Generate XDS.INP - Revision history

Kay: revision 1.25

2026-04-17T08:38:29Z

revision 1.25

← Older revision		Revision as of 10:38, 17 April 2026
Line 156:		Line 156:
	# revision 1.23 . KD 28/2/2026 remove setting negative DETECTOR_DISTANCE for adsc-CMOS1 - found with SBGrid 383 (PDB 5HV4)		# revision 1.23 . KD 28/2/2026 remove setting negative DETECTOR_DISTANCE for adsc-CMOS1 - found with SBGrid 383 (PDB 5HV4)
	# revision 1.24 . Jan Gebauer 14/03/2026 Implementation for ID30B Pilatus CdTe detector. Introduction of calc_CdTe_Silicon () for 5-25kEV range.		# revision 1.24 . Jan Gebauer 14/03/2026 Implementation for ID30B Pilatus CdTe detector. Introduction of calc_CdTe_Silicon () for 5-25kEV range.
	REVISION="1.24 (14-~~Mar~~-2026)"		# Revision 1.25 . KD 17/4/2026 Pilatus4 Si 2M at SLS. HDF5: subtract 1 from /entry/instrument/detector//saturation_value to obtain OFFSET
			REVISION="1.25 (17-Apr-2026)"

	#		#
Line 332:		Line 333:
	else		else
	h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME \| grep -i Eiger > /dev/null && DET=eiger		h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME \| grep -i Eiger > /dev/null && DET=eiger
	h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME \| grep -i "PILATUS4 CdTe 4M" > /dev/null && DET=eiger		# h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME \| grep -i "PILATUS4 CdTe 4M" > /dev/null && DET=eiger
			h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME \| grep -i PILATUS4 > /dev/null && DET=eiger
	fi		fi

Line 671:		Line 673:
	DLS=0		DLS=0
	OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME 2>/dev/null` \|\| DLS=1		OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME 2>/dev/null` \|\| DLS=1
			#special case of PILATUS4 Si 2M at SLS does not have /entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff but should be treated as Dectris - seems to be SLS own '
			if [ "$DET_SN" == "D029955" ]; then
			DLS=0
			fi
	if [ "$DLS" == 1 ]; then		if [ "$DLS" == 1 ]; then
	echo Eiger HDF5 from Diamond		echo Eiger HDF5 from Diamond
	# unfortunately h5dump 1.10 is required to get this right for the DLS .h5 files. This version is available at DLS but maybe not elsewhere		# unfortunately h5dump 1.10 is required to get this right for the DLS .h5 files. This version is available at DLS but maybe not elsewhere
	OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME \| awk '/$0$:/{print $2}'`		OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME \| awk '/$0$:/{print $2-1}'`
	# v0.95: fix the next 2 lines by taking care of negative values with the \- , and stop after first "(0)"		# v0.95: fix the next 2 lines by taking care of negative values with the \- , and stop after first "(0)"
	OSCILLATION_RANGE=`h5dump -d "/entry/data/omega" $FIRSTFRAME \| awk '/$0$: [\-0-9]/{print $3-$2;exit}'`		OSCILLATION_RANGE=`h5dump -d "/entry/data/omega" $FIRSTFRAME \| awk '/$0$: [\-0-9]/{print $3-$2;exit}'`
Line 685:		Line 691:
	echo Eiger HDF5 from Dectris		echo Eiger HDF5 from Dectris
	OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME \| awk '/$0$:/{print $2}'`		OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME \| awk '/$0$:/{print $2}'`
			if [ "$DET_SN" == "D029955" ]; then
			OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME \| awk '/$0$:/{print $2-1}'`
			fi
	OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME \| awk '/$0$: [0-9]/{print $2}'`		OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME \| awk '/$0$: [0-9]/{print $2}'`
	# STARTING_ANGLE: the \- was introduced in version 0.91 to allow negative values :		# STARTING_ANGLE: the \- was introduced in version 0.91 to allow negative values :
Line 1,195:		Line 1,204:
	UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known		UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known
	INCLUDE_RESOLUTION_RANGE=50 0 ! after CORRECT, insert high resol limit; re-run CORRECT		INCLUDE_RESOLUTION_RANGE=50 0 ! after CORRECT, insert high resol limit; re-run CORRECT
	! IDXREF ~~now~~ obeys INCLUDE_RESOLUTION_RANGE and EXCLUDE_RESOLUTION_RANGE to exclude ice-rings		! IDXREF obeys INCLUDE_RESOLUTION_RANGE and EXCLUDE_RESOLUTION_RANGE to exclude ice-rings

