How To's

HowTo Library

a

SysAdmin: OpenVMS

b

SysAdmin: Scanco

HowTo: Edit Scanco SCANCO_SUBMIT_COMMAND symbol

In directory DISK2:[MICROCT]MICROCT_SETUP_USER.COM add the following line:

$ SCANCO_SUBMIT_COMMAND :== SUBMIT/NOPRINT/QUE=SYS$SLOW /NOTIFY/LOG=SYS$SCRATCH:

Then end session and log in again.

Evaluation

HowTo: Start a 3D evaulation from the terminal

Warning: Do not change uct_evaulation_v4.com and ipl_fixed_batch_v4.com in .eval, but only work on your own file (i.e., eval_steve). First, an explanation of how the normal evaluation runs by hitting the 'Start 3d' button.

$ scanco_submit_command ue:uct_evaluation_v4.com/para=(xxx,yyy,zzz,…)

There are 8 parameters:

• P1: number of print outs of our results sheet
• P2: the ISQ filename
• P3-5: start x (pos x), y, z
• P6-8: dim x, y, z

The parameters p3-p8 come from the white bounding box. The problem is that when you start from the terminal you do not have these. This problem can be overcome by using the isq_to_aim_gobjbox.exe and then give the relevant parameters. You can $ run um: isq_to_aim_gobjbox.exe to see what it's asking for. By using gobjbox you do not need p3-p8. Therefore you can start the evaluation by giving:

$ scanco_submit_command ue:uct_evaluation_special_josh.com –/para=(1,dk0:[microct.data.0000275.0000245]c0000332.ISQ)

Note that you can make uct_evaluation_special_josh.com such that there is no need for P1 (change p2 to p1 in the script, etc). [Alternatively to using the gobjbox you could use the normal isq_to_aim, but hard code the dim and pos.] Then call whatever IPL files you want to call. Look into fixed_batch_v4 to see how we turn on the database always on the first line of every IPL part, and how we calculate parameters.

Writing Scripts

HowTo: Get information about a sample or measurement from database

The following will create a sys$scratch:info.txt file.

$ write_info

Errors and Fixes

HowTo: Fix "last slice" error problem when extracting AIM from ISQ

Sometimes the evaluation script (i.e., voi) converting the ISQ to an AIM fails because it tries to read one slice more than what is available in the ISQ data. The result of this failure is that the 3D analysis appears to fail and no .AIM or _SEG.AIM is created in the data directory. For example, it may have tried to read 261 slices, but there were only 260 slices available. The easiest work around is to make sure that the white bounding box in the uct_evaluation program does not include the last slice (largest Z dimension). Scanco is aware of this problem and will fix it in future software releases (V5.2).

HowTo: Use the new UCT_BACKUP software

New Features (i) You can now select multiple samples with the Shift and/or the Ctrl key; and (2) You can use the sample name filter field on top to display only names containing the filter string.

Start the move/copy by clicking on 'Start...' The 'Script...' button is for advanced users.

Advanced Users: Use of the 'Script...' button: this will generate a script, sys$scratch:archive.com, that you may submit in batch mode later (e.g. over night) by typing:

$ scanco_submit_command sys$scratch:archive.com/after=23:59

(In a multi-computer cluster setup, you may want to specify the exact queue name of the computer that has the tape hooked up by giving e.g. /que=sceval_fast )

Insert a tape, but do NOT mount the tape in the normal program. (If necessary: if it's a new tape, initialize it as usual). The batch job will be started one minute before midnight in the example above. $ show entry will show you that it is holding until then. See $ help submit /after and $ help dcl_tips date_time example for more help on this.

Little Reminder: While the tape is running and writing to it, DO NOT LOG OUT, DO NOT INTERRUPT THE PROGRAM! This would make that tape unusable from this point on - you could still read from that tape up to this point, but could not add more scans to this tape. What to do when tape is full? It then displays some message about continuing on another tape. Hit ctrl/c to interrupt the program, take a fresh tape, initialize it, select the remaining scans to archive again, hit 'start'.

And last but not least: WE STRONGLY URGE YOU TO DO THE WEEKLY BACKUP (SAFETY BACKUP OF USER DISK1 WITH YOUR DATABASES ON IT). Two users DID experience disk crashes last year, and without the weekly backup, you may still have all scans on the data disk (e.g. disk2), but without the databases you cannot tell which scans belong the which sample!

