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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_bshow__tomo_8tcl">
<title>/Users/bernard/b20/bsoft/tcltk/bshow_tomo.tcl File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/tcltk/bshow_tomo.tcl</primary></indexterm>
<para>

<para>Procedures to manage tomographic images. </para>
 
</para>
<simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1af5fc39d85d1ff5c03a3ada11e14f3a6b">Tomography</link></para>

<para>Dialog box to manage tomographic information. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a46087acc03c563fb392b74164882812b">setTiltAxis</link></para>

<para>Sets the tilt axis angle. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a06a4e8d204b7130048810da4a3f1c899">Tilts</link></para>

<para>Dialog box to set the tilts for a tomographic series. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ab19e3e243bdc70f4c9c2e48605e7ebb1">setTilts_and_DestroyWindow</link> w</para>

<para>Generates the tilt list for a tomographic series. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a3ca1a93f669b72f877cf10e027e180cb">readTlt</link></para>

<para>Reads tilt angles from a rawtlt file. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a0be4ba3a44b88b95f915574ac1ddce6e">drawTiltAxis</link></para>

<para>Draws the tilt axis on the canvas. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1aa35546eccdf9a42912418c00f5f3ac4f">markerSelect</link> x y</para>

<para>Selects a marker. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a69332d981cfa4d3286b4852cd74579bb">markerSelectAppend</link> x y</para>

<para>Appends marker at a location to list of selected markers. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a86ea7d832fed8d306bc5059bf2805ffe">markerSetSelection</link> x y</para>

<para>The marker selection is reset and set to within a rectangle. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a7b28a783fa731d2aae096b5d0842b3ce">markerCreateSelect</link> x y</para>

<para>Selects or creates a marker. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1aec9c77fadd944ad1167d897038f75310">markerGenerate</link></para>

<para>Generates markers from a seed. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a2a49409dfb83e08e1e4a53589c572e49">markerExtract</link></para>

<para>Extracts markers from a micrograph. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ab2511af584c84665230324ee530119c0">markerMove</link> x y</para>

<para>Moves the selected markers. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a82c5a5e2c010307852e8629be3f694cb">markerDraw</link> id</para>

<para>Draws a marker with an error line and label. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a4240ab5ae135c9d17029e7ca0a91e83a">markerDrawAll</link></para>

<para>Redraws all markers on the canvas. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1aa0c65ac918154f88c1815720f292a0a7">markerDelete</link> x y</para>

<para>Deletes the selected marker. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a8cabbde203ac6b95ab63779c7b543ed7">markerDeleteID</link> id</para>

<para>Deletes the selected marker. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a6236b38eebac5e647ba741dbf9b59ae6">markerDeleteSelected</link></para>

<para>Deletes all the selected markers. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a59172b12da3a7d0a91386091275ab792">markerDeleteSelectedAll</link></para>

<para>Deletes all the selected markers in all images. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a10ce5cf5c6bf25aa02e8775a27e40a95">markerDeleteAll</link></para>

<para>Deletes all markers. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a140a34b11b2442b5fdd05a921a26fd52">markerRenumber</link></para>

<para>Renumbers markers in the current micrograph. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a1ffe43d661b32b99680ed4b2ad1b9328">markerCenter</link></para>

<para>Centers markers in the current micrograph. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1af0373cb6dd2a9ca67af235af73592deb">markerFind</link> n</para>

<para>Finds markers in a file. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ab1ab3134464157738be15e6d1e869c6a">setEdge</link> edge</para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a9a2d9b4abce975a2c13ff1d73da06df1">markerSnap</link> x y</para>

<para>Centers the selected marker. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ae5e7ed553db8d22a9b52a7385f4249c5">updateResidual</link></para>

<para>Updates the residual calculation which also sets all marker residuals. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1aa3df66453e8a71af4bc4550b60146ab4">updateTomoTable</link></para>

<para>Updates the tomographic table from the micrograph parameters in memory. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a67307c4928876e46940d0334191778a0">updateMarkerParam</link></para>

<para>Updates marker parameters from the micrograph parameters in memory. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ac687a4356809c79adf5085d4e505d5a4">markerSetSelectFlag</link></para>

<para>Sets the selection flag for the selected markers. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ab6047eb8dfaa45cf9100f5dca605ea32">markerClearSelectFlag</link></para>

