Compaq mar345 User Manual

The

ar researc

rogram Manu

By Dr. Claudio Klein

X−ray Research G.m.b.H. Tel.: (+49) (40) 529−884−0 Segeberger Chaussee 34 Fax: (+49) (40) 529−884−20 D−22850 Norderstedt Mail: info@marresearch.com Germany Web: www.marresearch.com

ar345 Program Manual 2

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The mar345 Program Manual

Version 2.0

February 24, 2000

Written by Dr. Claudio Klein

This document contains proprietary and confidential information of X−ray Researc G.m.b.H.. The contents of this document may not be disclosed to third parties, copied o duplicated in any form, in whole or in part, without the prior written consent of X−ra Research G.m.b.H..

ossession, use, or copying of the software described in this publication

uthorized only pursuant to a valid written license from X−ray Research G.m.b.H.

arresearch and the marresearch logo are registered trademarks of X−ray Research

G.m.b.H..

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Contents

1 Introduction 4

1.1 Computer Requirements 4

1.2 Environment 4

2 Running mar345 5

2.1 Command Line 5

2.2 Input Files 6

2.3 Output Files 6

2.4 Basic Concept and Rules 7

2.5 Starting Up 8

3 User Interface 9

3.1 Main Window 9

3.2 Menu Bar 10

3.3 Scanner Status Area 11

3.4 Scanner Command Area 12

3.5 Editing Data Collection Parameters 13

3.6 Loading and Saving Data Collection Parameters 17

3.7 Moving Distance and Phi 18

3.8 Starting Data Collection 19

3.9 Stopping Data Collection 19

3.10 Single Scan 20

3.11 Shutter Timer 20

3.12 Getting Help 21

3.13 Hardware Status 21

3.14 X−ray Setup 22

3.15 Errors and Warningsp 23

4 Image Display 24

4.1 Display Window 24

4.2 Menu Bar 25

4.3 Image Area 27

4.4 Workr Area 29

4.5 Information Areas 29

4.6 Window Title 30

4.7 Colors Window 30

4.8 Cross−Section Window 32

5 Data Collection 34

5.1 Strategies 34

5.2 Checking Parameters 35

5.3 Warnings and Errors 35

5.4 End of Data Collection 35

6 Troubleshooting 36

ppendix 39

A Configuration File 39 B Calibration Files 40

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. Introduction

The program mar345 is a fully menu driven graphical user interface (GUI) for collecting an displaying images on a mar345 imaging plate system.

The program is provided as binary executable for several computer platforms and operatin systems:

− Silicon Graphics: IRIX 5.x, 6.x

− Digital: Compaq Tru Unix 4.x, 5.x

− Linux: RedHat 5.x, 6.x, SuSE 6.x

.1 Computer Requirements

− Motif 1.2.x shared libraries (except Linux).

− 8/16/24/32−bit colors X−windows terminal with 1280x1024 pixels.

− Standard Helvetica and Symbol fonts.

− 96 MB RAM memory or more.

.2 Environment

The program relies on definitions of the following environment variables:

− MARTABLEDIR Location of the scanner specific calibration files mar2300.XXX and mar3450.XXX and the corresponding configuration file config.XXX (where XXX = MAR_SCANNER_NO ).

− MAR_SCANNER_NO Three digit serial number, e.g. 049.

− MARLOGDIR Location of the log output files.

− MARHELPDIR Location of interactive help files.

The program relies on the correct network setup, i.e. the mar345 scanner must be accessibl by ping and telnet with IP−address 192.0.2.1.

For a description of the setup of the mar345 software suite, see the "mar345 Installatio

uide".

−

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. Running mar345

.1 Command Line

The program mar345 should be started by just typing "mar345". The program, however, understands the following command line options:

mar345 [−h] [−colors N] [−def XXXX] [−host HOST] [−keep]

[−more N] [−noxf] [−port PORT] [−setd]

The command line options are:

h Print a usage summary colors N Use N colors for drawing images.

Default: take N from configuration file.

def XXXX When starting the program, go to scanmode XXXX where

XXXX is 1200, 1600, 1800, 2000, 2300, 2400, 3000 or 3450.

Default: stay in current scan mode.

host HOST Connect to host HOST.

Default: take HOST from configuration file (usually 192.0.2.1)

keep Spiral images will be saved on disk.

Default: do not produce spiral files, only transformed images.

more N Log output level with N=0, 1, 2 or 3.

Use more > 0 only in case of hardware problems.

Default: N=0 (compact output)

noxf Spiral images will not be transformed into Cartesian images.

The program then requires much less memory, but images cannot be displayed.

Default: Do transform spiral images.

port PORT Connect to host HOST via socket port PORT.

