Squirrel Overview
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Transcript of Squirrel Overview
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
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4:00 PM4/29/2006
4:30 PM 5:00 PM 5:30 PM 6:00 PM
20015010050m/z
10-7
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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
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4:54 PM3/20/2006
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1 10 100 1000
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x10
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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
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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!