<para>Clears the selection flag for the selected markers. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1affd26645bc18468d6abbe7867c7db3a4">markerTable</link></para>

<para>Sets up the window for the marker table and updates it. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ad273229de20226bc636da37872a56cdd">updateMarkerTable</link></para>

<para>Updates the marker table. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a830352d054365f01d194a7fecc54a34c">moveCanvasTo</link> img_num loc</para>

<para>Centers the viewable canvas on the location in the image. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1af0a24806912ed57774e102d84167d5d0">goToMarker</link> w id isel img</para>

<para>Goes to a marker. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a165a6e7003459eef0bc1a1b4c8e89c30">markerNextResidual</link> w dir</para>

<para>Goes to the next marker based on its residual. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a8c3e811e2bf617436060fb75a566bb75">markerNextFOM</link> w dir</para>

<para>Goes to next marker based on its FOM. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a31a8b9fb704662f8eac491ff7bcfe3d1">markerAcceptModelLocation</link></para>

<para>Accepts the model locations of selected markers. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a0cb08f84a9d1a14c747088a6859e022b">alignAverageFrames</link></para>

<para>Aligns a series of frames from dose fractionation. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1afd881d88abfcb5fd116816ec339bfff5">doAlignAverageFrames</link> w</para>

<para>Aligns and averages frames. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a7d0b20a25a3da9fdd1edff870e55d4b9">normalizeImages</link></para>

<para>Normalizes a series of images based on simple statistics. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1abe7476ffe19173f2ea0bbafaaf256fc0">doNormalizeImages</link> w</para>

<para>Normalizes images. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ae73ff91ba408975ff0b788377bb1acc0">findTiltAxis</link></para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a5e715ca364a65e7cc811abd8a0e4147e">doFindTiltAxis</link> w</para>

<para>Executes the tilt axis search. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a68a99a5cfaf0a1a2af6f9f8fffa3c6e7">markerTransfer</link></para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a59be90bdadb677c93e60e9eceef7f643">doMarkerTransfer</link> w</para>

<para>Executes the marker transfer. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a9beb0198dc17d8ff5040bbb6d3d7e495">markerTrack</link></para>

<para>Tracks the markers through the tilt series. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ab3af8f9a793afdda6a570e1bdc03c055">doMarkerTrack</link> w</para>

<para>Executes marker tracking. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a8c06ac70125706cc261b7ac3fda9a0f3">markerRefine</link></para>

<para>Refines marker positions and micrograph geometry. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a3354db64340999cbd0a941a4647d84a3">doMarkerRefine</link> w</para>

<para>Does a refinement of markers or views. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1aace5de681b93191a6d46b685c0d62bc1">refineMarker</link></para>

<para>Refines one marker position. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a20ec2b8f52029efb836d325d524edef4">tomoPowerSpectra</link></para>

<para>Dialog box for calculating tilt-adjusted power spectra. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a3ddba3d63b4d50a997eff0b248c12808">doTomoPowerSpectra</link> w</para>

<para>Calculating tilt-adjusted power spectra. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a36f87581b176eb8394b9cc6b9cb1714c">tomoResolution</link></para>

<para>Estimates the resolution of images in a tilt series. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a9b24887c93abbf41e0fef7d4edb099af">doTomoResolution</link> w</para>

<para>Executes estimation of the resolution of the tilt series. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1aa39599c900107e0744952eb8060564ae">tomoReconstruct</link></para>

<para>Reconstructs a tomogram. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ac9e9237f967224c44ec29bd66ec685d8">doTomoReconstruct</link> w</para>

<para>Executes tomogram reconstruction. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1a29a7cd751a75ccc4b41d569c4d30df5b">tomoDenoise</link></para>

<para>Denoises a tomogram. </para>
</listitem>
            <listitem><para><link linkend="_bshow__tomo_8tcl_1ab560fd1a2a0b02812dc8c23151f33a09">doTomoDenoise</link> w</para>

<para>Executes tomogram denoising. </para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Procedures to manage tomographic images. </para>

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

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

<para>Created: 20021112 </para>

<para>Modified: 20180730 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_bshow__tomo_8tcl_1a0cb08f84a9d1a14c747088a6859e022b"/>    <section>
    <title>alignAverageFrames()</title>
<indexterm><primary>alignAverageFrames</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>alignAverageFrames</secondary></indexterm>
<para><computeroutput>alignAverageFrames</computeroutput></para><para>

