Scanco User Instructions

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OpenVMS Basics

OpenVMS

OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.


Session Manager

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command $ vue .



Session

Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

Views (directory shortcuts)

The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

Commands and Utilities

Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

Applications

Under applications you can launch various applications including:

  • DECterm: opens a DEC terminal
  • MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
  • Mozilla/Netscape: opens a web browser
  • XV: opens a screen capture program

DEC Terminal and Digital Command Language (DCL)

This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.


What is a symbol

DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols. Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL procedures, hold status information. 

$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]"	!A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS]	!Another way to define the symbol without quotations.
$ x == 3	                                !Store the value 3 in the symbol x.
$ SHOW SYMBOL x                                 !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x                        !Deletes the specified symbol, x.

Selected symbols on the Scanco system: 

$ UD	                            !Changes to the data directory.
$ UR	                            !Changes to the projects directory.
$ DISKS	                            !Shows the current disk usage.
$ DEC                                           !Opens a new DEC terminal.
$ EVE file.txt                      !Opens the file in the text editor.
$ AIX file.aim                      !Shows the processing log for an aim file. 
$ AIX -L file.aimThe                !"-L" is used to show the full log.
$ QUE	                            !Shows all entries in the queue.
$ GS file.ps or file.pdf            !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq     !Shows scan information for an *.isq or *.rsq file.

What is a logical

Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program. 

$ DEFINE UD DISK2:[XTREMECT2.DATA]  !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.

Selected logical on the micro-CT system: 

COM            !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD             !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6            !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR             !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE             !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU             !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS    !Logical pointing to the results directory MICROCT_USER:[RESULTS]

How to copy and paste using the mouse

In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.

List of common commands

$ DEC	                            !Open a new DEC terminal
$ VUE	                            !Start the session manager. Press enter after to regain prompt.
$ UCT	                            !Open the micro-CT control panel.
$ UCT_SAMPLE	                    !Start µCT Samples.
$ UCT_MEASUREMENT	            !Start µCT Tomography.
$ UCT_EVALUATION	            !Start µCT Evaluation Program.
$ UCT_3D	                    !Start µCT Ray.
$ UCT_BACKUP	                    !Start µCT Disk-Utility.
$ CD UD	                            !Change location to the data directory.
$ CD UR	                            !Change location to the projects directory.
$ CD SYS$SCRATCH	            !Change location to the scratch directory.
$ CD UCT_RESULTS	            !Change location to the results directory.
$ DIR UE	                    !List files in the evaluation directory.
$ DIR UU	                    !List files in the templates directory.
$ DIR COM	                    !List files in the commands directory.
$ UCT_LIST	                    !Extract results from the database.
$ AIX -L	                    !View the header of an AIM file.
$ CTHEADER	                    !View the header of an RSQ or ISQ file.
$ DISKS		                    !Show the current disk usage (all hard drives).
$ EVE	                            !Start the text editor.
$ LOGOUT	                    !End a session. For remote sessions, logout from the main (initial) login terminal.

How to move to a different directory

Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path. 

$ SET DEFAULT disk:[dir.subdir]	      !Moves to specified path.
$ SET DEFAULT [.subdir]		      !Moves one level into subdirectory subdir.

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM). 

$ CD subdir	                      !Moves into subdirectory subdir.
$ CD subdir1 subdir2	              !Moves into subdirectory subdir1, then into subdir2.
$ CD ..		                      !Moves up one level (i.e., out of one directory).

How to list the files in a directory

Use the DIRECTORY command, which may be abbreviated to DIR. 

$ DIR		                      !List everything in the current directory.
$ DIR disk:[dir.subdir]		      !Lists everything in the specified directory.
$ DIR/COL=1 *.aim	              !Lists all files with the extension .aim in a single column.
$ DIR/SINCE=TODAY		      !Lists all files created today.
$ dir [...*.aim]                      !The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ dir/size/grand_total [.subdir...]   !List the total size of all files in the SUBDIR directory. 
$ HELP DIR	                      !More information on the DIRECTORY command.

How to copy files

Use the COPY or BACKUP command. 

$ COPY file1.ext disk:[dir.subdir1]file2.ext          !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1]	              !Copy all .aim files (including all versions) to another location keeping the same name.
$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...]      !Copy the entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy the entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP COPY		                              !More information on the COPY command.
$ HELP BACKUP		                              !More information on the BACKUP command.

How to delete files

Use the DELETE command, which may be abbreviated to DEL. 

$ DEL myfile.txt;	              !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;*	              !Delete all versions of myfile.txt.
$ HELP DELETE		              !More information on the DELETE command.

Warning: Extreme caution! 

$ DEL *.*;*	                      !Delete everything in the current directory!

How to create a directory

Use the CREATE/DIR command. 

$ CREATE/DIR [.subdir]	              !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir]	      !Creates the subdirectory subdir at the specified path.

How to rename files and directories

Use the RENAME command. 

$ SET FILE/PROTECTION=O:RWED olddir.dir         !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext                !Renames oldfile.ext to newfile.ext.

How to check the queue

Use the SHOW QUEUE command, which may be abbreviated to SH QUE. 

$ SHOW QUEUE	                      !Shows all the queues, there are many!
$ SH QUE *FAST	                      !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW                        !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL	              !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL	      !Show only jobs that are currently executing for all users.

How to get queue information

Use the SHOW ENTRY command to obtain information about batch jobs in the queues. 

$ SHOW ENTRY	                      !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251	              !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL                 !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL                      !Shows all the batch jobs for all users.

How to FTP files

Use the FTP command. 

$ FTP 136.159.74.231	              !Connect to an FTP Server. Need to input user name and password.	
FTP> bin	                      !Set transfer mode to binary (.aim, .gobj, .isq, and most file types).
FTP> ascii	                      !Set transfer mode to ascii (.txt, .log, .com files).
FTP> mput *.aim	                      !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim	                      !Get all files with the .aim extension from the FTP server (mput = multiple get).
FTP> quit	                      !Disconnect from the FTP Server.

Scanning

User Tutorial

For XtremeCT II and I:

For MicroCT35, VivaCT40 and VivaCT80:

Evaluation

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