	FRIEDEL'S_LAW=FALSE ! This acts only on the CORRECT step		FRIEDEL'S_LAW=FALSE ! This acts only on the CORRECT step
Line 1,446:		Line 1,455:
	UNTRUSTED_RECTANGLE= 1295 1297 0 2181		UNTRUSTED_RECTANGLE= 1295 1297 0 2181
	UNTRUSTED_RECTANGLE= 1815 1817 0 2181		UNTRUSTED_RECTANGLE= 1815 1817 0 2181
			eof
			elif [ "$NX" == "1553" -a "$NY" == "1630" ]; then
			# Pilatus4 Si 2M ; v1.25
			cat >> XDS.INP << eof
			!masking non sensitive area of Pilatus4 Si 2M
			! UNTRUSTED_RECTANGLE= lines not needed because pixel counts are -1
	eof		eof

Kay: /* Usage */ mention xds-zcbf plugin

2026-03-17T13:00:06Z

Usage: mention xds-zcbf plugin

← Older revision		Revision as of 15:00, 17 March 2026
Line 7:		Line 7:
	For .h5 files you need to load the *master.h5 , and you don't need the quotation marks:		For .h5 files you need to load the *master.h5 , and you don't need the quotation marks:
	generate_XDS.INP /home/myname/frms/mydata_1_master.h5		generate_XDS.INP /home/myname/frms/mydata_1_master.h5
	XDS [https://xds.mr.mpg.de/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= supports] compression with gzip or bzip2. When specifying the frame name parameter of the script, you should leave out any .gz or .bz2 extension. Note that the processing of *.cbf.gz files can be made faster by loading the xds-zcbf.so plugin.		XDS [https://xds.mr.mpg.de/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= supports] compression with gzip or bzip2. When specifying the frame name parameter of the script, you should leave out any .gz or .bz2 extension. Note that the processing of *.cbf.gz files can be made faster by [[Installation\|loading]] the xds-zcbf.so [[LIB\|plugin]].

	For good interaction with [[XDSGUI]], it is advantageous to provide an ''absolute'' filename for the data files - one that starts with a slash ("/").		For good interaction with [[XDSGUI]], it is advantageous to provide an ''absolute'' filename for the data files - one that starts with a slash ("/").

Kay: /* Usage */

2026-03-17T12:58:09Z

Usage

← Older revision		Revision as of 14:58, 17 March 2026
Line 5:		Line 5:
	Usage is just (don't forget the quotation marks!):		Usage is just (don't forget the quotation marks!):
	generate_XDS.INP "/home/myname/frms/mydata_1_???.img"		generate_XDS.INP "/home/myname/frms/mydata_1_???.img"
	XDS [https://xds.mr.mpg.de/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= supports] bzip2~~-ed frames~~. ~~Thus, when~~ specifying the frame name parameter of the script, you should leave out any .bz2 extension.		For .h5 files you need to load the *master.h5 , and you don't need the quotation marks:
			generate_XDS.INP /home/myname/frms/mydata_1_master.h5
			XDS [https://xds.mr.mpg.de/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= supports] compression with gzip or bzip2. When specifying the frame name parameter of the script, you should leave out any .gz or .bz2 extension. Note that the processing of *.cbf.gz files can be made faster by loading the xds-zcbf.so plugin.

	For ~~improved~~ interaction with [[XDSGUI]], it is advantageous to provide an ''absolute'' filename for the data files - one that starts with a slash ("/").		For good interaction with [[XDSGUI]], it is advantageous to provide an ''absolute'' filename for the data files - one that starts with a slash ("/").

	== The script ==		== The script ==

Kay: /* The script */

2026-03-17T12:37:21Z

The script

← Older revision		Revision as of 14:37, 17 March 2026
Line 16:		Line 16:

	<pre>		<pre>

	#!/bin/bash		#!/bin/bash
	# purpose: generate XDS.INP		# purpose: generate XDS.INP

Kay: /* The script */ #!/bin/bash must be on its own line

2026-03-17T12:36:37Z

The script: #!/bin/bash must be on its own line

← Older revision		Revision as of 14:36, 17 March 2026
Line 15:		Line 15:
	<div class="mw-collapsible-content">		<div class="mw-collapsible-content">

	<pre>#!/bin/bash		<pre>
			#!/bin/bash
	# purpose: generate XDS.INP		# purpose: generate XDS.INP
	#		#

JanGeb: /* The script */ Added support for Pilatus 4M CdTe @ ID30B/ESRF (rev. 1.24)

