<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_mg__processing_8h">
<title>/Users/bernard/b20/bsoft/include/mg_processing.h File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/include/mg_processing.h</primary></indexterm>
<para>

<para>Header file for micrograph processing. </para>
 
</para>
<programlisting>#include &quot;ctf.h&quot;
#include &quot;symmetry.h&quot;
#include &quot;marker.h&quot;
#include &quot;View.h&quot;
#include &quot;Euler.h&quot;
#include &quot;Bstring.h&quot;
</programlisting><simplesect>
    <title>Classes    </title>
        <itemizedlist>
            <listitem><para>struct <link linkend="_struct_bframe">Bframe</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bparticle">Bparticle</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bfilnode">Bfilnode</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bfilament">Bfilament</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bbadarea">Bbadarea</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bstrucfac">Bstrucfac</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_blayerline">Blayerline</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bmicrograph">Bmicrograph</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bfield">Bfield</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_breconstruction">Breconstruction</link></para>
</listitem>
            <listitem><para>struct <link linkend="_struct_bproject">Bproject</link></para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Macros    </title>
        <itemizedlist>
            <listitem><para>#define <link linkend="_mg__processing_8h_1ae84172dd7ca73ab08d8b2f3e05e4a1bd">NFOM</link>   10</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1aed7e6e228b7fd67f42ee99ed71c173a6">MODE_PPS</link>   0</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1a7b7c8de8641ef3ea15dcabe51f383ab7">MODE_SCC</link>   1</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1a9ccbffa539e7ddf4266ed8b7bad27973">MODE_CCC</link>   2</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1ab8c52c1b4c021ed3e6b6b677bd2ac019">MODE</link>   3</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1a362a277b8fa83a46fbc7b4581decd0a7">FULL_ASU</link>   8</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1aa57ecac6e63249e8231a06817499de4c">MULTI_FILE</link>   16</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1ad0c43e5f420b67c107d8438c4133e943">APPLY_CTF</link>   32</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1a4efb1cd58f357b727017352c32459516">PART_LOG</link>   64</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1a77f715c5f3253bfde0474db82eb74a39">WRITE_PPX</link>   128</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1a315ca3b720b034606534af8cb26c66f6">CHECK_PPX</link>   256</para>
</listitem>
            <listitem><para>#define <link linkend="_mg__processing_8h_1a430974fce3ad38f27921beab66fdece6">_ProjectParamStructs_</link></para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Enumerations    </title>
        <itemizedlist>
            <listitem><para>enum <link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cf">FOMType</link> { 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa551a40f8bc3d35846bcb2ae6febb93b8">NoFOM</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa065fec74420cd18346040e497d71993b">FOM</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa31fea2d078f06af81b75a599eacc5544">FOM_CC</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfafb7b28c211352092896774d30fcdc430">FOM_CV</link>, 

<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa853bde58f48f6880c63975f331d07fcc">FOM_SNR</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfae32e29507c39f153deba7ace768695d3">FOM_CC_AVG</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa972c8989e3bb5a412f44e83ea8c02444">FOM_CC_STD</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfaf9d9f40a64cf52ce9a80c9dd68e8a1cc">FOM_HAND_A</link>, 

<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfaa574bba0b5509f16ca3967d48f16a9f9">FOM_HAND_B</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa325ae8565ed0b9da723eb4041d119789">FOM_PFT_CC</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa0f7cf6ba784ead8c5c1bef385f42a123">FOM_PFT_PRJ</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa558886b7c2e6aa390544613eb612805a">FOM_PFT_CMP</link>, 

<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa387a9049c8103c665076f444dc2a6b9d">FOM_RFACTORAB</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa262482a438211935eea644171d5bb4a6">COVERAGE</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa4796eb9aeaa0065da5f9d02fb4eae41b">FOM1</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa1b537fdabec28a0449a00c9a8e5c1b38">FOM2</link>, 

<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa698fcbc7f8c54f6c7f3eddb4ef024cff">FOM3</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa062705311781ab80b8511b3d49947c2a">FOM4</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa61415279d2d31f8f19fe24ad8be7eff2">FOM5</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfae3761d93cb832028164094e146a804d5">FOM6</link>, 

<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa658a3bec97657b45aae11d337cce801c">FOM7</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa20995c415282a30abdbec2715bbc220b">FOM8</link>, 
<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa3b7ec516a34eb052c38d7d9587a1e46a">FOM9</link>
 }</para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_struct_bproject">Bproject</link> * <link linkend="_mg__processing_8h_1a25b137bf513c310fe45bdcc537ccd6fa">project_init</link> ()</para>

<para>Initializes a micrograph processing project parameter structure. </para>
</listitem>
            <listitem><para><link linkend="_struct_bproject">Bproject</link> * <link linkend="_mg__processing_8h_1ad1f222bc7be0953672c332c6e46cdd38">project_create</link> (int nmg, int nrec)</para>

<para>Creates a micrograph processing project parameter structure. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a25d3404c481c541d872a3b413356d35b">project_equal_mg_part_files</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Sets micrograph and particle files to be the same. </para>
</listitem>
            <listitem><para><link linkend="_struct_bfield">Bfield</link> * <link linkend="_mg__processing_8h_1a88699a90fd28e99ae75a6917983d2bcf">field_add</link> (<link linkend="_struct_bfield">Bfield</link> **field, <link linkend="_class_bstring">Bstring</link> &amp;field_id)</para>

<para>Adds a field-of-view parameter structure to a linked list. </para>
</listitem>
            <listitem><para><link linkend="_struct_bfield">Bfield</link> * <link linkend="_mg__processing_8h_1a45810a20edb8af24806e4714c16c500d">field_find_id</link> (<link linkend="_struct_bfield">Bfield</link> *field, <link linkend="_class_bstring">Bstring</link> &amp;field_id)</para>

<para>Finds a field-of-view based on its identifier. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1aade03929a0337e4503da2409863ca1a0">field_find_micrograph</link> (<link linkend="_struct_bfield">Bfield</link> *field, int mg_select, int mg_index, double mg_ang)</para>

<para>Returns a pointer to a specific micrograph in a field-of-view structure based on a unique characteristic of that micrograph. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1a1eb0089167cd6208688f200f90862a3c">field_find_micrograph_n</link> (<link linkend="_struct_bfield">Bfield</link> *field, int n)</para>

<para>Returns a pointer to the nth micrograph in a field-of-view structure. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1a0f1c206ae9649cf3264251635461e9ca">field_find_micrograph_by_focus</link> (<link linkend="_struct_bfield">Bfield</link> *field, int focus_opt, int index)</para>

<para>Returns a pointer to the micrograph in a field-of-view structure based on the focus level and iteration index. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1a75786ba6e6327763d476677bb3886cf9">field_find_micrograph_by_rotang</link> (<link linkend="_struct_bfield">Bfield</link> *field, double rotang)</para>

<para>Returns a pointer to the micrograph in a field-of-view structure with the specified in-plane rotational angle. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1a09911941af317755d147a980ab5b5ef1">field_find_micrograph_by_tiltang</link> (<link linkend="_struct_bfield">Bfield</link> *field, double tiltang)</para>

<para>Returns a pointer to the micrograph in a field-of-view structure with the specified tilt angle. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1ab68ac92873bb04a571d551897be28818">field_find_zero_tilt_mg</link> (<link linkend="_struct_bfield">Bfield</link> *field)</para>

<para>Finds the micrograph closest to a zero degree tilt in a series. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1ac464f306aa2ec99c9b3fcc56db4a4a55">field_find_low_tilt_mg_with_markers</link> (<link linkend="_struct_bfield">Bfield</link> *field)</para>

<para>Finds the micrograph closest to a zero degree tilt in a series with markers. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1a84eceae3d7e32e0020f1367e700c5067">micrograph_add</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> **mg, <link linkend="_class_bstring">Bstring</link> &amp;mg_id)</para>

<para>Adds a micrograph parameter structure to a linked list. </para>
</listitem>
            <listitem><para><link linkend="_struct_bframe">Bframe</link> * <link linkend="_mg__processing_8h_1a773fc6768efab4512b2a5177adaa925f">frame_add</link> (<link linkend="_struct_bframe">Bframe</link> **frame, int pid)</para>

<para>Adds a movie frame parameter structure to a linked list. </para>
</listitem>
            <listitem><para><link linkend="_struct_bparticle">Bparticle</link> * <link linkend="_mg__processing_8h_1a0f7ed71becb7cca444d3fc3958ebfef6">particle_add</link> (<link linkend="_struct_bparticle">Bparticle</link> **part, int pid)</para>

<para>Adds a particle parameter structure to a linked list. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a576729ae5e5de904255d9ce75bf8bbc7">mg_part_links</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg)</para>

<para>Sets the links from particles to micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1af15de191006cbacd08c1de606733be2c">rec_part_links</link> (<link linkend="_struct_breconstruction">Breconstruction</link> *rec)</para>

<para>Sets the links from particles to reconstructions. </para>
</listitem>
            <listitem><para><link linkend="_struct_bparticle">Bparticle</link> * <link linkend="_mg__processing_8h_1a11b5d8faa9780cb1e293a7964ca5d045">part_find_first</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Finds the first particle in a project. </para>
</listitem>
            <listitem><para><link linkend="_struct_bfilament">Bfilament</link> * <link linkend="_mg__processing_8h_1a3c3409ebfdf0c3c9f76e512276daed15">filament_add</link> (<link linkend="_struct_bfilament">Bfilament</link> **fil, int pid)</para>

<para>Adds a filament parameter structure to a linked list. </para>
</listitem>
            <listitem><para><link linkend="_struct_bfilnode">Bfilnode</link> * <link linkend="_mg__processing_8h_1afd15ba5092d93cbf73031268d633c70e">filament_node_add</link> (<link linkend="_struct_bfilnode">Bfilnode</link> **fnode, int pid)</para>

<para>Adds a filament node parameter structure to a linked list. </para>
</listitem>
            <listitem><para>double <link linkend="_mg__processing_8h_1a81e8d85bf058042c71e7f2cee45ba6cb">filament_length</link> (<link linkend="_struct_bfilament">Bfilament</link> *fil)</para>

<para>Calculates the length of a filament. </para>
</listitem>
            <listitem><para><link linkend="_struct_breconstruction">Breconstruction</link> * <link linkend="_mg__processing_8h_1a019bf8ef2ecc6aadc2089aec61cf5cdb">reconstruction_add</link> (<link linkend="_struct_breconstruction">Breconstruction</link> **rec, <link linkend="_class_bstring">Bstring</link> &amp;rec_id)</para>

<para>Adds a reconstruction parameter structure to a linked list. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1ab65655cea9125617c8610d258ee0afe6">project_count_fields</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the fields in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1ae7ec8c0272ecc20f2e00134bd115c6c6">project_count_micrographs</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the micrographs in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1af94c66caf43ea55ce68b469b0c353205">project_count_mg_selected</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the selected micrographs in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a2b8f534ce8411fb9faae15b227c3cc0c">project_count_reconstructions</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the reconstructions in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a219067937f105e127cdeae560d170a28">project_count_rec_selected</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the selected reconstructions in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1abdcbe054bc2eb7387070ef0204eae53b">project_count_mg_particles</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the particles in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1ac78e776a3d10f232a11edd0adc416c07">project_count_mg_part_selected</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts the number of particles in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a11b83d64b7e65cdd6c2e491a02382782">project_count_mg_part_selected</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int num_select)</para>

<para>Counts the number of particles in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1aeeeacdda010c707cde1d2a8e8e14d626">project_count_mg_groups</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts the number of groups of particles in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a377da990cda46b5c6d05c59dec0b21e9">project_count_rec_particles</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the particles in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a9ed00f7aa3050401f5022b3092d4c01d">project_count_rec_part_selected</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the particles in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a6c1fe6a0c2a9e6634097fddd73d2096b">project_count_rec_groups</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts all the particles in the project structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1afbe966628abe7c5c63aeb0abe104d2d5">project_count_mg_filaments</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts the number of filaments in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a3a5ca4e452b8145a7d849a30debda167">project_count_mg_filament_nodes</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts the number of filament nodes in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a022e277e7acd99366640c185961f033e">project_count_rec_filaments</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts the number of filaments in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1ab6127567379d468759d5193c978d5112">project_count_rec_filament_nodes</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Counts the number of filaments in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a8b9440b7753c5e27937b70f2b91efab8">field_count</link> (<link linkend="_struct_bfield">Bfield</link> *field)</para>

