<?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="_bico_8cpp">
<title>/Users/bernard/b20/bsoft/src/bico.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/bico.cpp</primary></indexterm>
<para>

<para>Program to analyze icosahedral subtomograms. </para>
 
</para>
<programlisting>#include &quot;mg_processing.h&quot;
#include &quot;mg_reconstruct.h&quot;
#include &quot;rwmg.h&quot;
#include &quot;rwimg.h&quot;
#include &quot;rwsymop.h&quot;
#include &quot;symmetry.h&quot;
#include &quot;linked_list.h&quot;
#include &quot;utilities.h&quot;
#include &quot;options.h&quot;
#include &quot;timer.h&quot;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_bico_8cpp_1a0c4a59e86ee58e4d4b2000cbba30f1a5">project_ico_worst_vertex</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bimage">Bimage</link> *pref, <link linkend="_class_bimage">Bimage</link> *pmask, <link linkend="_class_bimage">Bimage</link> *pfsmask, double hires, double lores, double maxres)</para>

<para>Determines the special vertex for icosahedral symmetry and returns two maps. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_bico_8cpp_1a348e4c60dafc8a27f8128fa16b7ce20d">project_ico_opposite_vertex</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bimage">Bimage</link> *pmask, <link linkend="_class_bimage">Bimage</link> *pfsmask, double hires, double lores, double maxres)</para>

<para>Determines the special vertex for icosahedral symmetry and returns two maps. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_bico_8cpp_1a67ea0c855903cc381bedf009b8d20ee2">project_ico_best_c5</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_class_bimage">Bimage</link> *pref, <link linkend="_class_bimage">Bimage</link> *pmask, <link linkend="_class_bimage">Bimage</link> *pfsmask, double hires, double lores, double maxres)</para>

<para>Determines the best 5-fold orientation of the vertex wrt a reference. </para>
</listitem>
            <listitem><para>long <link linkend="_bico_8cpp_1aee13a3e857cc2d5cb8ecbea2e9e2c9a9">project_assign_special_vertex_orientations</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, <link linkend="_struct_bproject">Bproject</link> *project_specvert)</para>
</listitem>
            <listitem><para>int <link linkend="_bico_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627">main</link> (int argc, char **argv)</para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_bico_8cpp_1a04c2474d6defbcc34041672fba8c9823">img_read_orient_mask</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_class_bimage">Bimage</link> *pmask, <link linkend="_class_view">View</link> view)</para>
</listitem>
            <listitem><para>double <link linkend="_bico_8cpp_1a97de0d715f0f4ff08c3d9a978b074ea2">img_cc</link> (<link linkend="_class_bimage">Bimage</link> *p1, <link linkend="_class_bimage">Bimage</link> *p2, <link linkend="_class_bimage">Bimage</link> *pfsmask, double hires, double lores)</para>
</listitem>
            <listitem><para>long <link linkend="_bico_8cpp_1ae8b03a4dbc616c4d2baf9a701a107110">particle_worst_vertex</link> (<link linkend="_struct_bparticle">Bparticle</link> *vert, <link linkend="_class_bimage">Bimage</link> *pref, <link linkend="_class_bimage">Bimage</link> *pmask, <link linkend="_class_bimage">Bimage</link> *pfsmask, double hires, double lores)</para>
</listitem>
            <listitem><para>long <link linkend="_bico_8cpp_1af1e43f88fc1ccb00d831750a24c4b0d9">particle_cc_opposite_vertices</link> (<link linkend="_struct_bparticle">Bparticle</link> *vert, <link linkend="_class_bimage">Bimage</link> *pmask, <link linkend="_class_bimage">Bimage</link> *pfsmask, double hires, double lores)</para>
</listitem>
            <listitem><para>long <link linkend="_bico_8cpp_1a25c3c87aac2af79bf7725b192f22127d">particle_worst_opposite_vertex</link> (<link linkend="_struct_bparticle">Bparticle</link> *vert, <link linkend="_class_bimage">Bimage</link> *pref, <link linkend="_class_bimage">Bimage</link> *pmask, <link linkend="_class_bimage">Bimage</link> *pfsmask, double hires, double lores)</para>
</listitem>
            <listitem><para>long <link linkend="_bico_8cpp_1aa0416428f9b0281e97318a2c4e2e3091">particle_best_c5</link> (<link linkend="_struct_bparticle">Bparticle</link> *part, <link linkend="_class_bimage">Bimage</link> *pref, <link linkend="_class_bimage">Bimage</link> *pmask, <link linkend="_class_bimage">Bimage</link> *pfsmask, double hires, double lores)</para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_bico_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
            <listitem><para><link linkend="_fft_8h_1a61d23c567e69684715ea52482137a5e6">fft_plan</link> <link linkend="_bico_8cpp_1a6ecaa8728bab23c3a7d96fe0cadc75f2">planf</link></para>
</listitem>
            <listitem><para><link linkend="_fft_8h_1a61d23c567e69684715ea52482137a5e6">fft_plan</link> <link linkend="_bico_8cpp_1a9ec8849996c5e210d7b7e8e05b98639d">planb</link></para>
</listitem>
            <listitem><para>const char * <link linkend="_bico_8cpp_1a4de0ad4c7190962494815c0fa7f948df">use</link> []</para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Program to analyze icosahedral subtomograms. </para>

