SN_micro.xml

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<section id="Section-Tasks-Microstructure">
  <title>The Microstructure Page</title>

  <para>
    The &oof2; &micro; is the digitized representation of a physical
    microstructure and is the primary object upon which &oof2;
    operates.  The &micro; is a container for &skels; and &meshes;.
    The Microstructure Page in the main &oof2; window has two main
    purposes: it creates and manages &micro; objects, and it creates
    and manages <link
    linkend="Section-Concepts-Microstructure-Pixel_Group">pixel
    groups</link>.
  </para>

  <para>
    The anatomy of the Microstructure Page is shown in <xref
    linkend="Figure-MicroPage"/>.  The Microstructure Page
    <foreignphrase>per se</foreignphrase> starts below the <link
    linkend="Figure-MainWindow">Navigation Bar</link>.  At the top is
    the <emphasis>Microstructure Chooser</emphasis>, which selects the
    &micro; on which most of the other components of the page operate.
    Below that are <link
    linkend="Section-MicrostructurePage-Buttons">buttons</link> for
    manipulating &micros; and two panes, the <link
    linkend="Section-MicrostructurePage-InfoPane">Info Pane</link> and
    the <link linkend="Section-MicrostructurePage-GroupPane">Pixel
    Group Pane</link>.
  </para>

  <figure id="Figure-MicroPage">
    <title>
      The Microstructure Page
    </title>
    <mediaobject>
      <imageobject>
	    <imagedata fileref="FIGURES/gui/micropage.png" format="PNG"
                   contentwidth="802px"/>
      </imageobject>
    </mediaobject>
  </figure>
  <section id="Section-MicrostructurePage-Buttons">
    <title>Microstructure Page Buttons</title>
    <para>
      The buttons all correspond in a straightforward fashion to items
      in the <xref linkend="MenuItem-OOF.Microstructure"/> menu, and
      the details are provided there.  The first row of buttons is
      used to create a new &micro;. 
      <itemizedlist>
	<listitem>
	  <para>
	    Use the <guibutton>New...</guibutton> button to create a
	    completely new &micro; without any associated
	    &images; (<xref
	    linkend="MenuItem-OOF.Microstructure.New"/>).
	  </para>
	</listitem>
	<listitem>
	  <para>
	    Use the <guibutton>New from Image</guibutton> button to
	    create a &micro; from an &image; that's already loaded in
	    <emphasis>another</emphasis> &micro; (<xref
	    linkend="MenuItem-OOF.Microstructure.Create_From_Image"/>).
	  </para>
	</listitem>
	<listitem>
	  <para>
	    Use the <guibutton>New from Image File</guibutton> button
	    to load a new &image; and create a &micro; from it (<xref
	    linkend="MenuItem-OOF.Microstructure.Create_From_ImageFile"/>).
	  </para>
	</listitem>
	<listitem>
	  <para>
	    Use the <guibutton>New from Orientation Map</guibutton>
	    button to load a new <link
	    linkend="Section-Concepts-Microstructure-OrientationMap"><classname>Orientation
	    Map</classname></link> and create a &micro; from
	    it (<xref
	    linkend="MenuItem-OOF.Microstructure.Create_From_OrientationMap_File"/>).
	  </para>
	</listitem>
      </itemizedlist>
      After using any of these buttons, the Microstructure chooser at
      the top of the page will automatically switch to the new
      &micro;.
    </para>
    <para>
      Most of the <guilabel>New&hellip;</guilabel> buttons bring up a
      dialog box in which the name and size of the &micro; can be
      set. If any of these parameters is set to
      <userinput>automatic</userinput>, a suitable default value will
      be used. The manual pages for the menu commands explain what
      <userinput>automatic</userinput> means in each context.  In the
      &oof2; GUI, an input field will display
      <emphasis>&lt;automatic&gt;</emphasis> in italics when its value
      is <userinput>automatic</userinput>.  See <xref
      linkend="Object-automatic"/> for the details.
    </para>
    <para>
      The second row of buttons manipulate the &micro; that's
      selected in the Microstructure chooser.
      <itemizedlist>
	<listitem>
	  <formalpara>
	    <title>Rename</title>
	    <para>
	      Rename the current &micro; (<xref
	      linkend="MenuItem-OOF.Microstructure.Rename"/>).
	    </para>
	  </formalpara>
	</listitem>
	<listitem>
	  <formalpara>
	    <title>Copy</title>
	    <para>
	      Make a duplicate of the current &micro; (<xref
	      linkend="MenuItem-OOF.Microstructure.Copy"/>).  The copy
	      will include copies of all the &images; and <link
	      linkend="Section-Concepts-Microstructure-Pixel_Group">pixel
	      groups</link> in the original, but not the <link
	      linkend="Section-Concepts-Microstructure-OrientationMap">orientation
	      maps</link>, &skels;, or &meshes;.
	    </para>
	  </formalpara>
	</listitem>
	<listitem>
	  <formalpara>
	    <title>Delete</title>
	    <para>
	      Delete the current &micro;, as well as all of its
	      &skels; and &meshes; (<xref
	      linkend="MenuItem-OOF.Microstructure.Delete"/>).
	    </para>
	  </formalpara>
	</listitem>
	<listitem>
	  <formalpara>
	    <title>Save</title>
	    <para>
	      Save the current &micro; in a file (<xref
	      linkend="MenuItem-OOF.File.Save.Microstructure"/>).  The
	      only difference between the
	      <guibutton>Save...</guibutton> button and the
	      <guimenu>File/Save/Microstructure</guimenu> command in
	      the menubar is that the <guibutton>Save...</guibutton>
	      button saves the &micro; named in the Microstructure
	      Chooser, whereas the menubar command asks for a &micro;
	      in a dialog box.
	    </para>
	  </formalpara>
	</listitem>
      </itemizedlist>
    </para>
  </section>