How to do weekly backup: insert 'special' weekly backup tape, e.g. week_a, and just hit 'Full backup to tape'.

HowTo: Extract your results from the 3D database

Assuming you've used the scanco_submit_command to initialize your evaluations (either manually or through the uct_evaluation tool) then you can get all of your results stored into a text file that can be easily imported in Excel.

$ uct_list

The output text file will be stored in sys$scratch and you can ftp this to a PC so that it can be imported into excel and further analysis can be performed.

Importing into Excel requires setting a deliminator based on the space.

HowTo: Tabulate your LOG file results from 3D evaluations

Only use this if you have not used the standard uct_evaluation tool to generate your 3D evaluations (in which case see the HowTo related to the 3D database). You can tabulate the LOG files:

$ search xxxx.log "ov "

Or whatever you want to search for can be stored in a text file

$ search/output=sys$scratch:ov.txt xxxx.log "ov "

To search more than one log file, and get the output into one single file:

$ fda/output=xxx.txt search *.log "ov "

The fda means 'file do all' and is a script made by Scanco to do one command (search) on a wildcard of files (*.log). Then put all the ov.txt, tv.txt, name.txt etc. files into excel. Josh has made a .com file that does a similar job as described above.

HowTo: Import foreign data into the Scanco database

Only ISQ files can be imported into the database, however it is possible to convert other types of data into ISQ files (i.e., stacks of BMPs into ISQ).

PART 1:

After transfering your data to the VMS system (use the data disk disk2, NOT the user disk disk1), use the IPL commands /import_freeformat or /read_aim function to import your data for conversion to an ISQ.

For DICOM files, start IPL and run the /dicom function to import. For DICOM, if your object is a single 3D file (-multifile false) or many many individual slice files (-multifile true, and give beginning of filenames, and –extension).

There may be requests by IPL to convert your data to signed short or signed char from other data types. Obey these requests and do it by running the /convert_unsigned function.

Then, write the ISQ file.

ipl> toisq in dk0:[microct.data]D0000001.ISQ
    -square           true
    -original_pos     false

This writes the ISQ file. Note that the filename MUST have one letter followed by seven digits. The letters and numbers can be chosen freely.

PART 2:

Create a sample in the database and write down the sample and measurement number. Then, run:

$ run um:uct_import

And give the new ISQ file, the new sample-number and check that the feedback is correct (i.e., that the name from the database is matching the name from the ISQ file header).

Operator and controlfile can be left 0 if you want.

Then it changes the sample and measurement number in the ISQ file, makes the correct directory on dk0, and gives you the line on the screen of how to rename the file to the correct, new directory. Take this line and use it on the command line. Done!

You can now use the normal uct_evaluation program with this file.

Note, if you were importing an AIM file, delete the original file as it will have the wrong measurement indexes in its log header. You will have to produce the AIM file again from the ISQ so our database writes the evaluation results into the correct sample fields.

HowTo: Launch an editor such as EVE

On the command line

$ edit/display=decwindows/tpu fname.txt

HowTo: Edit a symbol set by Scanco such as AIX

Log in as user calibration

$ set proc/priv=bypass
$ cdc (changes to microct_common)
$ sea *.com aix

Edit that file which is called microct_setup_common.com

Another example: To make the backspace/insert keys work properly, edit the login.com and insert the line

$ set terminal/insert

Anywhere suitable.

HowTo: Convert CT numbers to mg HA/ccm

The two byte numbers (short) can be converted to mu values by first dividing by mu_scaling which is probably 4096. Then apply the slope and intercept to get mg HA/ccm. A typical slope may be 2.95e+02 and intercept -1.896e+02.

These numbers are available in the AIM header, or the ISQ header ($ run ut:ctheader). The conversion is as follows:

mg HA/ccm = (AIM/mu_scaling) * slope + intercept
mg HA/ccm = (AIM/4096) * 295.494 – 189.695

!---------------------------------------------------------------------- 
Mu_Scaling                    4096 
Calibration Data              55 kVp, 200mg HA wedge, 4096 scaling 
Calib. default unit type      2 (Density) 
Density: unit                 mg HA/ccm 
Density: slope                2.95493988e+02 
Density: intercept            -1.89695007e+02 
HU: mu water                  0.58200 
!----------------------------------------------------------------------

HowTo: Submit a job to the queue

$ submit/noprint /que=sys$slow ipl_voi_josh_m.com 
  - /log=sys$scratch:test.log

HowTo: Assign special 3D evaluation to the uct_evaluation tool

Warning: This is for advanced users ONLY. Do not attempt this without contacting Steve!

