Instructions for Fit2d2maud
Note to new users
Fit2d2maud was developped over 10 years ago. Personnaly, I do not use it anymore.
These days
- If I need to load data into MAUD, I perform this task directly within MAUD. The procedure is described in the texture analysis tutorials on Rudy Wenk's website
- If I want fit2d to save series of chi files after binning data at multiple azimuth, there is now a function within fit2d to do so. You should cake your data with the number of required azimuthal bins (e.g. 72 bins if you want 5° steps over 360°) and then select Output, Multi-Chiplot.
Also note that, as of June 2018, some recent versions of fit2d have bugs in the definition of the end azimuth when you try to run the fit2d2maud scripts (thanks to Kirsten Schulze for pointing this out).
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.
- a
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
integrate - First set of questions should be
OK - 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
start azimuth - select +2.5 as
end azimuth - 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
Intensity conservationtoNOandGeometrical corrections to intensitytoNOas well. Maud will do the intensity corrections by itself.
- select -2.5 as
- Click
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...
- select
Exit,Options,Z-Axix Labeland enter whatever you wish (I likeIntensity). - go back to the
Cakefunction.
- select
- The data can be saved into a text file, with a
chiextension. Proceed as follow- Select
Exit,Output, andChiplot - Choose your file name.
- Clik
OK. - Have a look at the file you just created. You can use it for plotting, or post-processing with many kinds of software.
- Select
- 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
chifiles - the directory that will be used to store the Maud data files
- click on
Create Macro for Fit2d - you'll be asked to define
basename,start azimuth,end azimuthandinterval. For instance, if you chooseagCalibforbasename,0forstart azimuth,360forend azimuthand5forinterval, the macro will create the followingchifiles
- Select the
cake function, 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
exchangebutton) - leave the diffraction mode:
Exit - enter the macro mode:
Macros / Log file - select
Run Macro, choose the file you just created (agCalib.macin my case), and fit2d should go ahead and create thechifiles (72 of them if you chose and interval of 5 degrees between 0 and 360 degrees).
Converting 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 esg:
- click on
Convert Chi to Esg - enter your
basename,start azimuth,end azimuthandinterval. - click
OK.
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.