<para>Counts the number of fields-of-view in a linked list. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a8c8fd17fd2e25fa143b54137504cb981">field_count_micrographs</link> (<link linkend="_struct_bfield">Bfield</link> *field)</para>

<para>Counts all the micrographs in the field-of-view structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1aa85a8cf575c3102cb40552403ef65445">field_count_mg_selected</link> (<link linkend="_struct_bfield">Bfield</link> *field)</para>

<para>Counts all the micrographs in the field-of-view structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1aeccd8a8335fcaf638970bdd8df8eca02">field_count_particles</link> (<link linkend="_struct_bfield">Bfield</link> *field)</para>

<para>Counts all the particles in the field-of-view structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a1b9c9f1f16f2cde664a0e66ce3e9e22d">micrograph_count</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg)</para>

<para>Counts the number of micrographs in a linked list. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a668b2fb525abf5f02bc4dceaa9bfe2b6">micrograph_count_particles</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg)</para>

<para>Counts all the particles in the micrograph structure. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a10778be3402dbb9922caded8fe0affd3">particle_count</link> (<link linkend="_struct_bparticle">Bparticle</link> *part)</para>

<para>Counts the number of particles in a linked list. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1aa63b3ac40737891c46a7b6b54a3d30f5">particle_count_selected</link> (<link linkend="_struct_bparticle">Bparticle</link> *part)</para>

<para>Counts the number of particles in a linked list. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1abd2ce8451867b8cd759c7526a04dbd15">filament_count</link> (<link linkend="_struct_bfilament">Bfilament</link> *fil)</para>

<para>Counts the number of filaments in a linked list of filaments. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a90f978ea4f28efcf0704b83df007c62f">filament_node_count</link> (<link linkend="_struct_bfilament">Bfilament</link> *fil)</para>

<para>Counts the number of filament nodes in a linked list of filaments. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a2ecd27087626538aead67b4680eabedd">project_kill</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Frees a whole project. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a551b2c584dd16bd057485003a2801ffa">field_kill</link> (<link linkend="_struct_bfield">Bfield</link> *field)</para>

<para>Frees a whole field-of-view structure. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1aac2cfa0e97d4f68525e858bc3ae40364">micrograph_kill</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg)</para>

<para>Frees a whole micrograph parameter structure. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a2b69dff52f2fcb6b0e1e39694b2a3a96">particle_kill</link> (<link linkend="_struct_bparticle">Bparticle</link> *part)</para>

<para>Frees a list of particles. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a3ee2658715e2f7c3af32aeed7c64ec1c">filament_kill</link> (<link linkend="_struct_bfilament">Bfilament</link> *fil)</para>

<para>Frees a list of filaments. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a35fd2be48fa9fd8c2d4f52121955f491">reconstruction_kill</link> (<link linkend="_struct_breconstruction">Breconstruction</link> *rec)</para>

<para>Frees a whole reconstruction parameter structure. </para>
</listitem>
            <listitem><para><link linkend="_struct_bparticle">Bparticle</link> * <link linkend="_mg__processing_8h_1a9678ea3ba7ef13987104207071d9a938">particle_copy</link> (<link linkend="_struct_bparticle">Bparticle</link> **partlist, <link linkend="_struct_bparticle">Bparticle</link> *part)</para>

<para>Adds one particle onto a list of particle parameters. </para>
</listitem>
            <listitem><para><link linkend="_struct_bparticle">Bparticle</link> * <link linkend="_mg__processing_8h_1a71aa16a9928deabf084c63c2a096b4bd">particle_copy</link> (<link linkend="_struct_bparticle">Bparticle</link> *partlist)</para>

<para>Copies a list of particle parameters to a new list. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> * <link linkend="_mg__processing_8h_1aa3fd204c1c90abf01c5b9a23c8f2886a">micrograph_copy</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg)</para>

<para>Copies a micrograph. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1af3004e278b3e2e1d6a73d9ad14a91c4c">project_update</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_struct_bproject">Bproject</link> *proj_new, int fom_index)</para>

<para>Updates an existing project with new information. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1aefee0cf4f70f4bb0c5b04cc898a61746">micrograph_update</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg, <link linkend="_struct_bmicrograph">Bmicrograph</link> *nu_mg, int fom_index, int flags)</para>

<para>Updates an existing micrograph with new information. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a8b0300342a1926860c5f00aaceaae329">reconstruction_update</link> (<link linkend="_struct_breconstruction">Breconstruction</link> *rec, <link linkend="_struct_breconstruction">Breconstruction</link> *nu_rec, int fom_index, int flags)</para>

<para>Updates an existing reconstruction with new information. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a69f1ed7884ccf41af26203eeef36175d">particle_update</link> (<link linkend="_struct_bparticle">Bparticle</link> **pnt_part, <link linkend="_struct_bparticle">Bparticle</link> *new_part, int fom_index)</para>

<para>Updates an existing particle with new information. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1af723b0c3832b459eabeb7e5d1eaafc98">project_merge_part_parameters</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_struct_bproject">Bproject</link> *partproject)</para>

<para>Puts particle parameters from one project into another. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a2d742963893ed82ccc163ff4a0bb33f9">project_set_part_links</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Sets the links from particles back to the micrographs and reconstructions. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a1ccae53c51e7761e60a95432871bf859">micrograph_set_part_links</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg)</para>

<para>Sets the links from particles back to the micrograph. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a118c1837845abfc4fd1a7cccea4ea0ea">reconstruction_set_part_links</link> (<link linkend="_struct_breconstruction">Breconstruction</link> *rec)</para>

<para>Sets the links from particles back to the reconstruction. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a996afef91cc83786c8b920577182a74f">project_divide</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, long n)</para>

<para>Divides a project into a number of micrograph subsets. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmicrograph">Bmicrograph</link> ** <link linkend="_mg__processing_8h_1ac7775046402a74604b11c5b5daa3b917">project_micrograph_array</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, long &amp;nmg)</para>

<para>Sets up an array of selected micrograph pointers. </para>
</listitem>
            <listitem><para><link linkend="_struct_bparticle">Bparticle</link> ** <link linkend="_mg__processing_8h_1a7d8e3d54d7cdbdc3bc6fa625cefd5aae">project_mg_particle_array</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int <link linkend="_tcltk__bmg_8cpp_1a66823305785303716aa59f76b0e3359d">part_select</link>, long &amp;npart)</para>

<para>Sets up an array of selected particle pointers. </para>
</listitem>
            <listitem><para><link linkend="_struct_bparticle">Bparticle</link> ** <link linkend="_mg__processing_8h_1afd534ce20c532c899a3de0a0d9272e44">project_rec_particle_array</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int <link linkend="_tcltk__bmg_8cpp_1a66823305785303716aa59f76b0e3359d">part_select</link>, long &amp;npart)</para>

<para>Sets up an array of selected particle pointers. </para>
</listitem>
            <listitem><para><link linkend="_struct_bparticle">Bparticle</link> ** <link linkend="_mg__processing_8h_1a934ea28ec4fdaebf09eba0cf9a09d92c">particle_array</link> (<link linkend="_struct_bparticle">Bparticle</link> *partlist, int <link linkend="_tcltk__bmg_8cpp_1a66823305785303716aa59f76b0e3359d">part_select</link>, long &amp;npart)</para>

<para>Sets up an array of selected particle pointers. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a3075fd6be8909579fc652695ab97dd85">project_revert_filenames</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_struct_bproject">Bproject</link> *project_old, int flag)</para>

<para>Reverts file names to what it was in an old project. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1ac0eab102922702421184be84cd9790e0">project_set_field_id</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int nseries, <link linkend="_class_bstring">Bstring</link> &amp;field_id)</para>

<para>Sets the field id&apos;s according to a regular series. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1ac1a5ab271d20f9d10e6249f2a4809222">project_show_hierarchy</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Shows the project hierarchy. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a5acf16ba92a77c0e854c480d19db058f">project_maximum_selection</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Finds the maximum slection number for a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1aeb9c4608e15f4cf4f6908a814e24e0d8">project_show_selection_numbers</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Shows the selection numbers for the particles in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a97fc171f988871c9c8fc370be3f1d37b">project_show_selected</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Shows the selected particles in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a52ad936e0c81e64a41492fb9bc7caba4">project_show_class_averages</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Shows the class averages in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1acd49f1260bf7041db25dd602f7ad834b">project_show_selected_parameters</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int <link linkend="_rw_d_m_8cpp_1ae83c07067345faf98c959261a0b7db76">show</link>)</para>

<para>Shows the selected particle parameters in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a587ed4a57b89d23febb068699287bbe8">project_show_parameter</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;tag)</para>

<para>Shows the particle parameter indicated by the tag in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1adfcf6d630e0006ef9e04261cadd40176">project_show_fom_histogram</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Shows a histogram of the FOM values. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1ad138583472ffebcbac75c249b76682ad">project_show_mag_histogram</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int bins, double increment)</para>

<para>Shows the histogram for magnification values for selected particles. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a8cb6072793702839f396256ddc2cb44c">project_dump</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;filename)</para>

<para>Dumps particle info in the project hierarchy. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a52af723733b19a7fde714bbdad1d2dbf">project_select_field</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;field_id)</para>

<para>Selects a field from the project and deletes the rest. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1ae686468b6ee193bd928049b85425e476">project_select_micrograph</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;mg_id)</para>

<para>Selects a micrograph from the project and deletes the rest. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1aee29d487e2a375832b196ac46b0694f4">project_set_micrograph_path</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;path)</para>

<para>Sets the path to micrograph files for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1ad65009a72674549e06c890235f29ffee">project_set_frame_path</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;path)</para>

<para>Sets the path to micrograph frames files for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1afd06e7a40a415af7fa3a7de73e92a96e">project_set_powerspectrum_path</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;path)</para>

<para>Sets the path to powerspectrum files for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a41d210cceebbdd0aa97df99a64e6964d">project_set_particle_path</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;path)</para>

<para>Sets the path to particle files for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a12cba281bae1f9834833568e64961c1d">project_set_filament_path</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;path)</para>

<para>Sets the path to filament files for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a22d446c5ff1b3fe7e1de4b7f19adb920">project_set_magnification</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, double mag)</para>

<para>Sets the magnification for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1acacec50ef8e493074e15030974084eb1">project_set_scan_sampling</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, double sampling)</para>

<para>Sets the scan sampling for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a29a9ff01ed19c0fd41edeb3182b4d28c">project_set_pixel_size</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, double pixel_size)</para>

<para>Sets the pixel size for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1ad250e318df7f1ff7bc6444fdb3d0d42b">project_set_tilt</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, double tilt_axis, double tilt_angle)</para>

<para>Sets the tilt parameters for all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1aeababf316e7b9e5c96b8ce4b26bfdd43">project_sort_by_tilt</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Sorts the micrographs in each field by tilt angle. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a0066207317aba6c6a3b3319166ba37d9">project_set_dose</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, double dose)</para>

<para>Sets the electron dose of all the micrographs. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1aa12f3b48677510ae94a0b068c6bd377e">project_set_micrograph_origins</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_vector3">Vector3</link>&lt; float &gt; origin)</para>

<para>Sets micrograph origins to the given origin. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1ab82fb8a5bc69b0b3c2aa2485b83e09f1">project_add_origins_to_coords</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Adds the particle origins to the micrograph coordinates. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a876f72881c0e2829e517aaf0df8acdea">project_flip_origins</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int flip)</para>

<para>Flip origin coordinates. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__processing_8h_1a5837277b95ef6a1dc1f39b98b9d759a3">project_renumber_particles</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>)</para>

<para>Renumbers particles. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1ac3e8f5e1616cc4e958cc5357eb3ab7b6">project_set_particle_box_size</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size)</para>

<para>Sets particle box size to the given value. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1aa0536e68060c07b48f4f4f9ca353743d">project_set_particle_box_size</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, long box_size)</para>

<para>Sets particle box size to the given value. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a6b50ea2d44fbded720f3b094e84a908d">project_set_particle_origins</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; origin)</para>

<para>Sets particle origins to given values. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1adac6093c933222b384c57b1c3ad69b77">project_set_particle_asu_views</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bstring">Bstring</link> &amp;symmetry_asu)</para>

