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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_model__map_8h">
<title>/Users/bernard/b20/bsoft/include/model_map.h File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/include/model_map.h</primary></indexterm>
<para>

<para>Header file for model to map conversions. </para>
 
</para>
<programlisting>#include &quot;rwmodel.h&quot;
#include &quot;rwimg.h&quot;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_struct_bmodel">Bmodel</link> * <link linkend="_model__map_8h_1a15d28538406e013800f454770f8a23b8">model_from_images</link> (<link linkend="_class_bimage">Bimage</link> *plist)</para>

<para>Creates one or more models from 3D images. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_model__map_8h_1ace5c2637baabd40bc9bf1cb04cd827f8">img_from_model</link> (<link linkend="_struct_bmodel">Bmodel</link> *<link linkend="_tcltk__bmodel_8cpp_1a828359eaa8de833b547ac96934f43841">model</link>, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; ori, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; size, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; sam, double sigma)</para>

<para>Calculates a map from model component coordinates. </para>
</listitem>
            <listitem><para>int <link linkend="_model__map_8h_1ae5536e83d268a99aad537ecb8158a019">model_catenate_maps</link> (<link linkend="_struct_bmodel">Bmodel</link> *<link linkend="_tcltk__bmodel_8cpp_1a828359eaa8de833b547ac96934f43841">model</link>, <link linkend="_class_bstring">Bstring</link> &amp;filename)</para>

<para>Concatenates all model maps into one multi-image file. </para>
</listitem>
            <listitem><para>int <link linkend="_model__map_8h_1a3263a0e5bfa5f6bd0021c7f9111890cd">model_shell_fit</link> (<link linkend="_struct_bmodel">Bmodel</link> *<link linkend="_tcltk__bmodel_8cpp_1a828359eaa8de833b547ac96934f43841">model</link>, double hires, double lores, int neg)</para>

<para>Fits a shell model as a rigid body to a map. </para>
</listitem>
            <listitem><para>int <link linkend="_model__map_8h_1a6d24b015aae3b64a002fb48434ce0c92">model_shell_radial_profile</link> (<link linkend="_struct_bmodel">Bmodel</link> *<link linkend="_tcltk__bmodel_8cpp_1a828359eaa8de833b547ac96934f43841">model</link>)</para>

<para>Calculates a radial profile from a shell model. </para>
</listitem>
            <listitem><para><link linkend="_class_bimage">Bimage</link> * <link linkend="_model__map_8h_1a85e7bfcd88d3f3b329eb7c47b0176f0a">model_shell_power_spectrum</link> (<link linkend="_struct_bmodel">Bmodel</link> *<link linkend="_tcltk__bmodel_8cpp_1a828359eaa8de833b547ac96934f43841">model</link>, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; size, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; origin, int ft_size, int ann_min, int ann_max, double hires, double lores)</para>

<para>Calculates a radial profile from a shell model. </para>
</listitem>
            <listitem><para>int <link linkend="_model__map_8h_1ac0676cc045f8488b4ca2413454a21b3a">model_component_symmetry</link> (<link linkend="_struct_bmodel">Bmodel</link> *<link linkend="_tcltk__bmodel_8cpp_1a828359eaa8de833b547ac96934f43841">model</link>, long nangles, long ann_min, long ann_max, long ann_width, long zmin, long zmax, long zinc, long minorder, long maxorder)</para>

<para>Determines the cyclic symmetry of components. </para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Header file for model to map conversions. </para>

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

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

<para>Created: 20081112 </para>

<para>Modified: 20160606 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_model__map_8h_1ace5c2637baabd40bc9bf1cb04cd827f8"/>    <section>
    <title>img_from_model()</title>
<indexterm><primary>img_from_model</primary><secondary>model_map.h</secondary></indexterm>
<indexterm><primary>model_map.h</primary><secondary>img_from_model</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link>* img_from_model (<link linkend="_struct_bmodel">Bmodel</link> * model, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; ori, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; size, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; sam, double sigma)</computeroutput></para><para>

