Metrology refinement - Revision history

Nicksauter at 21:59, 17 August 2015

2015-08-17T21:59:20Z

← Older revision		Revision as of 21:59, 17 August 2015
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	Most of these steps may be performed by general users, but some require editing the source code. Therefore, it may be suitable to consult the software authors. Please don't hesitate to ask for assistance regarding any aspect of this procedure.		Most of these steps may be performed by general users, but some require editing the source code. Therefore, it may be suitable to consult the software authors. Please don't hesitate to ask for assistance regarding any aspect of this procedure.

			This page is superseded by the Aug. 2014 tutorial documented here: [[L498_Thermolysin]]

	== Optical Metrology ==		== Optical Metrology ==

Nicksauter: /* Sub-pixel metrology corrections */

2014-07-16T19:07:17Z

Sub-pixel metrology corrections

← Older revision		Revision as of 19:07, 16 July 2014
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	== Sub-pixel metrology corrections ==		== Sub-pixel metrology corrections ==

			distl.tile_flags

Nicksauter at 18:28, 16 July 2014

2014-07-16T18:28:44Z

← Older revision		Revision as of 18:28, 16 July 2014
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	Once a suitable image is obtained, start the calibration tool with this command:		Once a suitable image is obtained, start the calibration tool with this command:

	# For silver behenate:		# For silver behenate:
	cxi.view <powder pattern image path> viewer.calibrate_silver=true distl.detector_format_version="CXI 7.1"		cxi.view <powder pattern image path> viewer.calibrate_silver=true distl.detector_format_version="CXI 7.1"

	Note, the flag distl.detector_format_version is a legacy requirement that will be phased out.		Note, the flag distl.detector_format_version is a legacy requirement that will be phased out.

Nicksauter at 16:57, 16 July 2014

2014-07-16T16:57:28Z

← Older revision		Revision as of 16:57, 16 July 2014
Line 13:		Line 13:
	Most of these steps may be performed by general users, but some require editing the source code. Therefore, it may be suitable to consult the software authors. Please don't hesitate to ask for assistance regarding any aspect of this procedure.		Most of these steps may be performed by general users, but some require editing the source code. Therefore, it may be suitable to consult the software authors. Please don't hesitate to ask for assistance regarding any aspect of this procedure.

	XPP beam line and back detector DS2 of CXI: The four quadrants are fixed to a back mount and may not move relative to one another. movable at CXI, necessitating pixel-level adjustments to individual quadrants. ''cctbx.xfel'' then refines tile positions to whole pixel, and then sub-pixel precision by calculating spot positions on a highly diffracting dataset and refining tile locations versus actual spot positions for each tile. This creates four levels of metrology information and corrections. These levels and the method of measuring and refining them are detailed below.

	=== Optical Metrology ===		== Optical Metrology ==

	LCLS provides initial tile placements. Periodically the detector is disassembled and re-built, necessitating new calibration information. The optical measurements are included in the ''cctbx.xfel'' in the source code and are reference by your ''pyana'' config file. See [[Preparatory_steps]] for more information.		LCLS provides initial tile placements. Periodically the detector is disassembled and re-built, necessitating new calibration information. The optical measurements are included in the ''cctbx.xfel'' in the source code and are reference by your ''pyana'' config file. See [[Preparatory_steps]] for more information.

	=== Quadrant positioning ===		== Quadrant positioning ==

	The CXI CSPAD detectors have quadrants on rails to allow re-sizing of the central hole. The second-level of metrology corrections consists of unit pixel corrections to entire quadrants using the cxi.view quadrant calibration tool. First, create a virtual powder pattern using averaging (see [preparatory steps]). Usually the standard deviation or maximum projection will show virtual powder ring. An image with strong rings to moderate resolution is desired. Once obtained, start the calibration tool with this command:		===Problem statement===

	cxi.view <~~virtual~~ powder pattern image path> viewer.calibrate_silver=true distl.detector_format_version="CXI 7.1"		The optical metrology step above determines only the sensor positions relative to the frames of reference of each quadrant; but not the absolute position of each quadrant in space. At the XPP instrument, the LCLS-provided initial tile placements may additionally place the quadrants, but this should be confirmed. At the CXI instrument, the forward detector DS1 has rail-mounted quadrants to allow re-sizing of the central hole. At CXI, quadrant placement should be assessed for both the forward and back (DS2) detectors.

