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. 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  g/m 3. 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. SQUIRREL (SeQUential Igor data RetRiEvaL) is an AMS data management and analysis tool. It is collection of code using the Igor software program. Silke Hings, Frank Drewnick James Allan, Jonny Croiser Ed Dunlea, Donna Sueper Tim Onasch And many other AMS Users! Ongoing, collaborative effort What is Squirrel?

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…) Familiarity with Igor * Publication-quality graphs * Users can write custom code Recreation of James Allan’s quad program * Generates mass spectra averages, size distributions, time trends; uses same frag list and batch files

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? 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! DAQ DATA REMAINS UNMODIFIED in original HDF files

10. Screen Shots AMS Panel Select Data to Act Upon Create, view todo waves Is it done yet? 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 Squirrel Credits, Web link Manipulate Output, Other Info

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

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

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

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

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

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

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

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

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

20. Screen Shots Corrections - Airbeam

21. Screen Shots Corrections - PToF

22. Screen Shots Frag Checks

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

24. 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) What do I need to do to use Squirrel?

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

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

27. Thanks to fellow coders Wearesquirrel ! Special thanks to James Allan Thanks in advance for the ongoing collaboration Thanks!