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Notes for PSI

Show free disk space

df -h /media/disk/

Rsync the files to HD

synchronisierung auf workstation ganz links

  • grosse disk einstecken
  • evtl. mit `sudo gparted` formatieren, damit wirklich alles leer ist…
  • evtl. mit `dmesg` schauen, was lso ist, wenn nix passiert
  • `cd ~`, damit im root-verzeichnis\
  • im terminal eingeben:
rsyncdir -t 60000 --no-g --exclude-from=exclude_file.txt /sls/X02DA/data/e11126/Data10/BeamTime /media/MedionHDDrive2GO/
`-t 60000`

erhoeht die abbruchzeit, damit synchronisation nicht gestoppt wird, falls mal laenger keine daten auf Data10 geschrieben werden. <note>–no-g konserviert die Gruppenzugehoerigkeit, und ist seit Beamtime 2010e evtl. noetig</note>


filelist, die die zu exkludierenden files enthaelt. in unserem fall meist


falls die rohdaten erwuenscht sind, dann `tif` aus dem exclude_file entfernen. `tif_ang` sind die resortierten 360grad-projektionen, die chris' skript mit hardlinks generiert. 'cpr' und 'fcr' kommen von der holotomography mir rajmund, rec_DMP entstehen, wenn mann falsche parameter bei der rekonstruktion eingibt.


Verzeichnis mit den Messdaten auf File-Server (einfach herauszufinden mit `pwd`)


Root-Verzeichnis der Daten auf der HD. Ohne z.B. 2009a, denn rsyncdir macht sonst `/media/disk/2009a/2009a/blabla`

am ende disk mit

eject /media/FestPlattenName


backup to archivftp.psi.ch

Start a Terminal and logon to the 6th node of the Cluster:

ssh e11126@x02da-cn-6

Change to the directory you need to send to the Backupserver with (for example)

cd Data3/2010a

or for example

cd Data10/2009f

Then you can generate a Textfile containing a List with Files to backup using the commands:

ls -d */tif > backupfile.txt
ls -d */rec* >> backupfile.txt
ls -d mrg/*/rec* >> backupfile.txt
ls -d mrg/*/tif* >> backupfile.txt #only if you want to backup the merged tiffs!
  • 'ls -d */tif' lists all the subdirectories containing the Projections in the directory you're in and '> backupfile.txt' writes the output of this command to a textfile with the chosen name.
  • The following commands look for other directories ('ls -d */rec*' looks for all instances of rec*-Directories, e.g. rec_8bit or rec_16bit) and appends them (using '»') to the same file. The appending is important, or else you'll loose what you've entered in the previous lines!
  • In the end we're also looking for Projections and Reconstructions in the 'mrg' subfolder, where we've written the merged Files using the widefieldscan-workflow.

To actually start the backup, you need to issue the following command (in the directory where you generated the backupfile):

bl-ftp2arch.sh -u e11126 -e david.haberthuer@psi.ch -b -P -f backupfile.txt

This starts the archiver-script for the Schittny-eAccount (-u), notifies David about success/failure (-e, email goes only to @psi-Addresses), performs the archival in the background (-b), asks for the archivFTP-Password (-P) and uses backupfile.txt as list of files to backup (-f).

If you want to monitor the progress, it's probably best if you run the command without the -b flag inside a screen-session, so you can hangup the terminal and come back.

Restore backup from archivftp.psi.ch

Either follow these steps on the TOMCAT-website or:

  • Connect to slslc05.psi.ch per SSH
  • Start gFTP to have a graphical interface to the FTP-server. Start it with issuing “gftp” in the terminal.
  • login as either e11126@archivftp.psi.ch or e10277@archivftp.psi.ch. The passwords are known by the Beamline-Crew or me.
  • Browse to the directory which you want to restore.
  • Try to transfer the data. Since archivftp.psi.ch stores everything on tape, you'll probably get an error the first time. Just retry after some minutes, then everything should work like a charm.


Falls jobs manuell submitted wurden und nicht mit dem RecoManager angeschaut werden koennen, dann kann auf x02da-cons-2

cd /usr/local/cluster/DiCoClient/
java -jar DiCoClient.jar

ausgefuehrt werden. Dies started den DicoClient (Distibuted Computing Client). Mit “lj ex a” sieht mensch alle momentan ausgefuehrten, der Rest wird mit “h” erklaert.

rename multiple files


rename R243b10_ R243b10_mrg R243b10_???.tif

or use workaround like below if “rename” does not work with more than 1000 files (seems to be the case over ssh/x-server…)

rename R243b10_0 R243b10_mrg0 R243b10_0???.tif
rename R243b10_1 R243b10_mrg1 R243b10_1???.tif
rename R243b10_2 R243b10_mrg2 R243b10_2???.tif
rename R243b10_3 R243b10_mrg3 R243b10_3???.tif
rename R243b10_4 R243b10_mrg4 R243b10_4???.tif

Camserver restart

rdesktop pc6189 -g 1250x950 -a 16

oder mit

alias | grep CCD

rausfinden, welcher PC momentan grad zustaendig ist…

Reset Camera

  • Start CamWare and take any picture (snap shot or movie)
  • Close CamWare
  • Start Image-Pro Plus
  • Start Camera Server FIFO

Image-Pro Plus

  • Camera control → Exposure, binning, etc.
  • Histogram (Histogram of image, directly linked to a particular image)
  • Flat: 40'000 - 50'000 counts.
  • Arithmetic and logical operations → divide image by flat → min. 2000 - 3000 counts in new images. If not → higher energy!!
  • Enhance - Display range: Gives histogram of current image and defines display range. May be use constantly.