Dectris PILATUS User Manual
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Dectris PILATUS User Manual

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USER MANUAL
PILATUS Detector Systems
Version 1.2

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  • Page 1 USER MANUAL PILATUS Detector Systems Version 1.2...

  • Page 2: Table Of Contents

    Main commands ................30 Variables..................31 Exposure series................32 Integration into other systems............32 9.4.1 Steps to bring up a PILATUS detector in a new environment:..33 Calibrating the detector ...............36 10.1 Principle...................36 10.2 Calibrating the detector manually ............37 10.3 Loading trim files manually ..............41 10.4 Adjusting the threshold level manually..........42...
  • Page 3 13.3 External Multi Trigger mode.............54 13.4 External Enable mode ..............54 13.5 Multiple Exposure mode ..............56 Appendix .....................57 14.1 Table of figures................57...

  • Page 4: Document History

    1 Document History Actual document Version Date status prepared checked released 6.2.2009 In Work 1.1 Changes Version Date Changes 31.08.2007 Various improvements 06.02.2009 Various improvements User_Manual-PILATUS-V1_2.doc 4/57...

  • Page 5: How To Use This Manual

    2 How to use this manual Before you start to operate the PILATUS detector system please read this manual thoroughly. This user manual has been especially designed for DECTRIS PILATUS detector systems. The technical specification of the detector system is also part of this user manual.

  • Page 6: Definitions Of Terms

    2.3 Definitions of terms Term Description Module control board Detector control board Bank control board Digital to Analog Converter User_Manual-PILATUS-V1_2.doc 6/57...

  • Page 7: Warnings

    With any over-current condition, immediately shut the detector down and restart it. • Opening the detector or the power supply housing without the explicit instructions from DECTRIS will void the warranty. • The Linux-OS on the PC has a customized Kernel to improve data throughput.

  • Page 8: System Description

    4 System Description 4.1 Overview A PILATUS detector system consists of the following components: • Detector • Analysis PC with SuSE Linux, the data acquisition tool camserver and the data analysis tool TVX • Power supply (where applicable) • Connecting cables...
  • Page 9 Figure 2 Principle of direct detection. A DECTRIS hybrid pixel detector is composed of a silicon sensor, which is a two-dimensional array of pn-diodes processed in high-resistivity silicon, connected to an array of readout channels designed with advanced CMOS technology (Figure 3). Each readout channel is connected to its corresponding detecting element through a microscopic indium ball, with a typical diameter of 18 um.
  • Page 10 DOUT Figure 4 Block diagramm of the CMOS chip The fundamental unit of the DECTRIS detectors consists of a single fully depleted monolithic silicon sensor with an 8 x 2 array of CMOS readout chips bump-bonded to it. Each sensor is a continuous array of 487 x 197 = 94965 pixels without dead areas and covers an active area of 83.8 x 33.5 mm...

  • Page 11: Software

    5 Software The operating software for the PILATUS detector system consists of two software components: • TVX Data acquisition control and data analysis software • Camserver Operating software for the detector Those two software packages are normally installed on one PC and communicate with each other through an internal socket connection.

  • Page 12: Overview Of Tvx

    TVX compiles and operates both on Linux and Mac OS X systems. Camserver, except the demo version, requires specific camera hardware for operation. Figure 8. TVX control and analysis layout schematic. User_Manual-PILATUS-V1_2.doc 12/57...

  • Page 13: Overview Of Camserver

    (e.g., a nfs mount) where any program can access them. See more on 9.4 6 Getting started See the appropriate chapter in the technical specification of your detector system. User_Manual-PILATUS-V1_2.doc 13/57...

  • Page 14: How To Operate The System

    Camserver is running on. In case TVX and Camserver are running on different machines the IP address and hostname should be adjusted in the following files: /home/det/p2_det/tvxrc /etc/hosts See also 9.4 how to integrate the detector into other systems. User_Manual-PILATUS-V1_2.doc 14/57...
  • Page 15 Figure 9 Shell showing the active path and the runtvx command. Figure 10 Screen after runtvx has initialized the detector and opened the Camserver and TVX window. User_Manual-PILATUS-V1_2.doc 15/57...

