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 ports no. 4441 to 4444. The port number
given on the command line overrides the default and the entry in the configuration
file.
- -s PORT
- Start TCP/IP-server on port PORT.
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. As
of program version 5.0, the program can also act as TCP/IP-server by listening
to connections on a given port number (see section TCP/IP-SERVER). The
command syntax is the same as for the ASCII-file input. 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. When not supplying
the image number in _NNN notation, the image number given on the IMAGE/FFRM
keyword will be appended to the root name.
Default: ROOT xtal_001
- IMAGe | FFRM <n>
- Optional image number to be appended
to the image root name given by the ROOT keyword. An additional underscore
character is appended to the root name in front of the 3-digit number.
Default: If no image is given, the root name is checked for a 3-digit ending.
- 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
In mar345s detectors, scanmode 4 to 7 have been replace by:
MODE 4 = 1150 pixels, 345 mm diameters, 0.15 mm pixelsize
MODE 5 = 1000 pixels, 300 mm diameters, 0.15 mm pixelsize
MODE 6 = 800 pixels, 240 mm diameters, 0.15 mm pixelsize
MODE 7 = 600 pixels, 180 mm diameters, 0.15 mm pixelsize
In some versions of the mar345s detectors, the 150 micron modes modes 0
to 4 have been replaced by the 100 micron modes 5 to 7.
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://www.bernstein-plus-sons.com/software/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.
As of version 5.0, the program
may accept input from a TCP/IP-socket. In the client/server-model, program
scan345 is the server and listens to a given port number for incoming
connections. The port number can be given on the command line by using option
’-s PORT_NUMBER’ or by providing a line in the configuration file:
SERVER PORT port_number WRITE n
The port number here specifies the port number to listen to. The option
"WRITE n" is optional and is going to dump the information that would
go into file mar.message (see above) as output on the TCP/IP-socket every
"n" seconds. The default is n=0, i.e. no message output will be generated
on the TCP/IP-socket.
- $MARTABLEDIR/mar2300.$MAR_SCANNER_NO:
-
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, marXperts
GmbH, Norderstedt, Germany
© Copyright 2000-2015 marXperts GmbH,
Norderstedt, Germany
|
| marXperts GmbH | Phone: +49 - (40) - 529 884-0 |
| Werkstr.
3 | FAX: +49 - (40) - 529 884-20 |
| D-22844 Norderstedt - GERMANY | info@marXperts.com |
| www.marXperts.com |
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