  <section id="Section-MicrostructurePage-InfoPane">
    <title>The Info Pane</title>
    <para>
      The Info Pane on the left lists the <link
      linkend="Section-Concepts-Microstructure-Coordinates">sizes</link>
      of the currently selected &micro;, as well as the names of any
      &images; and <link
      linkend="Section-Concepts-Microstructure-OrientationMap">orientation
      maps</link> it contains.
    </para>
  </section>
  <section id="Section-MicrostructurePage-GroupPane">
    <title>The Pixel Group Pane</title>
    <para>
      The Pixel Group Pane creates and manipulates <link
      linkend="Section-Concepts-Microstructure-Pixel_Group">pixel
      groups</link>.  Using pixel groups is in principle optional in
      &oof2;, but they provide a convenient way of storing and
      operating on sets of pixels.  The buttons on the left side and
      right sides of the pane correspond to items in the <xref
      linkend="MenuItem-OOF.PixelGroup"/> menu.  The center of the
      pane is a list of all of the pixel groups defined in the
      current &micro;. 
    </para>
    <para>
      The seven buttons to the left of the central list operate on the
      pixel groups themselves: creating a <link
      linkend="MenuItem-OOF.PixelGroup.New">new</link> group, <link
      linkend="MenuItem-OOF.PixelGroup.AutoGroup">automatically</link><footnote>
      <para>
        This command works differently from the
        <guibutton>Group</guibutton> on the <link
        linkend="Section-Tasks-Image">Image</link> page.  Compare
        <xref linkend="MenuItem-OOF.PixelGroup.AutoGroup"/> (this
        page) and <xref linkend="MenuItem-OOF.Image.AutoGroup"/>
        (Image page).
      </para>
      </footnote>
      putting all pixels into groups, <link
      linkend="MenuItem-OOF.PixelGroup.Rename">renaming</link> or
      <link linkend="MenuItem-OOF.PixelGroup.Copy">copying</link> an
      existing group, <link
      linkend="MenuItem-OOF.PixelGroup.Delete">deleting</link> a
      group, <link
      linkend="MenuItem-OOF.PixelGroup.DeleteAll">deleting all</link>
      groups, or setting a group's <link
      linkend="MenuItem-OOF.PixelGroup.Meshable">meshable</link> flag.
      All except for <guibutton>New</guibutton>,
      <guibutton>Auto</guibutton>, and <guibutton>Delete
      All</guibutton> operate on the pixel group that's currently
      selected in the list.
    </para>
    <para>
      The four buttons to the right of the central list operate on
      the <emphasis>contents</emphasis> of the currently selected
      group.  <link
      linkend="MenuItem-OOF.PixelGroup.AddSelection"><guibutton>Add</guibutton></link> button
      adds the <link
      linkend="Section-Concepts-Microstructure-PixelSelection">currently
      selected pixels</link> to the currently selected group.  The
      <link
	  linkend="MenuItem-OOF.PixelGroup.RemoveSelection"><guibutton>Remove</guibutton></link>
      button removes the currently selected pixels from the group,
      and the <link
      linkend="MenuItem-OOF.PixelGroup.Clear"><guibutton>Clear</guibutton></link>
      button empties the group entirely.  The <link
      linkend="MenuItem-OOF.PixelGroup.Query"><guibutton>Info</guibutton></link>
      button prints information about the group in the <link
      linkend="Section-Windows-Messages">Message window</link>.
    </para>
  </section>
</section>


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