  • Page 16: How To Use Tvx

    8 How to use TVX 8.1 Description of the directories In the default setup, all data for the use of the PILATUS detector system is in the directory /home/det/p2_det. Figure 11 Relevant directories and folders. Directory Description config Glossary (.gl) files for the detector...

  • Page 17: Main Commands

    >=, |, ||, &, &&) and special operators (<<, >>, !, :, <<=, etc.) in arbitrarily complicated expressions to perform sophisticated analyses and to construct custom scripts. In case of doubt, try it out you can’t hurt anything. User_Manual-PILATUS-V1_2.doc 17/57...
  • Page 18 Figure 12 The ‘menu’ of TVX. Many commands in TVX or Camserver require an input value or argument. Without the declaration of a value, the currently set value is shown. In this manual input values are shown in Italic. User_Manual-PILATUS-V1_2.doc 18/57...
  • Page 19 TVX and Camserver windows and start up again. setdac Sets all Digital Analog Converters (DAC) to the predefined values. imagepath path Image Path Without the input of a path it displays the current default path. With a declaration it changes the default User_Manual-PILATUS-V1_2.doc 19/57...
  • Page 20 Capture the default graph to filename Captures a displayed graph (and its zoom) as a .ppm (portable pixmap) file. connect [ip_address] Connect the socket connection from TVX to the Camserver at [ip_address] disconnect Disconnect the socket connection from TVX to User_Manual-PILATUS-V1_2.doc 20/57...

  • Page 21: Description Of The Image Display

    Coordinate: (0,0) Coordinate: (487,0) Zoom factor Selection tool Coordinate: (487,195) Color scheme Numerical values for the selection tool. Actual position of the cursor and the intensitiy of the pixel User_Manual-PILATUS-V1_2.doc 21/57...
  • Page 22 (det_dist, lamdba and pixel size) Display mode greys color lookup table with gray scale. spectral color lookup table with a spectral distribution (blue and User_Manual-PILATUS-V1_2.doc 22/57...
  • Page 23 The values are reversed - x-rays in the image become black rather than white. Useful for crystallographic images. Several test images and graphs are included in the system. Try the following: imagepath examples disp testimg.tif disp gray20bit.tif grafpath examples grafdemo More examples are in: /home/det/p2_det/programs/tvx/test/images -and- /home/det/p2_det/programs/tvx/test/graphs User_Manual-PILATUS-V1_2.doc 23/57...
  • Page 24 The size and position can be adjusted directly with the mouse or by typing the values directly into the boxes. The circle is used only as a positioning aid. Use the keyword integrate in the tvx window to display the result. User_Manual-PILATUS-V1_2.doc 24/57...

  • Page 25: Image Formats

    8.4 Image formats Due to the high dynamic range of 20 bits (1’000’000) of the PILATUS detectors, images are stored as 32 bit (unsigned) integers. These images can be viewed and analyzed with TVX or other image viewers. Many viewers do not support 32 bit TIFF files;...
  • Page 26 (rms), var (variance), xcen & ycen (centroid), box_x1, box_x2, box_y1 & box_y2 (corners of box). format n1[.n2] Control the number of digits to be printed (n1) or the number of decimal places (n2). User_Manual-PILATUS-V1_2.doc 26/57...

  • Page 27: Mask Files

    Note that a float input object returns a 32-bit integer mask. Because the generated file is a normal image you can use any of the image manipulation tools supplied in TVX to alter your mask image if you wish. User_Manual-PILATUS-V1_2.doc 27/57...

  • Page 28: User Defined Commands

    The brackets [ ] mean to substitute the enclosed argument as text with the number of digits specified by the format. With define one can create custom commands for the current session and eventually save them for reuse. Example: User_Manual-PILATUS-V1_2.doc 28/57...

  • Page 29: Glossary Files

    In case of multi-module detectors a file called t.gl is generated and used for automated trimbit calculation. Usually this file contains only a comment. 8.9 Various commands To see the temperature and humidity log of the detector, do: less $HOME/p2_det/config/camstat/TH.log User_Manual-PILATUS-V1_2.doc 29/57...

  • Page 30: How To Use Camserver

    (see section 13) extenable [fname] Start exposure defined by external exposure and store images in [fname]. (see section 13) help Type this in the TVX window for a discussion of how exposurenaming exposure series are named. dcb_init Re-initialize the DCB. User_Manual-PILATUS-V1_2.doc 30/57...