<para>Sets particle views within the asymmetric unit. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a153585f20c4d97a7e9285f6857e3cf7a">project_set_particle_asu_views</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_struct_bsymmetry">Bsymmetry</link> *sym)</para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1ab3dd826e459645bbab9daaa7147909cc">project_rotate_particle_views</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_view">View</link> view)</para>

<para>Rotates particle views with respect to a reference view. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a60d84303b4561d17729dabed733e9ca0">project_apply_map_magnifications</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int mag_num, float *mag)</para>

<para>Change particle pixel sizes for particles based on map magnifications. </para>
</listitem>
            <listitem><para><link linkend="_class_view">View</link> * <link linkend="_mg__processing_8h_1a48e44d868399e6ea7a48bd1143c40c87">views_from_project</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int selection)</para>

<para>Retrieves the particle views from a project. </para>
</listitem>
            <listitem><para><link linkend="_class_bstring">Bstring</link> <link linkend="_mg__processing_8h_1ad546987441fbc7af42ab2eda64275974">get_fom_tag</link> (<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cf">FOMType</link> fom_type)</para>

<para>Returns the tag associated with a particular FOM. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__processing_8h_1a2cf013b25c49556c6c988a5df0962da3">get_fom_tag</link> (<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cf">FOMType</link> fom_type, char *tag)</para>

<para>Returns the tag associated with a particular FOM. </para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Header file for micrograph processing. </para>

<para><formalpara><title>Author: </title>

<para>Bernard Heymann </para>
</formalpara>
<formalpara><title>Date: </title>

<para>Created: 20000426 </para>

<para>Modified: 20191015 </para>
</formalpara>
</para>
</section>
<section>
<title>Macro Definition Documentation</title>
<anchor xml:id="_mg__processing_8h_1a430974fce3ad38f27921beab66fdece6"/>    <section>
    <title>_ProjectParamStructs_</title>
<indexterm><primary>_ProjectParamStructs_</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>_ProjectParamStructs_</secondary></indexterm>
<para><computeroutput>#define _ProjectParamStructs_</computeroutput></para><para>
Definition at line 348 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1ad0c43e5f420b67c107d8438c4133e943"/>    <section>
    <title>APPLY_CTF</title>
<indexterm><primary>APPLY_CTF</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>APPLY_CTF</secondary></indexterm>
<para><computeroutput>#define APPLY_CTF   32</computeroutput></para><para>
Definition at line 24 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1a315ca3b720b034606534af8cb26c66f6"/>    <section>
    <title>CHECK_PPX</title>
<indexterm><primary>CHECK_PPX</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>CHECK_PPX</secondary></indexterm>
<para><computeroutput>#define CHECK_PPX   256</computeroutput></para><para>
Definition at line 27 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1a362a277b8fa83a46fbc7b4581decd0a7"/>    <section>
    <title>FULL_ASU</title>
<indexterm><primary>FULL_ASU</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FULL_ASU</secondary></indexterm>
<para><computeroutput>#define FULL_ASU   8</computeroutput></para><para>
Definition at line 22 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1ab8c52c1b4c021ed3e6b6b677bd2ac019"/>    <section>
    <title>MODE</title>
<indexterm><primary>MODE</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>MODE</secondary></indexterm>
<para><computeroutput>#define MODE   3</computeroutput></para><para>
Definition at line 21 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1a9ccbffa539e7ddf4266ed8b7bad27973"/>    <section>
    <title>MODE_CCC</title>
<indexterm><primary>MODE_CCC</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>MODE_CCC</secondary></indexterm>
<para><computeroutput>#define MODE_CCC   2</computeroutput></para><para>
Definition at line 20 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1aed7e6e228b7fd67f42ee99ed71c173a6"/>    <section>
    <title>MODE_PPS</title>
<indexterm><primary>MODE_PPS</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>MODE_PPS</secondary></indexterm>
<para><computeroutput>#define MODE_PPS   0</computeroutput></para><para>
Definition at line 18 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1a7b7c8de8641ef3ea15dcabe51f383ab7"/>    <section>
    <title>MODE_SCC</title>
<indexterm><primary>MODE_SCC</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>MODE_SCC</secondary></indexterm>
<para><computeroutput>#define MODE_SCC   1</computeroutput></para><para>
Definition at line 19 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1aa57ecac6e63249e8231a06817499de4c"/>    <section>
    <title>MULTI_FILE</title>
<indexterm><primary>MULTI_FILE</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>MULTI_FILE</secondary></indexterm>
<para><computeroutput>#define MULTI_FILE   16</computeroutput></para><para>
Definition at line 23 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1ae84172dd7ca73ab08d8b2f3e05e4a1bd"/>    <section>
    <title>NFOM</title>
<indexterm><primary>NFOM</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>NFOM</secondary></indexterm>
<para><computeroutput>#define NFOM   10</computeroutput></para><para>
Definition at line 16 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1a4efb1cd58f357b727017352c32459516"/>    <section>
    <title>PART_LOG</title>
<indexterm><primary>PART_LOG</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>PART_LOG</secondary></indexterm>
<para><computeroutput>#define PART_LOG   64</computeroutput></para><para>
Definition at line 25 of file mg_processing.h.</para>
    </section><anchor xml:id="_mg__processing_8h_1a77f715c5f3253bfde0474db82eb74a39"/>    <section>
    <title>WRITE_PPX</title>
<indexterm><primary>WRITE_PPX</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>WRITE_PPX</secondary></indexterm>
<para><computeroutput>#define WRITE_PPX   128</computeroutput></para><para>
Definition at line 26 of file mg_processing.h.</para>
</section>
</section>
<section>
<title>Enumeration Type Documentation</title>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cf"/>    <section>
    <title>FOMType</title>
<indexterm><primary>FOMType</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOMType</secondary></indexterm>
<para><computeroutput>enum <link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cf">FOMType</link></computeroutput></para><informaltable frame="all">
<title>Enumerator</title>
    <tgroup cols="2" align="left" colsep="1" rowsep="1">
      <colspec colname='c1'/>
      <colspec colname='c2'/>
<tbody>
<row><entry><indexterm><primary>NoFOM</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>NoFOM</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa551a40f8bc3d35846bcb2ae6febb93b8"/>NoFOM</entry><entry></entry></row><row><entry><indexterm><primary>FOM</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa065fec74420cd18346040e497d71993b"/>FOM</entry><entry></entry></row><row><entry><indexterm><primary>FOM_CC</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_CC</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa31fea2d078f06af81b75a599eacc5544"/>FOM_CC</entry><entry></entry></row><row><entry><indexterm><primary>FOM_CV</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_CV</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfafb7b28c211352092896774d30fcdc430"/>FOM_CV</entry><entry></entry></row><row><entry><indexterm><primary>FOM_SNR</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_SNR</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa853bde58f48f6880c63975f331d07fcc"/>FOM_SNR</entry><entry></entry></row><row><entry><indexterm><primary>FOM_CC_AVG</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_CC_AVG</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfae32e29507c39f153deba7ace768695d3"/>FOM_CC_AVG</entry><entry></entry></row><row><entry><indexterm><primary>FOM_CC_STD</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_CC_STD</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa972c8989e3bb5a412f44e83ea8c02444"/>FOM_CC_STD</entry><entry></entry></row><row><entry><indexterm><primary>FOM_HAND_A</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_HAND_A</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfaf9d9f40a64cf52ce9a80c9dd68e8a1cc"/>FOM_HAND_A</entry><entry></entry></row><row><entry><indexterm><primary>FOM_HAND_B</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_HAND_B</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfaa574bba0b5509f16ca3967d48f16a9f9"/>FOM_HAND_B</entry><entry></entry></row><row><entry><indexterm><primary>FOM_PFT_CC</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_PFT_CC</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa325ae8565ed0b9da723eb4041d119789"/>FOM_PFT_CC</entry><entry></entry></row><row><entry><indexterm><primary>FOM_PFT_PRJ</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_PFT_PRJ</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa0f7cf6ba784ead8c5c1bef385f42a123"/>FOM_PFT_PRJ</entry><entry></entry></row><row><entry><indexterm><primary>FOM_PFT_CMP</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_PFT_CMP</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa558886b7c2e6aa390544613eb612805a"/>FOM_PFT_CMP</entry><entry></entry></row><row><entry><indexterm><primary>FOM_RFACTORAB</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM_RFACTORAB</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa387a9049c8103c665076f444dc2a6b9d"/>FOM_RFACTORAB</entry><entry></entry></row><row><entry><indexterm><primary>COVERAGE</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>COVERAGE</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa262482a438211935eea644171d5bb4a6"/>COVERAGE</entry><entry></entry></row><row><entry><indexterm><primary>FOM1</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM1</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa4796eb9aeaa0065da5f9d02fb4eae41b"/>FOM1</entry><entry></entry></row><row><entry><indexterm><primary>FOM2</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM2</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa1b537fdabec28a0449a00c9a8e5c1b38"/>FOM2</entry><entry></entry></row><row><entry><indexterm><primary>FOM3</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM3</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa698fcbc7f8c54f6c7f3eddb4ef024cff"/>FOM3</entry><entry></entry></row><row><entry><indexterm><primary>FOM4</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM4</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa062705311781ab80b8511b3d49947c2a"/>FOM4</entry><entry></entry></row><row><entry><indexterm><primary>FOM5</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM5</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa61415279d2d31f8f19fe24ad8be7eff2"/>FOM5</entry><entry></entry></row><row><entry><indexterm><primary>FOM6</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM6</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfae3761d93cb832028164094e146a804d5"/>FOM6</entry><entry></entry></row><row><entry><indexterm><primary>FOM7</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM7</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa658a3bec97657b45aae11d337cce801c"/>FOM7</entry><entry></entry></row><row><entry><indexterm><primary>FOM8</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM8</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa20995c415282a30abdbec2715bbc220b"/>FOM8</entry><entry></entry></row><row><entry><indexterm><primary>FOM9</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>FOM9</secondary></indexterm>
<anchor xml:id="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cfa3b7ec516a34eb052c38d7d9587a1e46a"/>FOM9</entry><entry></entry></row>    </tbody>
    </tgroup>
</informaltable>
<para>
Definition at line 38 of file mg_processing.h.</para>
</section>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_mg__processing_8h_1a88699a90fd28e99ae75a6917983d2bcf"/>    <section>
    <title>field_add()</title>
<indexterm><primary>field_add</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_add</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bfield">Bfield</link>* field_add (<link linkend="_struct_bfield">Bfield</link> ** field, <link linkend="_class_bstring">Bstring</link> &amp; field_id)</computeroutput></para><para>

<para>Adds a field-of-view parameter structure to a linked list. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**field</entry>
                                <entry>
<para>pointer to any field-of-view in the list. </para>
</entry>
                            </row>
                            <row>
                                <entry>field_id</entry>
                                <entry>
<para>field identifier. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bfield* new field-of-view. <literallayout><computeroutput>The function allocates memory for a new field-of-view structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 120 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a8b9440b7753c5e27937b70f2b91efab8"/>    <section>
    <title>field_count()</title>
<indexterm><primary>field_count</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_count</secondary></indexterm>
<para><computeroutput>long field_count (<link linkend="_struct_bfield">Bfield</link> * field)</computeroutput></para><para>

<para>Counts the number of fields-of-view in a linked list. </para>
</para>

<para><literallayout><computeroutput>The function counts fields-of-view in the list from the given pointer,
and does not count fields-of-view prior to this one.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>pointer to any field-of-view in the list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of fields-of-view. </para>
</formalpara>
</para>
<para>
Definition at line 1053 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aa85a8cf575c3102cb40552403ef65445"/>    <section>
    <title>field_count_mg_selected()</title>
<indexterm><primary>field_count_mg_selected</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_count_mg_selected</secondary></indexterm>
<para><computeroutput>long field_count_mg_selected (<link linkend="_struct_bfield">Bfield</link> * field)</computeroutput></para><para>

<para>Counts all the micrographs in the field-of-view structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>field-of-view parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of micrographs of field. </para>
</formalpara>
</para>
<para>
Definition at line 1082 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a8c8fd17fd2e25fa143b54137504cb981"/>    <section>
    <title>field_count_micrographs()</title>
<indexterm><primary>field_count_micrographs</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_count_micrographs</secondary></indexterm>
<para><computeroutput>long field_count_micrographs (<link linkend="_struct_bfield">Bfield</link> * field)</computeroutput></para><para>