2026-03-16T14:00:04Z

The script: Added support for Pilatus 4M CdTe @ ID30B/ESRF (rev. 1.24)

@@ Line 15: / Line 15: @@
 <div class="mw-collapsible-content">
-<pre>
+<pre>#!/bin/bash
 # purpose: generate XDS.INP
+#
@@ Line 153: / Line 151: @@
 # revision 1.22 . KD 28/5/2025 UNTRUSTED_RECTANGLEs for Pilatus3 1M, S/N 10-0159
 # revision 1.23 . KD 28/2/2026 remove setting negative DETECTOR_DISTANCE for adsc-CMOS1 - found with SBGrid 383 (PDB 5HV4)
-REVISION="1.23 (28-Feb-2026)"
+# revision 1.24 . Jan Gebauer 14/03/2026 Implementation for ID30B Pilatus CdTe detector. Introduction of calc_CdTe_Silicon () for 5-25kEV range.
+#
@@ Line 180: / Line 179: @@
 # make sure the locale does not interfere with e.g. awk calculations:
 export LC_ALL="C"
+#
 # defaults:
@@ Line 214: / Line 247: @@
 CLUSTER_RADIUS=3.5
 REFINE_CORRECT="CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything"
 dname=$(dirname "$1")
@@ Line 294: / Line 328: @@
 else
   h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger
 fi
@@ Line 740: / Line 775: @@
    X_RAY_WAVELENGTH=`h5dump -d "/entry/instrument/beam/incident_wavelength" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
    NX=`h5dump -d "/entry/instrument/detector/detectorSpecific/x_pixels_in_detector" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
    NY=`h5dump -d "/entry/instrument/detector/detectorSpecific/y_pixels_in_detector" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
@@ Line 1,175: / Line 1,223: @@
 DETECTOR= $DETECTOR
 SENSOR_THICKNESS= $SENSOR_THICKNESS
 ! attention CCD detectors: for very high resolution (better than 1A) make sure to specify SILICON
 ! as about 32* what CORRECT.LP suggests (absorption of phosphor is much higher than that of silicon).
@@ Line 1,375: / Line 1,424: @@
 eof
      fi
 # Pilatus 12M
@@ Line 1,431: / Line 1,499: @@
 echo "spots in FRAME.cbf (or SHOW_HKL.cbf in versions since BUILT=20240723)!"
 rm -f tmp1 tmp2
-# end of generate_XDS.INP
+# end of generate_XDS.INP</pre>
 </div>
 </div>

Kay: revision 1.23 . KD 28/2/2026 remove setting negative DETECTOR_DISTANCE for adsc-CMOS1 - found with SBGrid 383 (PDB 5HV4)

2026-02-28T10:44:28Z

revision 1.23 . KD 28/2/2026 remove setting negative DETECTOR_DISTANCE for adsc-CMOS1 - found with SBGrid 383 (PDB 5HV4)

← Older revision		Revision as of 12:44, 28 February 2026
Line 152:		Line 152:
	# revision 1.21 . Thomas Hauß 12/03/2025 define for Bruker sfrm format DET= Bruker-sfrm and corresponding section		# revision 1.21 . Thomas Hauß 12/03/2025 define for Bruker sfrm format DET= Bruker-sfrm and corresponding section
	# revision 1.22 . KD 28/5/2025 UNTRUSTED_RECTANGLEs for Pilatus3 1M, S/N 10-0159		# revision 1.22 . KD 28/5/2025 UNTRUSTED_RECTANGLEs for Pilatus3 1M, S/N 10-0159
	REVISION="1.22 (28-~~May~~-~~2025~~)"		# revision 1.23 . KD 28/2/2026 remove setting negative DETECTOR_DISTANCE for adsc-CMOS1 - found with SBGrid 383 (PDB 5HV4)
			REVISION="1.23 (28-Feb-2026)"

	#		#
Line 503:		Line 504:
	ORGY=`grep BEAM_CENTER_Y tmp2 \| sed s/BEAM_CENTER_Y=//`		ORGY=`grep BEAM_CENTER_Y tmp2 \| sed s/BEAM_CENTER_Y=//`
	REVERSE_PHI="yes"		REVERSE_PHI="yes"
	DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 \| sed s/DISTANCE=/-/`		# DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 \| sed s/DISTANCE=/-/` found to be wrong with SBGrid-383 28.2.26 ->rev 1.23
			DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 \| sed s/DISTANCE=//`
	OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 \| sed s/OMEGA_DELTA=//`		OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 \| sed s/OMEGA_DELTA=//`
	DETECTOR_X_AXIS="-1 0 0"		DETECTOR_X_AXIS="-1 0 0"

