9. Labkey experience

   Importing data

   To add new ways to import data from different file types (say, dicom files), a new module should be made. Labkey is quite verbose on module insertion. Here they elaborate what modules can do. In the list is the pointer to a pipeline based on R scripts. While …

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10. Merlin log

    Status

    Merlin is the name of the PC that will run labkey. It can be accessed via:

    username@merlin.fmf.uni-lj.si
    

    Contact me if you want to have a username, however a valid reason should be specified.

    The ownership status of merlin is somewhat mixed. It belongs to …

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11. Notes on MC generation of umSetup data

    Generate config files for Gate script generation

    Location

    ~/software/build/gate\_tools/cpp
    

    File

    makePhantomConfig
    

    Setup

    ~/software/build/gate\_tools/config\_files/phantom{,2}\_{pc,grid}.cfg
    

    Generate Gate scripts

    Location

    ~/software/build/Gate/umSetup/scripts
    

    Scripts:

    For projects (uniform, edge) use:

    generateProject.sh
    

    For phantom use

    generatePhantom.sh …

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12. Dicom2ROOT

    Port Dicom files to ROOT

    I made a pluging that allows manipulation of images stored in the Dicom
    file format in ROOT. Basically, it is an IO (import/export) facility that reads and stores dicom images.

    The software is loadable via git:

    git clone http://www-f9.ijs.si/~studen/git …

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13. Process phantom

    How to process phantom data

    Make dir list:

    ls -d /data0/studen/data/Gate/umSetup/umSetup2_rod*_1 | 
    > /data0/studen/data/Gate/umSetup/umSetup2_1_phantom.dirlist
    

    Apply gate2um:

    cd ~/software/build/gate_tools/
    ./scripts/processList.sh /data0/studen/data/Gate/umSetup/umSetup2_1_phantom.dirlist |
    /data0/studen/data/imageRec/layout/setup0/gateSetup.in
    

    The last …

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14. Cloning a GIT repository in Windows

    Cloning a GIT repository in Windows

    GIT is a linux native. Therefore, all basic commands are command prompt oriented. However, windows explorer bindings are available in windows, and cloning becomes a simple task.

    Installing GIT

    GIT must be installed. If not, go to:

    git

    and download the latest version. Follow …

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15. Installing VMEDAQ (Mint)

    Some notes on installing VMEDAQ.

    DAQPP

    Didn't like to be installed anywhere but /usr area.

    Python

    A way to tell configure where to search for python is by using python-config.

    Check if python-config is around if not, install it as part of python-dev

    GLIB

    g_module_symbol is often missing in vmedaq …

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16. How to get SNR convergence plots

    SNR convergence

    Go to coinc/root_scripts directory. Most of the libraries are loaded by default once root is run.

    By hand, add:

    root [] .L estimatePSF.C+
    root [] .L scripts_buildTradeOffFromIterationData.C
    

    Then, load the data headers.

    root [] tagCollection tg
    root [] tg.parseFile("/data0/studen/data/imageRec/layout/setup2/tagMapSi.txt")
    

    I …

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17. AUTOCONF explained

    Autoconf

    Autoconf is a nice set of tools which should in principle help in compiling the software by finding appropriate libraries. In many years of usage of autoconf tools I can only say that I never quite saw its appeal. Not because of autotools itself, but because there is always …

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18. Installing Amide

    Amide compilation

    Amide is a nice visualization tool, and also free. However, this means one has to put some effort in installing it. First, to get the source, you need to have Mercurial version control software installed, because amide is maintained using it. Then go to your software directory, and …

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