<para>Counts all the micrographs in the field-of-view structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>field-of-view parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of micrographs of field. </para>
</formalpara>
</para>
<para>
Definition at line 1067 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aeccd8a8335fcaf638970bdd8df8eca02"/>    <section>
    <title>field_count_particles()</title>
<indexterm><primary>field_count_particles</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_count_particles</secondary></indexterm>
<para><computeroutput>long field_count_particles (<link linkend="_struct_bfield">Bfield</link> * field)</computeroutput></para><para>

<para>Counts all the particles in the field-of-view structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>field-of-view parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles in field. </para>
</formalpara>
</para>
<para>
Definition at line 1097 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a45810a20edb8af24806e4714c16c500d"/>    <section>
    <title>field_find_id()</title>
<indexterm><primary>field_find_id</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_find_id</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bfield">Bfield</link>* field_find_id (<link linkend="_struct_bfield">Bfield</link> * field, <link linkend="_class_bstring">Bstring</link> &amp; field_id)</computeroutput></para><para>

<para>Finds a field-of-view based on its identifier. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>pointer to first field-of-view in the list. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;field_id</entry>
                                <entry>
<para>field-of-view identifier. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bfield* field-of-view or NULL if not found. <literallayout><computeroutput>The function searches a linked list for the field-of-view
identifier and returns a pointer to that structure or NULL if
it cannot find it.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 152 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ac464f306aa2ec99c9b3fcc56db4a4a55"/>    <section>
    <title>field_find_low_tilt_mg_with_markers()</title>
<indexterm><primary>field_find_low_tilt_mg_with_markers</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_find_low_tilt_mg_with_markers</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* field_find_low_tilt_mg_with_markers (<link linkend="_struct_bfield">Bfield</link> * field)</computeroutput></para><para>

<para>Finds the micrograph closest to a zero degree tilt in a series with markers. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>field-of-view. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* micrograph closest to zero degrees tilt with markers. <literallayout><computeroutput>The first micrograph with the smallest deviation from zero degree
tilt with defined markers is returned.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 431 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aade03929a0337e4503da2409863ca1a0"/>    <section>
    <title>field_find_micrograph()</title>
<indexterm><primary>field_find_micrograph</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_find_micrograph</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* field_find_micrograph (<link linkend="_struct_bfield">Bfield</link> * field, int mg_select, int mg_index, double mg_ang)</computeroutput></para><para>

<para>Returns a pointer to a specific micrograph in a field-of-view structure based on a unique characteristic of that micrograph. </para>
</para>

<para><formalpara><title>Author: </title>

<para>David Belnap </para>
</formalpara>

                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>field-of-view. </para>
</entry>
                            </row>
                            <row>
                                <entry>mg_select</entry>
                                <entry>
<para>selection criterion. </para>
</entry>
                            </row>
                            <row>
                                <entry>mg_index</entry>
                                <entry>
<para>Reference by its index in field (for mg_ref_select=0|1|2). </para>
</entry>
                            </row>
                            <row>
                                <entry>mg_ang</entry>
                                <entry>
<para>Reference by micrograph rotation or tilt angle (for mg_ref_select=3|4). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* Pointer to the selected micrograph <literallayout><computeroutput>Calls functions that find a micrograph by index number within the
field, by focus level, in-plane rotational angle, tilt angle, or
tilt angle plus focus level or index number:

criterion                        mg_select   mg_index  mg_ang
--------------------------------------------------------------
nth closest-to-focus                 0           n        -
nth farthest-from-focus              1           n        -
index number in series (1...n)       2         index      -
in-plane rotation angle              3           -      angle
tilt angle                           4           -      angle
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 183 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a0f1c206ae9649cf3264251635461e9ca"/>    <section>
    <title>field_find_micrograph_by_focus()</title>
<indexterm><primary>field_find_micrograph_by_focus</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_find_micrograph_by_focus</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* field_find_micrograph_by_focus (<link linkend="_struct_bfield">Bfield</link> * field, int focus_opt, int iselect)</computeroutput></para><para>

<para>Returns a pointer to the micrograph in a field-of-view structure based on the focus level and iteration index. </para>
</para>

<para><formalpara><title>Author: </title>

<para>David Belnap and Bernard Heymann </para>
</formalpara>

                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>a field-of-view structure </para>
</entry>
                            </row>
                            <row>
                                <entry>focus_opt</entry>
                                <entry>
<para>0=closest-to-focus, 1=farthest-from-focus </para>
</entry>
                            </row>
                            <row>
                                <entry>iselect</entry>
                                <entry>
<para>0,1,...,n; select (index+1)th-closest or (index+1)th-farthest focus </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* mg Micrograph at specified focus level Loops through micrographs in the field-of-view. Orders focus values in an array from smallest to largest. Selects the (index+1)th closest-to-focus or farthest-from-focus value. (focus_opt determines whether the closest or farthest value is selected.) Loops through micrographs again to find the micrograph with the selected value. Tests if there are zero or multiple micrographs with the same focus value and exits program if so. Otherwise, the pointer to the micrograph with the specified focus level is returned. An example, if index=1 and focus_opt=0, a pointer to the 2nd closest-to-focus micrograph will be returned. To get the closest-to-focus or farthest-from-focus value, the index must be zero. </para>
</formalpara>
</para>
<para>
Definition at line 261 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a75786ba6e6327763d476677bb3886cf9"/>    <section>
    <title>field_find_micrograph_by_rotang()</title>
<indexterm><primary>field_find_micrograph_by_rotang</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_find_micrograph_by_rotang</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* field_find_micrograph_by_rotang (<link linkend="_struct_bfield">Bfield</link> * field, double rotang)</computeroutput></para><para>

<para>Returns a pointer to the micrograph in a field-of-view structure with the specified in-plane rotational angle. </para>
</para>

<para><formalpara><title>Author: </title>

<para>David Belnap and Bernard Heymann </para>
</formalpara>

                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>a field-of-view </para>
</entry>
                            </row>
                            <row>
                                <entry>rotang</entry>
                                <entry>
<para>in-plane rotational angle of micrograph (in radians) </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* mg Pointer to micrograph with rotang <literallayout><computeroutput>Loop through all micrographs in the field-of-view to find
micrograph with the specified angle.  Test if there are zero or
multiple micrographs with the same rotational angle, halt program 
if true.  If not true, then return pointer to the micrograph with 
the specified angle.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 318 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a09911941af317755d147a980ab5b5ef1"/>    <section>
    <title>field_find_micrograph_by_tiltang()</title>
<indexterm><primary>field_find_micrograph_by_tiltang</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_find_micrograph_by_tiltang</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* field_find_micrograph_by_tiltang (<link linkend="_struct_bfield">Bfield</link> * field, double tiltang)</computeroutput></para><para>

<para>Returns a pointer to the micrograph in a field-of-view structure with the specified tilt angle. </para>
</para>

<para><formalpara><title>Author: </title>

<para>David Belnap </para>
</formalpara>

                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>a field-of-view </para>
</entry>
                            </row>
                            <row>
                                <entry>tiltang</entry>
                                <entry>
<para>tilt angle of micrograph (in radians) </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* micrograph with rotang <literallayout><computeroutput>Loop through all micrographs in the field-of-view to find
micrograph with the specified tilt angle.  Test if there are zero
or multiple micrographs with the same angle, halt program if true.
If not true, then return pointer to the micrograph with the 
specified angle.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 362 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a1eb0089167cd6208688f200f90862a3c"/>    <section>
    <title>field_find_micrograph_n()</title>
<indexterm><primary>field_find_micrograph_n</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_find_micrograph_n</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* field_find_micrograph_n (<link linkend="_struct_bfield">Bfield</link> * field, int n)</computeroutput></para><para>

<para>Returns a pointer to the nth micrograph in a field-of-view structure. </para>
</para>

<para><formalpara><title>Author: </title>

<para>David Belnap and Bernard Heymann </para>
</formalpara>

                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>a field-of-view </para>
</entry>
                            </row>
                            <row>
                                <entry>n</entry>
                                <entry>
<para>nth micrograph index (first index number = 1) </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* Pointer to the nth micrograph <literallayout><computeroutput>Loop through micrographs in the field-of-view until the nth 
micrograph is reached.  Return pointer to that micrograph.
Tests whether n is within the appropriate range.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 223 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ab68ac92873bb04a571d551897be28818"/>    <section>
    <title>field_find_zero_tilt_mg()</title>
<indexterm><primary>field_find_zero_tilt_mg</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_find_zero_tilt_mg</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* field_find_zero_tilt_mg (<link linkend="_struct_bfield">Bfield</link> * field)</computeroutput></para><para>

<para>Finds the micrograph closest to a zero degree tilt in a series. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>field-of-view. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* micrograph closest to zero degrees tilt. <literallayout><computeroutput>The first micrograph with the smallest deviation from zero degree
tilt is returned.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 400 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a551b2c584dd16bd057485003a2801ffa"/>    <section>
    <title>field_kill()</title>
<indexterm><primary>field_kill</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>field_kill</secondary></indexterm>
<para><computeroutput>int field_kill (<link linkend="_struct_bfield">Bfield</link> * field)</computeroutput></para><para>

<para>Frees a whole field-of-view structure. </para>
</para>

<para><literallayout><computeroutput>Frees all the structures down the hierarchy.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*field</entry>
                                <entry>
<para>field-of-view parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 1261 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a3c3409ebfdf0c3c9f76e512276daed15"/>    <section>
    <title>filament_add()</title>
<indexterm><primary>filament_add</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>filament_add</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bfilament">Bfilament</link>* filament_add (<link linkend="_struct_bfilament">Bfilament</link> ** fil, int pid)</computeroutput></para><para>

<para>Adds a filament parameter structure to a linked list. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**fil</entry>
                                <entry>
<para>pointer to any filament in the list. </para>
</entry>
                            </row>
                            <row>
                                <entry>pid</entry>
                                <entry>
<para>filament number in file (starts at 1). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bfilament* new filament. <literallayout><computeroutput>The function allocates memory for a new filament structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 625 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1abd2ce8451867b8cd759c7526a04dbd15"/>    <section>
    <title>filament_count()</title>
<indexterm><primary>filament_count</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>filament_count</secondary></indexterm>
<para><computeroutput>long filament_count (<link linkend="_struct_bfilament">Bfilament</link> * fil)</computeroutput></para><para>

<para>Counts the number of filaments in a linked list of filaments. </para>
</para>

<para><literallayout><computeroutput>The function counts filaments in the list from the given pointer,
and does not count filaments prior to this one.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*fil</entry>
                                <entry>
<para>pointer to any filament in the list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filaments. </para>
</formalpara>
</para>
<para>
Definition at line 1187 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a3ee2658715e2f7c3af32aeed7c64ec1c"/>    <section>
    <title>filament_kill()</title>
<indexterm><primary>filament_kill</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>filament_kill</secondary></indexterm>
<para><computeroutput>int filament_kill (<link linkend="_struct_bfilament">Bfilament</link> * fil)</computeroutput></para><para>

<para>Frees a list of filaments. </para>
</para>

<para><literallayout><computeroutput>Frees all the structures down the hierarchy.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*fil</entry>
                                <entry>
<para>filament parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 1347 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a81e8d85bf058042c71e7f2cee45ba6cb"/>    <section>
    <title>filament_length()</title>
<indexterm><primary>filament_length</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>filament_length</secondary></indexterm>
<para><computeroutput>double filament_length (<link linkend="_struct_bfilament">Bfilament</link> * fil)</computeroutput></para><para>

<para>Calculates the length of a filament. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*fil</entry>
                                <entry>
<para>pointer to a filament. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>double length in coordinate units. <literallayout><computeroutput>The length is defined as the sum of the link lengths connecting the nodes.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 681 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1afd15ba5092d93cbf73031268d633c70e"/>    <section>
    <title>filament_node_add()</title>
<indexterm><primary>filament_node_add</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>filament_node_add</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bfilnode">Bfilnode</link>* filament_node_add (<link linkend="_struct_bfilnode">Bfilnode</link> ** fnode, int pid)</computeroutput></para><para>

<para>Adds a filament node parameter structure to a linked list. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**fnode</entry>
                                <entry>
<para>pointer to any filament node in the list. </para>
</entry>
                            </row>
                            <row>
                                <entry>pid</entry>
                                <entry>
<para>filament node number in file (starts at 1). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bfilnode* new filament node. <literallayout><computeroutput>The function allocates memory for a new filament node structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 655 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a90f978ea4f28efcf0704b83df007c62f"/>    <section>
    <title>filament_node_count()</title>
<indexterm><primary>filament_node_count</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>filament_node_count</secondary></indexterm>
<para><computeroutput>long filament_node_count (<link linkend="_struct_bfilament">Bfilament</link> * fil)</computeroutput></para><para>