Default: take PORT from configuration file (usually 4441)

setd The user may redefine the distance detector to crystal from

within the program. Default: Redefining the distance is disallowed..

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.2 Input Files

The program mar345 requires the following input files to work properly:

) $MARLOGDIR/mar345.dat

The program continuously saves edited parameters into this file. It is nice to find the progra in the same state where you left it at startup. However, if mar345.dat cannot be found program defaults will be used.

) $MARTABLEDIR/config.XXX

XXX is a 3−digit serial number. This file contains essential scanner specific information. Fo the scanner to produce valid data it is essential to have this file with all entries correspondin to valid parameters for the scanner. The program mar345 will use program defaults if this fi is not available.

) $MARTABLEDIR/mar2300.XXX

XXX is a 3−digit serial number. This file contains flat−field corrections and the geometry tab for transforming spiral images into Cartesian images for all scans at 0.15 mm pixelsize. Th file is scanner−specific and required to do scans in 0.15 mm pixel modes. The typical size o this file is 73 MB.

) $MARTABLEDIR/ma3450.XXX

Same as mar23000.XXX but used for all scans at 0.10 mm pixelsize. The typical size of th file is 103 MB.

See Appendix A and B for more information about input files.

.3 Output Files

The program mar345 writes all relevant messages to standard output but it also produce several types of log files, depending on the configuration. Since log files can be important t look at in case of software or hardware problems, the program creates different versions o log files named:

1.) $MARLOGDIR/log/mar.log.X (always)

2.) $MARLOGDIR/spy/mar.spy.X (configuration file entry: USE SPY)

3.) $MARLOGDIR/lp/mar.lp.X (configuration file entry: USE STATS)

where X is a number running from 1 to 99. All log files reside in the subdirectory assigend b the logical variable MARLOGDIR. In this directory, there is also a file called "last.log" tha contains only the version number of the latest (i.e. current) log file and a soft link of mar.lo to the latest mar.log.X file in subdirectory log. Accordingly, soft links are also set to file mar.spy and mar.lp if configured..Up to 99 copies of the log files will be kept and the cyclically overwritten.

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The contents of the different types of log files are as follows:

1.) mar.log: All messages on the terminal output.

2.) mar.spy: Native mar345 controller messages.

These messages become very important in case of hardware problems. Therefore, USE SPY should always be set. Note, that these files can become very large in size, so sufficien disk space should be available in $MARLOGDIR (up to 100 MB in total).

3.) mar.lp: Some image statistics like minimum, maximum and average intensity. Normally, these values are not of much interest, so

USE STATS should rather be the exception.

.4 Basic Concepts and Rules

The program has to perform different tasks:

− Allow user input (i.e. change data collection parameters, analyze images, etc.)

− Send commands to the scanner.

− Receive information from the scanner

− Transform spiral images into Cartesian images.

− Display transformed images. User input is done via the graphical user interface (see chapter 3). Communication with the scanner is realized through an Ethernet interface. Usually, the ho

computer features a dedicated Ethernet card for communicating with the scanner. Ho computer and scanner are linked via a so called "cross−over cable", i.e. a special RJ−45 typ cable that allows for directly connecting 2 computers without the need of a hub.

Transformation and data display requires some memory as well as CPU−time. Typicall

ar345 keeps the equivalent of 2.5 images in memory. When using 3450x3450 pixel image

this corresponds to 75 MB. Data collection should always have highest priority. However, there is no real protectio

against abuse of the computer by other processes. In particular, memory consuming dat processing jobs can cause drops in performance of the workstation to such a degree tha nothing else will work. Also network I/O can severly degrade the host computer performance e.g. when processing data across NFS−mounted disks!

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.5 Starting Up

Create a new window for running the program and type: "mar345". Do not run the program the background and do not use this window for other purposes. The program will sen important output to the window and you don’t want to miss it. At start up, the program will tell you something like:

=============================================================

Program : mar345 Version : 2.0.8 (Feb 16 2000) Scanner no. : 049 Scanner mode: 345 mm @ 0.15 mm Started on : Wed Feb 16 15:09:08 2000 LOG file is: /home/mar345/log/log/mar.log.58 SPY file is: /home/mar345/log/spy/mar.spy.58 STAT file is: /home/mar345/log/lp/mar.lp.58

=============================================================

It will also tell you if it is able to talk to the scanner. If environment variables are not set yo will be notified. Next, three windows will be created and automatically placed on the screen: a startup window, the mar345 main window and an empty image display window.

If the scanner is not turned on at all, by invoking program mar345 on the command line, yo will not get any feed back. This is because the program tries to open a network connection t the scanner and the program will sit there and wait until the scanner starts talking to it.

