Table of Contents
mar345 - data acquisition program for the 345mm mar research Imaging
Plate Detector System
mar345 [ OPTIONS ]
a Motif-based graphical user interface for operating the mar research
Imaging Plate Detector System. The program functions are:
- Send Commands
to the scanner.
- Display the scanner status.
- Transform spiral images into
- Display and analyze images.
The program features a scanner
control window (Main Window), a image display window and related subwindows.
The program versions 0.x for scanners with serial numbers < 044 support different
electronics than program versions 1.x ( for serial numbers >= 044 ). They
must not be mixed up!
With version 3.0 a way for externally feeding in commands
has been added. Simple commands (e.g. erase, open shutter, move phi, etc.)
as well as entire data collections can be started by creating a keyworded
command file (see below: EXTERNAL COMMANDS).
Command line options
always have precedence over value given in the configuration file. All
documentation about how to actually use the features of the graphical user
interface must be looked up in the html documentation.
The main window displays
the following scanner status information:
- -c, --colors COLORS
- No. of colors to use for image display.
Default: -c 64
- --debug NUMBER
- Sets an undocumented flag for debugging purposes.
Default: --debug 0
- --default SCANMODE
- Default scanmode to use for the mar345
detector. At program startup, the scanner will be set to the requested
Default: leave in current scanmode
- -host HOST
- Connect to host HOST. By
default, the scanner hostname is "mar345" (192.0.2.1). The host name giving
on the command line overrides the default and the entry in the configuration
- -h, --help
- Prints usage summary
- Do not connect to the mar345 detector,
but do run the program. Only a limited amount of things can be done without
- -k, --keep
- Write spiral images to disk during scan. By
default, only transformed images are saved.
- -m, --more LEVEL
- Verbose output;
the amount depends on the value of LEVEL, which may have a value between
0 and 3, higher values giving more information.
- -mar345s, -f
- Force usage
of fast mar345s scanmodes overriding the values in the configuration files.
Use with care. It will work only if the mar345 controller is capable of
using fast scan modes.
- At program startup, do not perform run through
- At program startup, do not perform a
self test (i.e. lasers, laser shutter, erase lamps). The default is to do
a self-test each time mar345 is started.
- Spiral images will not be
transformed and displayed during data collection. The default is to transform
- -[no]furnace TIME
- This works with a special compilation of program
mar345 version >= 2.5 only. <TIME> overrides the value given on keyword FURNACE
UPDATE <sec> in the configuration file. A value of 0 would turn off usage
and initialization of the furnace. So will the argument -nofurnace (leaving
off the time value). This option should be use when working with the mar345
with a furnace disconnected.
- -p, --port PORT
- Connect to port PORT. By default,
the connection will be established through ports 4441 to 4444. The port
number given on the command line overrides the default and the entry in
the configuration file.
- -s, --server PORT
- Listens to port PORT for incoming
connections. If the port number is given on the command line, the optional
keyword SERVER PORT in the configuration file will be ignored. When running
the program in TCP/IP-server mode, the program accepts command input via
- -off OFFSET
- Apply an offset to raw spiral data.
- -sc factor
- Apply a scale factor to raw spiral data.
- Allows users to redefine
the distance within the program. For safety reasons, this feature is disabled.
- -sn NNN
- Serial number of detector. By default, the serial number is taken
from environment variable $MAR_SCANNER_NO.
- -v, --verbose
- Increases verbosity
level. May be given several times.
- Current time.
- Current scanner
- Current scan mode (diameter and pixelsize).
- Current X-ray shutter
- Current image.
- Current distance.
- Current phi position.
- Current intensity.
- Current disk space.
Underneath the section with the scanner status information,
the following push buttons can be found:
data collection parameters, press the Collect button in the main window
and make your choice of programming a "Single Set", "Multiple Sets" (1-4
data sets), "MAD Data" for collecting MAD data (multiple anomalous dispersion)
or "Index Crystal" for collecting images with larger PHI movements inbetween.
The following input is required:
- Collect: Choice of programming
up to four data sets (see EDITING DATA COLLECTION PARAMETERS).
- Scan: Provides
a window for entering the output file name for a single scan.
- Erase: Turns
on the erase lamps and erases the imaging plate.
