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==Tables== ===Table 1 - Login and Software=== <table border="1"> <tr> <td valign="top" width="200">xuct</td> <td valign="top" width="500">login password</td> </tr> <tr> <td valign="top" width="200">eve, lse, e</td> <td valign="top" width="500"> text editors</td> </tr> <tr> <td valign="top" width="200">spa corelut</td> <td valign="top" width="500">spawn a process</td> </tr> <tr> <td valign="top" width="200">uct</td> <td valign="top" width="500">main program</td> </tr> <tr> <td valign="top" width="200">uct_evaluation</td> <td valign="top" width="500"> </td> </tr> <tr> <td valign="top" width="200">uct_3d</td> <td valign="top" width="500"> </td> </tr> <tr> <td valign="top" width="200">uct_backup</td> <td valign="top" width="500"> </td> </tr> <tr> <td valign="top" width="200">aix C0000104.AIM</td> <td valign="top" width="500">examine an AIM</td> </tr> <tr> <td valign="top" width="200">aio 13</td> <td valign="top" width="500">AIM filtrations (list of procedures)</td> </tr> <tr> <td valign="top" width="200">sap</td> <td valign="top" width="500">2d AIM viewing tool</td> </tr> <tr> <td valign="top" width="200">sap -s aimfile.aim</td> <td valign="top" width="500">Opens the given AIM in sap.</td> </tr> <tr> <td valign="top" width="200">pwindow /nowait</td> <td valign="top" width="500">capture a window as TIF, GIF, etc.</td> </tr> <tr> <td valign="top" width="200">viza /nowait</td> <td valign="top" width="500">3d viewer (requires mcubes result)</td> </tr> <tr> <td valign="top" width="200">mcubes</td> <td valign="top" width="500">marching cubes</td> </tr> <tr> <td valign="top" width="200">help <code>arg</code></td> <td valign="top" width="500"> </td> </tr> <tr> <td valign="top" width="200">sh sym <code>arg</code></td> <td valign="top" width="500"> </td> </tr> <tr> <td valign="top" width="200">aimod</td> <td valign="top" width="500">to alter the dim, pos, el_size_mm, etc of an aim. Use ‘e’ to end input parameters.</td> </tr> </table> ===Table 2 - Commands and Aliases=== <table border="1"> <tr> <td valign="top" width="200">ds</td> <td valign="top" width="500">directory, with file sizes</td> </tr> <tr> <td valign="top" width="200">dh</td> <td valign="top" width="500">directory, with whole path</td> </tr> <tr> <td valign="top" width="200">dh0</td> <td valign="top" width="500">for all the files in lower directories beginning with ‘0’.</td> </tr> <tr> <td valign="top" width="200">-</td> <td valign="top" width="500">to continue command to next line</td> </tr> <tr> <td valign="top" width="200">sh sym dd</td> <td valign="top" width="500">shows symbol value {executable, path}</td> </tr> <tr> <td valign="top" width="200">sh log ud</td> <td valign="top" width="500">shows a logical value {path}</td> </tr> <tr> <td valign="top" width="200">dec</td> <td valign="top" width="500">delete file (with confirmation)</td> </tr> <tr> <td valign="top" width="200">del</td> <td valign="top" width="500">delete file (no confirmation)</td> </tr> <tr> <td valign="top" width="200">decisq</td> <td valign="top" width="500">delete ISQ file</td> </tr> <tr> <td valign="top" width="200">sh dev ud (sdud)</td> <td valign="top" width="500">report disk space (38881940 blocks equals ~19GB)</td> </tr> <tr> <td valign="top" width="200">sdur</td> <td valign="top" width="500">report disk space on measurement disk</td> </tr> <tr> <td valign="top" width="200">onjane</td> <td valign="top" width="500">set display to jane (jane.ethz.ch)</td> </tr> <tr> <td valign="top" width="200">onblund</td> <td valign="top" width="500">set display to blund (blund.ethz.ch)</td> </tr> <tr> <td valign="top" width="200">cd scratch</td> <td valign="top" width="500">view scratch directory (e.g. see MEASUREMENT_233.LOG;1)</td> </tr> <tr> <td valign="top" width="200">sh que <nowiki>*reco*</nowiki></td> <td valign="top" width="500">show reconstruction queue (also, sq <nowiki>*reco*</nowiki>)</td> </tr> <tr> <td valign="top" width="200">sh que <nowiki>*meas*</nowiki></td> <td valign="top" width="500">show measurement queue</td> </tr> <tr> <td valign="top" width="200">sh que <nowiki>*eval*</nowiki></td> <td valign="top" width="500">show evaluation queue</td> </tr> <tr> <td valign="top" width="200">del <nowiki>/entry=#</nowiki></td> <td valign="top" width="500">delete a process off queue (use see to view entry numbers)</td> </tr> <tr> <td valign="top" width="200">tp0</td> <td valign="top" width="500">tape drive for backups</td> </tr> <tr> <td valign="top" width="200">sh dev tp0 /full</td> <td valign="top" width="500">shows all information about tape drive (including if somebody has mounted it).