<para>Aligns a series of frames from dose fractionation. </para>
</para>
<para>
Definition at line 1234 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1afd881d88abfcb5fd116816ec339bfff5"/>    <section>
    <title>doAlignAverageFrames()</title>
<indexterm><primary>doAlignAverageFrames</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doAlignAverageFrames</secondary></indexterm>
<para><computeroutput>doAlignAverageFrames w </computeroutput></para><para>

<para>Aligns and averages frames. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1284 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a5e715ca364a65e7cc811abd8a0e4147e"/>    <section>
    <title>doFindTiltAxis()</title>
<indexterm><primary>doFindTiltAxis</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doFindTiltAxis</secondary></indexterm>
<para><computeroutput>doFindTiltAxis w </computeroutput></para><para>

<para>Executes the tilt axis search. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1417 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a3354db64340999cbd0a941a4647d84a3"/>    <section>
    <title>doMarkerRefine()</title>
<indexterm><primary>doMarkerRefine</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doMarkerRefine</secondary></indexterm>
<para><computeroutput>doMarkerRefine w </computeroutput></para><para>

<para>Does a refinement of markers or views. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1643 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ab3af8f9a793afdda6a570e1bdc03c055"/>    <section>
    <title>doMarkerTrack()</title>
<indexterm><primary>doMarkerTrack</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doMarkerTrack</secondary></indexterm>
<para><computeroutput>doMarkerTrack w </computeroutput></para><para>

<para>Executes marker tracking. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1566 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a59be90bdadb677c93e60e9eceef7f643"/>    <section>
    <title>doMarkerTransfer()</title>
<indexterm><primary>doMarkerTransfer</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doMarkerTransfer</secondary></indexterm>
<para><computeroutput>doMarkerTransfer w </computeroutput></para><para>

<para>Executes the marker transfer. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1484 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1abe7476ffe19173f2ea0bbafaaf256fc0"/>    <section>
    <title>doNormalizeImages()</title>
<indexterm><primary>doNormalizeImages</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doNormalizeImages</secondary></indexterm>
<para><computeroutput>doNormalizeImages w </computeroutput></para><para>

<para>Normalizes 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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1348 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ab560fd1a2a0b02812dc8c23151f33a09"/>    <section>
    <title>doTomoDenoise()</title>
<indexterm><primary>doTomoDenoise</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doTomoDenoise</secondary></indexterm>
<para><computeroutput>doTomoDenoise w </computeroutput></para><para>

<para>Executes tomogram denoising. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1999 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a3ddba3d63b4d50a997eff0b248c12808"/>    <section>
    <title>doTomoPowerSpectra()</title>
<indexterm><primary>doTomoPowerSpectra</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doTomoPowerSpectra</secondary></indexterm>
<para><computeroutput>doTomoPowerSpectra w </computeroutput></para><para>

<para>Calculating tilt-adjusted power spectra. </para>
</para>
<para>
Definition at line 1742 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ac9e9237f967224c44ec29bd66ec685d8"/>    <section>
    <title>doTomoReconstruct()</title>
<indexterm><primary>doTomoReconstruct</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doTomoReconstruct</secondary></indexterm>
<para><computeroutput>doTomoReconstruct w </computeroutput></para><para>

<para>Executes tomogram 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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1911 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a9b24887c93abbf41e0fef7d4edb099af"/>    <section>
    <title>doTomoResolution()</title>
<indexterm><primary>doTomoResolution</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>doTomoResolution</secondary></indexterm>
<para><computeroutput>doTomoResolution w </computeroutput></para><para>

<para>Executes estimation of the resolution of the tilt series. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1818 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a0be4ba3a44b88b95f915574ac1ddce6e"/>    <section>
    <title>drawTiltAxis()</title>
<indexterm><primary>drawTiltAxis</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>drawTiltAxis</secondary></indexterm>
<para><computeroutput>drawTiltAxis</computeroutput></para><para>

<para>Draws the tilt axis on the canvas. </para>
</para>
<para>
Definition at line 354 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ae73ff91ba408975ff0b788377bb1acc0"/>    <section>
    <title>findTiltAxis()</title>
<indexterm><primary>findTiltAxis</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>findTiltAxis</secondary></indexterm>
<para><computeroutput>findTiltAxis</computeroutput></para><para>
Definition at line 1365 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1af0a24806912ed57774e102d84167d5d0"/>    <section>
    <title>goToMarker()</title>
<indexterm><primary>goToMarker</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>goToMarker</secondary></indexterm>
<para><computeroutput>goToMarker w id isel img </computeroutput></para><para>

