Document 7731065
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Transcript Document 7731065
Squirrel Overview
7th AMS Users Meeting
U of Minnesota, Minneapolis, Sun., Sept. 17, 2006 17:00
(Slightly modified in December, 2006)
Donna Sueper
Aerodyne, University of Colorado, Boulder
Outline
Squirrel Motivation
What, Why, How
Squirrel Analysis Flow Chart
Outline major steps, Quick & Thorough Analysis
Squirrel Features
AMS Igor Panel Screen Shots, Resulting Graphs
Squirrel Future
Bug list & Feature request
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 Allen’s quad program
* Generates mass spectra averages, size distributions, time trends;
uses same frag list and batch files
* WHAT IS NEW: size binned mass spectra
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
* 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?
RAW DATA REMAINS UNMODIFIED in
original HDF files
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’.
Intermediate HDF files, written to disk, hold
processed MS and PToF data
Processed and pre-processed data include open and closed MS sticks,
raw MS spectra, PToF sticks and PToF raw spectra.
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
Screen Shots
MS Tab
time series,
avg spectrum
PToF Tab
MS Tab
_p data
image,
avg size dist,
size binned spectrum
12
8
4
0
4:00 PM
4/29/2006
-3
Nitrate equivalent mass (µg m )
10
10
10
10
10
10
10
10
4:30 PM
5:00 PM
5:30 PM
6:00 PM
0
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
-5
-6
-7
50
100
m/z
150
200
Screen Shots
PToF Tab
image,
avg size dist,
size binned spectrum
PToF Tab
MS Tab
_p data
time series,
avg spectrum
1000
2
100
0
10
1
1000
-2
100
-4
10
1
10
100
1000
1
1000
100
25
10
20
1
10nm - 100 nm
-3
15
4:54 PM
3/20/2006
x10
NH4im_HiLhhh_dSO4im_HiLhhh_dNO3im_HiLhhh_d
4
10
5
0
40
60
80
100
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?
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/
(Email Donna Sueper for the username and password for downloading)
What is next for Squirrel?
Continued bug fixing
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
Where can I go for more Squirrel info?
http://cires.colorado.edu/jimenez-group/
ToFAMSResources/ToFSoftware/SquirrelInfo
Thanks!
Thanks to fellow coders
Special Thanks to James Allan
Thanks in advance for the ongoing collaboration
We are squirrel !