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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_mg__extract_8cpp">
<title>/Users/bernard/b20/bsoft/src/mg/mg_extract.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/mg/mg_extract.cpp</primary></indexterm>
<para>

<para>Functions to extract particles from micrographs. </para>
 
</para>
<programlisting>#include &quot;mg_extract.h&quot;
#include &quot;linked_list.h&quot;
#include &quot;spline.h&quot;
#include &quot;utilities.h&quot;
#include &lt;sys/stat.h&gt;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a601ccbd20e30a462486fa9f98096291e">mask_filament_particles</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_struct_bparticle">Bparticle</link> *partlist, int mask_width)</para>
</listitem>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a6d23673f8727975c2a59c185aa099e33">rotate_mask_filament_particles</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_struct_bparticle">Bparticle</link> *partlist, int rotation_axis, int back_flag, int mask_width)</para>
</listitem>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a52cdb0e5f1258b74a7deebfae262354d">particle_setup_filenames</link> (<link linkend="_struct_bparticle">Bparticle</link> *part, <link linkend="_class_bstring">Bstring</link> filename, <link linkend="_class_bstring">Bstring</link> partpath)</para>

<para>Sets up individual particle file names for extraction. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a56857662e7ec02cbcbd636eabb81085a">filament_setup_filenames</link> (<link linkend="_struct_bfilament">Bfilament</link> *fil, <link linkend="_class_bstring">Bstring</link> filename, <link linkend="_class_bstring">Bstring</link> filpath)</para>

<para>Sets up individual filament file names for extraction. </para>
</listitem>
            <listitem><para><link linkend="_class_vector3">Vector3</link>&lt; double &gt; * <link linkend="_mg__extract_8cpp_1aec90ecc0487320283bc31f566b8cddbc">vector3_spline_from_nodes</link> (<link linkend="_struct_bfilnode">Bfilnode</link> *fnode, long &amp;nspline)</para>

<para>Calculates a spline curve from a set of filament nodes. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__extract_8cpp_1a51fbf589e7048a0a43ae9980b02c843f">project_extract_particles</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, double scale, int back_flag, int norm_flag, int fill_type, double fill, int mask_width, int <link linkend="_string__util_8cpp_1add313f0fe82466f4c1c4622307d928bc">split</link>, <link linkend="_class_bstring">Bstring</link> &amp;partbase, <link linkend="_class_bstring">Bstring</link> &amp;partpath, <link linkend="_class_bstring">Bstring</link> &amp;partext)</para>

<para>Extracts particle images from micrographs defined in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__extract_8cpp_1a70e9d9f1721954bae56fc67f7e87f56e">micrograph_extract_particles</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg, <link linkend="_class_bimage">Bimage</link> *p, double scale, int back_flag, int norm_flag, double fill, int mask_width)</para>

<para>Extracts particle images from a micrograph. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__extract_8cpp_1abad317d61b8f91053e91bd5b2df0f1dc">reconstruction_extract_particles</link> (<link linkend="_struct_breconstruction">Breconstruction</link> *rec, <link linkend="_class_bimage">Bimage</link> *p, double scale, int back_flag, int norm_flag, double fill, int mask_width)</para>

<para>Extracts particle images from a reconstruction. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_mg__extract_8cpp_1a0ec9c62b2b79fc55187151ce525034af">particle_extract</link> (<link linkend="_struct_bparticle">Bparticle</link> *particles, <link linkend="_struct_bbadarea">Bbadarea</link> *bad_areas, <link linkend="_class_bimage">Bimage</link> *p, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; size, double scale, double bad_radius, int back_flag, int norm_flag, double fill, int mask_width)</para>

<para>Extracts particle images from an image. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_mg__extract_8cpp_1ad149a6b8b077f6fb0ca159b30011a08e">micrograph_extract_gold</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg, <link linkend="_class_bimage">Bimage</link> *p, double radius)</para>

