Diffusion Nanopore Tools (master) History

History
master8574c2881649e61e71381a3…

Jun 13 2019

Event detector is now running on the selected files. All the files have a…
8574c2881649
·Microtubulus <michael.graf> on Jun 13 2019, 17:07.
Plot axes fixes. Other layout fixes.
bd4fb7c71584
·Microtubulus <michael.graf> on Jun 13 2019, 13:05.

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.

Historymaster8574c2881649e61e71381a3…

Jun 13 2019

Jun 12 2019

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History
master8574c2881649e61e71381a3…