Table of Contents
scan345 - terminal program for doing scans and other operations on
the 345mm mar research Imaging Plate Detector System .
scan345
[ -h ] [ [ -keep ] [ -more LEVEL ] [ -host HOST ] [ -port PORT ]
scan345
is a program for performing scanner operations on the mar research Imaging
Plate Detector System without graphical user interface. Input is read from
a command file (see below). The program exists in two versions to cooperate
with different types of controllers. Version >=2.0 of scan345 cooperates
with scanners with serial no. > 043 only, while version 0.x of scan345 operates
with scanners from serial no. 001 to 043. Note, however, that even scanners
with serial numbers <= 043 may have been upgraded to behave like one of
the later models. For scan345 >= 2.0, all scanner functions can be used,
for scan345 < 2.0, available program functions are:
·- Scan the plate. This
involves transformation of spiral images into Cartesian images.
·- Change scan
mode.
·- Erase the plate.
- -keep
- Write spiral images to disk during scan.
By default, only transformed images are saved.
- -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.
- -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
file.
- -port PORT
- Connect to port PORT. By default, the connection will be
established through the arbitrary port no. 4123. The port number given on
the command line overrides the default and the entry in the configuration
file.
At startup, the program reads internal parameters from
a configuration file (see below). The program then connects to the scanner
via the BSD-socket-interface (Ethernet). If successful, the program waits
for input from file $MARLOGDIR/mar.com. This ASCII-file contains keyworded
commands. After the input has been processed, the file is deleted and the
specified command is sent to the scanner. The progress of an active command
is monitored in output file $MARLOGDIR/mar.message. The information in this
file refers to one task only. The file is truncated at the start of each
new task. If the specified command has finished, $MARLOGDIR/mar.message
is closed and the program looks for further commands from file $MARLOGDIR/mar.com.
Only one command can be processed at one time (the last COMMAND keyword
found in mar.com). All log information goes into standard output and into
the log file $MARLOGDIR/log/mar.log.NO (see below).
The following
keywords in $MARLOGDIR/mar.com are mandatory:
- COMMAND <task>
- Specifies the
task to execute. Can be: SCAN, ERASE, CHANGE, QUIT or LISTEN (scan345 < 2.0)
or SCAN, ERASE, CHANGE, QUIT, START, INIT, SHUTTER, EXPOSE, PHI, DISTANCE
and OMEGA (scan345 >= 2.0). A scan in a different scanmode automatically
involves a mode change. QUIT tells the scanner to exit from its listener
program, LISTEN (scan345 < 2.0 only) means, that the scanner will wait for
another connect request. No default.
With scan345 >= 2.0, the following commands
accept further input:
·- SHUTTER OPEN: Opens shutter
·- SHUTTER CLOSE: Closes
shutter
·- PHI MOVE <target>: Moves PHI to target (deg.).
·- PHI DEFINE <target>: Defines
PHI as target (deg.).
·- OMEGA MOVE <target>: Moves OMEGA to target (deg.).
·- OMEGA
DEFINE <target>: Defines OMEGA as target (deg.).
·- DISTANCE MOVE <target>: Moves
DISTANCE to target (mm).
·- DISTANCE DEFINE <target>: Defines DISTANCE as target
(mm).
·- INIT MIN: Initialize distance at near end of translation stage.
·- INIT
MAX: Initialize distance at far end of translation stage.
·- EXPOSE [<delta-phi>]
][<units>] [<oscillations>]: Makes an exposure with <oscillations> over <delta-phi>
degrees for <units> seconds or X-ray counts (default: seconds, unless COLLECT
DOSE given; see below). The additional arguments are optional, but if not
given here, they must be specified with keywords PHI and COLLECT (see below).
