How To's

Tips and Hints for OpenVMS

HowTo: Edit 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.

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.

HowTo: Get information about a sample or measurement from database

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

$ write_info

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.