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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_bsurf_8cpp">
<title>/Users/bernard/b20/bsoft/src/bsurf.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/bsurf.cpp</primary></indexterm>
<para>

<para>AFM image analysis and reconstruction. </para>
 
</para>
<programlisting>#include &quot;rwimg.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>int <link linkend="_bsurf_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627">main</link> (int argc, char **argv)</para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_bsurf_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
            <listitem><para>const char * <link linkend="_bsurf_8cpp_1a4de0ad4c7190962494815c0fa7f948df">use</link> []</para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>AFM image analysis and reconstruction. </para>

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

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

<para>Created: 19990124 </para>

<para>Modified: 20160604 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_bsurf_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627"/>    <section>
    <title>main()</title>
<indexterm><primary>main</primary><secondary>bsurf.cpp</secondary></indexterm>
<indexterm><primary>bsurf.cpp</primary><secondary>main</secondary></indexterm>
<para><computeroutput>int main (int argc, char ** argv)</computeroutput></para><para>
Definition at line 45 of file bsurf.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_bsurf_8cpp_1a4de0ad4c7190962494815c0fa7f948df"/>    <section>
    <title>use</title>
<indexterm><primary>use</primary><secondary>bsurf.cpp</secondary></indexterm>
<indexterm><primary>bsurf.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;bsurf&#32;[options]&#32;input.tif&#32;output.map&quot;</emphasis>,
<emphasis role="stringliteral">&quot;--------------------------------------------&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Calculates&#32;a&#32;3D&#32;surface&#32;from&#32;an&#32;AFM&#32;image.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Actions:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-expand&#32;10&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Surface&#32;expansion:&#32;value&#32;=&#32;new&#32;z&#32;dimension.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-threshold&#32;1.6,1&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Calculate&#32;a&#32;2D&#32;height&#32;image&#32;using&#32;this&#32;threshold&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;and&#32;direction:&#32;0=bottom&#32;up,&#32;1=top&#32;down.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-invert&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Invert&#32;inside&#32;&amp;&#32;outside&#32;(default&#32;not).&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;-datatype&#32;u&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Force&#32;writing&#32;of&#32;a&#32;new&#32;data&#32;type.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-positions&#32;2.5,6.3&#32;&#32;&#32;&#32;&#32;&#32;&#32;Z&#32;positions&#32;of&#32;surface&#32;minimum&#32;and&#32;maximum&#32;(angstrom).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-origin&#32;0.8,-10,15.7&#32;&#32;&#32;&#32;&#32;Set&#32;the&#32;origin&#32;(default&#32;from&#32;input&#32;image).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-sampling&#32;1.5,1.5,1.5&#32;&#32;&#32;&#32;Dimension&#32;scaling&#32;(default&#32;1,1,1&#32;A/pixel).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-resolution&#32;0.5,2.3&#32;&#32;&#32;&#32;&#32;&#32;Upper&#32;&amp;&#32;lower&#32;sigma&#32;bounds&#32;(default&#32;3.236,3.236).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-Density&#32;0.74&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Density&#32;within&#32;the&#32;surface&#32;(default&#32;0.81&#32;Da/A3).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Input:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-Stdev&#32;sd.map&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Standard&#32;deviation&#32;map&#32;(default&#32;no&#32;map).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
NULL
}
</programlisting><para>
Definition at line 18 of file bsurf.cpp.</para>
    </section><anchor xml:id="_bsurf_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>bsurf.cpp</secondary></indexterm>
<indexterm><primary>bsurf.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
