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Compaq mar345 manual

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Table of contents for the manual

  • Page 1

    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 The P rogram Manu al By Dr. Claudio Klein m ar researc h[...]

  • Page 2

    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.[...]

  • Page 3

    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 2.4 Basic Concept and Rules 7 2.5 Starting Up 8 3 User Interface 9 3.1 Main Window 9 3.2 [...]

  • Page 4

    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. The program is provided as binary executable for several computer platform[...]

  • Page 5

    m ar345 Program Manual 5 _ ____________________________________________________________________________________ _ 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[...]

  • Page 6

    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. It is nice to find the progra m in the same state where [...]

  • Page 7

    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. These messages become very important in case of hardware problems. Theref[...]

  • Page 8

    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. The program will sen d important output to the window a[...]

  • Page 9

    m ar345 Program Manual 9 _ ____________________________________________________________________________________ _ 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[...]

  • Page 10

    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 .2 Menu Bar The menu bar features two buttons: W indows Pops up [...]

  • Page 11

    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 . Shortcut: Ctrl+r. Q uit Quits program. Shortcut: Ctrl+q. 3 .3 Scan[...]

  • Page 12

    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. A good check fo r excessive computer activity is if the X−windo[...]

  • Page 13

    m ar345 Program Manual 1 3 _ ____________________________________________________________________________________ _ 3 .5 Editing Data Collection Parameters[...]

  • Page 14

    m ar345 Program Manual 1 4 _ ____________________________________________________________________________________ _ The Change Parameters window is used to program data collection parameters. Th e window comes in 4 slightly different flavours, depending on the button choice in the Colle ct M enu : − Single Data Set − Multiple Data Sets − Inde[...]

  • Page 15

    m ar345 Program Manual 1 5 _ ____________________________________________________________________________________ _ Table continued from previous page. _______________________________________________________________________ I tem Description ________________________________________________________________________ F irst image no. Image number of fi[...]

  • Page 16

    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. It is supposed that one wants to collect a number o f contiguous images at a certa[...]

  • Page 17

    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.e . using a certain oscillation range, a certain distance, etc.It is therefore useful to store[...]

  • Page 18

    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. One can also get separate windows for moving " ϕ " and " Distance " b[...]

  • Page 19

    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 . It is a good idea to always let the plate clean fir st be[...]

  • Page 20

    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. The directory, image root, image number and scan mod e can be selected. The output format al[...]

  • Page 21

    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. In the mar345−Help window, a he lp topic should then be selected fro m th[...]

  • Page 22

    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. This is most [...]

  • Page 23

    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. All relevant messages are displaye d automatically in the mar345−Er[...]

  • Page 24

    m ar345 Program Manual 2 4 _ ____________________________________________________________________________________ _ 4 . Image Display 4 .1 Display Window The image display window controls the most important display functions. It consists of different areas: Work area Information areas Menu bar Window title Image are a[...]

  • Page 25

    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 4.2.2). Shortcut: Alt+o . H elp Pops up the mar345−Help window.[...]

  • Page 26

    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. If you want all images to be displayed in the same way, select "Keep color scales" Shortcut: Ctrl+k R eset colors Rec[...]

  • Page 27

    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. ________________________________________________________________________ B utton Action Resul[...]

  • Page 28

    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. For this feature, use " Turn On 3D−plot " in the Options menu of view window o r toggle this option by pressing[...]

  • Page 29

    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. The double arrow will continous ly increase image [...]

  • Page 30

    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. 4 .7 Colors Window In this window,[...]

  • Page 31

    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). The dashed line [...]

  • Page 32

    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. The functions for the mar345−Cross section window widg[...]

  • Page 33

    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. L ower horizontal axis Length of line in mm units. L eft dashed red line Marks the[...]

  • Page 34

    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.e. crystal quality, beam properties, et c. The follow[...]

  • Page 35

    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. On the other hand, scan s take about 10% longer time and images are [...]

  • Page 36

    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[...]

  • Page 37

    m ar345 Program Manual 3 7 _ ____________________________________________________________________________________ _ Tabel continued from previous page. _______________________________________________________________________ No. Description _______________________________________________________________________ 1050 Message: "SHUTTER did not wo[...]

  • Page 38

    m ar345 Program Manual 3 8 _ ____________________________________________________________________________________ _ Tabel continued from previous page. _______________________________________________________________________ No. Description _______________________________________________________________________ 1101 Message: "No scan modes foun[...]

  • Page 39

    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.XXX, where XXX is the three−digit serial numbe r. Please refrain from cha[...]

  • Page 40

    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.XXX and mar3450.XXX, where XXX is the three−digit serial number. The file c[...]