Diffusion Nanopore Tools (master) History

History
masterea7575e2c37ff13f863f6d1…

Jun 12 2019

UI elements nearly finished. Plotting implemented. We will need to start to…
ea7575e2c37f
·Microtubulus <michael.graf> on Jun 12 2019, 17:38.
EventDetectorUI: file input with duplicate check. Filter for .dat and .log.
c46c0a63865b
·Microtubulus <michael.graf> on Jun 12 2019, 14:48.
Jochem's CUSUM eventPlots fix + UI files
b22aa27f135a
·Microtubulus <michael.graf> on Jun 12 2019, 13:23.
Rudimentary template for the UI.
0c8ace2b9651
·Microtubulus <michael.graf> on Jun 12 2019, 11:36.
I made some changes to the mainplotgui. Mainly coloring, so that voltages…
850d6bde662b
·Microtubulus <michael.graf> on Jun 12 2019, 10:50.

Jun 11 2019

Added relative delta for CUSUM fitting
f0ed91619c81
·deen on Jun 11 2019, 14:07.
Added more printing for debugging
5708b27f21a2
·deen on Jun 11 2019, 11:36.
Plotting with Currentdrop
3b21f3fa5b7a
·deen on Jun 11 2019, 11:26.
Added line in EventPlots for plotting in Jupyter Notebook
0a68ff931638
·deen on Jun 11 2019, 09:40.
Changed type of CUSUM fitted events to 'CUSUM'
96d8adf9e29d
·deen on Jun 11 2019, 09:39.
changed eventLengthCUSUM assignation
3e86162b8769
·deen on Jun 11 2019, 09:36.
CUSUM needs at least 2 levels, not 3
0456ec9b066d
·deen on Jun 11 2019, 09:34.
Reorganized so event adding is more clear
6546e6f62eaa
·deen on Jun 11 2019, 09:32.
modified printing
1c05b36cc2be
·deen on Jun 11 2019, 09:27.
Minor changes in printing
46a6544c0236
·deen on Jun 11 2019, 09:17.
Added saving of currentDrop for impulse
34ac37040d47
·deen on Jun 11 2019, 09:07.
modified verboseLevel and added check for integer
5ffc7919fc39
·deen on Jun 11 2019, 09:02.
bugfix
c21afa3fedea
·deen on Jun 11 2019, 08:58.
modified check
f65c960d7cdc
·deen on Jun 11 2019, 08:57.
Modified coefficients
7dfe94a20c40
·deen on Jun 11 2019, 08:50.

Jun 7 2019

Modified detection of events, added option to fit traces with function and use…
ebb436057178
·deen on Jun 7 2019, 17:59.

May 9 2019

Modified plotting of PSD
a0bf6cc71c88
·deen on May 9 2019, 10:58.

Apr 29 2019

merge
7004a7213899
·thakur on Apr 29 2019, 10:39.

Apr 26 2019

amazing edits and voltage based plotting by Jochem
f3ada36a22f3
·deen / thakur on Apr 26 2019, 17:28.

Apr 8 2019

Am idiot, moved up definition of slope, also cleaned up slightly
dba5e49293d7
·deen on Apr 8 2019, 15:35.
Add return for pore size from MakeIndividualIVs
2b36f610b798
·deen on Apr 8 2019, 15:31.

Apr 3 2019

Removed some prints
551a42365c11
·deen on Apr 3 2019, 16:01.
Modified where it is absolute
9717699af7d3
·deen on Apr 3 2019, 15:52.
Set to Mac OS
4b0a6e8f0475
·deen on Apr 3 2019, 15:43.
Default set to ExpFit
24bfd3aa08bb
·deen on Apr 3 2019, 15:35.
Merge remote-tracking branch 'origin/master'
5b31c6b182e4
·deen on Apr 3 2019, 15:34.
Absolute value for slope
e315497d510a
·deen on Apr 3 2019, 15:34.

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.

Historymasterea7575e2c37ff13f863f6d1…

Jun 12 2019

Jun 11 2019

Jun 7 2019

May 9 2019

Apr 29 2019

Apr 26 2019

Apr 8 2019

Apr 3 2019

Apr 2 2019

Apr 1 2019

Mar 22 2019

Mar 13 2019

Feb 28 2019

Feb 25 2019

Feb 19 2019

Jan 28 2019

Jan 27 2019

Jan 24 2019

Jan 16 2019

Jan 14 2019

Dec 12 2018

Dec 11 2018

Dec 10 2018

Dec 6 2018

Dec 5 2018

Dec 4 2018

Nov 29 2018

Nov 28 2018

Nov 23 2018

Nov 21 2018

Nov 20 2018

Nov 6 2018

Oct 29 2018

Oct 23 2018

Sep 26 2018

Sep 25 2018

History
masterea7575e2c37ff13f863f6d1…