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

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

<para>Created: 20180427 </para>

<para>Modified: 20180917 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_bico_8cpp_1a97de0d715f0f4ff08c3d9a978b074ea2"/>    <section>
    <title>img_cc()</title>
<indexterm><primary>img_cc</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>img_cc</secondary></indexterm>
<para><computeroutput>double img_cc (<link linkend="_class_bimage">Bimage</link> * p1, <link linkend="_class_bimage">Bimage</link> * p2, <link linkend="_class_bimage">Bimage</link> * pfsmask, double hires, double lores)</computeroutput></para><para>
Definition at line 216 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a04c2474d6defbcc34041672fba8c9823"/>    <section>
    <title>img_read_orient_mask()</title>
<indexterm><primary>img_read_orient_mask</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>img_read_orient_mask</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link>* img_read_orient_mask (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_class_bimage">Bimage</link> * pmask, <link linkend="_class_view">View</link> view)</computeroutput></para><para>
Definition at line 198 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627"/>    <section>
    <title>main()</title>
<indexterm><primary>main</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>main</secondary></indexterm>
<para><computeroutput>int main (int argc, char ** argv)</computeroutput></para><para>
Definition at line 62 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1aa0416428f9b0281e97318a2c4e2e3091"/>    <section>
    <title>particle_best_c5()</title>
<indexterm><primary>particle_best_c5</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>particle_best_c5</secondary></indexterm>
<para><computeroutput>long particle_best_c5 (<link linkend="_struct_bparticle">Bparticle</link> * part, <link linkend="_class_bimage">Bimage</link> * pref, <link linkend="_class_bimage">Bimage</link> * pmask, <link linkend="_class_bimage">Bimage</link> * pfsmask, double hires, double lores)</computeroutput></para><para>
Definition at line 362 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1af1e43f88fc1ccb00d831750a24c4b0d9"/>    <section>
    <title>particle_cc_opposite_vertices()</title>
<indexterm><primary>particle_cc_opposite_vertices</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>particle_cc_opposite_vertices</secondary></indexterm>
<para><computeroutput>long particle_cc_opposite_vertices (<link linkend="_struct_bparticle">Bparticle</link> * vert, <link linkend="_class_bimage">Bimage</link> * pmask, <link linkend="_class_bimage">Bimage</link> * pfsmask, double hires, double lores)</computeroutput></para><para>
Definition at line 285 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a25c3c87aac2af79bf7725b192f22127d"/>    <section>
    <title>particle_worst_opposite_vertex()</title>
<indexterm><primary>particle_worst_opposite_vertex</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>particle_worst_opposite_vertex</secondary></indexterm>
<para><computeroutput>long particle_worst_opposite_vertex (<link linkend="_struct_bparticle">Bparticle</link> * vert, <link linkend="_class_bimage">Bimage</link> * pref, <link linkend="_class_bimage">Bimage</link> * pmask, <link linkend="_class_bimage">Bimage</link> * pfsmask, double hires, double lores)</computeroutput></para><para>
Definition at line 329 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1ae8b03a4dbc616c4d2baf9a701a107110"/>    <section>
    <title>particle_worst_vertex()</title>
<indexterm><primary>particle_worst_vertex</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>particle_worst_vertex</secondary></indexterm>
<para><computeroutput>long particle_worst_vertex (<link linkend="_struct_bparticle">Bparticle</link> * vert, <link linkend="_class_bimage">Bimage</link> * pref, <link linkend="_class_bimage">Bimage</link> * pmask, <link linkend="_class_bimage">Bimage</link> * pfsmask, double hires, double lores)</computeroutput></para><para>
Definition at line 240 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1aee13a3e857cc2d5cb8ecbea2e9e2c9a9"/>    <section>
    <title>project_assign_special_vertex_orientations()</title>
<indexterm><primary>project_assign_special_vertex_orientations</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>project_assign_special_vertex_orientations</secondary></indexterm>
<para><computeroutput>long project_assign_special_vertex_orientations (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_struct_bproject">Bproject</link> * project_specvert)</computeroutput></para><para>
Definition at line 666 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a67ea0c855903cc381bedf009b8d20ee2"/>    <section>
    <title>project_ico_best_c5()</title>
<indexterm><primary>project_ico_best_c5</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>project_ico_best_c5</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link> * project_ico_best_c5 (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bimage">Bimage</link> * pref, <link linkend="_class_bimage">Bimage</link> * pmask, <link linkend="_class_bimage">Bimage</link> * pfsmask, double hires, double lores, double maxres)</computeroutput></para><para>