<para>Counts the number of filament nodes in a linked list of filaments. </para>
</para>

<para><literallayout><computeroutput>The function counts filament nodes in the list from the given pointer,
and does not count filaments prior to this one.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*fil</entry>
                                <entry>
<para>pointer to any filament in the list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filament nodes. </para>
</formalpara>
</para>
<para>
Definition at line 1205 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a773fc6768efab4512b2a5177adaa925f"/>    <section>
    <title>frame_add()</title>
<indexterm><primary>frame_add</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>frame_add</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bframe">Bframe</link>* frame_add (<link linkend="_struct_bframe">Bframe</link> ** frame, int pid)</computeroutput></para><para>

<para>Adds a movie frame parameter structure to a linked list. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**frame</entry>
                                <entry>
<para>pointer to any frame in the list. </para>
</entry>
                            </row>
                            <row>
                                <entry>pid</entry>
                                <entry>
<para>particle number in file (starts at 1). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bframe* new frame. <literallayout><computeroutput>The function allocates memory for a new frame structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 495 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ad546987441fbc7af42ab2eda64275974"/>    <section>
    <title>get_fom_tag()<computeroutput>[1/2]</computeroutput></title>
<indexterm><primary>get_fom_tag</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>get_fom_tag</secondary></indexterm>
<para><computeroutput><link linkend="_class_bstring">Bstring</link> get_fom_tag (<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cf">FOMType</link> fom_type)</computeroutput></para><para>

<para>Returns the tag associated with a particular FOM. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>fom_type</entry>
                                <entry>
<para>type of FOM. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para><link linkend="_class_bstring">Bstring</link> FOM tag. </para>
</formalpara>
</para>
<para>
Definition at line 3971 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a2cf013b25c49556c6c988a5df0962da3"/>    <section>
    <title>get_fom_tag()<computeroutput>[2/2]</computeroutput></title>
<indexterm><primary>get_fom_tag</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>get_fom_tag</secondary></indexterm>
<para><computeroutput>int get_fom_tag (<link linkend="_mg__processing_8h_1a9b8250bcd3dbae566bd5ef8a6089b1cf">FOMType</link> fom_type, char * tag)</computeroutput></para><para>

<para>Returns the tag associated with a particular FOM. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>fom_type</entry>
                                <entry>
<para>type of FOM. </para>
</entry>
                            </row>
                            <row>
                                <entry>*tag</entry>
                                <entry>
<para>FOM tag. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int string length of the new comment. </para>
</formalpara>
</para>
<para>
Definition at line 4009 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a576729ae5e5de904255d9ce75bf8bbc7"/>    <section>
    <title>mg_part_links()</title>
<indexterm><primary>mg_part_links</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>mg_part_links</secondary></indexterm>
<para><computeroutput>int mg_part_links (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg)</computeroutput></para><para>

<para>Sets the links from particles to micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*mg</entry>
                                <entry>
<para>pointer to micrograph. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 555 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a84eceae3d7e32e0020f1367e700c5067"/>    <section>
    <title>micrograph_add()</title>
<indexterm><primary>micrograph_add</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>micrograph_add</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* micrograph_add (<link linkend="_struct_bmicrograph">Bmicrograph</link> ** mg, <link linkend="_class_bstring">Bstring</link> &amp; mg_id)</computeroutput></para><para>

<para>Adds a micrograph parameter structure to a linked list. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**mg</entry>
                                <entry>
<para>pointer to any micrograph in the list. </para>
</entry>
                            </row>
                            <row>
                                <entry>mg_id</entry>
                                <entry>
<para>micrograph identifier. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* new micrograph. <literallayout><computeroutput>The function allocates memory for a new micrograph structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 461 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aa3fd204c1c90abf01c5b9a23c8f2886a"/>    <section>
    <title>micrograph_copy()</title>
<indexterm><primary>micrograph_copy</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>micrograph_copy</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>* micrograph_copy (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg)</computeroutput></para><para>

<para>Copies a micrograph. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*mg</entry>
                                <entry>
<para>micrograph structure to be copied. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph* new micrograph. </para>
</formalpara>
</para>
<para>
Definition at line 1529 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a1b9c9f1f16f2cde664a0e66ce3e9e22d"/>    <section>
    <title>micrograph_count()</title>
<indexterm><primary>micrograph_count</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>micrograph_count</secondary></indexterm>
<para><computeroutput>long micrograph_count (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg)</computeroutput></para><para>

<para>Counts the number of micrographs in a linked list. </para>
</para>

<para><literallayout><computeroutput>The function counts micrographs in the list from the given pointer,
and does not count micrographs prior to this one.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*mg</entry>
                                <entry>
<para>pointer to any micrograph in the list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of micrographs. </para>
</formalpara>
</para>
<para>
Definition at line 1118 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a668b2fb525abf5f02bc4dceaa9bfe2b6"/>    <section>
    <title>micrograph_count_particles()</title>
<indexterm><primary>micrograph_count_particles</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>micrograph_count_particles</secondary></indexterm>
<para><computeroutput>long micrograph_count_particles (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg)</computeroutput></para><para>

<para>Counts all the particles in the micrograph structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*mg</entry>
                                <entry>
<para>micrograph parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles in micrograph. </para>
</formalpara>
</para>
<para>
Definition at line 1132 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aac2cfa0e97d4f68525e858bc3ae40364"/>    <section>
    <title>micrograph_kill()</title>
<indexterm><primary>micrograph_kill</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>micrograph_kill</secondary></indexterm>
<para><computeroutput>int micrograph_kill (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg)</computeroutput></para><para>

<para>Frees a whole micrograph parameter structure. </para>
</para>

<para><literallayout><computeroutput>Frees all the structures down the hierarchy.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*mg</entry>
                                <entry>
<para>micrograph parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 1288 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a1ccae53c51e7761e60a95432871bf859"/>    <section>
    <title>micrograph_set_part_links()</title>
<indexterm><primary>micrograph_set_part_links</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>micrograph_set_part_links</secondary></indexterm>
<para><computeroutput>long micrograph_set_part_links (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg)</computeroutput></para><para>

<para>Sets the links from particles back to the micrograph. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*mg</entry>
                                <entry>
<para>micrograph parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles. </para>
</formalpara>
</para>
<para>
Definition at line 1928 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aefee0cf4f70f4bb0c5b04cc898a61746"/>    <section>
    <title>micrograph_update()</title>
<indexterm><primary>micrograph_update</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>micrograph_update</secondary></indexterm>
<para><computeroutput>int micrograph_update (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg, <link linkend="_struct_bmicrograph">Bmicrograph</link> * nu_mg, int fom_index, int flags)</computeroutput></para><para>

<para>Updates an existing micrograph with new information. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*mg</entry>
                                <entry>
<para>micrograph structure to be updated. </para>
</entry>
                            </row>
                            <row>
                                <entry>*nu_mg</entry>
                                <entry>
<para>micrograph structure with new information. </para>
</entry>
                            </row>
                            <row>
                                <entry>fom_index</entry>
                                <entry>
<para>index of FOM to select on. </para>
</entry>
                            </row>
                            <row>
                                <entry>flags</entry>
                                <entry>
<para>flags indicating which parts to update. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The new information is encoded as a micrograph structure.
All fields are updated if the new fields contain non-default data.
Defaults are defined here as zero-length strings or zeroes.
The particles in the original micrograph are matched by ID with 
those in the new micrograph and updated, with any new particles 
added from the new micrograph.
The bad area and marker coordinates are replaced if they exist 
in the new structure.
The new micrograph structure is not modified, except for deletion 
of bad areas and markers.

Flags:
    1   particles
    2   bad areas
    4   filaments
    8   structure factors
    16  layer lines
    32  markers
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 1670 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a11b5d8faa9780cb1e293a7964ca5d045"/>    <section>
    <title>part_find_first()</title>
<indexterm><primary>part_find_first</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>part_find_first</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bparticle">Bparticle</link>* part_find_first (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Finds the first particle in a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>pointer to project. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bparticle* first particle with a filename. <literallayout><computeroutput>The function searches for the first particle with a filename.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 589 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a0f7ed71becb7cca444d3fc3958ebfef6"/>    <section>
    <title>particle_add()</title>
<indexterm><primary>particle_add</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>particle_add</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bparticle">Bparticle</link>* particle_add (<link linkend="_struct_bparticle">Bparticle</link> ** part, int pid)</computeroutput></para><para>

<para>Adds a particle parameter structure to a linked list. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**part</entry>
                                <entry>
<para>pointer to any particle in the list. </para>
</entry>
                            </row>
                            <row>
                                <entry>pid</entry>
                                <entry>
<para>particle number in file (starts at 1). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bparticle* new particle. <literallayout><computeroutput>The function allocates memory for a new particle structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 527 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a934ea28ec4fdaebf09eba0cf9a09d92c"/>    <section>
    <title>particle_array()</title>
<indexterm><primary>particle_array</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>particle_array</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bparticle">Bparticle</link>** particle_array (<link linkend="_struct_bparticle">Bparticle</link> * partlist, int part_select, long &amp; npart)</computeroutput></para><para>

<para>Sets up an array of selected particle pointers. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*partlist</entry>
                                <entry>
<para>particle linked list. </para>
</entry>
                            </row>
                            <row>
                                <entry>part_select</entry>
                                <entry>
<para>particle selection (-1 if none). </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;npart</entry>
                                <entry>
<para>array length (modified). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bparticle** particle pointer array. <literallayout><computeroutput>FOM&apos;s of non-selected particles are zeroed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 2107 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a9678ea3ba7ef13987104207071d9a938"/>    <section>
    <title>particle_copy()<computeroutput>[1/2]</computeroutput></title>
<indexterm><primary>particle_copy</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>particle_copy</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bparticle">Bparticle</link>* particle_copy (<link linkend="_struct_bparticle">Bparticle</link> ** partlist, <link linkend="_struct_bparticle">Bparticle</link> * part)</computeroutput></para><para>

<para>Adds one particle onto a list of particle parameters. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**partlist</entry>
                                <entry>
<para>destination particle list. </para>
</entry>
                            </row>
                            <row>
                                <entry>*part</entry>
                                <entry>
<para>particle. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bparticle* new particle. </para>
</formalpara>
</para>
<para>
Definition at line 1409 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a71aa16a9928deabf084c63c2a096b4bd"/>    <section>
    <title>particle_copy()<computeroutput>[2/2]</computeroutput></title>
<indexterm><primary>particle_copy</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>particle_copy</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bparticle">Bparticle</link>* particle_copy (<link linkend="_struct_bparticle">Bparticle</link> * partlist)</computeroutput></para><para>

<para>Copies a list of particle parameters to a new list. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*partlist</entry>
                                <entry>
<para>source particle list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bparticle* new list. </para>
</formalpara>
</para>
<para>
Definition at line 1437 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a10778be3402dbb9922caded8fe0affd3"/>    <section>
    <title>particle_count()</title>
<indexterm><primary>particle_count</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>particle_count</secondary></indexterm>
<para><computeroutput>long particle_count (<link linkend="_struct_bparticle">Bparticle</link> * part)</computeroutput></para><para>

<para>Counts the number of particles in a linked list. </para>
</para>

<para><literallayout><computeroutput>The function counts particles in the list from the given pointer,
and does not count particles prior to this one.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*part</entry>
                                <entry>
<para>pointer to any particle in the list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles. </para>
</formalpara>
</para>
<para>
Definition at line 1151 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aa63b3ac40737891c46a7b6b54a3d30f5"/>    <section>
    <title>particle_count_selected()</title>
<indexterm><primary>particle_count_selected</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>particle_count_selected</secondary></indexterm>
<para><computeroutput>long particle_count_selected (<link linkend="_struct_bparticle">Bparticle</link> * part)</computeroutput></para><para>

<para>Counts the number of particles in a linked list. </para>
</para>

<para><literallayout><computeroutput>The function counts particles in the list from the given pointer,
and does not count particles prior to this one.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*part</entry>
                                <entry>
<para>pointer to any particle in the list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 1169 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a2b69dff52f2fcb6b0e1e39694b2a3a96"/>    <section>
    <title>particle_kill()</title>
<indexterm><primary>particle_kill</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>particle_kill</secondary></indexterm>
<para><computeroutput>int particle_kill (<link linkend="_struct_bparticle">Bparticle</link> * part)</computeroutput></para><para>