<para>Calculates a map from model component 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>*model</entry>
                                <entry>
<para>model. </para>
</entry>
                            </row>
                            <row>
                                <entry>ori</entry>
                                <entry>
<para>origin within new map. </para>
</entry>
                            </row>
                            <row>
                                <entry>size</entry>
                                <entry>
<para>size of new map. </para>
</entry>
                            </row>
                            <row>
                                <entry>sam</entry>
                                <entry>
<para>voxel size of new map. </para>
</entry>
                            </row>
                            <row>
                                <entry>sigma</entry>
                                <entry>
<para>gaussian sphere width. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* new map. </para>
</formalpara>
</para>
<para>
Definition at line 59 of file model_map.cpp.</para>
    </section><anchor xml:id="_model__map_8h_1ae5536e83d268a99aad537ecb8158a019"/>    <section>
    <title>model_catenate_maps()</title>
<indexterm><primary>model_catenate_maps</primary><secondary>model_map.h</secondary></indexterm>
<indexterm><primary>model_map.h</primary><secondary>model_catenate_maps</secondary></indexterm>
<para><computeroutput>int model_catenate_maps (<link linkend="_struct_bmodel">Bmodel</link> * model, <link linkend="_class_bstring">Bstring</link> &amp; filename)</computeroutput></para><para>

<para>Concatenates all model maps into one multi-image file. </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>*model</entry>
                                <entry>
<para>model. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;filename</entry>
                                <entry>
<para>new map file name. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The model map file name must be set and point to a valid file.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 158 of file model_map.cpp.</para>
    </section><anchor xml:id="_model__map_8h_1ac0676cc045f8488b4ca2413454a21b3a"/>    <section>
    <title>model_component_symmetry()</title>
<indexterm><primary>model_component_symmetry</primary><secondary>model_map.h</secondary></indexterm>
<indexterm><primary>model_map.h</primary><secondary>model_component_symmetry</secondary></indexterm>
<para><computeroutput>int model_component_symmetry (<link linkend="_struct_bmodel">Bmodel</link> * model, long nangles, long ann_min, long ann_max, long ann_width, long zmin, long zmax, long zinc, long minorder, long maxorder)</computeroutput></para><para>

<para>Determines the cyclic symmetry of components. </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>*model</entry>
                                <entry>
<para>model parameters. </para>
</entry>
                            </row>
                            <row>
                                <entry>nangles</entry>
                                <entry>
<para>number of angles. </para>
</entry>
                            </row>
                            <row>
                                <entry>ann_min</entry>
                                <entry>
<para>minimum annulus. </para>
</entry>
                            </row>
                            <row>
                                <entry>ann_max</entry>
                                <entry>
<para>maximum annulus. </para>
</entry>
                            </row>
                            <row>
                                <entry>ann_width</entry>
                                <entry>
<para>annular width. </para>
</entry>
                            </row>
                            <row>
                                <entry>zmin</entry>
                                <entry>
<para>minimum z limit. </para>
</entry>
                            </row>
                            <row>
                                <entry>zmax</entry>
                                <entry>
<para>maximum z limit. </para>
</entry>
                            </row>
                            <row>
                                <entry>zinc</entry>
                                <entry>
<para>z increment. </para>
</entry>
                            </row>
                            <row>
                                <entry>minorder</entry>
                                <entry>
<para>minimum cyclic order to search for. </para>
</entry>
                            </row>
                            <row>
                                <entry>maxorder</entry>
                                <entry>
<para>maximum cyclic order to search for. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 618 of file model_map.cpp.</para>
    </section><anchor xml:id="_model__map_8h_1a15d28538406e013800f454770f8a23b8"/>    <section>
    <title>model_from_images()</title>
<indexterm><primary>model_from_images</primary><secondary>model_map.h</secondary></indexterm>
<indexterm><primary>model_map.h</primary><secondary>model_from_images</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmodel">Bmodel</link>* model_from_images (<link linkend="_class_bimage">Bimage</link> * plist)</computeroutput></para><para>