<para>Extracts gold particle images from a micrograph. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_mg__extract_8cpp_1ae956c9add4c8e7e6c575b30e0f65e61b">reconstruction_extract_gold</link> (<link linkend="_struct_breconstruction">Breconstruction</link> *rec, <link linkend="_class_bimage">Bimage</link> *p, double radius)</para>

<para>Extracts gold particle images from a reconstruction. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_mg__extract_8cpp_1a252fc71654a1ec7e205d2fa694fa7319">marker_extract_gold</link> (<link linkend="_struct_bmarker">Bmarker</link> *<link linkend="_tcltk__bmarker_8cpp_1a1b8b1622a4b6e00330913aab6d5d941a">marker_list</link>, <link linkend="_class_bimage">Bimage</link> *p, int img_num, double radius)</para>

<para>Extracts gold particle images from an image. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__extract_8cpp_1a78275ddef801badc9e9a1ee7edf8cae7">project_extract_filaments</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int filament_width, int axis, <link linkend="_class_bstring">Bstring</link> &amp;<link linkend="_string__util_8cpp_1ae1cd0165442272bf85dc2d9461080a30">base</link>, <link linkend="_class_bstring">Bstring</link> &amp;path, <link linkend="_class_bstring">Bstring</link> &amp;ext, int <link linkend="_string__util_8cpp_1add313f0fe82466f4c1c4622307d928bc">split</link>)</para>

<para>Extracts filament images from micrographs defined in a project. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__extract_8cpp_1a77fbf79a9b6b82f3a809ec39831711ea">micrograph_extract_filaments</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg, <link linkend="_class_bimage">Bimage</link> *p, double width, int axis)</para>

<para>Extracts filament images from a micrograph. </para>
</listitem>
            <listitem><para>long <link linkend="_mg__extract_8cpp_1a23613b2d1fcd883f893fe2a6c2ea3e25">reconstruction_extract_filaments</link> (<link linkend="_struct_breconstruction">Breconstruction</link> *rec, <link linkend="_class_bimage">Bimage</link> *p, double width, int axis)</para>

<para>Extracts filament images from a micrograph. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_mg__extract_8cpp_1aa2a5f14d23705a074f0a6cf534a99339">filament_extract</link> (<link linkend="_struct_bfilament">Bfilament</link> *filaments, <link linkend="_class_bimage">Bimage</link> *p, double width, int axis)</para>

<para>Extracts filament images from a micrograph. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a4fda7f0af4198d127fd4f89902d0d8f6">project_filaments_to_particles</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, double boxing_interval, double rise, double angle)</para>

<para>Converts filaments to sets of particles. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a9c814f94135d307b754b970c523efc7a">micrograph_filaments_to_particles</link> (<link linkend="_struct_bmicrograph">Bmicrograph</link> *mg, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size, double boxing_interval, double rise, double angle)</para>

<para>Converts filaments to sets of particles. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a2fabeb0772dc3329e43794da9f9b198f">reconstruction_filaments_to_particles</link> (<link linkend="_struct_breconstruction">Breconstruction</link> *rec, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size, double boxing_interval, double rise, double angle)</para>

<para>Converts filaments to sets of particles. </para>
</listitem>
            <listitem><para><link linkend="_struct_bparticle">Bparticle</link> * <link linkend="_mg__extract_8cpp_1a66ae696c5d93392a6af3aba9a7e3ed16">filaments_to_particles</link> (<link linkend="_struct_bfilament">Bfilament</link> *filaments, double pixel_size, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size, double boxing_interval, double rise, double angle)</para>

<para>Converts filaments to sets of particles. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a95d641567edbbbf61afdd28bca22d0ce">project_mask_filament_particles</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int mask_width)</para>

<para>Masks particles extracted from filaments. </para>
</listitem>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a38cbca2c6f7b445bcc2eb87b10a698b5">project_rotate_mask_filament_particles</link> (<link linkend="_struct_bproject">Bproject</link> *<link linkend="_tcltk__bmodel_8cpp_1aea438e09dfc03683a0f49a05e9a69cac">project</link>, int rotation_axis, int back_flag, int mask_width)</para>