</td> </tr> <tr> <td valign="top" width="200">purge filename</td> <td valign="top" width="500">deletes all files except for the latest version.</td> </tr> <tr> <td valign="top" width="200">v1 filename</td> <td valign="top" width="500">renames the latest version to version 1.</td> </tr> <tr> <td valign="top" width="200">dsg</td> <td valign="top" width="500">type from project directory (ur) to get a report of disk space used by all projects.</td> </tr> <tr> <td valign="top" width="200">term</td> <td valign="top" width="500">opens a new terminal (new blund terminal).</td> </tr> <tr> <td valign="top" width="200">sb 1217</td> <td valign="top" width="500">show batch info after you know the process id from the <code>see</code> command.</td> </tr> <tr> <td valign="top" width="200">sb 1217/cont</td> <td valign="top" width="500">shows the continuous cpu usage. Type <code>e</code> to exit.</td> </tr> <tr> <td valign="top" width="200">qm</td> <td valign="top" width="500">In a busy terminal, type <code>qm s "this is done"</code> to send a mail to myself.</td> </tr> <tr> <td valign="top" width="200">qmm</td> <td valign="top" width="500">Type <code>qmm s “this is done”</code> to put a mail on <i>measurement</i> queue (<code>m</code>).</td> </tr> <tr> <td valign="top" width="200">qme</td> <td valign="top" width="500">Type <code>qme s “this is done” </code> to put a mail on <i>evaluation </i>queue (<code>e</code>).</td> </tr> <tr> <td valign="top" width="200">qmr</td> <td valign="top" width="500">Type <code>qmr s “this is done”</code> to put a mail on <i>reconstruction </i>queue (<code>r</code>).</td> </tr> <tr> <td valign="top" width="200">beep</td> <td valign="top" width="500">Makes a beep sound!</td> </tr> <tr> <td valign="top" width="200">se ipl</td> <td valign="top" width="500">To look at just the jobs with IPL in the job name.</td> </tr> <tr> <td valign="top" width="200">read_meas</td> <td valign="top" width="500">Takes a measurement number and reports info on it (i.e. backup tape name etc).</td> </tr> <tr> <td valign="top" width="200">sh que /all <nowiki>*$mou*</nowiki></td> <td valign="top" width="500">Show printer queue.</td> </tr> <tr> <td valign="top" width="200">sm</td> <td valign="top" width="500">show memory</td> </tr> <tr> <td valign="top" width="200">monitor/interval=1processes/topcpu</td> <td valign="top" width="500">Every 1 second update the cpu usage. Use ctrl-Z to quit. Type <code>monitor/interval=1 processes/topcpu</code></td> </tr> <tr> <td valign="top" width="200">ss</td> <td valign="top" width="500">show current system processes</td> </tr> <tr> <td valign="top" width="200">show proc</td> <td valign="top" width="500">to see who is user</td> </tr> <tr> <td valign="top" width="200">stop <code>jobname</code></td> <td valign="top" width="500">to kill a process</td> </tr> <tr> <td valign="top" width="200">onlocal</td> <td valign="top" width="500">make display on the local machine (i.e. if you’re at blund, display is at blund). or <code>SET DISP/CREATE/TRANSPORT=TCPIP/NODE=SCAPULA.EE.ETHZ.CH</code></td> </tr> <tr> <td valign="top" width="200">dk40</td> <td valign="top" width="500">sets disk to DISK40</td> </tr> <tr> <td valign="top" width="200">dk50</td> <td valign="top" width="500">sets disk to DISK50</td> </tr> <tr> <td valign="top" width="200">help lex</td> <td valign="top" width="500">returns the possible lexical commands for script files (e.g. <code>F$SEARCH</code>)</td> </tr> <tr> <td valign="top" width="200"> move files</td> <td valign="top" width="500"><code>rename myfiles*.* [.TEMP]</code></td> </tr> <tr> <td valign="top" width="200">move files</td> <td valign="top" width="500"><code>rename myfiles*.* [-], rename myfiles*.* [-.