- Initialize: Drives the
detector to its distance reference position.
- Open/Close Shutter: Opens and
closes the local X-ray shutter.
|Image root|||||Name root of images|||||lyso|
|Output format|||||new "mar345" or old "image"|||||mar345|
|Collect mode|||||TIME or X-ray
||||controlled PHI movement|||||(recommended)|
|First image no.|||||No. of first
|No. of images|||||No. of images in set (1-999)|||||120|
|PHI increment |||||PHI
movement between 2 |||||45 deg.|
|(Index crystal)|||||consecutive images||||
time per image|||||300 sec|
|Oscillations|||||PHI oscillations per image|||||1|
movement during|||||1.0 deg.|
|per image|||||one exposure||||
|PHI|||||PHI angle where data|||||0.0 deg.|
|Distance|||||Distance crystal-detector|||||150 mm|
In "Multiple Set" mode up
to 8 data sets may be programmed by editing these parameters. To use any
one of the programmed sets, the "Use" button must be explicitely pressed
for this set.
In ""MAD Data" mode, 2 data sets will be take (A and B). A starts at "Starting
PHI", B at "Starting PHI + 180 deg.". The first PHI-block of images will
be in set A, the second one in set B, the third one also in set B, but
at "Starting PHI + (images/block)* Delta-PHI + 180 deg.", the fourth one
again in set A at "Starting PHI + (images/block)*Delta-PHI ", etc. A PHI-block
denotes the smallest set of images that are contiguous in PHI. To obtain
the total number of images to be collected, just multiply the number of
PHI-blocks by the number of images per PHI-block. To alternate between both
sets, use 1 image per block. Note, that the smaller the number of images
per PHI-block the more PHI movements are required. For further illustration,
use the Help-button in the window.
In "Index Crystal" mode, the field "First image no." is replaced by the
field "PHI increment". The first image no. will always be 1. Before doing
the next exposure, the PHI axis drives to a new value that is "PHI increment"
degrees away from the previous image. The image no. for the new image is
calculated as: previous image no. + PHI increment/Delta PHI.
Data collection starts by pressing the "Go" button in the "Change
Parameters" window. A new window "Run Parameters" pops up and displays
the summary of the selected parameters. In this window, "Go" has to be pressed
again. By pressing "Go/Erase first" the plate will be cleaned before starting
the data collection. Note, that the plate will always be erase when moving
to larger scanned diameters.
If additional shell-commands have been configured
(see mar345_config_file) these shell-commands will be executed before actually
starting the data collection and/or each exposure.
During data collection,
the "Change Parameters" window cannot be obtained. If desired, the progress
of data collection can be traced by looking at the "Run Parameters" window
(select "Progress" in the menu bar of the main window or press "Ctrl+p"
in the main window). All essential information, however, is displayed in
the main window.
To stop data collection press
the yellow "Stop" button in the main window and select "Abort NOW" or "Stop
AFTER IMAGE" in the the "Run Parameters" window.
input fields for "Phi" and "Distance" in the "Change Parameters" window
are followed by two buttons: "Move" and "Set". By pressing "Move", the PHI
axis or the detector drives to the desired position. By pressing "Set",
the currently known values can be redefined.
order to open or close the shutter, normally one would just press the "Open/Close
Shutter" button in the main window. It is possible, however, to leave the
shutter open for a specified period time using an additional window that
can be obtained by choosing the "Shutter Timer" option in the "Windows"
submenu of the menu bar. This window displays a digital stop watch that
counts the time since the "Open Shutter" button was pressed. The shutter
will automatically close after the time specified in the entry field above
has elapsed. This will happen only if this window stays on the screen. When
closed, no further time limits are applied.
to diagnose hardware, in program version > 1.0 there is an additional window
that can be opened using the "Hardware" button in the "Windows" submenu
of the menu bar. In that window, hardware status is graphically displayed,
i.e. state of erase lamps, plate locking, etc. All hardware errors are logged
into standard output and into the log file. When using an optional "spy"
output file, each scanner operation is logged into that file. This can be
helpful for looking close at hardware problems.
some synchrotron beam lines, a shell command can be issued to modify the
current wavelength. In the config file, the "USE WAVE" keyword must be given.