<para>Rotates and masks particles extracted from filaments. </para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_mg__extract_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Functions to extract particles from micrographs. </para>

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

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

<para>Created: 20040406 </para>

<para>Modified: 20191001 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_mg__extract_8cpp_1aa2a5f14d23705a074f0a6cf534a99339"/>    <section>
    <title>filament_extract()</title>
<indexterm><primary>filament_extract</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>filament_extract</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link>* filament_extract (<link linkend="_struct_bfilament">Bfilament</link> * filaments, <link linkend="_class_bimage">Bimage</link> * p, double width, int axis)</computeroutput></para><para>

<para>Extracts filament images from 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>*filaments</entry>
                                <entry>
<para>filament parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>image. </para>
</entry>
                            </row>
                            <row>
                                <entry>width</entry>
                                <entry>
<para>width of box around filament to extract. </para>
</entry>
                            </row>
                            <row>
                                <entry>axis</entry>
                                <entry>
<para>helical axis alignment: x=1, y=2, z=3. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* multi-filament image. <literallayout><computeroutput>If the file names for individual filaments are specified, they are
used to write individual filaments to files.
Default axis alignment (for axis==0):
    2D images:  x-axis (1)
    3D images:  z-axis (3)
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 842 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a56857662e7ec02cbcbd636eabb81085a"/>    <section>
    <title>filament_setup_filenames()</title>
<indexterm><primary>filament_setup_filenames</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>filament_setup_filenames</secondary></indexterm>
<para><computeroutput>int filament_setup_filenames (<link linkend="_struct_bfilament">Bfilament</link> * fil, <link linkend="_class_bstring">Bstring</link> filename, <link linkend="_class_bstring">Bstring</link> filpath)</computeroutput></para><para>

<para>Sets up individual filament file names for extraction. </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>filament list. </para>
</entry>
                            </row>
                            <row>
                                <entry>filename</entry>
                                <entry>
<para>filament file name base. </para>
</entry>
                            </row>
                            <row>
                                <entry>filpath</entry>
                                <entry>
<para>filament path with optional wild card characters. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filaments. <literallayout><computeroutput>The filament path can have wildcard characters (&apos;?&apos;) that specify
the number of digits to use to insert numbers in the path and
the file name.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 85 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a66ae696c5d93392a6af3aba9a7e3ed16"/>    <section>
    <title>filaments_to_particles()</title>
<indexterm><primary>filaments_to_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>filaments_to_particles</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bparticle">Bparticle</link>* filaments_to_particles (<link linkend="_struct_bfilament">Bfilament</link> * filaments, double pixel_size, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size, double boxing_interval, double rise, double angle)</computeroutput></para><para>

<para>Converts filaments to sets of 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>*filaments</entry>
                                <entry>
<para>filament parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>pixel_size</entry>
                                <entry>
<para>sampling. </para>
</entry>
                            </row>
                            <row>
                                <entry>box_size</entry>
                                <entry>
<para>size of particle box. </para>
</entry>
                            </row>
                            <row>
                                <entry>boxing_interval</entry>
                                <entry>
<para>step size between boxes. </para>
</entry>
                            </row>
                            <row>
                                <entry>rise</entry>
                                <entry>
<para>rise per asymmetric unit in angstrom. </para>
</entry>
                            </row>
                            <row>
                                <entry>angle</entry>
                                <entry>
<para>angular rotation per asymmetric unit in radians. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bparticle* pointer to new list of particles. <literallayout><computeroutput>Particle coordinates are calculated along a spline curve through
the filament nodes, separated by half the given width.
Different filaments in a micrograph are indicated by the selection number.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 1021 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a252fc71654a1ec7e205d2fa694fa7319"/>    <section>
    <title>marker_extract_gold()</title>
<indexterm><primary>marker_extract_gold</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>marker_extract_gold</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link>* marker_extract_gold (<link linkend="_struct_bmarker">Bmarker</link> * marker_list, <link linkend="_class_bimage">Bimage</link> * p, int img_num, double radius)</computeroutput></para><para>

