mar research Graphical User Interface mar345 Guía de solución de problemas
X−ray Research G.m.b.H. Tel.: (+49) (40) 529−884−0
Segeberger Chaussee 34 Fax: (+49) (40) 529−884−20
Germany Web: www.marresearch.com
The
P
rogram Manu
al
By Dr. Claudio Klein
m
ar researc
h
m
ar345 Program Manual 2
_
____________________________________________________________________________________
_
The mar345 Program Manual
Version 2.0
February 24, 2000
Written by Dr. Claudio Klein
Copyright 2000 X−Ray Research G.m.b.H.
All Rights Reserved.
This document contains proprietary and confidential information of X−ray Researc
h
G.m.b.H.. The contents of this document may not be disclosed to third parties, copied o
r
duplicated in any form, in whole or in part, without the prior written consent of X−ra
y
Research G.m.b.H..
P
ossession, use, or copying of the software described in this publication
is
a
uthorized only pursuant to a valid written license from X−ray Research G.m.b.H.
m
arresearch and the marresearch logo are registered trademarks of X−ray Research
G.m.b.H..
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ar345 Program Manual 3
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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
A
ppendix 39
A Configuration File 39
B Calibration Files 40
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ar345 Program Manual 4
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1
. Introduction
The program mar345 is a fully menu driven graphical user interface (GUI) for collecting an
d
displaying images on a mar345 imaging plate system.
The program is provided as binary executable for several computer platforms and operatin
g
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
.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.
1
.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
e
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
n
G
uide".
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ar345 Program Manual 5
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2
. Running mar345
2
.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:
−
hPrint 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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ar345 Program Manual 6
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2
.2 Input Files
The program mar345 requires the following input files to work properly:
a
) $MARLOGDIR/mar345.dat
The program continuously saves edited parameters into this file. It is nice to find the progra
m
in the same state where you left it at startup. However, if mar345.dat cannot be found
,
program defaults will be used.
b
) $MARTABLEDIR/config.XXX
XXX is a 3−digit serial number. This file contains essential scanner specific information. Fo
r
the scanner to produce valid data it is essential to have this file with all entries correspondin
g
to valid parameters for the scanner. The program mar345 will use program defaults if this fi
le
is not available.
c
) $MARTABLEDIR/mar2300.XXX
XXX is a 3−digit serial number. This file contains flat−field corrections and the geometry tab
le
for transforming spiral images into Cartesian images for all scans at 0.15 mm pixelsize. Th
is
file is scanner−specific and required to do scans in 0.15 mm pixel modes. The typical size o
f
this file is 73 MB.
d
) $MARTABLEDIR/ma3450.XXX
Same as mar23000.XXX but used for all scans at 0.10 mm pixelsize. The typical size of th
is
file is 103 MB.
See Appendix A and B for more information about input files.
2
.3 Output Files
The program mar345 writes all relevant messages to standard output but it also produce
s
several types of log files, depending on the configuration. Since log files can be important t
o
look at in case of software or hardware problems, the program creates different versions o
f
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 Xis a number running from 1 to 99. All log files reside in the subdirectory assigend b
y
the logical variable MARLOGDIR. In this directory, there is also a file called "last.log" tha
t
contains only the version number of the latest (i.e. current) log file and a soft link of mar.lo
g
to the latest mar.log.X file in subdirectory log. Accordingly, soft links are also set to file
s
mar.spy and mar.lp if configured..Up to 99 copies of the log files will be kept and the
n
cyclically overwritten.
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ar345 Program Manual 7
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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
t
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.
2
.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
st
computer features a dedicated Ethernet card for communicating with the scanner. Ho
st
computer and scanner are linked via a so called "cross−over cable", i.e. a special RJ−45 typ
e
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
y,
m
ar345 keeps the equivalent of 2.5 images in memory. When using 3450x3450 pixel image
s
this corresponds to 75 MB.
Data collection should always have highest priority. However, there is no real protectio
n
against abuse of the computer by other processes. In particular, memory consuming dat
a
processing jobs can cause drops in performance of the workstation to such a degree tha
t
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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ar345 Program Manual 8
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2
.5 Starting Up
Create a new window for running the program and type: "mar345". Do not run the program
in
the background and do not use this window for other purposes. The program will sen
d
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
u
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
u
will not get any feed back. This is because the program tries to open a network connection t
o
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
rk
services, so a ping to the address of the scanner (usually 192.0.2.1) will work within 1
0
seconds after turning the scanner on. However, before starting communication with th
e
program mar345, the scanner must do first some initialization, i.e. drive the scanning head t
o
its default position (scan mode 2300) and lock the plate. Only when the plate is successful
ly
locked ("cling!") program mar345 can start talking to the scanner. You may, however, sta
rt
the program first and then turn on the scanner. The program really waits until a connectio
n
can be established.
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ar345 Program Manual 9
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3
. User Interface
3
.1 Main Window
M
enu Ba
r
S
canner Status Are
a
S
canner Command Are
a
C
ollect Men
u
P
rogress Ba
r
S
hutter Statu
s
T
ime until End of Data Se
t
C
urrent Tim
e
m
ar345 Program Manual 1 0
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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
3
.2 Menu Bar
The menu bar features two buttons:
W
indows Pops up the Windows submenu (3.2.1).
Shortcut: Alt+w.
H
elp Pops up the mar345−Help window.
Shortcut: F5.
3
.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:
D
isplay Pops up the mar 345−Display window.
Shortcut: F1.
P
rogress Pops up the mar345−Progress window.
Shortcut: F2.
X
−ray Setup Pops up the mar345−Setup window.
Shortcut: F3.
S
hutter Timer Pops up the mar345−Shutter Timer
window. Shortcut: F4.
L
og−file Pops up the mar345−Help window and
displays the current log file. Shortcut: F5.
H
ardware Pops up the mar345−Hardware Status
S
tatus window. Shortcut: F6.
E
rror Window Pops up the mar345−Error window and
displays the current errors. Shortcut: F7.
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