51.

Nov 28 2018

merge
2ef35a200eac
·thakur on Nov 28 2018, 11:22.

Nov 23 2018

-updated for csv files -semilog graphs
ac1107061311
·thakur on Nov 23 2018, 11:25.
Changed opening of abf files, current units appear to be in pA.
06756ab5ac7e
·deen on Nov 23 2018, 09:21.

Nov 21 2018

bugfix for using default extension if none is specified. Added string with…
4debbda11487
·deen on Nov 21 2018, 13:20.

Nov 20 2018

dated 20/11/2018
cf08f7c66c2b
·thakur on Nov 20 2018, 22:07.

Nov 6 2018

minor bug
4c63018c6ea0
·deen on Nov 6 2018, 15:42.
Merge remote-tracking branch 'origin/master'
d8f7aeba5740
·deen on Nov 6 2018, 15:39.
Added verbose options to most load functions and event detection and IV making.
72d130d353ae
·deen on Nov 6 2018, 15:37.

Oct 29 2018

Corrected typo for lenght --> length
1deb5d5da264
·thakur / Axopatch on Oct 29 2018, 18:20.

Oct 23 2018

Bugfix in CUSUM fitting, index -1. Added time for CUSUM fitting. Fix for…
1b48a3ac0be4
·deen on Oct 23 2018, 16:13.
fix
dfe0ecb79611
·deen on Oct 23 2018, 14:38.
Changed fit types. Added Standard error key (SE) that correctly captures the…
d4e385f6328a
·deen on Oct 23 2018, 14:37.

Sep 26 2018

Changed to Rough
aaef6f69371d
·deen on Sep 26 2018, 14:45.
Added voltage in plot
52897e16647e
·deen on Sep 26 2018, 14:43.
Misspelling......
b8b0a10ea649
·deen on Sep 26 2018, 14:27.
Bugfix, incorrectly estimating baseline
0304f8d4c759
·deen on Sep 26 2018, 14:24.
Added titlte
3661c2d7932e
·deen on Sep 26 2018, 14:02.
Minor bugfix for plotting if not fitted
62be1090664b
·deen on Sep 26 2018, 14:00.
Bugfix for opening data
d7388e3b03c0
·deen on Sep 26 2018, 13:09.
fixed plotting of events when clicked. Added option to show original trace with…
23cadb544365
·deen on Sep 26 2018, 11:35.
Changed name from Nanoporeplots to EventPlots. Added interactive plot, Split…
a8388ba67ded
·deen on Sep 26 2018, 09:42.

Sep 25 2018

Added interactive G-tau plot. Shows only CUSUM fitted events for now (with…
933b5123747b
·deen on Sep 25 2018, 17:19.
Removed plotting from nanoporeclases. Added CUSUM variables to nanoporeclasses.
1f6786480d9e
·deen on Sep 25 2018, 16:40.

Sep 21 2018

Changed saving of data
bde0ca0d1dab
·deen on Sep 21 2018, 16:09.
no message
c792e13c699c
·Microtubulus <michael.graf> on Sep 21 2018, 13:13.
Implement CUSUM in event detection
2a8396bb4a6d
·deen on Sep 21 2018, 13:02.
Fixed CUSUM function
38d9c4366802
·deen on Sep 21 2018, 12:53.
move to directory
c3550ed6e891
·deen on Sep 21 2018, 07:48.
Revert "Change directory for making IV"
b3c62d386c00
·deen on Sep 21 2018, 07:46.
Merge remote-tracking branch 'origin/master'
3b3cb8f58ddd
·deen on Sep 21 2018, 07:39.
Change directory for making IV
2e1d4a0e578d
·deen on Sep 21 2018, 07:39.

Sep 20 2018

Merge remote-tracking branch 'origin/master'
30bc3a694243
·deen on Sep 20 2018, 11:28.
added delay variable
5f63cce9e6e9
·deen on Sep 20 2018, 11:28.

Sep 12 2018

Merge remote-tracking branch 'origin/master'
29927513e285
·deen on Sep 12 2018, 15:16.
make type of coefficient all
451b6c50e0b3
·deen on Sep 12 2018, 15:16.
Added option for lowpass
2a248ed4f722
·branch: CUSUM
·deen on Sep 12 2018, 15:07.
Implemented CUSUM
d88f1af316db
·deen on Sep 12 2018, 11:20.

Sep 11 2018

Added Capacitance Measurement Code: CapacitanceCalc.py
abf170dbe284
·Microtubulus <michael.graf> on Sep 11 2018, 17:53.

Sep 10 2018

Merge branch 'master' of https://c4science.ch/diffusion/5484/nanopore-tools
bbda3fc18b16
·Microtubulus <michael.graf> on Sep 10 2018, 16:39.
osmotixvsconcdifference
e6a5c296a5e1
·Microtubulus <michael.graf> on Sep 10 2018, 16:39.
Redox
06472a371340
·Microtubulus <michael.graf> on Sep 10 2018, 16:34.
Added option to save as CSV
0f999a824045
·deen on Sep 10 2018, 10:04.

Sep 7 2018

Check if directory for saving exists, otherwise make it
6175240322bf
·deen on Sep 7 2018, 13:37.
variable changes
d9ad6bb5c745
·deen on Sep 7 2018, 13:31.
Forgot to remove append
142711bf3427
·Jochem on Sep 7 2018, 13:30.
bug needs to be string
53eba428216e
·Jochem on Sep 7 2018, 13:28.
Assertion bug, changed layout
c586f9ef2da1
·Jochem on Sep 7 2018, 13:27.
Added option to force run and option to cut out the saved chunks before…
531c52b5c6e1
·Jochem on Sep 7 2018, 13:20.
Estimate the impulse response length of the filter to improve calculation speed
8c5513d52bcc
·Jochem on Sep 7 2018, 11:28.
Merge remote-tracking branch 'origin/master'
401a6116ee17
·Chimera_2nd on Sep 7 2018, 10:52.
Can load Chimera files as well now
671b9a4959da
·Chimera_2nd on Sep 7 2018, 10:51.

Sep 6 2018

Added option to skip fitting if the batchevents has already been done with the…
2fb6a1c505c2
·Jochem on Sep 6 2018, 13:42.
Changed filename of EventDetection. Added possibility to directly run…
84359bf20bde
·Jochem on Sep 6 2018, 13:15.

Sep 5 2018

Merge remote-tracking branch 'origin/master'
44d1d2696158
·Jochem on Sep 5 2018, 17:29.

Historymaster58aa4022814834d9ee4de96…

Apr 2 2019

Apr 1 2019

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History
master58aa4022814834d9ee4de96…