<para>Extracts gold particle images from an image. </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>*marker_list</entry>
                                <entry>
<para>marker parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>image. </para>
</entry>
                            </row>
                            <row>
                                <entry>img_num</entry>
                                <entry>
<para>sub-image number. </para>
</entry>
                            </row>
                            <row>
                                <entry>radius</entry>
                                <entry>
<para>radius of gold particle. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* multi-particle image. </para>
</formalpara>
</para>
<para>
Definition at line 610 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a601ccbd20e30a462486fa9f98096291e"/>    <section>
    <title>mask_filament_particles()</title>
<indexterm><primary>mask_filament_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>mask_filament_particles</secondary></indexterm>
<para><computeroutput>int mask_filament_particles (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_struct_bparticle">Bparticle</link> * partlist, int mask_width)</computeroutput></para><para>
Definition at line 1162 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a77fbf79a9b6b82f3a809ec39831711ea"/>    <section>
    <title>micrograph_extract_filaments()</title>
<indexterm><primary>micrograph_extract_filaments</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>micrograph_extract_filaments</secondary></indexterm>
<para><computeroutput>long micrograph_extract_filaments (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg, <link linkend="_class_bimage">Bimage</link> * p, double width, int axis)</computeroutput></para><para>

<para>Extracts filament images from 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 parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>micrograph image. </para>
</entry>
                            </row>
                            <row>
                                <entry>width</entry>
                                <entry>
<para>width of box around filament to extract. </para>
</entry>
                            </row>
                            <row>
                                <entry>axis</entry>
                                <entry>
<para>helical axis alignment: x=1, y=2, z=3. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filaments. </para>
</formalpara>
</para>
<para>
Definition at line 783 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1ad149a6b8b077f6fb0ca159b30011a08e"/>    <section>
    <title>micrograph_extract_gold()</title>
<indexterm><primary>micrograph_extract_gold</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>micrograph_extract_gold</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link>* micrograph_extract_gold (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg, <link linkend="_class_bimage">Bimage</link> * p, double radius)</computeroutput></para><para>

<para>Extracts gold particle images from 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 parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>micrograph image. </para>
</entry>
                            </row>
                            <row>
                                <entry>radius</entry>
                                <entry>
<para>radius of gold particle. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* multi-particle image. </para>
</formalpara>
</para>
<para>
Definition at line 573 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a70e9d9f1721954bae56fc67f7e87f56e"/>    <section>
    <title>micrograph_extract_particles()</title>
<indexterm><primary>micrograph_extract_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>micrograph_extract_particles</secondary></indexterm>
<para><computeroutput>long micrograph_extract_particles (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg, <link linkend="_class_bimage">Bimage</link> * p, double scale, int back_flag, int norm_flag, double fill, int mask_width)</computeroutput></para><para>

<para>Extracts particle images from 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 parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>micrograph image. </para>
</entry>
                            </row>
                            <row>
                                <entry>scale</entry>
                                <entry>
<para>scale to extract (usually 1). </para>
</entry>
                            </row>
                            <row>
                                <entry>back_flag</entry>
                                <entry>
<para>background correction flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>norm_flag</entry>
                                <entry>
<para>normalization flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>fill</entry>
                                <entry>
<para>value to fill in new regions. </para>
</entry>
                            </row>
                            <row>
                                <entry>mask_width</entry>
                                <entry>
<para>filament mask width, if 0, don&apos;t apply. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles. </para>
</formalpara>
</para>
<para>
Definition at line 332 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a9c814f94135d307b754b970c523efc7a"/>    <section>
    <title>micrograph_filaments_to_particles()</title>
<indexterm><primary>micrograph_filaments_to_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>micrograph_filaments_to_particles</secondary></indexterm>
<para><computeroutput>int micrograph_filaments_to_particles (<link linkend="_struct_bmicrograph">Bmicrograph</link> * mg, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size, double boxing_interval, double rise, double angle)</computeroutput></para><para>