This will display a "Set"-button for the wavelength in the "Change Parameters"
window. When pressed, a shell command ($MARLOGDIR/mar345-set.csh, see below)
will be executed. No further input is allowed while task in progress. There
is no feedback that actually checks if the actual wavelength is the desired
Shell commands may be executed at the beginning
of a programmed data set and/or before starting an exposure. Input fields
are provided if keyword "USE SHELL" is given in the configuration file.
No further input is allowed while the shell command is running. Shell commands
make use of existing shell script files that may be edited for further
customization (see below).
If a positive value for parameter
COMMAND in the configuration file (see man page mar345_config_file) has
been given, the program accepts commands from a keyworded ASCII-file $MARCOMMANDFILE
which defaults to $MARLOGDIR/mar.com. Likewise, if a positive port number
for parameter SERVER PORT in the configuration file (see man page mar345_config_file)
has been given, the program accepts commands from the given port of a TCP/IP-socket
in the same ASCII syntax as defined in $MARCOMMANDFILE.
Simple commands (e.g. erase, open shutter, move phi, etc.) as well as entire
data collections can be started this way. After evaluating MARCOMMANDFILE,
the file is deleted. If a certain task or procedure is active, only commands
ABORT or STOP will be accepted. All other commands will be executed after
the current procedure has finished. When setting up a data collection, the
parameters given in MARCOMMANDFILE will overwrite the settings for either
SINGLE SET, INDEX CRYSTAL or MAD DATA. Parameters that are not specified
will be taken from the GUI, otherwise. This way, any combination of graphical
editing and external commands is achieved.
An active task or procedure will write additional output into file $MARLOGDIR/mar.message.
This file will contain information about the progress of a procedure. A
new procedure is going to overwrite the file. This file may be used by other
external programs for synchronization with further actions.
The syntax for file MARCOMMANDFILE is as follows (see also EXAMPLES for
- COMMAND <string>
- Specifies the hardware command or procedure
to be executed. This keyword must be given as first line in MARCOMMANDFILE
when driving the program via MARCOMMANDFILE. When driving the program via
a TCP/IP-socket, the COMMAND line must be given as the last part of the
instructions! <string> is one of:
- SHUTTER OPEN - Opens the shutter
- SHUTTER CLOSE - Closes the shutter
- Shuts down the program
- CHANGE - Change current scanmode
- ERASE - Erases
the image plate
- SCAN - Scans the image plate and produces an image
[MIN] - Initializes the distance to far [or near] end
- COLLECT [SINGLE | INDEX
| MAD ] - Starts a data collection run, either as single data set, index
crystal or MAD data set.
- PHI MOVE <deg> - moves PHI to <deg>
- PHI DEFINE <deg> -
defines PHI as <deg>
- DISTANCE MOVE <mm> - moves DISTANCE to <mm>
- DISTANCE DEFINE
<mm> - defines DISTANCE as <mm>
- ABORT - aborts current movements and stops data
- STOP - stops data collection after finishing current image
The following additional keywords in MARCOMMANDFILE are meaningful only
for COMMAND COLLECT or COMMAND SCAN. If they are not provided, the corresponding
entries in the GUI from either SINGLE SET, INDEX CRYSTAL or MAD SET are
used for data collection. Note that when doing SCANS, the output file name
will be composed of the directory (DIRE), the root name (ROOT), a three
digit number starting with FFRM and the image extension depending on the
format (e.g. .mar1200).
|Keyword|||||Arguments|||||Example|||||Analogy in GUI|
|DOSE|||||<dose>|||||100|||||X-ray dose (units)|
|FFRM|||||<number>|||||1|||||First image no.|
|BLOC|||||<number>|||||2|||||No. of PHI blocks|
|COM2|||||<strings>|||||?|||||Shell command 2|
The only effect of the following keywords will be that the provided values
will be used as image header information.
|CHI |||||<deg>|||||0.0|||||Chi position|
The following keywords will overwrite the entries in the "X-ray Setup"-window
of the GUI.
|Keyword|||||Arguments|||||Example|||||Analogy in GUI|
<mA>|||||50 100|||||X-ray kV, mA|
|SLIT|||||<x> <y>|||||0.3 0.35|||||Collimator X,Y|
|BEAM|||||<x> <y>|||||0.1 0.2|||||Deviation X,Y|
The image display
window can be obtained by selecting the "Display" button in the menu bar
of the main window or by typing "Ctrl+d". During data collection, newly
collected images are displayed automatically. While the scanner is not
scanning, other images may be loaded from disk using the "Files" option
in the "Windows" submenu of the menu bar.
magnification factors, select "Auto/100%", "100%", "75%" or "50%" in the
menu bar, where 100% means: 1 pixel on the screen is 1 pixel in the image.