  • Page 31: Variables

    (see section 13) nexpframe [N] Query or set the number of exposures per frame. This is the number of times to enable the detector before reading out the image (see section 13) User_Manual-PILATUS-V1_2.doc 31/57...

  • Page 32: Exposure Series

    9.3 Exposure series With PILATUS detector systems, it is possible to take image series with a frame rate of up to 300Hz (depending on the system) and a shortest exposure time of 1 µs. All timings are controlled by a crystal clock on the DCB.

  • Page 33: Steps To Bring Up A Pilatus Detector In A New Environment

    Simply capture 'camdbg.out' and send it to DECTRIS. The Camserver program of the PILATUS detector provides a simple to use interface for either EPICS or SPEC. Several clients for these protocols have been written at the Swiss Light Source (SLS) of the Paul Scherrer Institut (PSI).
  • Page 34 Then, in tvx, type "help command_name". Further sources of information: $HOME/p2_det/tvxrc $HOME/p2_det/camrc $HOME/p2_det/programs/tvx/00README $HOME/p2_det/programs/tvx/tvx/00README.SLS $HOME/p2_det/programs/tvx/docs/* $HOME/p2_det/programs/tvx/camera/camserver/00README $HOME/p2_det/programs/tvx/camera/camserver/docs/case_definitions.txt $HOME/p2_det/programs/tvx/camera/camserver/docs/README.camserver_c ommands $HOME/p2_det/programs/tvx/camera/camserver/slsp2det_cam/docs/* $HOME/p2_det/config/* $HOME/p2_det/config/trim_gls/* To see the details of the current configuration of camserver, do: cat $HOME/p2_det/config/camstat/HWVersions User_Manual-PILATUS-V1_2.doc 34/57...
  • Page 35 Further documentation of the system and of all commands can be viewed by: konqueror $HOME/p2_det/programs/tvx/docs/html/index.html -or- firefox $HOME/p2_det/programs/tvx/docs/html/index.html User_Manual-PILATUS-V1_2.doc 35/57...

  • Page 36: Calibrating The Detector

    PILATUS detectors possess an adjustable threshold to suppress fluorescence, which can be useful in many experiments. The calibration of the PILATUS detector is necessary, because every pixel has a different characteristic, sensitivity and count rate due to voltage drops and nonlinearities in the analog amplifiers.

  • Page 37: Calibrating The Detector Manually

    TVX window: get “trim_gls/p2_trim_det.gl” (the quotation marks are required). You will be prompted to enter a name for the directory in which the trim files will be stored; this should be a directory that does not already exist. A format User_Manual-PILATUS-V1_2.doc 37/57...
  • Page 38 “mean_vs_vtrm” graph (Figure 17). Set Vtrm to a level well below the inflection point of the S curve, e.g. vt=1.35, where no pixels are counting. However the procedure suggests a value that is almost always correct. User_Manual-PILATUS-V1_2.doc 38/57...
  • Page 39 The system will now run through a trim bit scan and vary all 64 possibilities of the trimbits. The next prompt will occur in a few hours depending on flux of the x-ray source. Figure 18 Result of the trimbit scan User_Manual-PILATUS-V1_2.doc 39/57...
  • Page 40 Table 1: Recommended Values for Vcmp and Vtrim for standard settings and energies between 6 and 12 keV. These values can be used together with the glossary trimscan_only.gl, where you directly enter Vtrim and Vcmp for the targeted energy. User_Manual-PILATUS-V1_2.doc 40/57...

  • Page 41: Loading Trim Files Manually

    The trim files will be loaded and a comparison between loaded trims and assigned trims is made. If everything has worked correctly you should see exactly 100 counts per pixel. Command Description trimdet N Set all trimbits to N show setdac Shows the command used to set the DACs User_Manual-PILATUS-V1_2.doc 41/57...

  • Page 42: Adjusting The Threshold Level Manually

    Values for setvcmp between 0 .. 0.8. Figure 20 Value of Vcomp (x) for a specified energy Zero sets threshold level very high and no x-rays are registered; 0.8 sets threshold level very low and all x-rays and some noise are counted. User_Manual-PILATUS-V1_2.doc 42/57...

