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Generate XDS.INP: Difference between revisions

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Generate XDS.INP (view source)

Revision as of 14:01, 22 June 2010

5,359 bytes added ,  22 June 2010
fix QX scaling in case of mccd_xdsparams.pl usage; add code of mccd_xdsparams.pl
(fixes; start script with <pre> and end with </pre> for easier cut-and-paste)
(fix QX scaling in case of mccd_xdsparams.pl usage; add code of mccd_xdsparams.pl)
Line 91: Line 91:
       # find QX, ORGX and ORGY:
       # find QX, ORGX and ORGY:
       QX=`grep Pixelsizex tmp2 | sed s/Pixelsizex=//`
       QX=`grep Pixelsizex tmp2 | sed s/Pixelsizex=//`
      QX=`echo "scale=10; $QX/1000000" |bc -l `
       NX=`grep pixelsin1line tmp2 | sed s/#pixelsin1line=//`
       NX=`grep pixelsin1line tmp2 | sed s/#pixelsin1line=//`


Line 124: Line 126:
   ORGXINT=`echo "scale=0; $ORGX/1" | bc -l `
   ORGXINT=`echo "scale=0; $ORGX/1" | bc -l `
   if [ $ORGXINT -lt $NXBYFOUR ]; then
   if [ $ORGXINT -lt $NXBYFOUR ]; then
    QX=`echo "scale=10; $QX/1000000" |bc -l `
#    echo ORGX ORGY QX = $ORGX $ORGY $QX
#    echo ORGX ORGY QX = $ORGX $ORGY $QX
     ORGX=`echo "scale=1; $ORGX/$QX" | bc -l`
     ORGX=`echo "scale=1; $ORGX/$QX" | bc -l`
Line 246: Line 247:
rm tmp1 tmp2
rm tmp1 tmp2


</pre>
For MarCCD data, generate_XDS.INP relies on mccd_xdsparams.pl which is below, and should also be in your $PATH . Alternatively, catmar (which can be downloaded from http://www.marresearch.com/download.html) may be used.
<pre>
#!/usr//bin/perl -w
#
#
#                        Copyright 2004
#                              by
#                The Board of Trustees of the
#              Leland Stanford Junior University
#                      All rights reserved.
#
#                      Disclaimer Notice
#
#    The items furnished herewith were developed under the sponsorship
# of the U.S. Government.  Neither the U.S., nor the U.S. D.O.E., nor the
# Leland Stanford Junior University, nor their employees, makes any war-
# ranty, express or implied, or assumes any liability or responsibility
# for accuracy, completeness or usefulness of any information, apparatus,
# product or process disclosed, or represents that its use will not in-
# fringe privately-owned rights.  Mention of any product, its manufactur-
# er, or suppliers shall not, nor is it intended to, imply approval, dis-
# approval, or fitness for any particular use.  The U.S. and the Univer-
# sity at all times retain the right to use and disseminate the furnished
# items for any purpose whatsoever.
#
#                      Permission Notice
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTA-
# BILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO
# EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
# THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# MARCDD image header format
#
# TIFF header 1024 bytes
# Private frame header 3072 bytes
## file/header format parameters 256 bytes
## data statistics 128 bytes
## more statistics 256 bytes
## goniostat parameters 128 bytes
### xtal_to_detector int32 (mm*1000)
### beam_x int32 (pixel*1000)
### beam_y int32 (pixel*1000)
## detector parameters 128 bytes
### detector_type int32
### pixelsize_x int32 (nanometers
### pixelsize_y int32 (nanometers
##X-ray source parameters 128 bytes
die "ERROR: Missing Argument. \nUsage: $0 [options] <image_filename>\n" unless @ARGV;
while ($_ = $ARGV[0], /^-/) {
        shift;
        last if /^--$/;
        # if (/^-D(.*)/) { $debug = $1 }
        if (/^-v/)    { $verbose = 1 }
        # ...          # other switches
}
open ( FILE, '<', $ARGV[0] ) or
        die ( "ERROR: Cannot open file" );
seek ( FILE, 1024+80, 0 );
read ( FILE , $size_fast, 4 );
read ( FILE , $size_slow, 4 );
seek ( FILE, 1024+256+128+256, 0 );
read ( FILE , $xtal_to_detector, 4 );
read ( FILE , $beam_x, 4 );
read ( FILE , $beam_y, 4 );
seek ( FILE, 1024+256+128+256+16, 0);
read ( FILE , $exp, 4 ); #exp time x 1000
seek ( FILE, 1024+256+128+256+44, 0);
read ( FILE , $start_phi, 4 ); #start phi x 1000
seek ( FILE, 1024+256+128+256+76, 0);
read ( FILE , $end_phi, 4 ); #end phi x 1000
seek ( FILE, 1024+256+128+256+128, 0 );
read ( FILE , $detector_type, 4 );
read ( FILE , $pixelsize_x, 4 );
read ( FILE , $pixelsize_y, 4 );
seek ( FILE, 1024+256+128+256+128+128+12, 0 );
read ( FILE , $wavelength, 4 ); #wavelength x 10000
close ( FILE );
$size_fast = unpack ('i*' ,$size_fast);
$size_slow = unpack ('i*' ,$size_slow);
$xtal_to_detector =unpack('i*' ,$xtal_to_detector) / 1000;
$detector_type =unpack('i*' ,$detector_type);
$beam_x = unpack ('i*' ,$beam_x) / 1000 ; # pixels
$beam_y = unpack ('i*' ,$beam_y) / 1000 ; # pixels
$beam_xc = $size_fast - $beam_x ;
$beam_yc = $size_fast - $beam_y ;
$pixelsize_x = unpack ('i*' ,$pixelsize_x) / 1000000 ;  # mm
$pixelsize_y = unpack ('i*' ,$pixelsize_y) / 1000000 ;  # mm
$beam_x_mm = $beam_x * $pixelsize_x  ; # mm
$beam_y_mm = $beam_y * $pixelsize_y ; # mm
$exp = unpack ('i*' ,$exp) / 1000 ; #seconds
$start_phi = unpack ('i*' ,$start_phi); #mdeg
$end_phi = unpack ('i*' ,$end_phi); #mdeg
$osc = ($end_phi - $start_phi)/1000; # deg
$wavelength = unpack ('i*' ,$wavelength)/100000  ; #A
if ($verbose) {
        print "NX= ${size_fast} NY= ${size_slow} QX= ${pixelsize_x} QY= ${pixelsize_y} \n";
        print "DETECTOR_DISTANCE= ${xtal_to_detector} \n";
        print "ORGX= ${beam_xc}  ORGY= ${beam_yc} \n";
        print "OSCILLATION_RANGE= ${osc} \n";
        print "X-RAY_WAVELENGTH= ${wavelength} \n";
} else {
        print "$size_fast,$size_slow", "\n";
        print "$xtal_to_detector", "\n";
        print "$beam_x_mm,$beam_y_mm", "\n";
        print "$pixelsize_x", "\n";
        print "$exp","\n";
        print "$osc","\n";
        print "$wavelength","\n";
}
exit
</pre>
</pre>
Kay
Bureaucrats
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