<para>Converts filaments to sets of 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>*mg</entry>
                                <entry>
<para>micrograph parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>box_size</entry>
                                <entry>
<para>size of particle box. </para>
</entry>
                            </row>
                            <row>
                                <entry>boxing_interval</entry>
                                <entry>
<para>step size between boxes. </para>
</entry>
                            </row>
                            <row>
                                <entry>rise</entry>
                                <entry>
<para>rise per asymmetric unit in angstrom. </para>
</entry>
                            </row>
                            <row>
                                <entry>angle</entry>
                                <entry>
<para>angular rotation per asymmetric unit in radians. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of filaments converted. <literallayout><computeroutput>Particle coordinates are calculated along a spline curve through
the filament nodes, separated by half the given width.
Different filaments in a micrograph are indicated by the selection number.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 948 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a0ec9c62b2b79fc55187151ce525034af"/>    <section>
    <title>particle_extract()</title>
<indexterm><primary>particle_extract</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>particle_extract</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link>* particle_extract (<link linkend="_struct_bparticle">Bparticle</link> * particles, <link linkend="_struct_bbadarea">Bbadarea</link> * bad_areas, <link linkend="_class_bimage">Bimage</link> * p, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; size, double scale, double bad_radius, int back_flag, int norm_flag, double fill, int mask_width)</computeroutput></para><para>

<para>Extracts particle images from an image. </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>*particles</entry>
                                <entry>
<para>particle parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*bad_areas</entry>
                                <entry>
<para>bad area parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>image. </para>
</entry>
                            </row>
                            <row>
                                <entry>size</entry>
                                <entry>
<para>size of box to extract. </para>
</entry>
                            </row>
                            <row>
                                <entry>scale</entry>
                                <entry>
<para>scale to extract (usually 1). </para>
</entry>
                            </row>
                            <row>
                                <entry>bad_radius</entry>
                                <entry>
<para>radius of bad area. </para>
</entry>
                            </row>
                            <row>
                                <entry>back_flag</entry>
                                <entry>
<para>background correction flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>norm_flag</entry>
                                <entry>
<para>normalization flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>fill</entry>
                                <entry>
<para>value to fill in new regions. </para>
</entry>
                            </row>
                            <row>
                                <entry>mask_width</entry>
                                <entry>
<para>filament mask width, if 0, don&apos;t apply. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* multi-particle image. <literallayout><computeroutput>If the background flag is specified, the particle mask is set in the 
background, defined as outside the inscribing circle.
The mask is set within every bad area in the micrograph and
transferred to the mask for a particle where it overlaps.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 403 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a52cdb0e5f1258b74a7deebfae262354d"/>    <section>
    <title>particle_setup_filenames()</title>
<indexterm><primary>particle_setup_filenames</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>particle_setup_filenames</secondary></indexterm>
<para><computeroutput>int particle_setup_filenames (<link linkend="_struct_bparticle">Bparticle</link> * part, <link linkend="_class_bstring">Bstring</link> filename, <link linkend="_class_bstring">Bstring</link> partpath)</computeroutput></para><para>

<para>Sets up individual particle file names for extraction. </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>particle list. </para>
</entry>
                            </row>
                            <row>
                                <entry>filename</entry>
                                <entry>
<para>particle file name base. </para>
</entry>
                            </row>
                            <row>
                                <entry>partpath</entry>
                                <entry>
<para>particle path with optional wild card characters. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles. <literallayout><computeroutput>The particle path can have wildcard characters (&apos;?&apos;) that specify
the number of digits to use to insert numbers in the path and
the file name.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 35 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a78275ddef801badc9e9a1ee7edf8cae7"/>    <section>
    <title>project_extract_filaments()</title>
<indexterm><primary>project_extract_filaments</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>project_extract_filaments</secondary></indexterm>
<para><computeroutput>long project_extract_filaments (<link linkend="_struct_bproject">Bproject</link> * project, int filament_width, int axis, <link linkend="_class_bstring">Bstring</link> &amp; base, <link linkend="_class_bstring">Bstring</link> &amp; path, <link linkend="_class_bstring">Bstring</link> &amp; ext, int split)</computeroutput></para><para>