When the scanner is turned on, the scanner controller will start very quickly basic netwo services, so a ping to the address of the scanner (usually 192.0.2.1) will work within 1 seconds after turning the scanner on. However, before starting communication with th program mar345, the scanner must do first some initialization, i.e. drive the scanning head t its default position (scan mode 2300) and lock the plate. Only when the plate is successful locked ("cling!") program mar345 can start talking to the scanner. You may, however, sta the program first and then turn on the scanner. The program really waits until a connectio can be established.

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. User Interface

enu Ba

.1 Main Window

ime until End of Data Se

urrent Tim

rogress Ba

hutter Statu

ollect Men

canner Status Are

canner Command Are

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The main window controls the most important scanner functions. It consists of different areas

− a menu bar

− the scanner status area

− the scanner command area

.2 Menu Bar

The menu bar features two buttons:

indows Pops up the Windows submenu (3.2.1).

Shortcut: Alt+w.

elp Pops up the mar345−Help window.

Shortcut: F5.

.2.1 Windows Submenu

The Windows submenu pops up if the "Windows" button in the menu bar was pressed or if "Alt+w" was pressed while the pointer was in the main window.

The Windows submenu features the following buttons:

isplay Pops up the mar 345−Display window.

Shortcut: F1.

rogress Pops up the mar345−Progress window.

Shortcut: F2.

−ray Setup Pops up the mar345−Setup window. Shortcut: F3.

hutter Timer Pops up the mar345−Shutter Timer

window. Shortcut: F4.

og−file Pops up the mar345−Help window and

displays the current log file. Shortcut: F5.

ardware Pops up the mar345−Hardware Status

tatus window. Shortcut: F6. rror Window Pops up the mar345−Error window and

displays the current errors. Shortcut: F7.

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ove Distance Pops up the mar345−Distance window. Shortcut: F8. ove Phi Pops up the mar345−Phi window. Shortcut: F9.

eset Scanner Reboots the scanner reboot. Shortcut: Ctrl+r.

uit Quits program. Shortcut: Ctrl+q.

.3 Scanner Status Area

The status area provides at all times all necessary information about the current status of th scanner.This part of the user interface changes dynamically according to the current scanne operation. It features the following items: _______________________________________________________________________

tem Description

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arresearch / During data collection, this field shows the time it takes

ime until End to finish all active or queued data sets.

urrent Time Displays local computer time.

rogress Bar If the scanner is performing an operation, the progress of this

operation will be displayed with a colored progress bar and an appropriate text string.

hutter Status Shows the state of the local X−ray beam shutter (open or

closed).

urrent Image Shows the name of the current image leaving out the

directory and file name extension.

urrent Mode Shows the current scanmode of the scanner. urrent Distance Shows the current distance of detector to crystal. urrent Phi Shows the current position of the PHI axis.

ntensity Displays the current intensity reading of the selected

ionization chamber.

ree disk space Shows how many MB of disk space are available on the

disk where the current image will be written to.

________________________________________________________________________ Under normal conditions, the program retrieves status information from the scanner once

second. The time and the free disk space will be updated less frequently.

S E

d e

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ote: Timing is a crucial issue when operating the scanner. If the computer is very bus doing other computations, the internal clock of the program will work slower. A good check fo excessive computer activity is if the X−windows server is not able to repaint the user interac at a reasonable speed.

.4 Scanner Command Area

The buttons in the command area can be used to send commands directly to the scanner o to pop up further windows, i.e. the mar345−Scan and mar345−Change Paramete windows. The functions of the individual buttons are: _______________________________________________________________________

utton Description

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ollect Changes layout of the button choices, i.e. the Collect Menu buttons are

displayed.

can Pops up the mar345−Scan window. rase Immediately starts to erase the imaging plate. Erasing is identical to doing

a scan, but no data are taken.

nitialize The scanner will move to its distance reference position (usually at the far en

of the translation stage). This distance initialization may have to be done if th scanner looses the information about the distance for some reasons. The re− ference positions are taken from the configuration file. The detector move− ment has to be confirmed. The configuration file will be reread when pressing this button.

pen Shutter Opens (or closes) the local X−ray beam shutter.

________________________________________________________________________ And in the Collect Menu there are:

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ingle Set Pops up the mar345−Change Parameters window for programming

a single data set.

ultiple Sets Pops up the mar345−Change Parameters window for programming

up to 64 data sets.

ndex Crystal Pops up the mar345−Change Parameters window for programming

a small number of images to be used for indexing a crystal.

AD Data Pops up the mar345−Change Parameters window for programming

a data collection typical for anomalous and/or MAD data.

ancel Returns to the original layout. ________________________________________________________________________

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