With scan345 >= 2.2, the SCAN command accepts additional input:
·- SCAN ERASE
<n> ADD <m>: After finishing one scan, the plate may optionally be erase <n>
times, additionally. Note that one complete erase cycle consists of a scan
plus approx. 15 seconds of erase. Optionally, data from <m> subsequent scans
can be added to the first scan. The program will write out resulting images
after each scan cycle containing the sum of added data. The resulting output
file will be overwritten until <m>+1 scans are completed. When saving spiral
files, the raw spiral data will be stored as <root>.<c>.sXXXX where <c> = a,b,c,d,
etc.. The defaults are: SCAN ERASE 0 ADD 0
With scan345 >= 2.0, instead of
COMMAND, the following keywords can be used to access the whole range of
commands for the scanner and base:
·- IPS <no> <mode> <par1> <par2> <par3> <par4> <par5>
<str>:
·- SYSTEM <command>
Either IPS or SYSTEM will overwrite all COMMAND keywords.
Use these keywords very carefully and only after consulting mar research.
The following keywords in $MARLOGDIR/mar.com are mandatory only when doing
a scan:
- DIRECTORY <directory>
- Specifies the output directory for image
files.
Default: DIRECTORY current_directory
- ROOT <root>
- Specifies the root name
of the output image when doing scans. The syntax is: <string>_<no>, where <string>
is any string and <no> is a three digit number, e.g. 001.
Default: ROOT xtal_001
- MODE <scanmode>
- Specifies the scan mode. The number
range from 0 to 7. The scanmodes are as follows:
MODE 0 = 2300 pixels, 345 mm diameters, 0.15 mm pixelsize
MODE 1 = 2000 pixels, 300 mm diameters, 0.15 mm pixelsize
MODE 2 = 1600 pixels, 240 mm diameters, 0.15 mm pixelsize
MODE 3 = 1200 pixels, 180 mm diameters, 0.15 mm pixelsize
MODE 4 = 3450 pixels, 345 mm diameters, 0.10 mm pixelsize
MODE 5 = 3000 pixels, 300 mm diameters, 0.10 mm pixelsize
MODE 6 = 2400 pixels, 240 mm diameters, 0.10 mm pixelsize
MODE 7 = 1800 pixels, 180 mm diameters, 0.10 mm pixelsize
Default: MODE 0
- FORMAT <format>
- Specifies the image output format. For scan345
< 2.0 available formats are: 0 = spiral output only, 1 = mar345 style output,
3 = image style output. For scan345 >= 2.0, available format specifiers are:
MAR345, IMAGE and SPIRAL.
In scan345 >= 3.0, the imgCIF/CBF output format has been added. CBF and imgCIF
differ in the way the binary data are encoded: CBF uses binary encoding
and is somewhat more compact while in the imgCIF format, the data are ASCII-encoded.
The format specifier to use is: CBF and CIF. For more details about CBF/imgCIF
see http://ndbserver.rutgers.edu/mmcif/cbf/.
It is strongly recommended to use the mar345 format!
Default: FORMAT MAR345 (or FORMAT 1 in scan345 < 2.0)
The following keywords
in $MARLOGDIR/mar.com are optional. Their only purpose is to fill up image
header entries with meaningful values. It is strongly suggested to pass
at least the PHI, DISTANCE and WAVELENGTH parameters to the program.
- DISTANCE
<distance>
- Specifies the distance crystal-detector in mm.
Default: 100 mm.
- WAVELENGTH <lambda>
- Specifies the used wavelength in Angstroem.
Default: Taken from configuration file
- PHI <start> <end> <oscillations>
- Specifies
the starting and ending values of the PHI axis in degrees, as well as the
number of oscillations used.
Default: Taken from configuration file
- OMEGA <start> <end> <oscillations>
- Specifies
the starting and ending values of the OMEGA axis in degrees, as well as
the number of oscillations used.
Default: Taken from configuration file
- CHI <chi>
- Specifies the position
of the CHI axis in degrees.
Default: Taken from configuration file
- THETA <2-theta>
- Specifies the position
of the 2-THETA axis in degrees.
