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Squirrel Overview

Squirrel Overview. Donna Sueper. Aerodyne, University of Colorado, Boulder. AMS Data Analysis Tasks, Intro. The data acquisition software (DAQ) saves: * Values such as flow rate, airbeam, maximum m/z; one value per run. DAQ data sets: ParVal, InfoVal, RunInfo, CommonParVal

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Squirrel Overview

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  1. Squirrel Overview Donna Sueper Aerodyne, University of Colorado, Boulder

  2. AMS Data Analysis Tasks, Intro The data acquisition software (DAQ) saves: * Values such as flow rate, airbeam, maximum m/z; one value per run. DAQ data sets: ParVal, InfoVal, RunInfo, CommonParVal * Raw mass spectra values for Open, Closed, possibly PToF data DAQ sets: MSOpen, MSClosed, possibly MSClosed_w, etc., PToF * Sticks spectra for Closed, Diff, possibly PToF data DAQ sets: MSSDiff, MSSClosed, PToFStick The specifics about what is saved and when can be found through the DAQ manual, available at: http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/Downloads/Supplemental/ToF-AMS_DAQ_UM_v30.pdf One can open an hdf file within Igor (or other software programs) to load the DAQ data for analysis. In Igor go to Data - Load Waves – New HDF5 Browser. Then change the file type to all files (not .h5) and select a file. You should see something like:

  3. AMS Data Analysis Tasks, Intro

  4. AMS Data Analysis Tasks, Intro • An AMS data analysis should include: • Review of DAQ values and settings to ensure consistency of data from one run to the next. • Application of conversion factors to translate ion signal to mg/m3. • Checking and/or recalculation of raw spectra to sticks • Sticks to speciated aerosol loadings • Do these steps for many runs

  5. Outline • Squirrel Motivation What, Why, How • Squirrel Analysis Flow Chart Outline major steps, Quick & Complete Analysis • Squirrel Features AMS Igor Panel Screen Shots, Resulting Graphs • Squirrel Future Bug list & Feature requests • Closing Remarks

  6. What is Squirrel? • SQUIRREL (SeQUential Igor data RetRiEvaL) is an AMS data management and analysis tool. It is collection of code using the Igor software program. • Ongoing, collaborative effort Silke Hings, Frank Drewnick James Allan, Jonny Croiser Ed Dunlea, Donna Sueper Tim Onasch And many other AMS Users!

  7. Why Squirrel? • Aerodyne AMS generates large data sets • * Not feasible to load all data into memory • * The squirrel approach is to load sufficient data for task at hand (diagnostics, quick look…) • Recreation of James Allan’s quad program • * Generates mass spectra averages, size distributions, time trends; uses same frag list and batch files • Familiarity with Igor • * Publication-quality graphs • * Users can write custom code

  8. How does Squirrel work? • Access Raw HDF files generated from DAQ • * HDF is a general purpose file format for storing scientific data • * DAQ data remains on the disk in randomly accessible HDF format • Create intermediate HDF files (pre-processing) • * Files name example: AMS_intermediate_000001.hdf • * Some operations which create intermediate files: conversion to Hz, stick recalculation, application of DC markers for PToF size distributions • Select runs to analyze via Todo waves • * Todo waves are made up of run numbers, have a special format • * For quad users, Todo waves are generalized and versatile mask waves

  9. How does Squirrel access data? • DAQ DATA REMAINS UNMODIFIED in original HDF files • Intermediate HDF files, written to disk, hold processed MS and PToF data Pre-processed data include open and closed MS sticks (MSSOpen, MSSClosed, MSSDiff, raw MS spectra (MSOpen, MSClosed, MSDiff), PToF sticks (PToF_Stick) and PToF raw (PToF) spectra. • MSSDiff_p matrix stays in memory MSSDiff_p = stick values of difference spectra, rows are run #s, columns are m/z. The ‘_p’ indicates that it is ‘pre-processed’. • This has implications for how to organize, store Igor experiments!