  • Page 43: Adjusting The Analog Amplifier Manually

    10.5 Adjusting the analog amplifier manually The frequency response and consequently the count rate of the analog amplifier can be adjusted. PILATUS II Pixel Cell Pixsel 6 Bit Latch Pixsel + DAC CNT/RO Pulse Global Comp 20 bit φ φ...
  • Page 44 Figure 22 Step response at various Vrf settings Figure 23 Calibration curves for different amplifier settings Vrf. User_Manual-PILATUS-V1_2.doc 44/57...

  • Page 45: Loading Trim Files And Setting The Threshold Automatically

    3 – 6 keV Midg -0.2 Standard settings for energies between 5 – 18 keV lowg -0.3 Fast setting with low gain for best performance at high energies and high rates: 7 – 30 keV User_Manual-PILATUS-V1_2.doc 45/57...
  • Page 46 The information about the relevant trimfiles is stored in /home/det/p2_det/config/cam_data/calibrations.def In this file, the names of the trimfiles and the corresponding parameters are stored. In case new trim-files are generated, the directories should be copied to /home/det/p2_det/config/calibration and the information should be entered in calibrations.def User_Manual-PILATUS-V1_2.doc 46/57...

  • Page 47: Creating A Flat Field Correction Image

    Both a mask file and a flat field correction image will be created and copied into the directory ~/p2_det/correct. The final step will delete the working directory created under the images directory. User_Manual-PILATUS-V1_2.doc 47/57...

  • Page 48: Using The Flat Field Correction Image

    The camserver command “LdFlatField” will cause imagename camserver to apply a specified flat field correction to every image taken. The file specified (the same as in the abover paragraph) is a floating-point TIFF file with mean value near 1.0. User_Manual-PILATUS-V1_2.doc 48/57...

  • Page 49: Factory Calibration And Correction

    Correction The following calibrations are done at our premises: 1) Threshold calibration The PILATUS detector systems come fully calibrated. See the system information sheet in your user handbook for more information about the calibrated energies and settings. The discriminator thresholds in the individual pixels are set by an automated procedure (described above).
  • Page 50 It is also easy to incorporate these data as a post-acquisition step. The gaps between the modules can optionally be flagged with -1 (zero is the default). Both of these flags are used by XDS. User_Manual-PILATUS-V1_2.doc 50/57...

  • Page 51: External Triggering

    Starts the external trigger mode and waits for the trigger ExtMtrigger [image External multi trigger name] Starts the external multi trigger mode and waits for the trigger Extenable [image External enable name] Starts the external enable mode and waits for the gate pulse User_Manual-PILATUS-V1_2.doc 51/57...

  • Page 52: External Trigger Mode

    “expp” will repeat the cycle for “ni” images. The image number is only incremented during the trigger mode, if you reissue the command “extt imagename.tif” the system will start writing images from “imagename_00001.tif” and overwrite existing data. User_Manual-PILATUS-V1_2.doc 52/57...
  • Page 53 The maximum jitter is ~15 ns with an average delay of 177 ns. Figure 25. Delay and jitter. User_Manual-PILATUS-V1_2.doc 53/57...

  • Page 54: External Multi Trigger Mode

    Variables “delay”, “expt”, “expp”, etc. are not used in external enable mode. The image number is only incremented during the exposure series; if you reissue the command “extt imagename.tif” it will start writing images from “imagename_00001.tif” and overwrite existing data. User_Manual-PILATUS-V1_2.doc 54/57...
  • Page 55 This can be seen in the oscilliscope image below. Figure 27. Oscilloscope trace of the typical delay between enable signal and exposure. User_Manual-PILATUS-V1_2.doc 55/57...

  • Page 56: Multiple Exposure Mode

    Fempto project at the SLS. This also eliminate the need to wait 3 ms between exposures; however at least 3ms is needed for the image readout after nexpf eposures. Figure 28. Osciloscope image of the multiple exposure mode. User_Manual-PILATUS-V1_2.doc 56/57...

  • Page 57: Appendix

    14.1 Table of figures Figure 1 Overview of the PILATUS detector system setup......8 Figure 2 Principle of direct detection..............9 Figure 3 The detector module, the basic element of all DECTRIS detector systems......................9 Figure 4 Block diagramm of the CMOS chip..........10 Figure 5 Normal operation with TVX and Camserver on one computer..11...

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