Default: Taken from configuration file
- TIME <exposure-time>
- Specifies the
used exposure time in seconds.
Default: TIME 60.0
- COLLECT <mode>
- Specifies the type of exposures: TIME
controlled or X-ray DOSE controlled. In scan345 < 2.0, enter COLLECT 0 (time
mode) or COLLECT 1 (dose mode), in scan345 >= 2.0 give, COLLECT TIME <time>
or COLLECT DOSE <dose>.
Default: COLL TIME 60.0 (scan345 >= 2.0) or COLL 1 (scan345 < 2.0)
- SOURCE
<X-ray_source>
- String to specify the type of X-ray source.
Default: Taken from configuration file
- FILTER <monochromator>
- String to
specify the type of monochromator used.
Default: Taken from configuration file
- REMARK <remark>
- String for additional
comments.
Default: None
- BEAM <slit_X> <slit_Y>
- Specifies the aperture of the collimator
in X and Y.
Default: Taken from configuration file.
- POLARIZATION <pol>
- Specifies the
polarization factor of the beam.
Default: Taken from configuration file.
- POWER <kV> <mA>
- Specifies the power
settings of the X-ray source (kiloVolt, milliAmps).
Default: Taken from configuration file.
The following logical
names must be assigned:
- MARTABLEDIR:
- Location of scanner specific calibration
and configuration files.
- MAR_SCANNER_NO
- Serial number of scanner.
- MARLOGDIR
- Directory where log files will go.
The program requires the
following input files:
- $MARTABLEDIR/mar2300.$MAR_SCANNER_NO:
- Scanner specific
calibration table used for transformation of the images collected with
0.15 mm pixelsize.
- $MARTABLEDIR/mar3450.$MAR_SCANNER_NO:
- Scanner specific
calibration table used for transformation of the images collected with
0.10 mm pixelsize.
- $MARTABLEDIR/config.$MAR_SCANNER_NO:
- Scanner specific configuration
file (Ascii).
- $MARLOGDIR/mar.com.
- Keyworded ASCII file containing commands
and other parameters.
Besides the desired image, the program
produces the following output files:
- $MARLOGDIR/last.log:
- Contains the version
number of the latest log file.
- $MARLOGDIR/mar.log_NO (scan345 < 2.0 only):
- Latest log file. NO ranges from 1 to 99 and is increased with each call
of program mar345. If NO > 99, NO = 1.
- $MARLOGDIR/log/mar.log.NO (scan345 >=
2.0 only):
- Latest log file. NO ranges from 1 to 99 and is increased with
each call of program mar345. If NO > 99, NO = 1.
- $MARLOGDIR/spy/mar.spy.NO (scan345
>= 2.0 only):
- Latest spy file. Output will be produced only if "USE SPY" is
given in the configuration file.
- $MARLOGDIR/mar.status (scan345 >= 2.0
only):
- Current scanner status: DISTANCE, PHI, currently active tasks and
hardware bits (currently undocumented). The current status will be updated
approx. once per second. This file is being used only if "USE STATUS" is
given.
- $MARLOGDIR/mar.message.
- This file will be truncated at the start of
each new task. The progress of the current command will be logged into this
file. If the task has finished, the file will be closed.
- scan345
-port 4532 -host mars
mar345_config_file, mar345, marView, marTools,
mar345xf, mar345_formats, marpack, marcvt.
Claudio Klein, Marresearch
G.m.b.H., Norderstedt, Germany
© Copyright 2000-2004 Marresearch G.m.b.H.,
Norderstedt, Germany
|
| Marresearch G.m.b.H. | Phone: +49 - (40) - 529 884-0 |
| Hans-Boeckler-Ring
17 | FAX: +49 - (40) - 529 884-20 |
| D-22851 Norderstedt - GERMANY | info@marresearch.com |
| www.marrresearch.com |
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