<para>Goes to a marker. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                            <row>
                                <entry>id</entry>
                                <entry>
<para>marker identifier </para>
</entry>
                            </row>
                            <row>
                                <entry>isel</entry>
                                <entry>
<para>offset in table ? </para>
</entry>
                            </row>
                            <row>
                                <entry>img</entry>
                                <entry>
<para>micrograph index </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1086 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a31a8b9fb704662f8eac491ff7bcfe3d1"/>    <section>
    <title>markerAcceptModelLocation()</title>
<indexterm><primary>markerAcceptModelLocation</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerAcceptModelLocation</secondary></indexterm>
<para><computeroutput>markerAcceptModelLocation</computeroutput></para><para>

<para>Accepts the model locations of selected markers. </para>
</para>
<para>
Definition at line 1215 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a1ffe43d661b32b99680ed4b2ad1b9328"/>    <section>
    <title>markerCenter()</title>
<indexterm><primary>markerCenter</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerCenter</secondary></indexterm>
<para><computeroutput>markerCenter</computeroutput></para><para>

<para>Centers markers in the current micrograph. </para>
</para>
<para>
Definition at line 764 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ab6047eb8dfaa45cf9100f5dca605ea32"/>    <section>
    <title>markerClearSelectFlag()</title>
<indexterm><primary>markerClearSelectFlag</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerClearSelectFlag</secondary></indexterm>
<para><computeroutput>markerClearSelectFlag</computeroutput></para><para>

<para>Clears the selection flag for the selected markers. </para>
</para>
<para>
Definition at line 952 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a7b28a783fa731d2aae096b5d0842b3ce"/>    <section>
    <title>markerCreateSelect()</title>
<indexterm><primary>markerCreateSelect</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerCreateSelect</secondary></indexterm>
<para><computeroutput>markerCreateSelect x y </computeroutput></para><para>

<para>Selects or creates a marker. </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>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Marker position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 474 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1aa0c65ac918154f88c1815720f292a0a7"/>    <section>
    <title>markerDelete()</title>
<indexterm><primary>markerDelete</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerDelete</secondary></indexterm>
<para><computeroutput>markerDelete x y </computeroutput></para><para>

<para>Deletes the selected marker. </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>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Marker position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 684 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a10ce5cf5c6bf25aa02e8775a27e40a95"/>    <section>
    <title>markerDeleteAll()</title>
<indexterm><primary>markerDeleteAll</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerDeleteAll</secondary></indexterm>
<para><computeroutput>markerDeleteAll</computeroutput></para><para>

<para>Deletes all markers. </para>
</para>
<para>
Definition at line 741 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a8cabbde203ac6b95ab63779c7b543ed7"/>    <section>
    <title>markerDeleteID()</title>
<indexterm><primary>markerDeleteID</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerDeleteID</secondary></indexterm>
<para><computeroutput>markerDeleteID id </computeroutput></para><para>

<para>Deletes the selected marker. </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>id</entry>
                                <entry>
<para>Marker identifier. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 700 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a6236b38eebac5e647ba741dbf9b59ae6"/>    <section>
    <title>markerDeleteSelected()</title>
<indexterm><primary>markerDeleteSelected</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerDeleteSelected</secondary></indexterm>
<para><computeroutput>markerDeleteSelected</computeroutput></para><para>

<para>Deletes all the selected markers. </para>
</para>
<para>
Definition at line 714 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a59172b12da3a7d0a91386091275ab792"/>    <section>
    <title>markerDeleteSelectedAll()</title>
<indexterm><primary>markerDeleteSelectedAll</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerDeleteSelectedAll</secondary></indexterm>
<para><computeroutput>markerDeleteSelectedAll</computeroutput></para><para>

<para>Deletes all the selected markers in all images. </para>
</para>
<para>
Definition at line 729 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a82c5a5e2c010307852e8629be3f694cb"/>    <section>
    <title>markerDraw()</title>
<indexterm><primary>markerDraw</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerDraw</secondary></indexterm>
<para><computeroutput>markerDraw id </computeroutput></para><para>

