Adapting to SGE pipeline

To nicely construct the calls to prj2sinSGE we need to have more
parameters. These are either read from the LogFile (default) or input by
the user. LogFile reading thus expanded.
Calls to prj2sinSGE are constructed a bit differently.
Since SGE takes care of sheduling, we can simply submit everything and
wait for it to finish. Theoretically we can thus remove lots of the
logic about checking folders, etc.
The calls are probably not correct yet, since Fede explained them to me
in 10 minutes. This version was used for a very first test, the bottom
of the file still contains the old version...
Fully adapted to SGE pipeline

After lots of testing and correcting the commandline calls for
prj2sinSGE (with Fedes and Annabelles help) several times, the script
now generates cprs at the selected ROI, and reconstructs them into
correctly named folders. Some further tests, then bringing it into
production.
Pretty output and final debugging (JobID)

Output to both log and console is now a bit prettier and meaningful. The
Job ID was not always reliably detected, sometimes we got back a string
with the location of the log-file folder. The script now looks if the
number it gets back is an 'int', otherwise it breaks the script and
let's the user retry. Cause of the problem is unknown, also to Fede :)
We also need flats!

We cannot directly go from cprs to recs, we need fltps. Thus copying a
whole block inbetween, where flats are calculated. Unfortunately this
still does not work, even when Fede helps me to debug the command-line
calls. Escalating it to Alain.
Changing description of options, introducing new "SlicesAround" option
and renaming "Range" to "Magnitude", which seems better.
Further debugging and (hopefully final) corrections

Correcting typo which hindered reconstructions to be calculated, I
forgot to add the slice number to the location of the fltp folder...
Alain suggested to slice to ROI to an even number of files, this seems
to help with the script running through all of the tasks.
Save the commandline call to the Logfile, this can help with debugging.
Nicer job-names and nicer output to the console all-around.
Workaround for renumbered reconstructions

Since we're using a ROI, the slice numbering is way off. We thus look at
only at slice the middle slice of (2 * options.SliceAround), which is
the middle slice of the ROI we reconstructed.
Merge branch 'SGE'