Generate XDS.INP: Difference between revisions

Generate XDS.INP (view source)

Revision as of 10:50, 2 July 2012

63 bytes added , 2 July 2012

→‎The script: version 0.26

Kay

Bureaucrats

2,720

edits

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 # revision 0.23 . KD 1/2012 - add UNTRUSTED_QUADRILATERAL, remove MINIMUM_ZETA (0.05 is default now)
 # revision 0.24 . KD 3/2012 - remove revision 0.10 since XDS now takes much longer paths
-# revision 0.25 . KD 3/2012 - remove revision 0.22 for PSI Pilatus 2M; see http://www.globalphasing.com/autoproc/wiki/index.cgi?TroubleShootingKnownIssues
+# revision 0.25 . KD 3/2012 - remove revision 0.22 for PSI Pilatus 2M; see http://www.globalphasing.com/autoproc/wiki/index.cgi?
-REVISION="0.25 (30-Mar-2012)"
+# revision 0.26 . KD 7/2012 - Mac-compatibility: replace od flags --skip-bytes= and --read-bytes= with -j and -N (thanks to Oliver Clarke for working this out!)
+TroubleShootingKnownIssues
+REVISION="0.26 (02-Jul-2012)"
 #
 # usage: e.g. generate_XDS.INP "frms/mydata_1_???.img"
@@ Line 50: / Line 52: @@
 # known problems:
 # - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below);
 # - the same might be a problem for MAR headers, too (not sure about this)
+# - on Mac OS X, Xcode (from http://developer.apple.com/tools/xcode) might be needed - not sure about this
 #
 # notes for debugging of the script:
@@ Line 119: / Line 122: @@
    # use first frame of dataset to obtain parameters
-   # offsets are documented; values can be find in mccd_xdsparams.pl script
+   # offsets are documented; values can be found in mccd_xdsparams.pl script
    let SKIP=1024+80
-   NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   NX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    let SKIP=$SKIP+4
-   NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   NY=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    let SKIP=1720
-   DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   DETECTOR_DISTANCE=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l`
    let SKIP=1024+256+128+256+4
-   ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   ORGX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    ORGX=`echo "scale=2; $ORGX/1000" | bc -l `
    let SKIP=$SKIP+4
-   ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   ORGY=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    ORGY=`echo "scale=2; $ORGY/1000" | bc -l `
    let SKIP=1024+256+128+256+44
-   PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   PHISTART=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    let SKIP=1024+256+128+256+76
-   PHIEND=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   PHIEND=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l`
    let SKIP=1024+256+128+256+128+4
-   QX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   QX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    QX=`echo "scale=10; $QX/1000000" |bc -l `
    let SKIP=$SKIP+4
-   QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   QY=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    QY=`echo "scale=10; $QY/1000000" |bc -l `
    let SKIP=1024+256+128+256+128+128+12
-   X_RAY_WAVELENGTH=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
+   X_RAY_WAVELENGTH=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
    X_RAY_WAVELENGTH=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l`