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<?xml version="1.0"?>
<!DOCTYPE book PUBLIC "-//OASIS//DTD DocBook XML V4.3//EN"
               "http://www.oasis-open.org/docbook/xml/4.3/docbookx.dtd"
[
  <!ENTITY % local.common.attrib "xmlns:xi  CDATA  #FIXED 'http://www.w3.org/2003/XInclude'">
]>
<book id="index">
  <bookinfo>
    <title>CrystFEL Reference Manual</title>
    <releaseinfo>
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      For libcrystfel from CrystFEL 0.4.3.
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    </releaseinfo>
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    <abstract>
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    This is the internal documentation for CrystFEL.  Unless you are looking at
    the code, writing new programs or fixing bugs, you should not need to read
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    this.  You might use the information here when reading the code or to better
    understand how the software works, or refer to it when creating a new
    program within the suite.
    </abstract>
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  </bookinfo>

  <chapter>
    <title>Images</title>
        <xi:include href="xml/image.xml"/>
  </chapter>

  <chapter>
    <title>Handling reflection data</title>
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        <abstract>There are three main reflection list thingies.</abstract>
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        <xi:include href="xml/reflist.xml"/>
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        <xi:include href="xml/reflist-utils.xml"/>
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  </chapter>

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  <chapter>
    <title>Unit cells</title>
        <xi:include href="xml/unitcell.xml"/>
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        <xi:include href="xml/cell-utils.xml"/>
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  </chapter>

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  <chapter>
    <title>Statistics and R-factors</title>
        <xi:include href="xml/statistics.xml"><xi:fallback /></xi:include>
  </chapter>

  <chapter>
    <title>Symmetry</title>
        <xi:include href="xml/symmetry.xml"><xi:fallback /></xi:include>
  </chapter>

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  <chapter>
    <title>Integer Matrices</title>
        <xi:include href="xml/integer_matrix.xml"><xi:fallback /></xi:include>
  </chapter>

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  <chapter>
    <title>Indexing</title>
        <xi:include href="xml/indexing.xml"><xi:fallback /></xi:include>
  </chapter>

  <chapter>
    <title>Detector</title>
        <xi:include href="xml/detector.xml"><xi:fallback /></xi:include>
  </chapter>

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  <chapter>
    <title>HDF5</title>
        <xi:include href="xml/hdf5-file.xml"><xi:fallback /></xi:include>
  </chapter>
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  <chapter>
    <title>Stream</title>
        <xi:include href="xml/stream.xml"><xi:fallback /></xi:include>
  </chapter>

  <chapter>
    <title>Render</title>
        <xi:include href="xml/render.xml"><xi:fallback /></xi:include>
  </chapter>
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  <chapter>
    <title>Parallel programming</title>
        <xi:include href="xml/thread-pool.xml"><xi:fallback /></xi:include>
  </chapter>

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  <chapter>
    <title>Miscellaneous</title>
        <xi:include href="xml/quaternion.xml"/>
        <xi:include href="xml/utils.xml"/>
  </chapter>

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  <chapter>
    <title>Information for developers</title>
        <xi:include href="xml/coding-standards.xml"><xi:fallback /></xi:include>
  </chapter>

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  <index id="api-index-full">
    <title>API Index</title>
    <xi:include href="xml/api-index-full.xml"><xi:fallback /></xi:include>
  </index>

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</book>