Python code used for interacting with data generated by qNano.
extractor.py - extracts .irbd files into .dat files [Current(nA) with time(s)]
execute with the following linux command: $ od -A d -t f8 -w32 Raw_data.irbd |./extractor.py > Raw_data.dat
od translates the binary into a form python can interface with, then pipes the output to the .dat file, which can later be read line-by-line
locator.py - locates and returns a list of all 'blockade_1.csv' type files in a directory, copies and renames them with their parent directory's name and sticks them in a file called 'data' in the parent directory
xml_interpreter.py - extracts parameters from the .xml file accompanying each qNano recording.
options are: (followed by an example) "SrAperture"->A6006 "SrDilution"->1 "SrElectrolyteID"->SEB "SrExperiment"->Elf_charge_paper_review "SrFileName"->c:\Izon Data\Elf_charge_paper_review\B86_pH6_0.5V_30.1.12_b\B86_pH6_0.5V_30.1.12_b.irbd "SrNotes" "SrPartNumber" "SrPressure"->0 "SrRawConcentration"->0 "SrSampleName"->B86_pH6_0.5V_30.1.12_b "SrSize"->0 "SrType"->Sample "SrZetaPotential"->0 "SrRecordTime"->2012-01-30T15:32:12.5739991+13:00 "SrBandwidthFilter"->0 "SrBandwidthFilterOn"->false
baseline_comparison.py - extracts baselines of all plots and overlays on the same graph. N.B. baselines vary wildly - but normalization (\frac{\Delta I}{I} of events seems to account for most effects.
bibliography_plot.py Uses bibitex functionality to extract information including year and author from .bib library and plot grouping by shared authors.
plotting_functions.py - performs a standard Cumulcative Count experimental plot including: -cubic and parabolic fitting and inflection point printing to external file -mean FWHM plotting and gaussian fit to extract mean and st-dev values -baseline current plots overlaid with mean normalised blockades -comparison plot between mean, media and mode FWHM fitting -N.B. this only works with blockade_1.csv files generated with the izon command line software, that have then been calibrated to convert a time into an applied pressure.
Python_analysis_plots.zip - a collection of plot generated by continuous pressure variation and the fitting and plotting methods decribed in Multiplot_comparison_final.py with some example data. Plots compare: -averaging methods, mean, median and mode -sample size on maxima location (1,10, 20, 30) with each method -CC method with FWHM (easily extended to include FWQM)
Multiplot_comparison_final.py - a collection of functions for intereacting with qNano FWHM and CC data, useful for statistical investigations of the various fitting averaging and maxima location methods,
N.B. These should ideally be combined with others into a generic class file that can interact with ALL qNano produced data (it's on my to do list) and give a bunch of functions in order to better understand it.
RMS_noise.png - plot comparing the RMS noise of our qNano with applied voltage dictating the acceptable RMS region (+/-0.5V)
porebias.png - observed pore bias at various strectch. Still not clear why this is
irbd_analysis.py - performs a primitive extraction of events from an qNano .irbd file after it has been converted to .dat using translator.py above -Current version simply extract datapoints for events and puts them in a list of lists at the end called 'event_points' and 'time_points' that correspond directly to each other. The next version will also output a .csv of FWHM, duration, baseline current, start time, blockade magnitude etc
this is a test