<para>Frees a list of particles. </para>
</para>

<para><literallayout><computeroutput>Frees all the structures down the hierarchy.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*part</entry>
                                <entry>
<para>particle parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 1323 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a69f1ed7884ccf41af26203eeef36175d"/>    <section>
    <title>particle_update()</title>
<indexterm><primary>particle_update</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>particle_update</secondary></indexterm>
<para><computeroutput>int particle_update (<link linkend="_struct_bparticle">Bparticle</link> ** pnt_part, <link linkend="_struct_bparticle">Bparticle</link> * nu_part, int fom_index)</computeroutput></para><para>

<para>Updates an existing particle with new information. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**pnt_part</entry>
                                <entry>
<para>particle structure list to be updated. </para>
</entry>
                            </row>
                            <row>
                                <entry>*nu_part</entry>
                                <entry>
<para>particle structure list with new information. </para>
</entry>
                            </row>
                            <row>
                                <entry>fom_index</entry>
                                <entry>
<para>index of FOM to select on. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The new information is encoded as a particle structure.
All fields are updated if the new fields contain non-default data.
Defaults are defined here as zeroes.
The new particle structure is not modified.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 1817 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ab82fb8a5bc69b0b3c2aa2485b83e09f1"/>    <section>
    <title>project_add_origins_to_coords()</title>
<indexterm><primary>project_add_origins_to_coords</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_add_origins_to_coords</secondary></indexterm>
<para><computeroutput>int project_add_origins_to_coords (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Adds the particle origins to the micrograph coordinates. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The coordinates of particles from a micrograph and particle origins
in an image processing parameter structure are added. The old
micrograph coordinates are overwritten with the results.
Requirement: The box radius for picked particles must be specified.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3563 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a60d84303b4561d17729dabed733e9ca0"/>    <section>
    <title>project_apply_map_magnifications()</title>
<indexterm><primary>project_apply_map_magnifications</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_apply_map_magnifications</secondary></indexterm>
<para><computeroutput>int project_apply_map_magnifications (<link linkend="_struct_bproject">Bproject</link> * project, int mag_num, float * mag)</computeroutput></para><para>

<para>Change particle pixel sizes for particles based on map magnifications. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>mag_num</entry>
                                <entry>
<para>number of maps; </para>
</entry>
                            </row>
                            <row>
                                <entry>*mag</entry>
                                <entry>
<para>array of map magnifications. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3880 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ab65655cea9125617c8610d258ee0afe6"/>    <section>
    <title>project_count_fields()</title>
<indexterm><primary>project_count_fields</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_fields</secondary></indexterm>
<para><computeroutput>long project_count_fields (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the fields in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of fields in project. </para>
</formalpara>
</para>
<para>
Definition at line 731 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a3a5ca4e452b8145a7d849a30debda167"/>    <section>
    <title>project_count_mg_filament_nodes()</title>
<indexterm><primary>project_count_mg_filament_nodes</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_mg_filament_nodes</secondary></indexterm>
<para><computeroutput>long project_count_mg_filament_nodes (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts the number of filament nodes in a project. </para>
</para>

<para><literallayout><computeroutput>The function counts all the filament nodes in a project.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filament nodes. </para>
</formalpara>
</para>
<para>
Definition at line 983 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1afbe966628abe7c5c63aeb0abe104d2d5"/>    <section>
    <title>project_count_mg_filaments()</title>
<indexterm><primary>project_count_mg_filaments</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_mg_filaments</secondary></indexterm>
<para><computeroutput>long project_count_mg_filaments (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts the number of filaments in a project. </para>
</para>

<para><literallayout><computeroutput>The function counts all the filaments in a project.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filaments. </para>
</formalpara>
</para>
<para>
Definition at line 960 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aeeeacdda010c707cde1d2a8e8e14d626"/>    <section>
    <title>project_count_mg_groups()</title>
<indexterm><primary>project_count_mg_groups</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_mg_groups</secondary></indexterm>
<para><computeroutput>long project_count_mg_groups (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts the number of groups of particles in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of groups in project. </para>
</formalpara>
</para>
<para>
Definition at line 879 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ac78e776a3d10f232a11edd0adc416c07"/>    <section>
    <title>project_count_mg_part_selected()<computeroutput>[1/2]</computeroutput></title>
<indexterm><primary>project_count_mg_part_selected</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_mg_part_selected</secondary></indexterm>
<para><computeroutput>long project_count_mg_part_selected (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts the number of particles in a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. <literallayout><computeroutput>The function counts all the selected particles in a project.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 833 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a11b83d64b7e65cdd6c2e491a02382782"/>    <section>
    <title>project_count_mg_part_selected()<computeroutput>[2/2]</computeroutput></title>
<indexterm><primary>project_count_mg_part_selected</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_mg_part_selected</secondary></indexterm>
<para><computeroutput>long project_count_mg_part_selected (<link linkend="_struct_bproject">Bproject</link> * project, int num_select)</computeroutput></para><para>

<para>Counts the number of particles in a project. </para>
</para>

<para><literallayout><computeroutput>The function counts all the selected particles in a project.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project. </para>
</entry>
                            </row>
                            <row>
                                <entry>num_select</entry>
                                <entry>
<para>selection number. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 857 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1abdcbe054bc2eb7387070ef0204eae53b"/>    <section>
    <title>project_count_mg_particles()</title>
<indexterm><primary>project_count_mg_particles</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_mg_particles</secondary></indexterm>
<para><computeroutput>long project_count_mg_particles (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the particles in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles in project. </para>
</formalpara>
</para>
<para>
Definition at line 811 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1af94c66caf43ea55ce68b469b0c353205"/>    <section>
    <title>project_count_mg_selected()</title>
<indexterm><primary>project_count_mg_selected</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_mg_selected</secondary></indexterm>
<para><computeroutput>long project_count_mg_selected (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the selected micrographs in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of micrographs selected in project. </para>
</formalpara>
</para>
<para>
Definition at line 763 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ae7ec8c0272ecc20f2e00134bd115c6c6"/>    <section>
    <title>project_count_micrographs()</title>
<indexterm><primary>project_count_micrographs</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_micrographs</secondary></indexterm>
<para><computeroutput>long project_count_micrographs (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the micrographs in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of micrographs in project. </para>
</formalpara>
</para>
<para>
Definition at line 746 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ab6127567379d468759d5193c978d5112"/>    <section>
    <title>project_count_rec_filament_nodes()</title>
<indexterm><primary>project_count_rec_filament_nodes</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_rec_filament_nodes</secondary></indexterm>
<para><computeroutput>long project_count_rec_filament_nodes (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts the number of filaments in a project. </para>
</para>

<para><literallayout><computeroutput>The function counts all the filaments in a project.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filaments. </para>
</formalpara>
</para>
<para>
Definition at line 1029 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a022e277e7acd99366640c185961f033e"/>    <section>
    <title>project_count_rec_filaments()</title>
<indexterm><primary>project_count_rec_filaments</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_rec_filaments</secondary></indexterm>
<para><computeroutput>long project_count_rec_filaments (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts the number of filaments in a project. </para>
</para>

<para><literallayout><computeroutput>The function counts all the filaments in a project.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filaments. </para>
</formalpara>
</para>
<para>
Definition at line 1008 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a6c1fe6a0c2a9e6634097fddd73d2096b"/>    <section>
    <title>project_count_rec_groups()</title>
<indexterm><primary>project_count_rec_groups</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_rec_groups</secondary></indexterm>
<para><computeroutput>long project_count_rec_groups (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the particles in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles in project. </para>
</formalpara>
</para>
<para>
Definition at line 937 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a9ed00f7aa3050401f5022b3092d4c01d"/>    <section>
    <title>project_count_rec_part_selected()</title>
<indexterm><primary>project_count_rec_part_selected</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_rec_part_selected</secondary></indexterm>
<para><computeroutput>long project_count_rec_part_selected (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the particles in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles in project. </para>
</formalpara>
</para>
<para>
Definition at line 919 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a377da990cda46b5c6d05c59dec0b21e9"/>    <section>
    <title>project_count_rec_particles()</title>
<indexterm><primary>project_count_rec_particles</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_rec_particles</secondary></indexterm>
<para><computeroutput>long project_count_rec_particles (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the particles in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles in project. </para>
</formalpara>
</para>
<para>
Definition at line 902 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a219067937f105e127cdeae560d170a28"/>    <section>
    <title>project_count_rec_selected()</title>
<indexterm><primary>project_count_rec_selected</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_rec_selected</secondary></indexterm>
<para><computeroutput>long project_count_rec_selected (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the selected reconstructions in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of reconstructions selected in project. </para>
</formalpara>
</para>
<para>
Definition at line 795 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a2b8f534ce8411fb9faae15b227c3cc0c"/>    <section>
    <title>project_count_reconstructions()</title>
<indexterm><primary>project_count_reconstructions</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_count_reconstructions</secondary></indexterm>
<para><computeroutput>long project_count_reconstructions (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Counts all the reconstructions in the project structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of reconstructions in project. </para>
</formalpara>
</para>
<para>
Definition at line 780 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ad1f222bc7be0953672c332c6e46cdd38"/>    <section>
    <title>project_create()</title>
<indexterm><primary>project_create</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_create</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bproject">Bproject</link>* project_create (int nmg, int nrec)</computeroutput></para><para>

<para>Creates a micrograph processing project parameter structure. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>nmg</entry>
                                <entry>
<para>number of micrograph structures. </para>
</entry>
                            </row>
                            <row>
                                <entry>nrec</entry>
                                <entry>
<para>number of reconstruction structures. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bproject* project parameter structure. <literallayout><computeroutput>The function allocates memory for the project structure, a field-of-view structure,
and the requested number of micrographs and reconstructions.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 47 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a996afef91cc83786c8b920577182a74f"/>    <section>
    <title>project_divide()</title>
<indexterm><primary>project_divide</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_divide</secondary></indexterm>
<para><computeroutput>long project_divide (<link linkend="_struct_bproject">Bproject</link> * project, long n)</computeroutput></para><para>

<para>Divides a project into a number of micrograph subsets. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>n</entry>
                                <entry>
<para>number of subsets. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of new projects created. <literallayout><computeroutput>Only selected micrographs are considered in the subdivision.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 1962 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a8cb6072793702839f396256ddc2cb44c"/>    <section>
    <title>project_dump()</title>
<indexterm><primary>project_dump</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_dump</secondary></indexterm>
<para><computeroutput>long project_dump (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; filename)</computeroutput></para><para>

<para>Dumps particle info in the project hierarchy. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;filename</entry>
                                <entry>
<para>output file name. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles dumped. </para>
</formalpara>
</para>
<para>
Definition at line 2974 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a25d3404c481c541d872a3b413356d35b"/>    <section>
    <title>project_equal_mg_part_files()</title>
<indexterm><primary>project_equal_mg_part_files</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_equal_mg_part_files</secondary></indexterm>
<para><computeroutput>int project_equal_mg_part_files (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Sets micrograph and particle files to be the same. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>If the micrograph file name exists, that is used, otherwise the
particle file name is used.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 87 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a876f72881c0e2829e517aaf0df8acdea"/>    <section>
    <title>project_flip_origins()</title>
<indexterm><primary>project_flip_origins</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_flip_origins</secondary></indexterm>
<para><computeroutput>int project_flip_origins (<link linkend="_struct_bproject">Bproject</link> * project, int flip)</computeroutput></para><para>

<para>Flip origin coordinates. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>flip</entry>
                                <entry>
<para>axes to flip. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The particle origins are reversed.
The specification of axes to flip is embedded in the flip number:
    first bit  - x
    second bit - y
    third bit  - z
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3605 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a25b137bf513c310fe45bdcc537ccd6fa"/>    <section>
    <title>project_init()</title>
<indexterm><primary>project_init</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_init</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bproject">Bproject</link>* project_init ( )</computeroutput></para><para>

<para>Initializes a micrograph processing project parameter structure. </para>
</para>

<para><formalpara><title>Returns: </title>

<para>Bproject* project parameter structure. <literallayout><computeroutput>The function allocates memory for the project structure.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 29 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a2ecd27087626538aead67b4680eabedd"/>    <section>
    <title>project_kill()</title>
<indexterm><primary>project_kill</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_kill</secondary></indexterm>
<para><computeroutput>int project_kill (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Frees a whole project. </para>
</para>