-]</code></td> </tr> <tr> <td valign="top" width="200">see</td> <td valign="top" width="500">see current processes (<code>show entry/by=executing /full</code>)</td> </tr> <tr> <td valign="top" width="200">se ipl/full</td> <td valign="top" width="500">see ipl processes on queue</td> </tr> <tr> <td valign="top" width="200">ss</td> <td valign="top" width="500">show system processes</td> </tr> <tr> <td valign="top" width="200">stop <<code>proc id</code>></td> <td valign="top" width="500">kill a system process (i.e. <code>stop UCT_LUT7BB8</code>)</td> </tr> <tr> <td valign="top" width="200">move</td> <td valign="top" width="500">move or rename a file</td> </tr> <tr> <td valign="top" width="200">copy</td> <td valign="top" width="500">duplicate file</td> </tr> <tr> <td valign="top" width="200">rename</td> <td valign="top" width="500">move/copy files</td> </tr> <tr> <td valign="top" width="200">rename test.dir [-]</td> <td valign="top" width="500">to move up</td> </tr> <tr> <td valign="top" width="200">rename test.dir [.models]</td> <td valign="top" width="500">change name to models</td> </tr> <tr> <td valign="top" width="200">more</td> <td valign="top" width="500">view file contents</td> </tr> <tr> <td valign="top" width="200">ud *224 0</td> <td valign="top" width="500">goto DISK40:[DATA.UCT.00000224.00000404]</td> </tr> <tr> <td valign="top" width="200">lo</td> <td valign="top" width="500">logout</td> </tr> <tr> <td valign="top" width="200">ur</td> <td valign="top" width="500">goto DISK40:[DATA.UCT.PROJECTS]</td> </tr> <tr> <td valign="top" width="200">or</td> <td valign="top" width="500">goto OBL projects</td> </tr> <tr> <td valign="top" width="200">ret</td> <td valign="top" width="500">return to previous directory</td> </tr> <tr> <td valign="top" width="200">tup</td> <td valign="top" width="500">check utility processing</td> </tr> <tr> <td valign="top" width="200">v1</td> <td valign="top" width="500">reduces to newest file</td> </tr> <tr> <td valign="top" width="200">dd</td> <td valign="top" width="500">directory, with dates</td> </tr> <tr> <td valign="top" width="200">d</td> <td valign="top" width="500">refresh</td> </tr> </table> ===Table 3 - File Definitions=== <table border="1" cellspacing="1" cellpadding="1"> <tr> <td valign="top" width="200">RSQ</td> <td valign="top" width="500">raw image file (contains projection data), created with scan</td> </tr> <tr> <td valign="top" width="200">ISQ</td> <td valign="top" width="500">reconstructed file (contains slice data), created from RSQ</td> </tr> <tr> <td valign="top" width="200">AIM</td> <td valign="top" width="500">discretized CT results, extracted from ISQ.</td> </tr> <tr> <td valign="top" width="200">RAW</td> <td valign="top" width="500">raw data (RSQ)</td> </tr> <tr> <td valign="top" width="200">IMA</td> <td valign="top" width="500">image data (AIM, ISQ, GOBJ).</td> </tr> </table> ===Table 4 - Reconstruction and Batch Jobs=== <table border="1" cellspacing="1" cellpadding="1"> <tr> <td valign="top" width="200">fan_reko_all [] 9.6</td> <td valign="top" width="500">reconstruct ISQ from RSQ in directory [] with a reconstruction angle of 9.6 (righthand-rule).</td> </tr> <tr> <td valign="top" width="200">fan_reko 9.6 [] 22 10</td> <td valign="top" width="500">reconstruct ISQ from RSQ, angle 9.6, directory [], first slice number, number of slices (optional queue name). Must reconstruct at least 2 slices. Get reconstruction angle from uct_evaluation (atan).</td> </tr> <tr> <td valign="top" width="200">fan_reco</td> <td valign="top" width="500">interactive reconstruction of single slices from RSQ data.</td> </tr> <tr> <td colspan="2" valign="top" width="702">subut MEASUREMENT_92.COM;1 /que=BLUND_MEASURE submeas #sample</td> </tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="500">submit a batch job</td> </tr> </table> ===Table 5 - Directory and File Organization=== <table border="1" cellspacing="1" cellpadding="1"> <tr> <td valign="top" width="200">data</td> <td valign="top" width="500">DISK40:[DATA.UCT.00000224.00000404]<br> C0000274.ISQ;1 {after reconstructing all slices}<br> C0000274.RSQ;1 {measurement output}<br> C0000274.AIM;1 {extracted from ISQ}</td> </tr> <tr> <td valign="top" width="200">projects</td> <td valign="top" width="500">DISK40:[DATA.UCT.PROJECTS.JAX]<br>00000216.DIR;1 :DISK40: [DATA.UCT.PROJECTS.JAX.00000216.00000354] :C0000229.AIM;1 :C0000229_GFILT.AIM;1 :C0000229_THRES.AIM;1<br> 00000217.DIR;1 {more data files as above, etc.