This will show how to set up $ eval_kyle: It is easy to set up multiple .COM files for the 3D evalulation tool, one such set-up is already prepared on your computer:

$ eval_special

will do something similar to $ voi where the normal contour program opens, but if you start the 3D eval, the special script um:uct_evaluation_special.com is called (associated with eval_special), which then in turn calls ipl_fixed_batch_special.com, where you can specify your own set of thresholds, etc.

So it is a daisy chain of files which we will need to follow to set up a special xxx_kyle.com script, and where ever we encounter _special.com, we copy and change it to _kyle.com.

So to set up $ eval_kyle you will need to do the following:

• 1. Edit microct_setup_user.com (double-click on file), please be careful here, it's very important! (and I hope you have done your 'weekly full backup' regularly, so you could always retrieve a good version of login.com...)

• 2. Then, towards to bottom and duplicate the line

$ eval_special :== @com:eval_var.com um:uct_evaluation_special.com and change duplicate to $ eval_kyle  :== @com:eval_var.com um:uct_evaluation_kyle.com

This will make this command eval_kyle available after you login freshly. Save and Exit.

• 3. Then go to disk1:[microct.eval] and copy the file uct_evaluation_special.com to the name uct_evaluation_kyle.com ('Commands', 'Copy ...', BUT CLICK ON THE THREE DOTS and give new output name.

If you do not see the eval_special: go to terminal, $ dir ue:*special*.com and take it from the microct_common directory)

• 4. Edit the _kyle.com file: at the top, change ipl_......_special.com to _kyle.com

• 5. Copy ipl_fixed_batch_special.com to ipl_fixed_batch_kyle.com

• 6. Edit ipl_fixed_batch_kyle.com to your liking. If you want $ eval_kyle to not perform the full evaluation, but only something akin to voi, then, in the steps above, copy uct_eval_voi.com to uct_evaluation_kyle.com, and ipl_voi.com to ipl_fixed_batch_kyle.com (thus you take the voi script as template for the _kyle script).

• 7. Then open a new terminal ('applications', 'decterm'), $ eval_kyle should work now!

Notes: When you start the 3D eval, then $ que will show you your batch job with your name on it now!

And now a few more explanations how the whole thing works: in all eval programs, hitting 'Start 3d' just submits the logical uct_evaluation, $ show log uct_evaluation shows you that by default, this points to ue:uct_evaluation_v4.com.

Those little voi and eval_steve scripts then just temporarily redefine this logical so that a different script is submitted when you 'start 3d eval'.

About the corelut eval: Then we start a whole different eval program: the .exe_corelut. So, if you set up a eval_steve_c (or whatever you want to call it): Produce a eval_var_c.com in the directory commands (maybe copy from microct_common to [microct.commands]), and there, on the last line, instead of starting $ uct_evaluation (the normal program), replace by $ evalc which starts the .exe_corelut - and because the eval_var.com has over-ridden the uct_evaluation logical just before, then you are starting different script upon starting 3d eval. NB: we have a logical AND a symbol called uct_evalution. Sorry for confusion. Symbol uct_evaluation starts normal eval program, so this is what you replace by symbol evalc now).

HowTo: Create your own IPL script tips

To make a script that would submit a job to the queue with the command as follows:

$ @um:ipl_eval_only.com 'aim_file' 'gobj_file' 'p1' 0

you need to create your own IPL file would be translated to the following command:

$ submit /noprint /que=sys$slow ue:IPL_VOI_JOSH_M.COM 
  - /log=sys$scratch:test.log /para=('aim_file','gobj_file','seg_file')

The IPL file would look something like this…

$   if p1 .EQS. "" 
$ 	THEN 
$	write sys$output "Give DK0:[xxx]C0001234_SEG.aim on the line."
$	write sys$output "Or: "
$	write sys$output "Type $ scanco_submit_command um:ipl_eval_autostart/para=(dk0:[xxx]c00123_seg.aim) "
$ 	exit
$   endif
$
$ gobj_file = p1-F$PARSE(p1,,,"VERSION")-"_SEG.AIM" + ".GOBJ"
$ aim_file = p1-F$PARSE(p1,,,"VERSION")-"_SEG.AIM" + ".AIM"
$
$!
$ @um:ipl_eval_only.com 'aim_file' 'gobj_file' 'p1' 0
$ exit