  10. Screen Shots AMS Panel Squirrel Credits, Web link Select Analysis Action * Always read top to bottom, left to right * Buttons make things go * Checkboxes indicate options * Gold buttons are popular * Most default setting are appropriate * Italicized items aren’t functional Select Data to Act Upon Create, view todo waves Manipulate Output, Other Info Is it done yet?

  11. Squirrel Data Analysis Flow Chart Quick Look Get Index HDF Index Tab Pre-Process _p data (DAQ sticks) time series, avg spectrum image, avg size dist, size binned spectrum MS Tab PToF Tab

  12. Screen Shots HDF tab Output In this data set, oscillation due to v/w mode switching Get Index Pre-Process _p data Get Index Output = Diagnostics Plot Pre-Process Output = History Window

  13. Screen Shots MS Tab _p data image, avg size dist, size binned spectrum time series, avg spectrum MS Tab PToF Tab

  14. Screen Shots PToF Tab _p data image, avg size dist, size binned spectrum time series, avg spectrum MS Tab PToF Tab

  15. Squirrel Data Analysis Flow Chart Quick Look Complete Look Get Index Get Index Check m/z calibration Check baseline Modify SI HDF Index Tab HDF Index Tab m/z fitting params baseline fitting params Ion_user Pre-Process Pre-Process _p data (DAQ sticks) _p data (recalc sticks) time series avgs, etc. size dist, mass spec, image, etc. time series avgs, etc. size dist, mass spec, image, etc. MS Tab MS Tab PToF Tab PToF Tab

  16. Screen Shots Check m/z calibration View fit info for many runs Choose which peaks to fit View peak fits for individual runs Filter out bad runs

  17. Screen Shots Check baseline Choose fitting parameters View many runs Choose stick compliment parameters View details of one run

  18. Screen Shots Modify SI Change these values IF daq values wrong

  19. Squirrel Data Analysis Flow Chart Quick Look Complete Look Get Index Get Index Check m/z calibration Check baseline Modify SI HDF Index Tab HDF Index Tab m/z fitting params baseline fitting params Ion_user Pre-Process Pre-Process _p data (DAQ sticks) _p data (recalc sticks) time series avgs, etc. size dist, mass spec, image, etc. time series avgs, etc. size dist, mass spec, image, etc. Airbeam MS Tab MS Tab corr_fact PToF Tab PToF Tab Corrections Tab Do Corrections PToF _p data (dc marker) Calc Loadings Tweak Frag table Loading waves Frag Checks Tab Diagnostics Plot

  20. Screen Shots Corrections - Airbeam

  21. Screen Shots Corrections - PToF

  22. Screen Shots Frag Checks

  23. Squirrel Data Analysis Flow Chart Quick Look Complete Look Get Index Get Index Check m/z calibration Check baseline Modify SI HDF Index Tab HDF Index Tab m/z fitting params baseline fitting params Ion_user Pre-Process Pre-Process _p data (DAQ sticks) _p data (recalc sticks) time series avgs, etc. size dist, mass spec, image, etc. time series avgs, etc. size dist, mass spec, image, etc. Airbeam MS Tab MS Tab corr_fact PToF Tab PToF Tab Corrections Tab Do Corrections PToF _p data (dc marker) Calc Loadings Tweak Frag table Loading waves Frag Checks Tab Diagnostics Plot

  24. What do I need to do to use Squirrel? • Version 5.05A or more of Igor • HDF5 xop to be placed in your Igor Extensions folder • Latest Squirrel software, a packed Igor template http://cires.colorado.edu/jimenez-group/ ToFAMSResources/ToFSoftware/SquirrelInfo/ (Email Donna Sueper for the username and password for downloading)

  25. What is next for Squirrel? • Continued bug fixing • Implement existing feature requests * Journal interface * Misc panel & graph tweaking

  26. Where can I go for more Squirrel info? • http://cires.colorado.edu/jimenez-group/wiki/index.php/ToF-AMS_Analysis_Software

  27. Thanks! • Thanks to fellow coders • Special thanks to James Allan • Thanks in advance for the ongoing collaboration We are squirrel !

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