Transcript Slide 1

Squirrel Overview
Donna Sueper
Aerodyne, 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/jimenezgroup/ToFAMSResources/ToFSoftware/Downloads/Supplemental/ToFAMS_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:
AMS Data Analysis Tasks, Intro
AMS Data Analysis Tasks, Intro
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 mg/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 Chart
Outline major steps, Quick & Complete Analysis
 Squirrel Features
AMS Igor Panel Screen Shots, Resulting Graphs
 Squirrel Future
Bug list & Feature requests
 Closing Remarks
What is Squirrel?
 SQUIRREL (SeQUential Igor data RetRiEvaL) is an
AMS data management and analysis tool. It is
collection of code using the Igor software program.
 Ongoing, collaborative effort
Silke Hings, Frank Drewnick
James Allan, Jonny Croiser
Ed Dunlea, Donna Sueper
Tim Onasch
And many other AMS Users!
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…)
 Recreation of James Allan’s quad program
* Generates mass spectra averages, size distributions, time trends;
uses same frag list and batch files
 Familiarity with Igor
* Publication-quality graphs
* Users can write custom code
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?
 DAQ DATA REMAINS UNMODIFIED in
original HDF files
 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!
Screen Shots
AMS Panel
Squirrel Credits, Web link
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
Select Data to Act Upon
Create, view todo waves
Manipulate Output, Other Info
Is it done yet?
Squirrel Data Analysis Flow Chart
HDF Index Tab
Quick Look
Get Index
Pre-Process
time series,
avg spectrum
PToF Tab
MS Tab
_p data (DAQ sticks)
image,
avg size dist,
size binned spectrum
Screen Shots
HDF tab Output
Get Index
Pre-Process
_p data
Get Index Output =
Diagnostics Plot
Pre-Process Output =
History Window
In this data set, oscillation due to v/w mode switching
Screen Shots
MS Tab
time series,
avg spectrum
PToF Tab
MS Tab
_p data
image,
avg size dist,
size binned spectrum
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Nitrate equivalent mass (µg m )
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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
-1
-2
-3
-4
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m/z
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Screen Shots
PToF Tab
image,
avg size dist,
size binned spectrum
PToF Tab
MS Tab
_p data
time series,
avg spectrum
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NH4im_HiLhhh_dSO4im_HiLhhh_dNO3im_HiLhhh_d
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Squirrel Data Analysis Flow Chart
Complete Look
HDF Index Tab
Get Index
Pre-Process
size dist,
mass spec,
image, etc.
Check m/z calibration
m/z fitting params
Pre-Process
_p data (recalc sticks)
MS Tab
time series
avgs, etc.
PToF Tab
MS Tab
_p data (DAQ sticks)
Get Index
time series
avgs, etc.
PToF Tab
HDF Index Tab
Quick Look
size dist,
mass spec,
image, etc.
Check baseline
baseline fitting params
Modify SI
Ion_user
Screen Shots
Check m/z calibration
View fit info
for many runs
Choose which
peaks to fit
View peak fits
for individual runs
Filter out bad runs
Screen Shots
Check baseline
Choose stick
compliment
parameters
View details of
one run
Choose fitting
parameters
View many
runs
Screen Shots
Modify SI
Change these
values IF daq
values wrong
Squirrel Data Analysis Flow Chart
Complete Look
HDF Index Tab
Get Index
Pre-Process
m/z fitting params
Check baseline
Modify SI
baseline fitting params
Ion_user
Pre-Process
Airbeam
corr_fact
Do Corrections
PToF
size dist,
mass spec,
image, etc.
Corrections Tab
time series
avgs, etc.
Frag Checks Tab
size dist,
mass spec,
image, etc.
Check m/z calibration
_p data (recalc sticks)
MS Tab
time series
avgs, etc.
PToF Tab
MS Tab
_p data (DAQ sticks)
Get Index
PToF Tab
HDF Index Tab
Quick Look
_p data (dc marker)
Calc Loadings
Loading waves
Tweak
Frag table
Diagnostics
Plot
Screen Shots
Corrections - Airbeam
Screen Shots
Corrections - PToF
Screen Shots
Frag Checks
Squirrel Data Analysis Flow Chart
Complete Look
HDF Index Tab
Get Index
Pre-Process
m/z fitting params
Check baseline
Modify SI
baseline fitting params
Ion_user
Pre-Process
Airbeam
corr_fact
Do Corrections
PToF
size dist,
mass spec,
image, etc.
Corrections Tab
time series
avgs, etc.
Frag Checks Tab
size dist,
mass spec,
image, etc.
Check m/z calibration
_p data (recalc sticks)
MS Tab
time series
avgs, etc.
PToF Tab
MS Tab
_p data (DAQ sticks)
Get Index
PToF Tab
HDF Index Tab
Quick Look
_p data (dc marker)
Calc Loadings
Loading waves
Tweak
Frag table
Diagnostics
Plot
What do I need to do to use Squirrel?
 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 is next for Squirrel?
 Continued bug fixing
 Implement existing feature requests
* Journal interface
* Misc panel & graph tweaking
Where can I go for more Squirrel info?
http://cires.colorado.edu/jimenez-group/wiki/index.php/ToFAMS_Analysis_Software
Thanks!
 Thanks to fellow coders
 Special thanks to James Allan
 Thanks in advance for the ongoing collaboration
We are squirrel !