<para><literallayout><computeroutput>Frees all the structures down the hierarchy.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 1224 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a5acf16ba92a77c0e854c480d19db058f"/>    <section>
    <title>project_maximum_selection()</title>
<indexterm><primary>project_maximum_selection</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_maximum_selection</secondary></indexterm>
<para><computeroutput>long project_maximum_selection (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Finds the maximum slection number for a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long maximum selection number. </para>
</formalpara>
</para>
<para>
Definition at line 2364 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1af723b0c3832b459eabeb7e5d1eaafc98"/>    <section>
    <title>project_merge_part_parameters()</title>
<indexterm><primary>project_merge_part_parameters</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_merge_part_parameters</secondary></indexterm>
<para><computeroutput>int project_merge_part_parameters (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_struct_bproject">Bproject</link> * partproject)</computeroutput></para><para>

<para>Puts particle parameters from one project into another. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure with all parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*partproject</entry>
                                <entry>
<para>project parameter structure with particle parameters. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 1876 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a7d8e3d54d7cdbdc3bc6fa625cefd5aae"/>    <section>
    <title>project_mg_particle_array()</title>
<indexterm><primary>project_mg_particle_array</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_mg_particle_array</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bparticle">Bparticle</link>** project_mg_particle_array (<link linkend="_struct_bproject">Bproject</link> * project, int part_select, long &amp; npart)</computeroutput></para><para>

<para>Sets up an array of selected particle pointers. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>part_select</entry>
                                <entry>
<para>particle selection (-1 if none). </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;npart</entry>
                                <entry>
<para>array length (modified). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bparticle** particle pointer array. <literallayout><computeroutput>FOM&apos;s of non-selected particles are zeroed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 2029 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ac7775046402a74604b11c5b5daa3b917"/>    <section>
    <title>project_micrograph_array()</title>
<indexterm><primary>project_micrograph_array</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_micrograph_array</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmicrograph">Bmicrograph</link>** project_micrograph_array (<link linkend="_struct_bproject">Bproject</link> * project, long &amp; nmg)</computeroutput></para><para>

<para>Sets up an array of selected micrograph pointers. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;nmg</entry>
                                <entry>
<para>array length (modified). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmicrograph** micrograph pointer array. <literallayout><computeroutput>FOM&apos;s of non-selected micrographs are zeroed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 2001 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1afd534ce20c532c899a3de0a0d9272e44"/>    <section>
    <title>project_rec_particle_array()</title>
<indexterm><primary>project_rec_particle_array</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_rec_particle_array</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bparticle">Bparticle</link>** project_rec_particle_array (<link linkend="_struct_bproject">Bproject</link> * project, int part_select, long &amp; npart)</computeroutput></para><para>

<para>Sets up an array of selected particle pointers. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>part_select</entry>
                                <entry>
<para>particle selection (-1 if none). </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;npart</entry>
                                <entry>
<para>array length (modified). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bparticle** particle pointer array. <literallayout><computeroutput>FOM&apos;s of non-selected particles are zeroed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 2071 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a5837277b95ef6a1dc1f39b98b9d759a3"/>    <section>
    <title>project_renumber_particles()</title>
<indexterm><primary>project_renumber_particles</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_renumber_particles</secondary></indexterm>
<para><computeroutput>long project_renumber_particles (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Renumbers particles. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long total number of particles. <literallayout><computeroutput>For each micrograph the particles are renumbered starting from 1.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3656 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a3075fd6be8909579fc652695ab97dd85"/>    <section>
    <title>project_revert_filenames()</title>
<indexterm><primary>project_revert_filenames</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_revert_filenames</secondary></indexterm>
<para><computeroutput>int project_revert_filenames (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_struct_bproject">Bproject</link> * project_old, int flag)</computeroutput></para><para>

<para>Reverts file names to what it was in an old project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>*project_old</entry>
                                <entry>
<para>project parameter structure with old file names. </para>
</entry>
                            </row>
                            <row>
                                <entry>flag</entry>
                                <entry>
<para>1=mg, 2=ps, 4=rec, 8=part, 16=frames. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 2135 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ab3dd826e459645bbab9daaa7147909cc"/>    <section>
    <title>project_rotate_particle_views()</title>
<indexterm><primary>project_rotate_particle_views</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_rotate_particle_views</secondary></indexterm>
<para><computeroutput>int project_rotate_particle_views (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_view">View</link> view)</computeroutput></para><para>

<para>Rotates particle views with respect to a reference view. </para>
</para>

<para><formalpara><title>Author: </title>

<para>Eduardo Sanz-Garcia </para>
</formalpara>

                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>view</entry>
                                <entry>
<para>reference view. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3838 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a52af723733b19a7fde714bbdad1d2dbf"/>    <section>
    <title>project_select_field()</title>
<indexterm><primary>project_select_field</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_select_field</secondary></indexterm>
<para><computeroutput>int project_select_field (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; field_id)</computeroutput></para><para>

<para>Selects a field from the project and deletes the rest. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;field_id</entry>
                                <entry>
<para>field to select. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3074 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ae686468b6ee193bd928049b85425e476"/>    <section>
    <title>project_select_micrograph()</title>
<indexterm><primary>project_select_micrograph</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_select_micrograph</secondary></indexterm>
<para><computeroutput>int project_select_micrograph (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; mg_id)</computeroutput></para><para>

<para>Selects a micrograph from the project and deletes the rest. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;mg_id</entry>
                                <entry>
<para>micrograph to select. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3106 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a0066207317aba6c6a3b3319166ba37d9"/>    <section>
    <title>project_set_dose()</title>
<indexterm><primary>project_set_dose</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_dose</secondary></indexterm>
<para><computeroutput>int project_set_dose (<link linkend="_struct_bproject">Bproject</link> * project, double dose)</computeroutput></para><para>

<para>Sets the electron dose of all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>dose</entry>
                                <entry>
<para>electron dose (electrons/angstrom). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3508 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ac0eab102922702421184be84cd9790e0"/>    <section>
    <title>project_set_field_id()</title>
<indexterm><primary>project_set_field_id</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_field_id</secondary></indexterm>
<para><computeroutput>int project_set_field_id (<link linkend="_struct_bproject">Bproject</link> * project, int nseries, <link linkend="_class_bstring">Bstring</link> &amp; field_id)</computeroutput></para><para>

<para>Sets the field id&apos;s according to a regular series. </para>
</para>

<para><literallayout><computeroutput>The micrograph data blocks must be arranged in a regular order with
every nseries micrographs from the same field-of-view.
The field id&apos;s are taken from the first micrograph id in a series.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>nseries</entry>
                                <entry>
<para>number of micrographs per field-of-view. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;field_id</entry>
                                <entry>
<para>a user-specified field ID. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 2203 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a12cba281bae1f9834833568e64961c1d"/>    <section>
    <title>project_set_filament_path()</title>
<indexterm><primary>project_set_filament_path</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_filament_path</secondary></indexterm>
<para><computeroutput>int project_set_filament_path (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; path)</computeroutput></para><para>

<para>Sets the path to filament files for all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;path</entry>
                                <entry>
<para>path to filament files. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>If the requested path is &quot;.&quot; or &quot;./&quot;, the path is completely removed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3304 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ad65009a72674549e06c890235f29ffee"/>    <section>
    <title>project_set_frame_path()</title>
<indexterm><primary>project_set_frame_path</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_frame_path</secondary></indexterm>
<para><computeroutput>int project_set_frame_path (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; path)</computeroutput></para><para>

<para>Sets the path to micrograph frames files for all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;path</entry>
                                <entry>
<para>path to micrograph frames files. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>If the requested path is &quot;.&quot; or &quot;./&quot;, the path is completely removed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3196 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a22d446c5ff1b3fe7e1de4b7f19adb920"/>    <section>
    <title>project_set_magnification()</title>
<indexterm><primary>project_set_magnification</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_magnification</secondary></indexterm>
<para><computeroutput>int project_set_magnification (<link linkend="_struct_bproject">Bproject</link> * project, double mag)</computeroutput></para><para>

<para>Sets the magnification for all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>mag</entry>
                                <entry>
<para>magnification. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3355 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aa12f3b48677510ae94a0b068c6bd377e"/>    <section>
    <title>project_set_micrograph_origins()</title>
<indexterm><primary>project_set_micrograph_origins</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_micrograph_origins</secondary></indexterm>
<para><computeroutput>int project_set_micrograph_origins (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_vector3">Vector3</link>&lt; float &gt; origin)</computeroutput></para><para>

<para>Sets micrograph origins to the given origin. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>origin</entry>
                                <entry>
<para>particle origin. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>For each micrograph the micrograph origin is set to the given origin.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3531 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aee29d487e2a375832b196ac46b0694f4"/>    <section>
    <title>project_set_micrograph_path()</title>
<indexterm><primary>project_set_micrograph_path</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_micrograph_path</secondary></indexterm>
<para><computeroutput>int project_set_micrograph_path (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; path)</computeroutput></para><para>

<para>Sets the path to micrograph files for all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;path</entry>
                                <entry>
<para>path to micrograph files. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>If the requested path is &quot;.&quot; or &quot;./&quot;, the path is completely removed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3167 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a2d742963893ed82ccc163ff4a0bb33f9"/>    <section>
    <title>project_set_part_links()</title>
<indexterm><primary>project_set_part_links</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_part_links</secondary></indexterm>
<para><computeroutput>long project_set_part_links (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Sets the links from particles back to the micrographs and reconstructions. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles. </para>
</formalpara>
</para>
<para>
Definition at line 1906 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1adac6093c933222b384c57b1c3ad69b77"/>    <section>
    <title>project_set_particle_asu_views()<computeroutput>[1/2]</computeroutput></title>
<indexterm><primary>project_set_particle_asu_views</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_particle_asu_views</secondary></indexterm>
<para><computeroutput>int project_set_particle_asu_views (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; symmetry_asu)</computeroutput></para><para>

<para>Sets particle views within the asymmetric unit. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;symmetry_asu</entry>
                                <entry>
<para>point group string. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>For each micrograph or reconstruction the particle view is set to within the asymmetric unit.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3792 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a153585f20c4d97a7e9285f6857e3cf7a"/>    <section>
    <title>project_set_particle_asu_views()<computeroutput>[2/2]</computeroutput></title>
<indexterm><primary>project_set_particle_asu_views</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_particle_asu_views</secondary></indexterm>
<para><computeroutput>int project_set_particle_asu_views (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_struct_bsymmetry">Bsymmetry</link> * sym)</computeroutput></para><para>
Definition at line 3805 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ac3e8f5e1616cc4e958cc5357eb3ab7b6"/>    <section>
    <title>project_set_particle_box_size()<computeroutput>[1/2]</computeroutput></title>
<indexterm><primary>project_set_particle_box_size</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_particle_box_size</secondary></indexterm>
<para><computeroutput>int project_set_particle_box_size (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size)</computeroutput></para><para>

<para>Sets particle box size to the given value. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>box_size</entry>
                                <entry>
<para>particle box size. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>For each micrograph or reconstruction the particle box size is set 
to the given radius and the particle origins are adjusted as well.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3693 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aa0536e68060c07b48f4f4f9ca353743d"/>    <section>
    <title>project_set_particle_box_size()<computeroutput>[2/2]</computeroutput></title>
<indexterm><primary>project_set_particle_box_size</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_particle_box_size</secondary></indexterm>
<para><computeroutput>int project_set_particle_box_size (<link linkend="_struct_bproject">Bproject</link> * project, long box_size)</computeroutput></para><para>

<para>Sets particle box size to the given value. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>box_size</entry>
                                <entry>
<para>particle box size. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>For each micrograph or reconstruction the particle box size is set 
to the given radius and the particle origins are adjusted as well.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3738 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a6b50ea2d44fbded720f3b094e84a908d"/>    <section>
    <title>project_set_particle_origins()</title>
<indexterm><primary>project_set_particle_origins</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_particle_origins</secondary></indexterm>
<para><computeroutput>int project_set_particle_origins (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; origin)</computeroutput></para><para>

<para>Sets particle origins to given values. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>origin</entry>
                                <entry>
<para>particle origin. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>For each micrograph or reconstruction the particle origin is set to the given origin.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3757 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a41d210cceebbdd0aa97df99a64e6964d"/>    <section>
    <title>project_set_particle_path()</title>
<indexterm><primary>project_set_particle_path</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_particle_path</secondary></indexterm>
<para><computeroutput>int project_set_particle_path (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; path)</computeroutput></para><para>