<para>Draws a marker with an error line and label. </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>id</entry>
                                <entry>
<para>Marker identifier. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 600 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a4240ab5ae135c9d17029e7ca0a91e83a"/>    <section>
    <title>markerDrawAll()</title>
<indexterm><primary>markerDrawAll</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerDrawAll</secondary></indexterm>
<para><computeroutput>markerDrawAll</computeroutput></para><para>

<para>Redraws all markers on the canvas. </para>
</para>
<para>
Definition at line 656 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a2a49409dfb83e08e1e4a53589c572e49"/>    <section>
    <title>markerExtract()</title>
<indexterm><primary>markerExtract</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerExtract</secondary></indexterm>
<para><computeroutput>markerExtract</computeroutput></para><para>

<para>Extracts markers from a micrograph. </para>
</para>
<para>
Definition at line 542 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1af0373cb6dd2a9ca67af235af73592deb"/>    <section>
    <title>markerFind()</title>
<indexterm><primary>markerFind</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerFind</secondary></indexterm>
<para><computeroutput>markerFind n </computeroutput></para><para>

<para>Finds markers in a 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>n</entry>
                                <entry>
<para>Image number. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 778 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1aec9c77fadd944ad1167d897038f75310"/>    <section>
    <title>markerGenerate()</title>
<indexterm><primary>markerGenerate</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerGenerate</secondary></indexterm>
<para><computeroutput>markerGenerate</computeroutput></para><para>

<para>Generates markers from a seed. </para>
</para>
<para>
Definition at line 530 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ab2511af584c84665230324ee530119c0"/>    <section>
    <title>markerMove()</title>
<indexterm><primary>markerMove</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerMove</secondary></indexterm>
<para><computeroutput>markerMove x y </computeroutput></para><para>

<para>Moves the selected markers. </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>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Mouse position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 564 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a8c3e811e2bf617436060fb75a566bb75"/>    <section>
    <title>markerNextFOM()</title>
<indexterm><primary>markerNextFOM</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerNextFOM</secondary></indexterm>
<para><computeroutput>markerNextFOM w dir </computeroutput></para><para>

<para>Goes to next marker based on its FOM. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                            <row>
                                <entry>dir</entry>
                                <entry>
<para>direction: min, lower, higher, max </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1163 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a165a6e7003459eef0bc1a1b4c8e89c30"/>    <section>
    <title>markerNextResidual()</title>
<indexterm><primary>markerNextResidual</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerNextResidual</secondary></indexterm>
<para><computeroutput>markerNextResidual w dir </computeroutput></para><para>

<para>Goes to the next marker based on its residual. </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>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                            <row>
                                <entry>dir</entry>
                                <entry>
<para>direction: min, lower, higher, max </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1109 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a8c06ac70125706cc261b7ac3fda9a0f3"/>    <section>
    <title>markerRefine()</title>
<indexterm><primary>markerRefine</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerRefine</secondary></indexterm>
<para><computeroutput>markerRefine</computeroutput></para><para>

<para>Refines marker positions and micrograph geometry. </para>
</para>
<para>
Definition at line 1595 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a140a34b11b2442b5fdd05a921a26fd52"/>    <section>
    <title>markerRenumber()</title>
<indexterm><primary>markerRenumber</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerRenumber</secondary></indexterm>
<para><computeroutput>markerRenumber</computeroutput></para><para>

<para>Renumbers markers in the current micrograph. </para>
</para>
<para>
Definition at line 752 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1aa35546eccdf9a42912418c00f5f3ac4f"/>    <section>
    <title>markerSelect()</title>
<indexterm><primary>markerSelect</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerSelect</secondary></indexterm>
<para><computeroutput>markerSelect x y </computeroutput></para><para>

<para>Selects a marker. </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>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Marker position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 398 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a69332d981cfa4d3286b4852cd74579bb"/>    <section>
    <title>markerSelectAppend()</title>
<indexterm><primary>markerSelectAppend</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerSelectAppend</secondary></indexterm>
<para><computeroutput>markerSelectAppend x y </computeroutput></para><para>

<para>Appends marker at a location to list of selected markers. </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>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Cursor position in window coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 433 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ac687a4356809c79adf5085d4e505d5a4"/>    <section>
    <title>markerSetSelectFlag()</title>
<indexterm><primary>markerSetSelectFlag</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerSetSelectFlag</secondary></indexterm>
<para><computeroutput>markerSetSelectFlag</computeroutput></para><para>