It is possible to further magnify areas within the image by selecting a
zoom area in the displayed image (see ZOOM MODE). In ZOOM MODE, the available
zoom factors are: 1, 2, 4, 8, ... 512.
With the "Options"
button in the menu bar, the following options can be toggled:
In the image area, the 3 mouse buttons have the following
- Keep/Hide statistics (average and max. intensity).
not keep view.
- Keep/Do not keep color scales.
- Reset colors.
- Next image.
- Zoom options.
"Integrate" is available in ZOOM MODE only.
The contents of the displayed image area is integrated.
"Keep view" means: when loading a new image, the same area and magnification
will be drawn. "Keep view" also implies "Keep colors". If a crosssection
has been drawn, it will be displayed as well.
"Keep color scales" means: when loading a new image, the image will be
drawn in the same way as the previous image (see IMAGE COLORS).
"Reset colors" means: reinitialize image colors.
"Next image" means: load the next image (image number incremented by one).
"Previous image" means: load the previous image (image number decremented
"Zoom options" means: in IMAGE MODE and zoom factors less than 100%, by
default every "N’th pixel" is displayed only and the ones inbetween are
ignored. While this method may hide some features in the image, it is much
faster than computing the "Average pixel" or the "Maximum pixel". "Average
pixel" tends to give a smoother look. In "Maximum pixel" mode, reflections
will appear stronger, but you will also see more noise (e.g. cosmics).
Normally, 32 colors are distributed in equidistant
intensity bins between a minimum (Min) and maximum (Max) value. All pixel
values > Max are drawn in one color and all values < Min in another color.
Min usually is 0, but Max is calculated such that 99.998 % of all pixels
in the image have intensities <= Max. The Max and Min can be entered on the
left hand side of the image display window (upper left and lower left corner,
respectively) or in the "Colors" window which can be obtained by selecting
the "Colors" option in the "Windows" submenu or by typing "Ctrl+o". In the
"Colors" window, the histogram of the pixel values in the image is displayed,
i.e. the inetnsity of a pixel versus its frequency. In the histogram plot,
two dashed bars mark the Min and Max values. To change Min or Max, enter
values in the corresponding fields (and press RETURN!) or move the left
or right bar using the left or right mouse button, respectively. Warning:
each operation requires recalculation of the whole image (CPU!!!).
- Left mouse button:
- Draws a line from point A to point B and
displays the pixel values along that line in a separate window (see CROSS
- Center mouse button:
- Displays x,y-coordinates, intensity and resolution
of the selected pixel (upper right area) and the minimum, maximum, average
and sigma of a box of 100x100 pixels (red box) around the selected pixel
(upper left area).
- Right mouse button:
- Draws a box from point A to point
B and displays the image area within that box in the image display window
with the corresponding magnification factor ("ZOOM MODE"). To get back to
normal "IMAGE MODE", the "Back" button in the menu bar must be pressed
(or "Alt+b" typed). In ZOOM MODE, the right mouse button has a different
function: when pressed, the magnified area is recentered at the pixel under
the mouse pointer.
color schemes, select "Gray scales" or "Gray scales" or "Rainbow". By dragging
the center mouse button in the histogram plot or in the color area of the
image display window, colors can be redistributed.
can be obtained by pressing the left mouse button in the image area of
the display window. The cross section plot can be used for measuring distances
and thus getting an estimate of cell constants. In the plot area two dashed
lines can be moved around by pressing the left (left bar) and right (right
bar) mouse button, respectively. The distance between bars is given in pixels
and mm. The upper horizontal scale in the plot area is the length of line
in pixel units, the lower one the length in mm.
To calculate cell constants,
the no. of peaks between the left and the right distance measuring bar must
be entered. Place the bars on top of two peaks. The no. of peaks must include
the first and last one.
