Benutzeranleitung / Produktwartung Graphical User Interface mar345 des Produzenten Compaq
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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.
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.
m ar345 Program Manual 3 _ ____________________________________________________________________________________ _ 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.
m ar345 Program Manual 4 _ ____________________________________________________________________________________ _ 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.
m ar345 Program Manual 5 _ ____________________________________________________________________________________ _ 2 . Running mar345 2 .1 Command Line The program mar345 should be started by just typing " mar345 ".
m ar345 Program Manual 6 _ ____________________________________________________________________________________ _ 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.
m ar345 Program Manual 7 _ ____________________________________________________________________________________ _ 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.
m ar345 Program Manual 8 _ ____________________________________________________________________________________ _ 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.
m ar345 Program Manual 9 _ ____________________________________________________________________________________ _ 3 . User Interface 3 .1 Main Window M enu Ba r S canner Status Are a S canner Command .
m ar345 Program Manual 1 0 _ ____________________________________________________________________________________ _ 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 .
m ar345 Program Manual 1 1 _ ____________________________________________________________________________________ _ M ove Distance Pops up the mar345−Distance window. Shortcut: F8. M ove Phi Pops up the mar345−Phi window. Shortcut: F9. R eset Scanner Reboots the scanner reboot .
m ar345 Program Manual 1 2 _ ____________________________________________________________________________________ _ N ote: Timing is a crucial issue when operating the scanner. If the computer is very bus y doing other computations, the internal clock of the program will work slower.
m ar345 Program Manual 1 3 _ ____________________________________________________________________________________ _ 3 .5 Editing Data Collection Parameters.
m ar345 Program Manual 1 4 _ ____________________________________________________________________________________ _ The Change Parameters window is used to program data collection parameters.
m ar345 Program Manual 1 5 _ ____________________________________________________________________________________ _ Table continued from previous page. _______________________________________________________________________ I tem Description ________________________________________________________________________ F irst image no.
m ar345 Program Manual 1 6 _ ____________________________________________________________________________________ _ In MAD Data mode " No. of images " is replaced by " No. of ϕ blocks " and a field for enterin g the number of images per ϕ block.
m ar345 Program Manual 1 7 _ ____________________________________________________________________________________ _ 3 .6 Loading and Saving Data Collection Parameters Crystallographers often collect data of a certain crystal type in always the same way, i.
m ar345 Program Manual 1 8 _ ____________________________________________________________________________________ _ 3 .7 Moving Distance and Phi The detector position and the ϕ axis can be moved by pressing buttons in th e m ar345−Change Parameters window.
m ar345 Program Manual 1 9 _ ____________________________________________________________________________________ _ 3 .8 Starting Data Collection Data collection can be started by pressing the " Go "o r" Go/Erase first " button in th e m ar345−Change Parameters window .
m ar345 Program Manual 2 0 _ ____________________________________________________________________________________ _ 3 .10 Single Scan A single scan can be done by pressing the " Scan " button in the main window. Th e m ar345−Scan window pops up.
m ar345 Program Manual 2 1 _ ____________________________________________________________________________________ _ 3 .12 Getting Help Interactive help can be obtained b y pressing the " Help " button in th e menu bar of the main window or b y pressing the F5 key.
m ar345 Program Manual 2 2 _ ____________________________________________________________________________________ _ 3 .14 X−ray Setup When producing images during data collection many parameters concerning the curren t experiment are automatically written into the output image headers, so this information ca n be retrieved later on.
m ar345 Program Manual 2 3 _ ____________________________________________________________________________________ _ 3 .15 Errors and Warnings During operation, i.e. data collection or other tasks, the scanner itself or the program mar34 5 might produce error messages or warnings.
m ar345 Program Manual 2 4 _ ____________________________________________________________________________________ _ 4 . Image Display 4 .1 Display Window The image display window controls the most important display functions.
m ar345 Program Manual 2 5 _ ____________________________________________________________________________________ _ 4 .2 Menu Bar The menu bar features the following buttons: W indows Pops up the Windows submenu (see 4.2.1). Shortcut: Alt+w . O ptions Pops up the Options submenu (see 4.
m ar345 Program Manual 2 6 _ ____________________________________________________________________________________ _ D o not/Keep color scales Normally, if a new image is loaded, the program recalculates a new color scheme.
m ar345 Program Manual 2 7 _ ____________________________________________________________________________________ _ 4 .3 Image Area In this area, the image is displayed. With the pointer (3−way mouse button) several addition al functions can be accessed.
m ar345 Program Manual 2 8 _ ____________________________________________________________________________________ _ At zoom factors > 4 one can obtain a 3−dimensional representation of the magnified portio n of the image.
m ar345 Program Manual 2 9 _ ____________________________________________________________________________________ _ 4 .4 Work Area 4 .4.1 Load Buttons By pressing the single left or right arrow one can decrease or increase the current imag e number and load the previous or next image, respectively.
m ar345 Program Manual 3 0 _ ____________________________________________________________________________________ _ 4 .6 Window Title In this area, the image name and some parameters extracted from the image header (total number of pixels along x, number of pixels with intensities larger than 65535) are displayed.
m ar345 Program Manual 3 1 _ ____________________________________________________________________________________ _ The functions of the mar345−Colors window widgets are: G rey scales Selection of coloring mode. Alternatives: Blue scales, Rainbow . M in All pixels with intensities <= Min are drawn white (black in Blue scales).
m ar345 Program Manual 3 2 _ ____________________________________________________________________________________ _ 4 .8 Cross−Section Window This window is used for displaying cross sections through the image. The window can b e obtained by pressing the left mouse button in the image area.
m ar345 Program Manual 3 3 _ ____________________________________________________________________________________ _ The plot area of the window shows the following features: V ertical axis Interpolated intensities U pper horizontal axis Length of line in pixel units.
m ar345 Program Manual 3 4 _ ____________________________________________________________________________________ _ 5 . Data Collection 5 .1 Strategies While some general rules apply how to collect data best, a sensible choice of data collectio n parameters depends on individual circumstances, i.
m ar345 Program Manual 3 5 _ ____________________________________________________________________________________ _ The decision about what pixelsize to choose is slightly more difficult. In general, the fine st pixelsize of 0.1mm is more efficient and yields slightly better data.
m ar345 Program Manual 3 6 _ ____________________________________________________________________________________ _ 6 . Troubleshooting Both the computer and the scanner can produce fatal errors and warnings. All messages ar e numbered. Messages with message numbers < 1000 come directly from the scanne r controller and are potentially serious.
m ar345 Program Manual 3 7 _ ____________________________________________________________________________________ _ Tabel continued from previous page.
m ar345 Program Manual 3 8 _ ____________________________________________________________________________________ _ Tabel continued from previous page.
m ar345 Program Manual 3 9 _ ____________________________________________________________________________________ _ A ppendix A . Configuration File Each scanner has a scanner specific configuration file. This file must reside in directo ry $MARTABLEDIR and is called config.
m ar345 Program Manual 4 0 _ ____________________________________________________________________________________ _ B . Calibration Files Each scanner comes with 2 scanner specific calibration files. These files must reside in directory $MARTABLEDIR and are called mar2300.
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