<para>Sets the path to particle files for all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;path</entry>
                                <entry>
<para>path to particle files. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>If the requested path is &quot;.&quot; or &quot;./&quot;, the path is completely removed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3254 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a29a9ff01ed19c0fd41edeb3182b4d28c"/>    <section>
    <title>project_set_pixel_size()</title>
<indexterm><primary>project_set_pixel_size</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_pixel_size</secondary></indexterm>
<para><computeroutput>int project_set_pixel_size (<link linkend="_struct_bproject">Bproject</link> * project, double pixel_size)</computeroutput></para><para>

<para>Sets the pixel size for all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>pixel_size</entry>
                                <entry>
<para>pixel size. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3398 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1afd06e7a40a415af7fa3a7de73e92a96e"/>    <section>
    <title>project_set_powerspectrum_path()</title>
<indexterm><primary>project_set_powerspectrum_path</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_powerspectrum_path</secondary></indexterm>
<para><computeroutput>int project_set_powerspectrum_path (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; path)</computeroutput></para><para>

<para>Sets the path to powerspectrum files for all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;path</entry>
                                <entry>
<para>path to powerspectrum files. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>If the requested path is &quot;.&quot; or &quot;./&quot;, the path is completely removed.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 3225 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1acacec50ef8e493074e15030974084eb1"/>    <section>
    <title>project_set_scan_sampling()</title>
<indexterm><primary>project_set_scan_sampling</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_scan_sampling</secondary></indexterm>
<para><computeroutput>int project_set_scan_sampling (<link linkend="_struct_bproject">Bproject</link> * project, double sampling)</computeroutput></para><para>

<para>Sets the scan sampling for all the micrographs. </para>
</para>

<para><literallayout><computeroutput>Sampling is isotropic.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>sampling</entry>
                                <entry>
<para>sampling. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3378 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ad250e318df7f1ff7bc6444fdb3d0d42b"/>    <section>
    <title>project_set_tilt()</title>
<indexterm><primary>project_set_tilt</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_set_tilt</secondary></indexterm>
<para><computeroutput>int project_set_tilt (<link linkend="_struct_bproject">Bproject</link> * project, double tilt_axis, double tilt_angle)</computeroutput></para><para>

<para>Sets the tilt parameters for all the micrographs. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>tilt_axis</entry>
                                <entry>
<para>micrograph tilt axis angle. </para>
</entry>
                            </row>
                            <row>
                                <entry>tilt_angle</entry>
                                <entry>
<para>micrograph tilt angle. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3427 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a52ad936e0c81e64a41492fb9bc7caba4"/>    <section>
    <title>project_show_class_averages()</title>
<indexterm><primary>project_show_class_averages</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_show_class_averages</secondary></indexterm>
<para><computeroutput>long project_show_class_averages (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Shows the class averages in a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of class averages. </para>
</formalpara>
</para>
<para>
Definition at line 2645 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1adfcf6d630e0006ef9e04261cadd40176"/>    <section>
    <title>project_show_fom_histogram()</title>
<indexterm><primary>project_show_fom_histogram</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_show_fom_histogram</secondary></indexterm>
<para><computeroutput>long project_show_fom_histogram (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Shows a histogram of the FOM values. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 2831 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ac1a5ab271d20f9d10e6249f2a4809222"/>    <section>
    <title>project_show_hierarchy()</title>
<indexterm><primary>project_show_hierarchy</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_show_hierarchy</secondary></indexterm>
<para><computeroutput>long project_show_hierarchy (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Shows the project hierarchy. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 2253 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1ad138583472ffebcbac75c249b76682ad"/>    <section>
    <title>project_show_mag_histogram()</title>
<indexterm><primary>project_show_mag_histogram</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_show_mag_histogram</secondary></indexterm>
<para><computeroutput>long project_show_mag_histogram (<link linkend="_struct_bproject">Bproject</link> * project, int bins, double increment)</computeroutput></para><para>

<para>Shows the histogram for magnification values for selected particles. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>bins</entry>
                                <entry>
<para>number of bins. </para>
</entry>
                            </row>
                            <row>
                                <entry>increment</entry>
                                <entry>
<para>increment between bins. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 2928 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a587ed4a57b89d23febb068699287bbe8"/>    <section>
    <title>project_show_parameter()</title>
<indexterm><primary>project_show_parameter</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_show_parameter</secondary></indexterm>
<para><computeroutput>long project_show_parameter (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bstring">Bstring</link> &amp; tag)</computeroutput></para><para>

<para>Shows the particle parameter indicated by the tag in a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;tag</entry>
                                <entry>
<para>parameter tag. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 2783 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a97fc171f988871c9c8fc370be3f1d37b"/>    <section>
    <title>project_show_selected()</title>
<indexterm><primary>project_show_selected</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_show_selected</secondary></indexterm>
<para><computeroutput>long project_show_selected (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Shows the selected particles in a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 2446 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1acd49f1260bf7041db25dd602f7ad834b"/>    <section>
    <title>project_show_selected_parameters()</title>
<indexterm><primary>project_show_selected_parameters</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_show_selected_parameters</secondary></indexterm>
<para><computeroutput>long project_show_selected_parameters (<link linkend="_struct_bproject">Bproject</link> * project, int show)</computeroutput></para><para>

<para>Shows the selected particle parameters in a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>show</entry>
                                <entry>
<para>selection number to show. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 2674 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aeb9c4608e15f4cf4f6908a814e24e0d8"/>    <section>
    <title>project_show_selection_numbers()</title>
<indexterm><primary>project_show_selection_numbers</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_show_selection_numbers</secondary></indexterm>
<para><computeroutput>long project_show_selection_numbers (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Shows the selection numbers for the particles in a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles selected. </para>
</formalpara>
</para>
<para>
Definition at line 2391 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1aeababf316e7b9e5c96b8ce4b26bfdd43"/>    <section>
    <title>project_sort_by_tilt()</title>
<indexterm><primary>project_sort_by_tilt</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_sort_by_tilt</secondary></indexterm>
<para><computeroutput>int project_sort_by_tilt (<link linkend="_struct_bproject">Bproject</link> * project)</computeroutput></para><para>

<para>Sorts the micrographs in each field by tilt angle. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 3490 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1af3004e278b3e2e1d6a73d9ad14a91c4c"/>    <section>
    <title>project_update()</title>
<indexterm><primary>project_update</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>project_update</secondary></indexterm>
<para><computeroutput>int project_update (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_struct_bproject">Bproject</link> * proj_new, int fom_index)</computeroutput></para><para>

<para>Updates an existing project with new information. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure to be updated. </para>
</entry>
                            </row>
                            <row>
                                <entry>*proj_new</entry>
                                <entry>
<para>project parameter structure with new information. </para>
</entry>
                            </row>
                            <row>
                                <entry>fom_index</entry>
                                <entry>
<para>index of FOM to select on. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0.</para>
</formalpara>
<literallayout><computeroutput>The new information is encoded as a project hierarchy.
The original project hierarchy is searched for the micrograph ID
tags that correspond to the original project hierarchy and those
micrograph parameters are updated. Because the micrograph ID tags
should be unique in themselves, the field ID tags are ignored and
the two project hierarchies may have different field designations.
If a micrograph ID from the new project hierarchy is not found in
the original project hierarchy, it is added.
The new project hierarchy is not modified.
</computeroutput></literallayout> </para>
<para>
Definition at line 1601 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1af15de191006cbacd08c1de606733be2c"/>    <section>
    <title>rec_part_links()</title>
<indexterm><primary>rec_part_links</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>rec_part_links</secondary></indexterm>
<para><computeroutput>int rec_part_links (<link linkend="_struct_breconstruction">Breconstruction</link> * rec)</computeroutput></para><para>

<para>Sets the links from particles to reconstructions. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*rec</entry>
                                <entry>
<para>pointer to reconstruction. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 571 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a019bf8ef2ecc6aadc2089aec61cf5cdb"/>    <section>
    <title>reconstruction_add()</title>
<indexterm><primary>reconstruction_add</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>reconstruction_add</secondary></indexterm>
<para><computeroutput><link linkend="_struct_breconstruction">Breconstruction</link>* reconstruction_add (<link linkend="_struct_breconstruction">Breconstruction</link> ** rec, <link linkend="_class_bstring">Bstring</link> &amp; rec_id)</computeroutput></para><para>

<para>Adds a reconstruction parameter structure to a linked list. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>**rec</entry>
                                <entry>
<para>pointer to any reconstruction in the list. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;rec_id</entry>
                                <entry>
<para>reconstruction identifier. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Breconstruction* new reconstruction. <literallayout><computeroutput>The function allocates memory for a new micrograph structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 704 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a35fd2be48fa9fd8c2d4f52121955f491"/>    <section>
    <title>reconstruction_kill()</title>
<indexterm><primary>reconstruction_kill</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>reconstruction_kill</secondary></indexterm>
<para><computeroutput>int reconstruction_kill (<link linkend="_struct_breconstruction">Breconstruction</link> * rec)</computeroutput></para><para>

<para>Frees a whole reconstruction parameter structure. </para>
</para>

<para><literallayout><computeroutput>Frees all the structures down the hierarchy.
</computeroutput></literallayout></para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*rec</entry>
                                <entry>
<para>reconstruction parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 1377 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a118c1837845abfc4fd1a7cccea4ea0ea"/>    <section>
    <title>reconstruction_set_part_links()</title>
<indexterm><primary>reconstruction_set_part_links</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>reconstruction_set_part_links</secondary></indexterm>
<para><computeroutput>long reconstruction_set_part_links (<link linkend="_struct_breconstruction">Breconstruction</link> * rec)</computeroutput></para><para>

<para>Sets the links from particles back to the reconstruction. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*rec</entry>
                                <entry>
<para>reconstruction parameter structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles. </para>
</formalpara>
</para>
<para>
Definition at line 1943 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a8b0300342a1926860c5f00aaceaae329"/>    <section>
    <title>reconstruction_update()</title>
<indexterm><primary>reconstruction_update</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>reconstruction_update</secondary></indexterm>
<para><computeroutput>int reconstruction_update (<link linkend="_struct_breconstruction">Breconstruction</link> * rec, <link linkend="_struct_breconstruction">Breconstruction</link> * nu_rec, int fom_index, int flags)</computeroutput></para><para>

<para>Updates an existing reconstruction with new information. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*rec</entry>
                                <entry>
<para>reconstruction structure to be updated. </para>
</entry>
                            </row>
                            <row>
                                <entry>*nu_rec</entry>
                                <entry>
<para>reconstruction structure with new information. </para>
</entry>
                            </row>
                            <row>
                                <entry>fom_index</entry>
                                <entry>
<para>index of FOM to select on. </para>
</entry>
                            </row>
                            <row>
                                <entry>flags</entry>
                                <entry>
<para>flags indicating which parts to update. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The new information is encoded as a reconstruction structure.
The update is only done if the FOM of the new reconstruction is better.
All fields are updated if the new fields contain non-default data.
Defaults are defined here as zero-length strings or zeroes.
The particles in the original reconstruction are matched by ID with 
those in the new reconstruction and updated, with any new particles 
added from the new reconstruction.
The bad area and marker coordinates are replaced if they exist 
in the new structure.
The new reconstruction structure is not modified, except for deletion 
of bad areas and markers.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 1772 of file mg_processing.cpp.</para>
    </section><anchor xml:id="_mg__processing_8h_1a48e44d868399e6ea7a48bd1143c40c87"/>    <section>
    <title>views_from_project()</title>
<indexterm><primary>views_from_project</primary><secondary>mg_processing.h</secondary></indexterm>
<indexterm><primary>mg_processing.h</primary><secondary>views_from_project</secondary></indexterm>
<para><computeroutput><link linkend="_class_view">View</link>* views_from_project (<link linkend="_struct_bproject">Bproject</link> * project, int selection)</computeroutput></para><para>

<para>Retrieves the particle views from a project. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*project</entry>
                                <entry>
<para>project parameter structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>selection</entry>
                                <entry>
<para>selection number (-1 selects positives, 0 selects all). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>View* linked list of views. </para>
</formalpara>
</para>
<para>
Definition at line 3925 of file mg_processing.cpp.</para>
</section>
</section>
</section>
