1. run_peaksearch(.bat, .sh, macosx) versus peaksearch(.exe)?
In your application directory, you may find a script file and an executable. Please launch script file run_peaksearch that launches PeakSearch. This will not be the case if you use PeakSearch inside Fable (which is the preferred way). In that case you do not have to worry about this..
As Java and Python technologies are melded, script files set your PYTHONPATH to the ImageD11 Python scripts available in your peaksearch/python directory.
If you launch the PeakSearch program directly, be sure to have installed fabio, ImageD11 (both available on SourceForge), PIL, and Numpy (and perhaps others as described in the ImageD11 documentation).
2. In image chooser, I don't want to retrieve .cor files and I just want .edf files stored in the selected directories...
In the menu Window | Preferences | Fabio Files include only edf as File type.
If you want to load all files readable by fabio, select the button "Restore Defaults". You can also add other extensions if you like. To include files that do not have an extension, you can use ".", however, it is preferable that you don't have image files without an extension.

3. Fabio / fabio file: kesako ?
Fabio is a Fable input/ouput library written in Python.
By fabio files, I mean a file format readble by this Python program.
Fabio is used in Java via Jep (Java Embedded Python, http://jepp.sourceforge.net/) to read header content and images.
Fabio supports a wide variety of formats e.g. EDF, TIF, Bruker, ADSC,
Mar345, MarCCD, OXD, GE. In order to use fabio to read files you must install
Python 2.5 or later on.
4. What do you mean by stem ?
This is the name of the image files without the digit part; It is used by Peaksearch.
For example, if a directory contains:
- imageforThisExperiment_0000.edf
- imageforThisExperiment_0001.edf
- imageforThisExperiment_0002.edf
- imageforThisExperiment_0003.edf
- imageforThisExperiment_0004.edf,
- experiment.par
- otherfile.chi
the stem of the image files is
"imageforThisExperiment"
. When running PeakSearch from a directory that is different from the one the image files are in, you can include the path to the image files in the stem. Note that if you do this, then the .spt files will include the path in the file names written in the files, perhaps making them non-portable.
4. Wow! I have relaunched the program, and I don't have the same perspective as previously ?
When you re-launch the application, the perspective you had before exiting is restored.
For example, if you quit the application with 2D peaks view opened, you will have this view, but no file loaded. You can always use Window | Reset Perspective to restore the default perspective. For more information on perspectives see the Workbench section under Fable in the Help.