Squirrel Overview

Donna SueperAerodyne, 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* 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 theDAQ 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:

AMS Data Analysis Tasks, Intro

AMS Data Analysis Tasks, IntroAn 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/m3.• Checking and/or recalculation of raw spectra to sticks• Sticks to speciated aerosol loadings• Do these steps for many runs

Outline Squirrel Motivation

What, Why, How

Squirrel Analysis Flow ChartOutline major steps, Quick & Complete Analysis

Squirrel FeaturesAMS Igor Panel Screen Shots, Resulting Graphs

Squirrel FutureBug list & Feature requests

Closing Remarks

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?

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

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

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

Screen ShotsAMS Panel

Select Data to Act UponCreate, 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

Get Index

Pre-ProcessH

DF

Ind

ex T

ab

Quick Look

PT

oF T

abtime series,avg spectrum

image,avg size dist,size binned spectrum

_p data (DAQ sticks)

MS

Tab

Squirrel Data Analysis Flow Chart

Screen ShotsHDF 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

12

8

4

0

4:00 PM4/29/2006

4:30 PM 5:00 PM 5:30 PM 6:00 PM

20015010050m/z

10-7

10-6

10-5

10-4

10-3

10-2

10-1

100

Nitr

ate

equi

vale

nt m

ass

(µg

m-3

) MSSD all 112.709 MSSD Air 110.953 MSSD Water -0.762827 MSSD NO3 0.133794 MSSD SO4 0.257086 MSSD Org 0.703696 MSSD NH4 0.166322 MSSD Chl 0.00246195

Screen ShotsMS Tab

PT

oF

Ta

b image,avg size dist,size binned spectrum

_p data

time series,avg spectrum

MS

Ta

b

1

10

100

1000

NO

3im

_H

iLh

hh

_d

4:54 PM3/20/2006

1

10

100

1000

SO

4im

_H

iLh

hh

_d

1

10

100

1000

NH

4im

_H

iLh

hh

_d

4

2

0

-2

-4

1 10 100 1000

25

20

15

10

5

0

x10

-3

100806040

10nm - 100 nm

Screen ShotsPToF Tab

PT

oF

Ta

b image,avg size dist,size binned spectrum

_p data

time series,avg spectrum

MS

Ta

b

Get Index

Pre-ProcessHD

F I

nd

ex

Ta

b

Quick LookP

To

F T

abtime series

avgs, etc.

size dist,mass spec,image, etc.

_p data (DAQ sticks)

Complete Look

Pre-ProcessHD

F I

nd

ex

Ta

b

Get Index

Check m/z calibration

_p data (recalc sticks)

m/z fitting params

MS

Ta

b

Check baseline

baseline fitting params

Squirrel Data Analysis Flow Chart

PT

oF

Ta

btime seriesavgs, etc.

size dist,mass spec,image, etc.

MS

Ta

b

Modify SI

Ion_user

Screen ShotsCheck m/z calibration

Choose whichpeaks to fit

View peak fitsfor individual runs

View fit infofor many runs

Filter out bad runs

Screen ShotsCheck baseline

Choose stick compliment parameters

Choose fitting parameters

View many runs

View details of one run

Screen ShotsModify SI

Change these values IF daq values wrong

Get Index

Pre-ProcessHD

F I

nd

ex

Ta

b

Quick LookP

To

F T

abtime series

avgs, etc.

size dist,mass spec,image, etc.

_p data (DAQ sticks)

Complete Look

Pre-ProcessHD

F I

nd

ex

Ta

b

Get Index

Check m/z calibration

Co

rre

ctio

ns

Ta

b

_p data (recalc sticks)

m/z fitting params

MS

Ta

b

Check baseline

baseline fitting params

Squirrel Data Analysis Flow Chart

PT

oF

Ta

btime seriesavgs, etc.

size dist,mass spec,image, etc.

MS

Ta

b

Modify SI

Ion_user

Fra

g C

he

cks

Ta

bTweak

Frag table

Do Corrections

corr_fact

Calc Loadings

Airb

ea

mP

To

F

_p data (dc marker)

Loading waves DiagnosticsPlot

Screen ShotsCorrections - Airbeam

Screen ShotsCorrections - PToF

Screen ShotsFrag Checks

Get Index

Pre-ProcessHD

F I

nd

ex

Ta

b

Quick LookP

To

F T

abtime series

avgs, etc.

size dist,mass spec,image, etc.

_p data (DAQ sticks)

Complete Look

Pre-ProcessHD

F I

nd

ex

Ta

b

Get Index

Check m/z calibration

Co

rre

ctio

ns

Ta

b

_p data (recalc sticks)

m/z fitting params

MS

Ta

b

Check baseline

baseline fitting params

Squirrel Data Analysis Flow Chart

PT

oF

Ta

btime seriesavgs, etc.

size dist,mass spec,image, etc.

MS

Ta

b

Modify SI

Ion_user

Fra

g C

he

cks

Ta

bTweak

Frag table

Do Corrections

corr_fact

Calc Loadings

Airb

ea

mP

To

F

_p data (dc marker)

Loading waves DiagnosticsPlot

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?

Implement existing feature requests

* Journal interface

* Misc panel & graph tweaking

What is next for Squirrel?

Continued bug fixing

Where can I go for more Squirrel info?

http://cires.colorado.edu/jimenez-group/wiki/index.php/ToF-AMS_Analysis_Software

Thanks to fellow coders

We are squirrel !

Special thanks to James Allan

Thanks in advance for the ongoing collaboration

Thanks!