Advanced Photon Source at Argonne National Laboratory   APS USAXS instrument
USAXS instrument at the Advanced Photon Source,
X-ray science division, beamline 15ID (ChemMatCARS)

Advanced Photon Source

A U.S. Department of Energy, Office of Science,
Office of Basic Energy Sciences national synchrotron x-ray research facility

 
 
Argonne Home > Advanced Photon Source > USAXS >

Important links:

USAXS web page

Irena 2 (software for SAS modeling)

Nika 1 (software for SAS area detector  data reduction )

Irena 2 movies

Indra 2 (software for USAXS data reduction)

Some other useful code for Igor Pro I wrote:


Cromer-Lieberman code for IgorPro (ver. 4.0): AtomicFormFactors

Clementine, package for modeling decay kinetics

Other useful links…

Home page of Pete Jemian (more SAS)

APS SAS web page

"Clementine", package for modeling decay kinetics using MEM and Least square fitting

  Clementine project is hosted on Igor Exchange site: http://www.igorexchange.com/project/Clementine.

Release 1.1 (first public release) was posted 10/30/2008.

Clementine package was developed to model decay kinetics processes using either maximum entropy (MEM, included) or least square fitting. The math of analysis (decay times are "tau") is :
MEM: signal(time) = FlatOffset + sum (P(Tau) * exp(- time/tau))
LSQF: signal(time) = FlatOffset + sum (P(Tau) * exp(- (time+TimeShift)/tau))
The package will :
MEM : Generate the distribution of P(Tau) values using Maximum Entropy method over user defined number of bins in tau (log-spaced)
LSQF : Model (and least square fit) sum of for up to 5 different P(tau), TimeShift, and tau combinations. Both P(tau) and tau can be fitted.

The code loosely follows following manuscripts:
Zs. Ablonczy , A. Lukacs , E. Papp, Application of the maximum entropy method to absorption kinetic rate processes, Biophysical Chemistry 104 (2003) 249–258
and
A. K. LIVESEY AND J. C. BROCHON , ANALYZING THE DISTRIBUTION OF DECAY CONSTANTS IN PULSE-FLUORIMETRY USING THE MAXIMUM ENTROPY METHOD, BIOPHYSICAL JOURNAL VOLUME 52 (1987), pg. 693-706.

The package consists of :
Load_Clementine.ipf > this file should be in (or linked to) "Igor Procedures"
DecayModeling_Load.ipf > this file should be in (or linked to)"User Procedures/Clementine"
DecayModeling_GUI.ipf > this file should be in (or linked to) "User Procedures/Clementine"
DecayModeling_1.ipf > this file should be in (or linked to) "User Procedures/Clementine"
DecayModeling_2.ipf > this file should be in (or linked to) "User Procedures/Clementine"
DecayModeling.ifh > the help file, should be in (or linked to) "Igor help files"
you also need
MaxEntPackage.ipf > this file should be in (or linked to) "User Procedures/Maximum Entropy"

Loading the package : select "Load Clementine MEM modeling" in the macro menu.
This will load the necessary procedure files in Igor, compile them and add in the "Macros" menu command "MEM Decay fitting".
Selecting command "MEM Decay fitting" from macros menu will open main control window.
For more details, please, read included help file (accessible by button from main control window).
*********************************************************
Data input
There are various data types Clementine can use:

a. one signal wave with x-scaling in seconds - with or without errors wave.
This is raw data from instrument which measures in fixed data intervals the signal. Such data are not properly spaced for MEM analysis. They need to be rebinned to log-time scaling. Check the check box "Rebin the data". If you have these data, you can also use Instrument response function.

b. two waves (signal/time)
In this case you have signal and associated time for each point. If you need to, you can still rebin the data on log scale. But you cannot use instrument response function...

c. Three waves (signal/time/errors)
In this case you have three waves - signal, error for signal, and times. You cannot use instrument response function, but you can rebin the data, if necessary.

 


        

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This page last modified: 2008-10-30 11:12 AM