			===Method===
			cctbx includes a special GUI to adjust quadrant positions visually, based on connectivity of concentric rings on a powder pattern. True powders can be used (silver behenate), or a powder pattern can be synthesized by averaging protein crystal Bragg patterns from an entire run (see [[Preparatory_steps]]). If protein patterns are averaged, it is most useful to view powder rings on a standard deviation or composite maximum image; rings on the average image itself tend to be faint.

			Once a suitable image is obtained, start the calibration tool with this command:

			# For silver behenate:
			cxi.view <powder pattern image path> viewer.calibrate_silver=true distl.detector_format_version="CXI 7.1"

	Note, the flag distl.detector_format_version is a legacy requirement that will be phased out.		Note, the flag distl.detector_format_version is a legacy requirement that will be phased out.

			Usually the standard deviation or maximum projection will show virtual powder ring. An image with strong rings to moderate resolution is desired.

	Once loaded, you will see your image and many red rings, incidentally corresponding to the diffraction pattern of silver behenate. Additionally, a separate settings panel will be present with 8 input boxes corresponding to the x and y offsets of each of the four quadrants, UL, UR, LL, and LR (upper and lower, left and right). Manually adjust the offsets until the powder rings are circular through the whole image, using the red rings as guides. These corrections will but put into your phil parameters file in the distl quad_translations entry in this form:		Once loaded, you will see your image and many red rings, incidentally corresponding to the diffraction pattern of silver behenate. Additionally, a separate settings panel will be present with 8 input boxes corresponding to the x and y offsets of each of the four quadrants, UL, UR, LL, and LR (upper and lower, left and right). Manually adjust the offsets until the powder rings are circular through the whole image, using the red rings as guides. These corrections will but put into your phil parameters file in the distl quad_translations entry in this form:
Line 35:		Line 44:
	Where the numbers are listed in this order: ULX ULY, URX URY, LLX LLY, LRX, LRY		Where the numbers are listed in this order: ULX ULY, URX URY, LLX LLY, LRX, LRY

	=== Unit pixel metrology corrections ===		== Unit pixel metrology corrections ==

			''cctbx.xfel'' then refines tile positions to whole pixel, and then sub-pixel precision by calculating spot positions on a highly diffracting dataset and refining tile locations versus actual spot positions for each tile.


	=== Sub-pixel metrology corrections ===		== Sub-pixel metrology corrections ==

Nicksauter at 23:23, 15 July 2014

2014-07-15T23:23:06Z

← Older revision		Revision as of 23:23, 15 July 2014
Line 14:		Line 14:

	XPP beam line and back detector DS2 of CXI: The four quadrants are fixed to a back mount and may not move relative to one another. movable at CXI, necessitating pixel-level adjustments to individual quadrants. ''cctbx.xfel'' then refines tile positions to whole pixel, and then sub-pixel precision by calculating spot positions on a highly diffracting dataset and refining tile locations versus actual spot positions for each tile. This creates four levels of metrology information and corrections. These levels and the method of measuring and refining them are detailed below.		XPP beam line and back detector DS2 of CXI: The four quadrants are fixed to a back mount and may not move relative to one another. movable at CXI, necessitating pixel-level adjustments to individual quadrants. ''cctbx.xfel'' then refines tile positions to whole pixel, and then sub-pixel precision by calculating spot positions on a highly diffracting dataset and refining tile locations versus actual spot positions for each tile. This creates four levels of metrology information and corrections. These levels and the method of measuring and refining them are detailed below.


	~~Of the operations of ''cctbx.xfel'', calculating and refining metrology is the operation most suited to beam line staff and the authors of the software.~~

	=== Optical Metrology ===		=== Optical Metrology ===

	LCLS provides initial tile placements. Periodically the detector is disassembled and re-built, necessitating new calibration information. The optical measurements are included in the ''cctbx.xfel'' in the source code and are reference by your ''pyana'' config file. See [~~preparatory steps~~] for more information.		LCLS provides initial tile placements. Periodically the detector is disassembled and re-built, necessitating new calibration information. The optical measurements are included in the ''cctbx.xfel'' in the source code and are reference by your ''pyana'' config file. See [[Preparatory_steps]] for more information.