Some more handy IPL sequences are:

$    INPUT = F$SEARCH("UCT_MEASUREMENT_DATA:[*.*''P1']*.RSQ",1)

and then you just need to give meas. number as P1 (and maybe slice range as p2),

$ if p2 .eqs. "" then p2 := A

OR, some nice starts are:

$    IF P3 .EQS. ""
$    THEN
$      WRITE SYS$OUTPUT "P1: Measurement Number to duplicate"
$      WRITE SYS$OUTPUT "P2: New Sample Number from Database"
$      WRITE SYS$OUTPUT "P3: New Start Letter of ISQ file"
$      WRITE SYS$OUTPUT "P4: Optional: Operator Number"
$      WRITE SYS$OUTPUT "P5: Optional: Controlfile Number"
$      EXIT
$    ENDIF

where you say which parameters HAVE to be there (up to p3), and which ones are optional.

All together, the script may look like this:

$    IF P1 .EQS. "" 
$    THEN 
$      WRITE SYS$OUTPUT "P1: Measurement Number to reco" 
$      WRITE SYS$OUTPUT "P2: Optional: Slice number N or Range M:N. Auto:All" 
$      WRITE SYS$OUTPUT "P3: Optional: Queue. Auto: sys$slow" 
$      EXIT 
$    ENDIF 
$ if p2 .eqs. "" then p2 := A 
$ if p3 .eqs. "" then p3 := SYS$SLOW 
$ slices  = p2 
$ quename = p3 
$ INPUT = F$SEARCH("UCT_MEASUREMENT_DATA:[*.*''P1']*.RSQ",1) 
$ INPUT = INPUT - F$PARSE(INPUT,,,"VERSION") 
$ logfile = "sys$scratch:RECO_" + f$PARSE(input,,,"NAME") + ".LOG" 
$ submit/noprint/queue='quename' uct_reconstruction_file - 
    /para=('input','slices','logfile') 
$ exit

Note that uct_reconstruction_file is a logical that points to um:uct_reconstruction.com.

Logicals are preferred in scripts to make them more universal.

HowTo: Create a customized button in the session manager

The session manager part to enable the double-click on the AIM file: Session Manager, 'Options', 'Menu', enter new item SAP with command:

@decw$user_defaults:sap$vue

Then move that menu point into 'Applications' menu. Also: 'Options', 'File types', Create 'AIM' file type. Move 'rename', 'copy', 'purge' etc. into menu, Select 'SAP', click on 'Change double click', and also move SAP into menu.

HowTo: Import data onto the VMS system

Create a project directory (i.e., DK0:[MICROCT.PROJECTS.SB.RABBIT]). Use FTP to transfer AIM files from other sources to the directory. Run IPL and use the /toisq_from_aim command to generate ISQ files. Create entries in the data base (sample name/number using the data base entry tool).

Run $ run um:uct_import to import the newly created ISQs into the data base by the names entered above. (Note that um: is a logical for disk1:[microct.main] (directory), give the ISQ. Give the sample number, rest default, check and use rename command it gives you on screen. Remember, the ISQ name must be 8 characters long (1 character followed by seven digits)!!! Fill out a log sheet with the original AIM names that were imported, and the resulting ISQ names that were generated.

HowTo: Use uct_evaluation without importing ISQ into the database

In a terminal, $ def uct_default_isq xxxxxxxx.isq Then start the uct_evaluation tool (or voi, evalc). Hit cancel when asked for a file to read and the default ISQ that was set will be read.

HowTo: Export the VMS display to SUN or LINUX terminal

# - temple
$ - sceval
# xhost +
# ssh -X microct@sceval.ucalgary.ca
$ set display /create /transport=tcpip /node=temple.ucalgary.ca

HowTo: Monitor CPU usage with a program like TOP

$ monitor/interval=1 processes/topcpu

HowTo: Configure the EVE editor

The following file, called tpu.dat, should be installed in disk1:[microct.xdefaults]:

