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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
2
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
3
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
4
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
5
Screen ShotsHDF tab Output
Get Index OutputDiagnostics Plot
Pre-Process OutputHistory Window
Get Index
Pre-Process
_p data
12
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
7
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
8
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
9
Screen ShotsCorrections - Airbeam
Screen ShotsCorrections - PToF
10
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
11
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
12
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!