	=== Quadrant positioning ===		=== Quadrant positioning ===

Nicksauter at 23:20, 15 July 2014

2014-07-15T23:20:03Z

@@ Line 1: / Line 1: @@
-Indexing requires highly precise knowledge of pixel positions in laboratory space.  Due to the physics of the CSPAD detector and the brevity of the incident XFEL pulses, a parallelized integrating detector was necessary to build to be able to operate at the framing rates available at the LCLS.  64 asics are arranged in a tetragonal pattern, 2 asics per sensor, 8 sensors per quadrant and 4 quadrants per detector.  The placement of these tiles in physical space is measured by the beamline operators optically using electron microscopy.  The four quadrants are movable at CXI, necessitating pixel-level adjustments to individual quadrants.  ''cctbx.xfel'' then refines tile positions to whole pixel, and then sub-pixel precision by calculating spot positions on a highly diffracting dataset and refining tile locations versus actual spot positions for each tile.  This creates four levels of metrology information and corrections.  These levels and the method of measuring and refining them are detailed below.
+Accurate data integration requires highly precise knowledge of pixel positions in laboratory space (metrology).  Gaining this knowledge is especially difficult due to the [[CSPAD Pattern | segmented nature of the CSPAD detector]], which is tiled into 64 application-specific integrated circuits (ASICs).  The 64 ASICs are arranged in quadrants that are approximately 4-fold rotationally symmetric, with 8 sensors per quadrant and 2 ASICs per sensor.   The sensors are field-serviceable, and may therefore change from Run to Run.
-Of the operations of ''cctbx.xfel'', calculating and refining metrology is the operation most suited to beam line staff and the authors of the software.  Please don't hesitate to ask for assistance regarding any aspect of this procedure.
+We thus need to determine positions and rotations for all 64 tiles, ideally down to an accuracy on order of 10 microns. As a general overview, cctbx takes the following steps:
 === Optical Metrology ===

Hattne: Changed CS-PAD to CSPAD for consistency.

2014-03-14T18:10:58Z

Changed CS-PAD to CSPAD for consistency.

← Older revision		Revision as of 18:10, 14 March 2014
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	Indexing requires highly precise knowledge of pixel positions in laboratory space. Due to the physics of the ~~CS-PAD~~ detector and the brevity of the incident XFEL pulses, a parallelized integrating detector was necessary to build to be able to operate at the framing rates available at the LCLS. 64 asics are arranged in a tetragonal pattern, 2 asics per sensor, 8 sensors per quadrant and 4 quadrants per detector. The placement of these tiles in physical space is measured by the beamline operators optically using electron microscopy. The four quadrants are movable at CXI, necessitating pixel-level adjustments to individual quadrants. ''cctbx.xfel'' then refines tile positions to whole pixel, and then sub-pixel precision by calculating spot positions on a highly diffracting dataset and refining tile locations versus actual spot positions for each tile. This creates four levels of metrology information and corrections. These levels and the method of measuring and refining them are detailed below.		Indexing requires highly precise knowledge of pixel positions in laboratory space. Due to the physics of the CSPAD detector and the brevity of the incident XFEL pulses, a parallelized integrating detector was necessary to build to be able to operate at the framing rates available at the LCLS. 64 asics are arranged in a tetragonal pattern, 2 asics per sensor, 8 sensors per quadrant and 4 quadrants per detector. The placement of these tiles in physical space is measured by the beamline operators optically using electron microscopy. The four quadrants are movable at CXI, necessitating pixel-level adjustments to individual quadrants. ''cctbx.xfel'' then refines tile positions to whole pixel, and then sub-pixel precision by calculating spot positions on a highly diffracting dataset and refining tile locations versus actual spot positions for each tile. This creates four levels of metrology information and corrections. These levels and the method of measuring and refining them are detailed below.