<para>Sets the selection flag for the selected markers. </para>
</para>
<para>
Definition at line 938 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a86ea7d832fed8d306bc5059bf2805ffe"/>    <section>
    <title>markerSetSelection()</title>
<indexterm><primary>markerSetSelection</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerSetSelection</secondary></indexterm>
<para><computeroutput>markerSetSelection x y </computeroutput></para><para>

<para>The marker selection is reset and set to within a rectangle. </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>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Marker position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 447 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a9a2d9b4abce975a2c13ff1d73da06df1"/>    <section>
    <title>markerSnap()</title>
<indexterm><primary>markerSnap</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerSnap</secondary></indexterm>
<para><computeroutput>markerSnap x y </computeroutput></para><para>

<para>Centers the selected marker. </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>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Marker position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 845 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1affd26645bc18468d6abbe7867c7db3a4"/>    <section>
    <title>markerTable()</title>
<indexterm><primary>markerTable</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerTable</secondary></indexterm>
<para><computeroutput>markerTable</computeroutput></para><para>

<para>Sets up the window for the marker table and updates it. </para>
</para>
<para>
Definition at line 966 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a9beb0198dc17d8ff5040bbb6d3d7e495"/>    <section>
    <title>markerTrack()</title>
<indexterm><primary>markerTrack</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerTrack</secondary></indexterm>
<para><computeroutput>markerTrack</computeroutput></para><para>

<para>Tracks the markers through the tilt series. </para>
</para>
<para>
Definition at line 1506 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a68a99a5cfaf0a1a2af6f9f8fffa3c6e7"/>    <section>
    <title>markerTransfer()</title>
<indexterm><primary>markerTransfer</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>markerTransfer</secondary></indexterm>
<para><computeroutput>markerTransfer</computeroutput></para><para>
Definition at line 1441 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a830352d054365f01d194a7fecc54a34c"/>    <section>
    <title>moveCanvasTo()</title>
<indexterm><primary>moveCanvasTo</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>moveCanvasTo</secondary></indexterm>
<para><computeroutput>moveCanvasTo img_num loc </computeroutput></para><para>

<para>Centers the viewable canvas on the location in the 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>img_num</entry>
                                <entry>
<para>image number. </para>
</entry>
                            </row>
                            <row>
                                <entry>loc</entry>
                                <entry>
<para>location list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1063 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a7d0b20a25a3da9fdd1edff870e55d4b9"/>    <section>
    <title>normalizeImages()</title>
<indexterm><primary>normalizeImages</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>normalizeImages</secondary></indexterm>
<para><computeroutput>normalizeImages</computeroutput></para><para>

<para>Normalizes a series of images based on simple statistics. </para>
</para>
<para>
Definition at line 1304 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a3ca1a93f669b72f877cf10e027e180cb"/>    <section>
    <title>readTlt()</title>
<indexterm><primary>readTlt</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>readTlt</secondary></indexterm>
<para><computeroutput>readTlt</computeroutput></para><para>

<para>Reads tilt angles from a rawtlt file. </para>
</para>
<para>
Definition at line 326 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1aace5de681b93191a6d46b685c0d62bc1"/>    <section>
    <title>refineMarker()</title>
<indexterm><primary>refineMarker</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>refineMarker</secondary></indexterm>
<para><computeroutput>refineMarker</computeroutput></para><para>

<para>Refines one marker position. </para>
</para>
<para>
Definition at line 1663 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ab1ab3134464157738be15e6d1e869c6a"/>    <section>
    <title>setEdge()</title>
<indexterm><primary>setEdge</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>setEdge</secondary></indexterm>
<para><computeroutput>setEdge edge </computeroutput></para><para>
Definition at line 831 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a46087acc03c563fb392b74164882812b"/>    <section>
    <title>setTiltAxis()</title>
<indexterm><primary>setTiltAxis</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>setTiltAxis</secondary></indexterm>
<para><computeroutput>setTiltAxis</computeroutput></para><para>

<para>Sets the tilt axis angle. </para>
</para>
<para>
Definition at line 253 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ab19e3e243bdc70f4c9c2e48605e7ebb1"/>    <section>
    <title>setTilts_and_DestroyWindow()</title>
<indexterm><primary>setTilts_and_DestroyWindow</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>setTilts_and_DestroyWindow</secondary></indexterm>
<para><computeroutput>setTilts_and_DestroyWindow w </computeroutput></para><para>