Kay: /* The script */ Pilatus3 1M

2025-05-28T17:11:56Z

The script: Pilatus3 1M

@@ Line 151: / Line 151: @@
 # revision 1.20 . KD 13/7/2024 Comment out line STRONG_PIXEL=4 in preparation for mid-2024 version of XDS.
 # revision 1.21 . Thomas Hauß 12/03/2025 define for Bruker sfrm format DET= Bruker-sfrm and corresponding section
-REVISION="1.21 (13-Mar-2025)"
+# revision 1.22 . KD 28/5/2025 UNTRUSTED_RECTANGLEs for Pilatus3 1M, S/N 10-0159
+#
@@ Line 1,344: / Line 1,345: @@
   UNTRUSTED_RECTANGLE=    0 4149   3812 3851
 eof
    elif [ "$NX" == "2463" -a "$NY" == "5071" ]; then
      : # handled above, before writing XDS.INP, untrusted regions come from site file

Hauss: Bruker-sfrm mentioned. TH

2025-03-13T16:09:45Z

Bruker-sfrm mentioned. TH

← Older revision		Revision as of 18:09, 13 March 2025
Line 2,342:		Line 2,342:
	== Limitations ==		== Limitations ==

	* The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus, Eiger), ADSC (Quantum), Rigaku (several types), MAR (CCD and image plate) detectors, and one Bruker detector. Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like ROTATION_AXIS, OSCILLATION_RANGE, X-RAY_WAVELENGTH, DETECTOR_DISTANCE, and XORG, YORG. For fine-tuning of detector parameters, see the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates].		* The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus, Eiger), ADSC (Quantum), Rigaku (several types), MAR (CCD and image plate) detectors, and one Bruker detector, and Bruker sfrm Version 18 . Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like ROTATION_AXIS, OSCILLATION_RANGE, X-RAY_WAVELENGTH, DETECTOR_DISTANCE, and XORG, YORG. For fine-tuning of detector parameters, see the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates].
	* The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has an anomalous signal.''' The authors do not take any responsibility for problems arising from incorrect sign of the anomalous signal, nor - obviously! - for any other mischief arising in or from data processing.		* The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has an anomalous signal.''' The authors do not take any responsibility for problems arising from incorrect sign of the anomalous signal, nor - obviously! - for any other mischief arising in or from data processing.
	* At some beamlines, the ROTATION_AXIS needs to be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. The frame headers do not have this information, but for some beamlines the correct value has been implemented in the script. For other beamlines, the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction of XDS.INP. The correct choice can be enforced by you with a [[Generate_XDS.INP#Site_Files\|site file]]. Pls also see the article [[Beamline notes]].		* At some beamlines, the ROTATION_AXIS needs to be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. The frame headers do not have this information, but for some beamlines the correct value has been implemented in the script. For other beamlines, the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction of XDS.INP. The correct choice can be enforced by you with a [[Generate_XDS.INP#Site_Files\|site file]]. Pls also see the article [[Beamline notes]].

Hauss: added section for Bruker-sfrm data format. TH

2025-03-13T15:55:42Z

added section for Bruker-sfrm data format. TH

@@ Line 150: / Line 150: @@
 # revision 1.19 . KD 14/10/2023 Pilatus 12M at DLS I23 has reverse phi. Fix download commands.
 # revision 1.20 . KD 13/7/2024 Comment out line STRONG_PIXEL=4 in preparation for mid-2024 version of XDS.
-REVISION="1.20 (13-Jul-2024)"
+# revision 1.21 . Thomas Hauß 12/03/2025 define for Bruker sfrm format DET= Bruker-sfrm and corresponding section
+#
@@ Line 284: / Line 285: @@
   grep -q MARCONTROL tmp2 && DET=OLDMAR
   grep -q "WAVELENGTH=0.0" tmp2 && DET=experimental-ED
 else
   h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger
@@ Line 955: / Line 961: @@
    DIRECTION_OF_DETECTOR_X_AXIS="$R1 0 $R3"
 # end of Bruker-cbf section
 else
    echo should never come here
@@ Line 1,103: / Line 1,205: @@
 eof
 # --------- Append additional detector-specific parameters ----------
-if [ "$DET" == "Bruker-cbf" ]; then
+if [ "$DET" == "Bruker-cbf" -o "$DET" == "Bruker-sfrm" ]; then
    echo "DELPHI=15 ! refine less often than the default of 5" >> XDS.INP
 elif [ "$DET" == "adsc-CMOS1" ]; then