<para>Extracts filament images from micrographs defined 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>micrograph project. </para>
</entry>
                            </row>
                            <row>
                                <entry>filament_width</entry>
                                <entry>
<para>extracted filament width. </para>
</entry>
                            </row>
                            <row>
                                <entry>axis</entry>
                                <entry>
<para>helical axis alignment: x=1, y=2, z=3. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;base</entry>
                                <entry>
<para>file name base. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;path</entry>
                                <entry>
<para>path to filament file. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;ext</entry>
                                <entry>
<para>filament file extension. </para>
</entry>
                            </row>
                            <row>
                                <entry>split</entry>
                                <entry>
<para>flag to split filaments into individual files. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filaments, &lt;0 on error. </para>
</formalpara>
</para>
<para>
Definition at line 674 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a51fbf589e7048a0a43ae9980b02c843f"/>    <section>
    <title>project_extract_particles()</title>
<indexterm><primary>project_extract_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>project_extract_particles</secondary></indexterm>
<para><computeroutput>long project_extract_particles (<link linkend="_struct_bproject">Bproject</link> * project, double scale, int back_flag, int norm_flag, int fill_type, double fill, int mask_width, int split, <link linkend="_class_bstring">Bstring</link> &amp; partbase, <link linkend="_class_bstring">Bstring</link> &amp; partpath, <link linkend="_class_bstring">Bstring</link> &amp; partext)</computeroutput></para><para>

<para>Extracts particle images from micrographs defined 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>micrograph project. </para>
</entry>
                            </row>
                            <row>
                                <entry>scale</entry>
                                <entry>
<para>scale to extract (usually 1). </para>
</entry>
                            </row>
                            <row>
                                <entry>back_flag</entry>
                                <entry>
<para>background correction flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>norm_flag</entry>
                                <entry>
<para>normalization flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>fill_type</entry>
                                <entry>
<para>FILL_AVERAGE, FILL_BACKGROUND, FILL_USER. </para>
</entry>
                            </row>
                            <row>
                                <entry>fill</entry>
                                <entry>
<para>value to fill in new regions. </para>
</entry>
                            </row>
                            <row>
                                <entry>mask_width</entry>
                                <entry>
<para>filament mask width, if 0, don&apos;t apply. </para>
</entry>
                            </row>
                            <row>
                                <entry>split</entry>
                                <entry>
<para>flag to split images into separate files. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;partbase</entry>
                                <entry>
<para>file name base. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;partpath</entry>
                                <entry>
<para>path to particle file. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;partext</entry>
                                <entry>
<para>particle file extension. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles, &lt;0 on error. </para>
</formalpara>
</para>
<para>
Definition at line 160 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a4fda7f0af4198d127fd4f89902d0d8f6"/>    <section>
    <title>project_filaments_to_particles()</title>
<indexterm><primary>project_filaments_to_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>project_filaments_to_particles</secondary></indexterm>
<para><computeroutput>int project_filaments_to_particles (<link linkend="_struct_bproject">Bproject</link> * project, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size, double boxing_interval, double rise, double angle)</computeroutput></para><para>