<para>Generates the tilt list for a tomographic series. </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>w</entry>
                                <entry>
<para>the window to destroy. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 306 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a06a4e8d204b7130048810da4a3f1c899"/>    <section>
    <title>Tilts()</title>
<indexterm><primary>Tilts</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>Tilts</secondary></indexterm>
<para><computeroutput>Tilts</computeroutput></para><para>

<para>Dialog box to set the tilts for a tomographic series. </para>
</para>
<para>
Definition at line 264 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a29a7cd751a75ccc4b41d569c4d30df5b"/>    <section>
    <title>tomoDenoise()</title>
<indexterm><primary>tomoDenoise</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>tomoDenoise</secondary></indexterm>
<para><computeroutput>tomoDenoise</computeroutput></para><para>

<para>Denoises a tomogram. </para>
</para>
<para>
Definition at line 1946 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1af5fc39d85d1ff5c03a3ada11e14f3a6b"/>    <section>
    <title>Tomography()</title>
<indexterm><primary>Tomography</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>Tomography</secondary></indexterm>
<para><computeroutput>Tomography</computeroutput></para><para>

<para>Dialog box to manage tomographic information. </para>
</para>
<para>
Definition at line 27 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a20ec2b8f52029efb836d325d524edef4"/>    <section>
    <title>tomoPowerSpectra()</title>
<indexterm><primary>tomoPowerSpectra</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>tomoPowerSpectra</secondary></indexterm>
<para><computeroutput>tomoPowerSpectra</computeroutput></para><para>

<para>Dialog box for calculating tilt-adjusted power spectra. </para>
</para>
<para>
Definition at line 1681 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1aa39599c900107e0744952eb8060564ae"/>    <section>
    <title>tomoReconstruct()</title>
<indexterm><primary>tomoReconstruct</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>tomoReconstruct</secondary></indexterm>
<para><computeroutput>tomoReconstruct</computeroutput></para><para>

<para>Reconstructs a tomogram. </para>
</para>
<para>
Definition at line 1844 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a36f87581b176eb8394b9cc6b9cb1714c"/>    <section>
    <title>tomoResolution()</title>
<indexterm><primary>tomoResolution</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>tomoResolution</secondary></indexterm>
<para><computeroutput>tomoResolution</computeroutput></para><para>

<para>Estimates the resolution of images in a tilt series. </para>
</para>
<para>
Definition at line 1770 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1a67307c4928876e46940d0334191778a0"/>    <section>
    <title>updateMarkerParam()</title>
<indexterm><primary>updateMarkerParam</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>updateMarkerParam</secondary></indexterm>
<para><computeroutput>updateMarkerParam</computeroutput></para><para>

<para>Updates marker parameters from the micrograph parameters in memory. </para>
</para>
<para>
Definition at line 919 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ad273229de20226bc636da37872a56cdd"/>    <section>
    <title>updateMarkerTable()</title>
<indexterm><primary>updateMarkerTable</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>updateMarkerTable</secondary></indexterm>
<para><computeroutput>updateMarkerTable</computeroutput></para><para>

<para>Updates the marker table. </para>
</para>
<para>
Definition at line 1044 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1ae5e7ed553db8d22a9b52a7385f4249c5"/>    <section>
    <title>updateResidual()</title>
<indexterm><primary>updateResidual</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>updateResidual</secondary></indexterm>
<para><computeroutput>updateResidual</computeroutput></para><para>

<para>Updates the residual calculation which also sets all marker residuals. </para>
</para>
<para>
Definition at line 860 of file bshow_tomo.tcl.</para>
    </section><anchor xml:id="_bshow__tomo_8tcl_1aa3df66453e8a71af4bc4550b60146ab4"/>    <section>
    <title>updateTomoTable()</title>
<indexterm><primary>updateTomoTable</primary><secondary>bshow_tomo.tcl</secondary></indexterm>
<indexterm><primary>bshow_tomo.tcl</primary><secondary>updateTomoTable</secondary></indexterm>
<para><computeroutput>updateTomoTable</computeroutput></para><para>

<para>Updates the tomographic table from the micrograph parameters in memory. </para>
</para>
<para>
Definition at line 871 of file bshow_tomo.tcl.</para>
</section>
</section>
</section>