<para>Determines the best 5-fold orientation of the vertex wrt a reference. </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>parameter structure with all parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pref</entry>
                                <entry>
<para>reference map. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pmask</entry>
                                <entry>
<para>real space mask. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pfsmask</entry>
                                <entry>
<para>frequency space mask. </para>
</entry>
                            </row>
                            <row>
                                <entry>hires</entry>
                                <entry>
<para>maximum resolution for correlation. </para>
</entry>
                            </row>
                            <row>
                                <entry>lores</entry>
                                <entry>
<para>minimum resolution for correlation. </para>
</entry>
                            </row>
                            <row>
                                <entry>maxres</entry>
                                <entry>
<para>maximum resolution for reconstruction. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* two reconstructions. <literallayout><computeroutput>The function compares opposite vertices of the twelve for every particle
to identify the pair that is most dissimilar. 
One of these is a candidate for the special vertex.
A reference map is then calculated from all the rest of the vertices.
The previously selected pair is then correlated agiants the reference
and the one with the worst coefficient selected as final candidate.
Two averages are calculated, the first for the non-special vertices,
and the second for the special vertices.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 606 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a348e4c60dafc8a27f8128fa16b7ce20d"/>    <section>
    <title>project_ico_opposite_vertex()</title>
<indexterm><primary>project_ico_opposite_vertex</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>project_ico_opposite_vertex</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link> * project_ico_opposite_vertex (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bimage">Bimage</link> * pmask, <link linkend="_class_bimage">Bimage</link> * pfsmask, double hires, double lores, double maxres)</computeroutput></para><para>

<para>Determines the special vertex for icosahedral symmetry and returns two maps. </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>parameter structure with all parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pmask</entry>
                                <entry>
<para>real space mask. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pfsmask</entry>
                                <entry>
<para>frequency space mask. </para>
</entry>
                            </row>
                            <row>
                                <entry>hires</entry>
                                <entry>
<para>maximum resolution for correlation. </para>
</entry>
                            </row>
                            <row>
                                <entry>lores</entry>
                                <entry>
<para>minimum resolution for correlation. </para>
</entry>
                            </row>
                            <row>
                                <entry>maxres</entry>
                                <entry>
<para>maximum resolution for reconstruction. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* two reconstructions. <literallayout><computeroutput>The function compares opposite vertices of the twelve for every particle
to identify the pair that is most dissimilar. 
One of these is a candidate for the special vertex.
A reference map is then calculated from all the rest of the vertices.
The previously selected pair is then correlated agiants the reference
and the one with the worst coefficient selected as final candidate.
Two averages are calculated, the first for the non-special vertices,
and the second for the special vertices.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 511 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a0c4a59e86ee58e4d4b2000cbba30f1a5"/>    <section>
    <title>project_ico_worst_vertex()</title>
<indexterm><primary>project_ico_worst_vertex</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>project_ico_worst_vertex</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link> * project_ico_worst_vertex (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_bimage">Bimage</link> * pref, <link linkend="_class_bimage">Bimage</link> * pmask, <link linkend="_class_bimage">Bimage</link> * pfsmask, double hires, double lores, double maxres)</computeroutput></para><para>

