1. Usage of reconstruction software

    README for observer_tools software

    The package observer_tools is intended for analysis and reconstruction of probe data. The package is pretty disorganized in its current versions as it was heavily modified to suit particular goals that came about during reconstruction.

    The package consists of three modules:

    • observer module. This module contains …
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  2. Theta Hat

    How to evaluate phantom data

    For SNR one needs to determine the expected data projection

    $$\bar{Y}=M\lambda$$

    where $\lambda$ is the true object (digital reference object, say)
    and M is the system matrix. Moreover, one needs the average reconstructed image $\check{\lambda}$ which is the reconstruction of $\bar …

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  3. High res PET calibration

    Process si calibration run

    Parse the data using observer and decoderSiSparse. Typical configuration file processSi257.config looks like this:

    #run with decoderSiSparse
files=/storage/data/20161206/si/Am241_si257_thr180_adj3_
eventsDotOut=/storage/data/20161206/si/out/Am241_si257_thr180_adj3.out
nPedestal=10000
configFile=/storage/data/imageRec/layout/setupOSU/setup257.in

    The configuration file setup257 …

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  5. BGO ring at JSI

    BGO ring at JSI and how to operate it

    Flood calibration

    Data colletction

    Run

    vmedaq ~/.vmedaq/bgo_ring.xml

    Set coincidence module to OR. Make sure the GATE width is long enough for peak of the signal to be recorded. Store data into flood directory

    Data processing

    Command is 

    bin/decoderBgoFloodNoFPGA …
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  6. Labkey upgrade

    Backup

    A backup of all data (database + files) (~/scripts/backup.sh):

    tar cvzf /mnt/disk/merlin/data0.tgz /data0 [92G]

    A backup of software: tomcat8, labkey, apache:

    tar cvzf /mnt/disk/merlin/tomcat8.tgz /usr/share/tomcat8 [21M]
tar cvzf /mnt/disk/merlin/tomcat8_catalina.tgz /var/lib/tomcat8 [7.5M …
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  7. How to look at execPSF image

    Look at an image produced by execPSF

    root [0] .x loadLibs_rodMeasurement.C
root [1] va_data va;
root [2] va.parse("/data0/studen/data/imageRec/studies/general/match_harmonized/Fischer_final.cfg")
root [] TH2D h2;
root [] getImage(h2,va,0);

    The long way

    root [6] va.img.set_value<int>("dirlistnData",100000,0)
root …
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  8. Installing observer at OSU

    Installing ROOT

    Most of the software is obtained through git. In most cases, I use the latest version, although switching to older is also possible. Building root takes a while.

    gamma@linux-nakn:~> cd /data/software/src/
#install cmake if neccesary
gamma@linux-nakn:/data/software/build/root> sudo zypper install cmake …
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  9. Setup of the hires PET PC

    Installing VMEDAQ (short version)

    Install dependencies

    gamma@linux-nakn:~> sudo zypper install kernel-devel git autoconf \
    libtool python-devel python3-devel zlib-devel gtk2-devel \
    python-gtk-devel gtk-doc libxml2-devel libglade2-devel mlocate
    make automake gcc pkg-config

    The SIS1100 driver:

    gamma@linux-nakn:~>cd /data/software/packages
gamma@linux-nakn:/data/software/packages> wget http://www.struck.de/sis1100-2 …
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  10. Nordugrid ARC on merlin

    Installing grid interface software on Merlin

    Following instructions on Sling:

    apt-get install nordugrid-arc-client nordugrid-arc-plugins-globus

    Then update list of metapackets by updating /etc/apt/sources.list and get the certificates:

    wget -q -O - https://dist.eugridpma.info/distribution/igtf/current/GPG-KEY-EUGridPMA-RPM-3 | sudo apt-key add -

    Update the apt cache, including the new …

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