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Squirrel Overview

Donna Sueper

7th AMS Users MeetingU of Minnesota, Minneapolis, Sun., Sept. 17, 2006 17:00

Aerodyne, University of Colorado, Boulder

OutlineSquirrel Motivation What, Why, How

Squirrel Analysis Flow ChartOutline major steps, Quick & Thorough Analysis

Squirrel FeaturesAMS Igor Panel Screen Shots, Resulting Graphs

Squirrel FutureBug list & Feature request

Closing Remarks

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SQUIRREL (SeQUential Igor data RetRiEvaL) is an AMS data management and analysis tool for Igor

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’ quad program* Generates mass spectra averages, size distributions, time trends;

uses same frag list and batch files* WHAT IS NEW: size binned mass spectra

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How does Squirrel work?

Access Raw HDF files generated from DAQ* HDF is a general purpose file format for storing scientific data* Raw 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 (open and closed MS sticks, raw MS spectra, PToF sticks and PToF raw spectra)

MSSDiff_p matrix (run vs m/z sticks) stays in memory

This has implications for how to organize, store Igor experiments!!!

RAW DATA REMAINS UNMODIFIED in original HDF files

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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-Process

HD

F In

dex

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

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Screen ShotsHDF tab Output

Get Index OutputDiagnostics Plot

Pre-Process OutputHistory Window

Get Index

Pre-Process

_p data

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8

4

0

4:00 PM4/29/2006

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

Screen ShotsMS Tab

PTo

F Ta

b image,avg size dist,size binned spectrum

_p data

time series,avg spectrum

MS

Tab

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

6

1

10

100

1000

NO

3im

_HiL

hhh_

d

4:54 PM3/20/2006

1

10

100

1000

SO4i

m_H

iLhh

h_d

1

10

100

1000

NH

4im

_HiL

hhh_

d

4

2

0

-2

-4

1 10 100 1000

Screen ShotsPToF Tab

25

20

15

10

5

0

x10-3

100806040

10nm - 100 nm

PTo

F Ta

b image,avg size dist,size binned spectrum

_p data

time series,avg spectrum

MS

Tab

Get Index

Pre-ProcessHD

F In

dex

Tab

Quick Look

PTo

F Ta

btime seriesavgs, etc.

size dist,mass spec,image, etc.

_p data (DAQ sticks)

Thorough Look

Pre-ProcessHD

F In

dex

Tab Get Index

Check m/z calibration

_p data (recalc sticks)

m/z fitting params

MS

Tab

Check baselinebaseline fitting params

Squirrel Data Analysis Flow ChartP

ToF

Tabtime series

avgs, etc.

size dist,mass spec,image, etc.

MS

Tab

Modify SIIon_user

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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

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Screen ShotsModify SI

Change these values IF daqvalues wrong

Get Index

Pre-ProcessHD

F In

dex

Tab

Quick Look

PTo

F Ta

btime seriesavgs, etc.

size dist,mass spec,image, etc.

_p data (DAQ sticks)

Thorough Look

Pre-ProcessHD

F In

dex

Tab Get Index

Check m/z calibration

Cor

rect

ions

Tab

_p data (recalc sticks)

m/z fitting params

MS

Tab

Check baselinebaseline fitting params

Squirrel Data Analysis Flow ChartP

ToF

Tabtime series

avgs, etc.

size dist,mass spec,image, etc.

MS

Tab

Modify SIIon_user

Frag

Che

cks

Tab

TweakFrag table

Do Corrections

corr_fact

Calc Loadings

Airb

eam

PTo

F

_p data (dc marker)

Loading waves DiagnosticsPlot

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Screen ShotsCorrections - Airbeam

Screen ShotsCorrections - PToF

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Screen ShotsFrag Checks

Get Index

Pre-ProcessHD

F In

dex

Tab

Quick Look

PTo

F Ta

btime seriesavgs, etc.

size dist,mass spec,image, etc.

_p data (DAQ sticks)

Thorough Look

Pre-ProcessHD

F In

dex

Tab Get Index

Check m/z calibration

Cor

rect

ions

Tab

_p data (recalc sticks)

m/z fitting params

MS

Tab

Check baselinebaseline fitting params

Squirrel Data Analysis Flow ChartP

ToF

Tabtime series

avgs, etc.

size dist,mass spec,image, etc.

MS

Tab

Modify SIIon_user

Frag

Che

cks

Tab

TweakFrag table

Do Corrections

corr_fact

Calc Loadings

Airb

eam

PTo

F

_p data (dc marker)

Loading waves DiagnosticsPlot

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Latest version 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/

What do I need to do to use Squirrel?

Implement existing feature requests

* Error Analysis* Normalize PToF to MS* Finish Jose’s Mission Diagnostics Panel* Think about using 4 separate correction factors* Journal interface* Misc panel & graph tweaking

What is next for Squirrel?Continued bug fixing

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Where can I go for more Squirrel info?

http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/SquirrelInfo

Thanks to fellow coders

We are squirrel !

Special Thanks to James Allan

Thanks in advance for the ongoing collaboration

Thanks!