<para>Determines the special vertex for icosahedral symmetry and returns two maps. </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>parameter structure with all parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pref</entry>
                                <entry>
<para>reference map. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pmask</entry>
                                <entry>
<para>real space mask. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pfsmask</entry>
                                <entry>
<para>frequency space mask. </para>
</entry>
                            </row>
                            <row>
                                <entry>hires</entry>
                                <entry>
<para>maximum resolution for correlation. </para>
</entry>
                            </row>
                            <row>
                                <entry>lores</entry>
                                <entry>
<para>minimum resolution for correlation. </para>
</entry>
                            </row>
                            <row>
                                <entry>maxres</entry>
                                <entry>
<para>maximum resolution for reconstruction. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* two reconstructions. <literallayout><computeroutput>The function correlates each vertex with the reference, and selects the one
out of the twelve for each particle with the worst coefficient as the 
likely special vertex.
Two averages are calculated, the first for the non-special vertices,
and the second for the special vertices.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 423 of file bico.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_bico_8cpp_1a9ec8849996c5e210d7b7e8e05b98639d"/>    <section>
    <title>planb</title>
<indexterm><primary>planb</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>planb</secondary></indexterm>
<para><computeroutput><link linkend="_fft_8h_1a61d23c567e69684715ea52482137a5e6">fft_plan</link> planb</computeroutput></para><para>
Definition at line 24 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a6ecaa8728bab23c3a7d96fe0cadc75f2"/>    <section>
    <title>planf</title>
<indexterm><primary>planf</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>planf</secondary></indexterm>
<para><computeroutput><link linkend="_fft_8h_1a61d23c567e69684715ea52482137a5e6">fft_plan</link> planf</computeroutput></para><para>
Definition at line 24 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a4de0ad4c7190962494815c0fa7f948df"/>    <section>
    <title>use</title>
<indexterm><primary>use</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>use</secondary></indexterm>
<para><computeroutput>const char* use[]</computeroutput></para><emphasis role="strong">Initial value:</emphasis><programlisting>=&#32;{
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Usage:&#32;bico&#32;[options]&#32;tomo.star&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-------------------------------&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Analyzes&#32;icosahedral&#32;subtomograms.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Actions:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-find&#32;opp&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Type&#32;of&#32;correlation:&#32;worst,&#32;opposite,&#32;c5.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Parameters:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-verbose&#32;7&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Verbosity&#32;of&#32;output.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-resolution&#32;15.6,200&#32;&#32;&#32;&#32;&#32;Resolution&#32;limits&#32;for&#32;cross-correlation&#32;(default&#32;0,inf).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-maxresolution&#32;9.5&#32;&#32;&#32;&#32;&#32;&#32;&#32;Maximum&#32;reconstruction&#32;resolution&#32;limit&#32;(default&#32;Nyquist).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Input:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-reference&#32;image.map&#32;&#32;&#32;&#32;&#32;Reference&#32;for&#32;cross-correlation.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-mask&#32;image.map&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Real&#32;space&#32;mask.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-Mask&#32;fsmask.mrc&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Frequency&#32;space&#32;mask&#32;(missing&#32;data).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-special&#32;vert.star&#32;&#32;&#32;&#32;&#32;&#32;&#32;Parameter&#32;file&#32;with&#32;special&#32;vertex&#32;orientations.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Output:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-output&#32;file.star&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Output&#32;parameter&#32;file.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-reconstruction&#32;file.ext&#32;Reconstruction&#32;file&#32;name.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
NULL
}
</programlisting><para>
Definition at line 35 of file bico.cpp.</para>
    </section><anchor xml:id="_bico_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>bico.cpp</secondary></indexterm>
<indexterm><primary>bico.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