<para>Converts filaments to sets of 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 parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>box_size</entry>
                                <entry>
<para>size of particle box. </para>
</entry>
                            </row>
                            <row>
                                <entry>boxing_interval</entry>
                                <entry>
<para>step size between boxes. </para>
</entry>
                            </row>
                            <row>
                                <entry>rise</entry>
                                <entry>
<para>rise per asymmetric unit in angstrom. </para>
</entry>
                            </row>
                            <row>
                                <entry>angle</entry>
                                <entry>
<para>angular rotation per asymmetric unit in radians. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of filaments converted. <literallayout><computeroutput>Particle coordinates are calculated along a spline curve through
the filament nodes, separated by half the given width.
Different filaments in a micrograph are indicated by the selection number.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 914 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a95d641567edbbbf61afdd28bca22d0ce"/>    <section>
    <title>project_mask_filament_particles()</title>
<indexterm><primary>project_mask_filament_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>project_mask_filament_particles</secondary></indexterm>
<para><computeroutput>int project_mask_filament_particles (<link linkend="_struct_bproject">Bproject</link> * project, int mask_width)</computeroutput></para><para>

<para>Masks particles extracted from filaments. </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 parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>mask_width</entry>
                                <entry>
<para>width of mask to apply. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of particles masked. <literallayout><computeroutput>The orientation of the filament is inferred from the view angle and
the adjacent regions are set to the background.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 1083 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a38cbca2c6f7b445bcc2eb87b10a698b5"/>    <section>
    <title>project_rotate_mask_filament_particles()</title>
<indexterm><primary>project_rotate_mask_filament_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>project_rotate_mask_filament_particles</secondary></indexterm>
<para><computeroutput>int project_rotate_mask_filament_particles (<link linkend="_struct_bproject">Bproject</link> * project, int rotation_axis, int back_flag, int mask_width)</computeroutput></para><para>

<para>Rotates and masks particles extracted from filaments. </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 parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>rotation_axis</entry>
                                <entry>
<para>axis to rotate to: 1=x, 2=y, 3=z. </para>
</entry>
                            </row>
                            <row>
                                <entry>back_flag</entry>
                                <entry>
<para>background correction flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>mask_width</entry>
                                <entry>
<para>width of mask to apply. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of particles masked. <literallayout><computeroutput>The orientation of the filament is inferred from the view angle and
the particle is rotated to orient the filament axis along a cartesian axis. 
The mask is applied and adjacent regions are set to the background.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 1115 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a23613b2d1fcd883f893fe2a6c2ea3e25"/>    <section>
    <title>reconstruction_extract_filaments()</title>
<indexterm><primary>reconstruction_extract_filaments</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>reconstruction_extract_filaments</secondary></indexterm>
<para><computeroutput>long reconstruction_extract_filaments (<link linkend="_struct_breconstruction">Breconstruction</link> * rec, <link linkend="_class_bimage">Bimage</link> * p, double width, int axis)</computeroutput></para><para>

<para>Extracts filament images from 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>*rec</entry>
                                <entry>
<para>reconstruction parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>reconstruction image. </para>
</entry>
                            </row>
                            <row>
                                <entry>width</entry>
                                <entry>
<para>width of box around filament to extract. </para>
</entry>
                            </row>
                            <row>
                                <entry>axis</entry>
                                <entry>
<para>helical axis alignment: x=1, y=2, z=3. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of filaments. </para>
</formalpara>
</para>
<para>
Definition at line 809 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1ae956c9add4c8e7e6c575b30e0f65e61b"/>    <section>
    <title>reconstruction_extract_gold()</title>
<indexterm><primary>reconstruction_extract_gold</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>reconstruction_extract_gold</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link>* reconstruction_extract_gold (<link linkend="_struct_breconstruction">Breconstruction</link> * rec, <link linkend="_class_bimage">Bimage</link> * p, double radius)</computeroutput></para><para>

<para>Extracts gold particle images from a 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 parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>reconstruction image. </para>
</entry>
                            </row>
                            <row>
                                <entry>radius</entry>
                                <entry>
<para>radius of gold particle. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* multi-particle image. </para>
</formalpara>
</para>
<para>
Definition at line 591 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1abad317d61b8f91053e91bd5b2df0f1dc"/>    <section>
    <title>reconstruction_extract_particles()</title>
<indexterm><primary>reconstruction_extract_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>reconstruction_extract_particles</secondary></indexterm>
<para><computeroutput>long reconstruction_extract_particles (<link linkend="_struct_breconstruction">Breconstruction</link> * rec, <link linkend="_class_bimage">Bimage</link> * p, double scale, int back_flag, int norm_flag, double fill, int mask_width)</computeroutput></para><para>