#
# DECTPU V3.1 1993-04-22 15:50 defaults
# CHANGED B.KOLLER 21-JUN-90
#
# Copyright (c) 1993 Digital Equipment Corporation.  All rights reserved.
#
#
# The following are all the resource names that DECTPU supports.
#
Tpu.Tpu$MainWindow.Title:		DECTPU Copyright © Digital Equipment Corporation 1992.  All Rights Reserved.
Tpu.Tpu$MainWindow.ApplicationTitle:	DECTPU
Tpu.Tpu$MainWindow.IconName:		DECTPU
Tpu.Tpu$MainWindow.X:			610
Tpu.Tpu$MainWindow.Y:			0
#
# The following resource names are commented out so that users can specify
# *rows and *columns and have DECTPU obey those directives.  If DECTPU finds
# finds no resource names governing the number of rows and columns it should
# have, it uses 24 rows and 80 columns.
#
#
Tpu.Tpu$MainWindow.Columns:	80
Tpu.Tpu$MainWindow.Rows:	56
*EVE_MENU_BAR*background:	#ADADADADADAD
Tpu*XmScrollBar*background:	#ADADADADADAD
Tpu*XmDialogShell*background:	#ADADADADADAD
Tpu*XmMenuShell*background:	#ADADADADADAD
*background:			white
Tpu*condensedFont: OFF
Tpu*fontSetSelection: 0

# 0 = big font
# 1 = little font
# 2 = GS font (German Standard)
# 3 = Fine font (used only for non-latin 1 fonts?)

HowTo: Redefine the submit command

• Check the current setting:

$ show sym *submit*

then change que by editing the MICROCT_SETUP_USER.COM file add the following line (this will supersede the setting standard setting)

$ SCANCO_SUBMIT_COMMAND :== SUBMIT/NOPRINT/QUE=SYS$SLOW /NOTIFY/LOG=SYS$SCRATCH:

all on one line...

then, end session and log in again.

HowTo: Extract patient name from database

$ mcr um:uct_info 1234

will show you sample-name of sample-number 1234

$ mcr um:uct_info -m 1234

will give you some (stupid) info about meas 1234

Note: If you use this function all the time, put the following into microct_setup_user.com

$ uct_info  :== $um:uct_info

and then the usage info will even be correct

HowTo: Extract disk usage information

To look at the RSQs in the database

$ dir/siz dk0:[microct.data...]*.rsq

the three dots means all subdirectories.

Other useful commands:

$ ctheader xxxxxx.isq

or

$ ctheader xxxxxx.rsq

shows you header.

$ fda command file-wildcard

does a 'file do all' of the command on all the given wildcard filenames.

$ pipe xxxx | search sys$pipe "patient"

is the pipe command in VMS.

So all three combined:

$ pipe fda ctheader dk0:[microct.data...]*.rsq | search sys$pipe "patient name"

or any other field you want to search for!

Other ideas:

$ write_info

gives you a file sys$scratch:info.txt with info in it (leave defaults to get all samples ever scanned, otherwise 'zoom' in on some samples.)

Check out the search command:

$ help search

and /match=and or /match=or

HowTo: Understand difference between mcr and run

The command mcr is the same as run, but only with mcr you can hand over 'in-line' parameters to an .exe file:

$ run ut:ctheader.exe c000124.isq

does not work, but you have to say

$ mcr ut:ctheader.exe c000124.isq

But funnily if you define a symbol in microct_setup_user.com (or login.com),

$ ctheader :== $ut:ctheader.exe

with just neither run nor mcr, but the 'funny' $ sign, then you can also hand over the ISQ name in-line.

Small detail with big effect...

HowTo: Make commands available to all users with symbols or paths

DCL$PATH is one way to do that, WE don't use it...

$ def dcl$path disk1:[microct.main],disk1:[microct.util]

then, if you type $ uct_t it will first try to

$ @uct_t.com and then $ r uct_t.exe

however, we usually define it by giving full path:

$ progx :== $disk1:[microct.main]progx.exe
$ com_proc_x :== @disk1:[microct.main]procedure.com

then, you can just type the shortcut ('symbol' in VMS language)

we use the 'cd' to set the default path, you may also use this in your command procedure:

proc.com:

$ cd 'p1'
$ dir *.*/size

$ define COM disk1:[microct.commands]
$ p :== @COM:PROC.COM

these both go into login.com

then, you can just type:

$ p disk4:[microct.data.0000007.000009]*.ISQ

HowTo: Shut down the Alpha stations and start up again

Warning: Do not do this unless absolutely necessary.

For shutdown

At the login screen, type "shutdown"/no password and hit enter. Then, you can turn the computer off at the prompt.

Then, you may turn the disk array off (unplug it as there is no power switch).

After you move the computer, power on the disk array and then the computer.