The following logical names must be
The program requires the following input
- Location of scanner specific calibration and configuration
- Serial number of scanner.
- Directory where
log files will go.
- Directory containing help files (optional).
- If the environment variable MARSTATUSFILE is not defined,
the default file name will be $MARLOGDIR/mar345.status. For a description,
- If the environment variable MARMESSAGEFILE is
not defined, the default file name will be $MARLOGDIR/mar.message. For a
description, see below.
The program produces the following
- Scanner specific calibration
table used for transformation of the images collected with 0.15 mm pixelsize.
- Scanner specific calibration table
used for transformation of the images collected with 0.10 mm pixelsize.
- Scanner specific configuration file (Ascii).
file for interactive help.
- $MARLOGDIR/mar345.dat (optional):
- Contains latest
data collection parameters.
- $MARLOGDIR/mar345.PAR (optional):
- Stores the
latest DISTANCE and PHI values on disk. The scanner does not keep these
values in memory, so the software has to tell the scanner which values
to use (or reinitialize). This file is used only on versions 0.x!
- Shell script for changing wavelength. This file must be executable.
The actual command to change the wavelength must be given. The script is
called when pressing the "Set"-wavelength button. Argument no. 1 is the wavelength
as given in the input field.
- $MARLOGDIR/mar345-com1.csh (optional):
script for a shell command to be executed before starting a data set. The
number of arguments is variable. The first argument is the name of the
program to be called.
- $MARLOGDIR/mar345-com2.csh (optional):
- Shell script
for a shell command to be executed before starting an exposure. The number
of arguments is variable. The first argument is the name of the program
to be called.
- MARCOMMANDFILE ($MARLOGDIR/mar.com, optional since version
- Keyworded ASCII file for setting up simple hardware commands (shutter,
erase, etc.) as well as an entire data collection. The file will be deleted
after succesful evaluation.
- Contains the version number of the latest
- $MARLOGDIR/mar.log_NO (version 0.x) or $MARLOGDIR/log/mar.log.NO:
- Latest log file. NO ranges from 1 to 99 and is increased with each call
of program mar345. If NO > 99, NO = 1.
- $MARLOGDIR/MAR345.NO.LP (version 0.x)
- Optional output, if keyword USE STATS is given
in the config file (see mar345_config_file). The NO ranges from 1 to 99
and is increased with each call of program mar345. If NO > 99, NO = 1.
(version > 1.0 only):
- Optional output, if keyword USE SPY is given in the
config file (see mar345_config_file).
- Optional output of
a status file updated in regular interval, containing the most relevant
status information. To enable output, use keyword STATUS <interval> in the
configuration file. The interval is in milliseconds. If the environment variable
MARSTATUSFILE is not defined, the default file name will be $MARLOGDIR/mar345.status.
- Optional output of a progress file when using external command
files (see MARCOMMANDFILE). This file contains the most relevant status
information about the progress of an active task. To enable output, use
keyword COMMAND <interval> in the configuration file. The interval is in milliseconds.
The default file name is $MARLOGDIR/mar.message
- data directory:
image files and data collection summaries (.SUMMARY and .html).
program will automatically set links $MARLOGDIR/mar.log and optionally $MARLOGDIR/mar.lp
and $MARLOGDIR/mar.spy to the latest files in use.
set argc = $#argv
set NUM = 2
set cmd = $1
while ( $NUM <= $argc )
set cmd = ( $cmd $argv[$NUM] )
# Actual command
The following command file would start a data
collection for images lyso_001.mar2000 to lyso_090.mar2000 starting at PHI=0
with an oscillation width of 1 deg. per image:
COMMAND COLLECT SINGLE
The following command file would move the distance to 250 mm:
COMMAND DISTANCE MOVE 250.0
marView, marTools, mar345xf, mar345_formats, mar345_config_file,
Claudio Klein, marXperts GmbH, Norderstedt, Germany
© Copyright 2000-2017 marXperts GmbH, Norderstedt, Germany
|marXperts GmbH||Phone: +49 - (40) - 529 884-0|
|Werkstr. 3|| FAX: +49 - (40) - 529 884-20|
Norderstedt - GERMANY||info@marXperts.com|
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