Instructions for Fit2d2maud
The process has to be performed in several steps
- bin one orientation manually,
- create a fit2d macro with Fit2d2maud,
- run the macro to slice the 2-D image automatically.
Binning of diffraction data with Fit2d: manual
First, we should fit2d to obtain one slice of data. This step is necessary to calibrate the few paramaters needed by fit2d.
Here's the trick:
- Load up your data (or calibration file) into fit2d.
beam center, select the best option...
Start azimuth, could be zero if you have full diffraction rings.
End azimuth, could be start+360 if you have full diffraction rings.
Inner Limit, can be beam center, or any point before the rings you're interested in.
Outer Limit, should be after the rings you're interested in.
- In the cake menu, choose
- First set of questions should be
- In the second set of questions, we want to a slice of data between azimuth -2.5 and azimuth 2.5, integrated onto a 1-D spectrum, therefore
- select -2.5 as
- select +2.5 as
- select 1 as
number of azimuthal bins
- Intensity corrections... There are options in fit2d to apply corrections to the integrated intensity. For the results of fit2d to be compatible with MAUD, you want to set
Geometrical corrections to intensityto
NOas well. Maud will do the intensity corrections by itself.
- select -2.5 as
OKand fit2d will integrate your slice of data.
- On Linux platforms, there may be a bug: the Y-Axis will be labelled with strange symbols or nothing at all: THIS HAS TO BE CORRECTED!! otherwise the rest of the analysis will crash...
Z-Axix Labeland enter whatever you wish (I like
- go back to the
- The data can be saved into a text file, with a
chiextension. Proceed as follow
- Choose your file name.
- Have a look at the file you just created. You can use it for plotting, or post-processing with many kinds of software.
- on a mac or windows: double click on the file
- on unix: type
java -jar fit2d2maud.jar
- the wavelength and sample to detector distance
- the directory with the diffraction data
- the directory that will contain the
- the directory that will be used to store the Maud data files
- click on
Create Macro for Fit2d
- you'll be asked to define
interval. For instance, if you choose
interval, the macro will create the following
- Select the
cakefunction, if you used the cake function already, you won't get any question. Otherwise, you'll be asked for
Binning of diffraction data with Fit2d: automatic
For the analysis of radial diffraction patterns, one has to bin the data over a large number of orientations. One could repeat the process above by hand, but 5 degrees slices over 360 degrees represent 72
chi files, so creating them by hand could take a while. Luckily, one can script fit2d and things become easier...
In any case, the process above has to be performed at least once: to calibrate parameters such as inner and outer radius, but also to correct the nasty bug on Z-Axis label on unix platforms.
To create macro files for Fit2d, one can use this sofware,
Fit2d2maud. Simply download the archive a run it:
You will be asked to define
I strongly recommend that you use separate directories for all of those...
Once everything is set up,
agCalib_0.chi for a slice integrated between -2.5 and 2.5 agCalib_5.chi for a slice integrated between 2.5 and 7.5 agCalib_10.chi for a slice integrated between 7.5 and 12.5 .... agCalib_360.chi for a slice integrated between 357.5 and 2.5
- Macro will be saved in a file
basename.macin your data directory.
Running the macro
- in fit2d, make sure that you have the image of the 2-D diffraction pattern (play with the
- leave the diffraction mode:
- enter the macro mode:
Macros / Log file
Run Macro, choose the file you just created (
agCalib.macin my case), and fit2d should go ahead and create the
chifiles (72 of them if you chose and interval of 5 degrees between 0 and 360 degrees).
chi file series for use in Maud
In Maud, data are stored in a file with an
esg extension. They contain all data for all azimuth angles within a single text file. The fit2d2maud software can convert series of
chi files into
- click on
Convert Chi to Esg
- enter your
Fit2d2maud will read all
chi files and create a big
esg file for use in Maud. In my case, I have 72
chi files, each of them is 50 kbytes, and the
esg file is 2.3 Mbytes, so it takes a few seconds... but it works.