<para>Extracts particle images from a 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 parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>*p</entry>
                                <entry>
<para>micrograph image. </para>
</entry>
                            </row>
                            <row>
                                <entry>scale</entry>
                                <entry>
<para>scale to extract (usually 1). </para>
</entry>
                            </row>
                            <row>
                                <entry>back_flag</entry>
                                <entry>
<para>background correction flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>norm_flag</entry>
                                <entry>
<para>normalization flag. </para>
</entry>
                            </row>
                            <row>
                                <entry>fill</entry>
                                <entry>
<para>value to fill in new regions. </para>
</entry>
                            </row>
                            <row>
                                <entry>mask_width</entry>
                                <entry>
<para>filament mask width, if 0, don&apos;t apply. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>long number of particles. </para>
</formalpara>
</para>
<para>
Definition at line 363 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a2fabeb0772dc3329e43794da9f9b198f"/>    <section>
    <title>reconstruction_filaments_to_particles()</title>
<indexterm><primary>reconstruction_filaments_to_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>reconstruction_filaments_to_particles</secondary></indexterm>
<para><computeroutput>int reconstruction_filaments_to_particles (<link linkend="_struct_breconstruction">Breconstruction</link> * rec, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; box_size, double boxing_interval, double rise, double angle)</computeroutput></para><para>

<para>Converts filaments to sets of 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>*rec</entry>
                                <entry>
<para>reconstruction parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>box_size</entry>
                                <entry>
<para>size of particle box. </para>
</entry>
                            </row>
                            <row>
                                <entry>boxing_interval</entry>
                                <entry>
<para>step size between boxes. </para>
</entry>
                            </row>
                            <row>
                                <entry>rise</entry>
                                <entry>
<para>rise per asymmetric unit in angstrom. </para>
</entry>
                            </row>
                            <row>
                                <entry>angle</entry>
                                <entry>
<para>angular rotation per asymmetric unit in radians. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of filaments converted. <literallayout><computeroutput>Particle coordinates are calculated along a spline curve through
the filament nodes, separated by half the given width.
Different filaments in a micrograph are indicated by the selection number.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 984 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1a6d23673f8727975c2a59c185aa099e33"/>    <section>
    <title>rotate_mask_filament_particles()</title>
<indexterm><primary>rotate_mask_filament_particles</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>rotate_mask_filament_particles</secondary></indexterm>
<para><computeroutput>int rotate_mask_filament_particles (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_struct_bparticle">Bparticle</link> * partlist, int rotation_axis, int back_flag, int mask_width)</computeroutput></para><para>
Definition at line 1213 of file mg_extract.cpp.</para>
    </section><anchor xml:id="_mg__extract_8cpp_1aec90ecc0487320283bc31f566b8cddbc"/>    <section>
    <title>vector3_spline_from_nodes()</title>
<indexterm><primary>vector3_spline_from_nodes</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>vector3_spline_from_nodes</secondary></indexterm>
<para><computeroutput><link linkend="_class_vector3">Vector3</link>&lt;double&gt;* vector3_spline_from_nodes (<link linkend="_struct_bfilnode">Bfilnode</link> * fnode, long &amp; nspline)</computeroutput></para><para>

<para>Calculates a spline curve from a set of filament nodes. </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>node list. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;nspline</entry>
                                <entry>
<para>number of elements in the spline array. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para><link linkend="_class_vector3">Vector3&lt;double&gt;</link>* array of spline coordinates. <literallayout><computeroutput>The node coordinates are copied into a new array used to calculate the spline array.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 127 of file mg_extract.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_mg__extract_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>mg_extract.cpp</secondary></indexterm>
<indexterm><primary>mg_extract.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
