Parameter file format

The parameter file is formatted with xml and is divided into subsections. Here the default parameter file is shown:

<reconstructor>
<userinformation>
    <operator>Anders Kaestner</operator>
    <instrument>ICON</instrument>
    <projectnumber>P11048</projectnumber>
    <sample>Curse tablet</sample>
    <comment>No comment</comment>
</userinformation>
<system>
    <memory>6000</memory>
    <loglevel>message</loglevel>
</system>
<projections>
    <dims>2048 2048</dims>
    <resolution>0.0135 0.0135</resolution>
    <firstindex>1</firstindex>
    <lastindex>625</lastindex>
    <projectionstep>1</projectionstep>
    <repeatline>false</repeatline>
    <scantype>sequential</scantype>
    <imagetype>projections</imagetype>
    <center>568</center>
    <translation>false</translation>
    <tiltangle>0</tiltangle>
    <tiltpivot>0</tiltpivot>
    <correcttilt>false</correcttilt>
    <filemask>tablet_####.fits</filemask>
    <path>/home/data/P11048_tablet/tomo/</path>
    <referencepath>/home/data/P11048_tablet/tomo/</referencepath>
    <obfilemask>ob_####.fits</obfilemask>
    <obfirstindex>1</obfirstindex>
    <obcount>5</obcount>
    <dcfilemask>dc_####.fits</dcfilemask>
    <dcfirstindex>1</dcfirstindex>
    <dccount>5</dccount>
    <roi>600 400 1700 432</roi>
    <doseroi>300 600 350 800</doseroi>
    <scanarc>0 360</scanarc>
</projections>

<matrix>
    <dims>1100 1100 32</dims>
    <rotation>0</rotation>
    <serialize>false</serialize>
    <path>/home/kaestner/work/svn/</path>
    <matrixname>tablet_####.tif</matrixname>
    <filetype>TIFF16bits</filetype>
    <firstindex>0</firstindex>
    <grayinterval>-1 0.728486</grayinterval>
</matrix>

<processchain>
    <preprocessing>
        <module>
            <modulename>FullLogNorm</modulename>
            <sharedobject>libStdPreprocModules.so</sharedobject>
            <active>true</active>
            <parameters>
                <uselut>false</uselut>
                <usenormregion>true</usenormregion>
            </parameters>
        </module>
        <module>
            <modulename>SpotClean2</modulename>
            <sharedobject>libStdPreprocModules.so</sharedobject>
            <active>true</active>
            <parameters>
                <gamma>0.03</gamma>
                <iterations>1</iterations>
                <maxlevel>12</maxlevel>
                <minlevel>0.0</minlevel>
                <sigma>0.005</sigma>
            </parameters>
        </module>
        <module>
            <modulename>MedianMixRingClean</modulename>
            <sharedobject>libStdPreprocModules.so</sharedobject>
            <active>true</active>
            <parameters>
                <threshold>0.01</threshold>
                <width>0.001</width>
            </parameters>
        </module>
        <module>
            <modulename>ProjectionFilterSingle</modulename>
            <sharedobject>libStdPreprocModules.so</sharedobject>
            <active>true</active>
            <parameters>
                <cutoff>0.5</cutoff>
                <filtertype>hamming</filtertype>
                <order>0</order>
                <usebias>true</usebias>
            </parameters>
        </module>
    </preprocessing>

    <backprojector>
        <module>
            <modulename>MultiProjBP</modulename>
            <sharedobject>libStdBackProjectors.so</sharedobject>
            <active>true</active>
            <parameters>
                <ProjectionBufferSize>16</ProjectionBufferSize>
                <SliceBlock>64</SliceBlock>
                <SubVolume>1</SubVolume>
            </parameters>
        </module>
    </backprojector>

</processchain>

Most of the parameters can be set with GUI. There are however some exceptions.

• \verb++ amount of memory available for reconstruction, unit mb.
• \verb++ number of projections to process simultaneously.
• \verb++ max number of slices to process in one processing block.

The buffer parameters have direct impact on the reconstruction time.