<para>Creates one or more models from 3D images. </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>*plist</entry>
                                <entry>
<para>list of images. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmodel* new model. <literallayout><computeroutput>The model ID&apos;s are derived from the image filenames.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 28 of file model_map.cpp.</para>
    </section><anchor xml:id="_model__map_8h_1a3263a0e5bfa5f6bd0021c7f9111890cd"/>    <section>
    <title>model_shell_fit()</title>
<indexterm><primary>model_shell_fit</primary><secondary>model_map.h</secondary></indexterm>
<indexterm><primary>model_map.h</primary><secondary>model_shell_fit</secondary></indexterm>
<para><computeroutput>int model_shell_fit (<link linkend="_struct_bmodel">Bmodel</link> * model, double hires, double lores, int neg)</computeroutput></para><para>

<para>Fits a shell model as a rigid body to a map. </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>*model</entry>
                                <entry>
<para>model. </para>
</entry>
                            </row>
                            <row>
                                <entry>hires</entry>
                                <entry>
<para>high resolution limit. </para>
</entry>
                            </row>
                            <row>
                                <entry>lores</entry>
                                <entry>
<para>low resolution limit. </para>
</entry>
                            </row>
                            <row>
                                <entry>neg</entry>
                                <entry>
<para>flag to set contrast negative. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The model map file name must be set and point to a valid file.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 192 of file model_map.cpp.</para>
    </section><anchor xml:id="_model__map_8h_1a85e7bfcd88d3f3b329eb7c47b0176f0a"/>    <section>
    <title>model_shell_power_spectrum()</title>
<indexterm><primary>model_shell_power_spectrum</primary><secondary>model_map.h</secondary></indexterm>
<indexterm><primary>model_map.h</primary><secondary>model_shell_power_spectrum</secondary></indexterm>
<para><computeroutput><link linkend="_class_bimage">Bimage</link>* model_shell_power_spectrum (<link linkend="_struct_bmodel">Bmodel</link> * model, <link linkend="_class_vector3">Vector3</link>&lt; long &gt; size, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; origin, int ft_size, int ann_min, int ann_max, double hires, double lores)</computeroutput></para><para>

<para>Calculates a radial profile from a shell model. </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>*model</entry>
                                <entry>
<para>model. </para>
</entry>
                            </row>
                            <row>
                                <entry>size</entry>
                                <entry>
<para>size of component density to extract. </para>
</entry>
                            </row>
                            <row>
                                <entry>origin</entry>
                                <entry>
<para>origin for extracted densities. </para>
</entry>
                            </row>
                            <row>
                                <entry>ft_size</entry>
                                <entry>
<para>Fourier transform size. </para>
</entry>
                            </row>
                            <row>
                                <entry>ann_min</entry>
                                <entry>
<para>minimum annulus for rotational alignment. </para>
</entry>
                            </row>
                            <row>
                                <entry>ann_max</entry>
                                <entry>
<para>maximum annulus for rotational alignment. </para>
</entry>
                            </row>
                            <row>
                                <entry>hires</entry>
                                <entry>
<para>high resolution limit for cross-correlation. </para>
</entry>
                            </row>
                            <row>
                                <entry>lores</entry>
                                <entry>
<para>low resolution limit for cross-correlation. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bimage* 0. <literallayout><computeroutput>The model map file name must be set and point to a valid file.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 344 of file model_map.cpp.</para>
    </section><anchor xml:id="_model__map_8h_1a6d24b015aae3b64a002fb48434ce0c92"/>    <section>
    <title>model_shell_radial_profile()</title>
<indexterm><primary>model_shell_radial_profile</primary><secondary>model_map.h</secondary></indexterm>
<indexterm><primary>model_map.h</primary><secondary>model_shell_radial_profile</secondary></indexterm>
<para><computeroutput>int model_shell_radial_profile (<link linkend="_struct_bmodel">Bmodel</link> * model)</computeroutput></para><para>

<para>Calculates a radial profile from a shell model. </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>*model</entry>
                                <entry>
<para>model. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The model map file name must be set and point to a valid file.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 240 of file model_map.cpp.</para>
</section>
</section>
</section>