	Of the operations of ''cctbx.xfel'', calculating and refining metrology is the operation most suited to beam line staff and the authors of the software. Please don't hesitate to ask for assistance regarding any aspect of this procedure.		Of the operations of ''cctbx.xfel'', calculating and refining metrology is the operation most suited to beam line staff and the authors of the software. Please don't hesitate to ask for assistance regarding any aspect of this procedure.
Line 9:		Line 9:
	=== Quadrant positioning ===		=== Quadrant positioning ===

	The CXI ~~CS-PAD~~ detectors have quadrants on rails to allow re-sizing of the central hole. The second-level of metrology corrections consists of unit pixel corrections to entire quadrants using the cxi.view quadrant calibration tool. First, create a virtual powder pattern using averaging (see [preparatory steps]). Usually the standard deviation or maximum projection will show virtual powder ring. An image with strong rings to moderate resolution is desired. Once obtained, start the calibration tool with this command:		The CXI CSPAD detectors have quadrants on rails to allow re-sizing of the central hole. The second-level of metrology corrections consists of unit pixel corrections to entire quadrants using the cxi.view quadrant calibration tool. First, create a virtual powder pattern using averaging (see [preparatory steps]). Usually the standard deviation or maximum projection will show virtual powder ring. An image with strong rings to moderate resolution is desired. Once obtained, start the calibration tool with this command:

	cxi.view <virtual powder pattern image path> viewer.calibrate_silver=true distl.detector_format_version="CXI 7.1"		cxi.view <virtual powder pattern image path> viewer.calibrate_silver=true distl.detector_format_version="CXI 7.1"

Aaron at 17:58, 25 October 2013

2013-10-25T17:58:28Z

← Older revision		Revision as of 17:58, 25 October 2013
Line 22:		Line 22:

	Where the numbers are listed in this order: ULX ULY, URX URY, LLX LLY, LRX, LRY		Where the numbers are listed in this order: ULX ULY, URX URY, LLX LLY, LRX, LRY

			=== Unit pixel metrology corrections ===

			=== Sub-pixel metrology corrections ===

Aaron: /* Quadrant positioning */

2013-10-25T17:57:42Z

Quadrant positioning

← Older revision		Revision as of 17:57, 25 October 2013
Line 15:		Line 15:
	Note, the flag distl.detector_format_version is a legacy requirement that will be phased out.		Note, the flag distl.detector_format_version is a legacy requirement that will be phased out.

	Once loaded, you will see your image and many red rings, incidentally corresponding to the diffraction pattern of silver behenate. Additionally, a separate settings panel will be present with		Once loaded, you will see your image and many red rings, incidentally corresponding to the diffraction pattern of silver behenate. Additionally, a separate settings panel will be present with 8 input boxes corresponding to the x and y offsets of each of the four quadrants, UL, UR, LL, and LR (upper and lower, left and right). Manually adjust the offsets until the powder rings are circular through the whole image, using the red rings as guides. These corrections will but put into your phil parameters file in the distl quad_translations entry in this form:

			distl {
			quad_translations = 2 -6 3 -6 -7 0 -1 -4
			}

			Where the numbers are listed in this order: ULX ULY, URX URY, LLX LLY, LRX, LRY

Aaron: /* Quadrant positioning */

2013-10-25T17:48:39Z

Quadrant positioning

← Older revision		Revision as of 17:48, 25 October 2013
Line 8:		Line 8:

	=== Quadrant positioning ===		=== Quadrant positioning ===

			The CXI CS-PAD detectors have quadrants on rails to allow re-sizing of the central hole. The second-level of metrology corrections consists of unit pixel corrections to entire quadrants using the cxi.view quadrant calibration tool. First, create a virtual powder pattern using averaging (see [preparatory steps]). Usually the standard deviation or maximum projection will show virtual powder ring. An image with strong rings to moderate resolution is desired. Once obtained, start the calibration tool with this command:

			cxi.view <virtual powder pattern image path> viewer.calibrate_silver=true distl.detector_format_version="CXI 7.1"

			Note, the flag distl.detector_format_version is a legacy requirement that will be phased out.

			Once loaded, you will see your image and many red rings, incidentally corresponding to the diffraction pattern of silver behenate. Additionally, a separate settings panel will be present with