}<br> COM.DIR;1 :DISK40:[DATA.UCT.PROJECTS.JAX.COM] :EVAL.COM;1 :IPL_SCANCO_V4.COM;1 :UCT_EVALUATION_FULL.COM;1<br> DOC.DIR;1 :Directory DISK40:[DATA.UCT.PROJECTS.JAX.DOC.IMG] :2D.DIR;1 {images from SAP usually} :3D.DIR;1 {images from viza usually} :LANDMARKS.DIR;1 {other images}<br> LOG.DIR;1 {evalution processing logs}</td> </tr> </table> ===Table 6 - AIO Procedures=== <table border="1" cellspacing="1" cellpadding="1"> <tr> <td valign="top" width="200"> <p align="left">AIO Procedures</p> </td> <td valign="top" width="500"> <p align="left">1. Different mathematical procedures.</p> <p align="left">2. Different mask procedures.</p> <p align="left">3. Exchange a slice with another slice in the AIM.</p> <p align="left">4. Reduce an AIM with cardinal reduction factors.</p> <p align="left">5. Calculate the relative positions of two AIMs.</p> <p align="left">6. Thresholding an AIM.</p> <p align="left">7. Thresholding and inverting an AIM.</p> <p align="left">8. Fill AIM with ramp function.</p> <p align="left">9. Calculate morphometric parameters from AIM.</p> <p align="left">10. Convert BID image to AIM with only one slice.</p> <p align="left">11. Mirror slices in AIM.</p> <p align="left">12. Interleaf slices in AIM.</p> <p align="left">13. Gaussian filtration of AIM.</p> <p align="left">14. Read single slice in AIM and convert to BID image.</p> <p align="left">15. Select AIM subimage (or MINIMAL).</p> <p align="left">16. SIBA bone remodeling module.</p> <p align="left">17. Flip, flop or flup AIM.</p> <p align="left">18. Convert AIM from YZ or XZ to XY representation.</p> <p align="left">19. Segmentation of AIM using region growing.</p> <p align="left">20. Segmentation of AIM using local thresholding.</p> <p align="left">21. Select cylindrical subvolume from AIM.</p> <p align="left">22. Calculate fist and second area moments from AIM.</p> </td> </tr> </table> ===Table 7 - EVE Editor Commands=== <table border="1" cellspacing="1" cellpadding="1"> <tr> <td valign="top" width="200">gold key</td> <td valign="top" width="500"><code><PF1></code></td> </tr> <tr> <td valign="top" width="200">copy</td> <td valign="top" width="500"><code><PF1><Remove></code> on VMS</td> </tr> <tr> <td valign="top" width="200">paste</td> <td valign="top" width="500"><code><Insert Here></code> on VMS <i>or </i> <code> <ctrl><insert></code> on PC</td> </tr> <tr> <td valign="top" width="200">cut</td> <td valign="top" width="500"><code><Remove> </code> on VMS <i>or </i><code><delete> </code> on PC</td> </tr> <tr> <td valign="top" width="200">learn</td> <td valign="top" width="500"><code><CTRL><K></code></td> </tr> <tr> <td valign="top" width="200">stop</td> <td valign="top" width="500"><code><CTRL><R> </code> (then give a key sequence such as <code><CTRL><Q></code>)</td> </tr> <tr> <td valign="top" width="200">repeat</td> <td valign="top" width="500"><code><PF1><#><(CTRL-Q)> </code> (the <code>CTRL-Q </code> depends on the given key sequence).</td> </tr> <tr> <td valign="top" width="200">find next</td> <td valign="top" width="500"><code><PF3></code></td> </tr> <tr> <td valign="top" width="200">enter search string</td> <td valign="top" width="500"><code><PF1><PF3></code></td> </tr> <tr> <td valign="top" width="200">replace string</td> <td valign="top" width="500"><code><PF1><S></code></td> </tr> <tr> <td valign="top" width="200">margins</td> <td valign="top" width="500">Mouse click bottom of window type: <code>set right 999</code></td> </tr> <tr> <td valign="top" width="200">kill line</td> <td valign="top" width="500"><code><PF4></code></td> </tr> <tr> <td valign="top" width="200">kill word</td> <td valign="top" width="500">- (minus key on number pad)</td> </tr> <tr> <td valign="top" width="200">advance next line</td> <td valign="top" width="500"><code>0</code> (zero on number pad)</td> </tr> <tr> <td valign="top" width="200">select text</td> <td valign="top" width="500"><code><CTRL><SPACE></code></td> </tr> <tr> <td colspan="2" valign="top" width="702">Further reference at <code>DISK1:[RAM.EDIT]TPU.ACCEL </code> where some of Ralph’s definitions are described.</td> </tr> </table>
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