Dectris PILATUS3 User Manual
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Dectris PILATUS3 User Manual

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User Manual
PILATUS3
This user manual is valid for the following PILATUS detectors:
PILATUS3 6M | PILATUS3 2M | PILATUS3 1M
PILATUS3 300K | PILATUS3 300K-W | PILATUS3 200K
Version:
V2.1
DECTRIS Ltd.
5400 Baden
Switzerland
www.dectris.com

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  • Page 1 User Manual PILATUS3 This user manual is valid for the following PILATUS detectors: PILATUS3 6M | PILATUS3 2M | PILATUS3 1M PILATUS3 300K | PILATUS3 300K-W | PILATUS3 200K Version: V2.1 DECTRIS Ltd. 5400 Baden Switzerland www.dectris.com...

  • Page 2: Table Of Contents

    6. Control the Detector 6.1. From the Detector Server 6.2. From a Specific Environment 6.2.1. Steps to Bring Up a PILATUS3 Detector in a New Environment 6.2.2. Testclients 7. How to use the PILATUS3 Detector through Camserver 7.1. Main Commands 7.1.1.
  • Page 3 9.2. Flag the Module Gaps 10. Adjust Crystallography Parameters 11. Flat Field Image 11.1. Using the Flat Field Correction Image in Camserver 12. How to Use the PILATUS3 Detector through TVX 12.1. Description of the Image Display 12.2. Analysis commands 12.3. Mask files 12.4.

  • Page 4: Document History

    20.06.2014 released SB, LK 1.2. Changes Version Date Changes 01.05.2013 First version 1.1.1 12.06.2013 Adapted CD 14.02.2014 Complete revision, final CD 20.06.2014 Moved system specific information to Technical Specifications. Minor changes. User Manual. PILATUS3. Version: V2.1 4/62...

  • Page 5: How To Use This Manual

    How to use this Manual Before you start to operate the PILATUS3 detector system please read the User Manual and the Technical Documentation included in the documentation package carefully. This document has been designed for the PILATUS3 detector systems. 2.1.

  • Page 6: Explanation Of Symbols

    .. Shell commands are written in blue and italic ExpTime Camserver commands are in written italic Disp TVX commands are written in bold italic exposem TVX macros are written in underlined, bold, italic User Manual. PILATUS3. Version: V2.1 6/62...

  • Page 7: Disclaimer

    DECTRIS Ltd. bears no responsibility or liability for damage of any kind, also for indirect or consequential damage resulting from the use of this system. DECTRIS Ltd. is the sole owner of all user rights related to the contents of the manual (in particular information, images or materials), unless otherwise indicated. Without the written permission of DECTRIS Ltd.

  • Page 8: Warnings

    Place the protective cover on the detector when it is not in use.  Opening the detector or the power supply housing without explicit instructions from DECTRIS Ltd. will void the warranty.  DO NOT INSTALL ADDITIONAL SOFTWARE OR CHANGE THE OPERATING SYSTEM on the detector server except for necessary network configurations.

  • Page 9: System Description

    System Description 4.1. Overview A PILATUS3 detector system consists of the following components:  Detector  Detector server  Cooling unit  PILATUS Processing Unit (depending on the system) Max. 3 bar, 23°C Cooling PILATUS Unit Detector (optional) Closed circuit...

  • Page 10: Hardware

    However, the detector cannot withstand a direct synchrotron beam. Figure 1. Principle of direct detection. A DECTRIS Ltd. 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 2).
  • Page 11 Figure 3. Design of each pixel. See text for details. The fundamental unit of the DECTRIS Ltd. detectors, the module, consists of a single fully depleted monolithic silicon sensor with an 8 x 2 array of CMOS readout chips bump-bonded to it.
  • Page 12 However, counter paralyzation limits the maximum usable count rate. In PILATUS3 detectors, the instant retrigger technology re-evaluates the pulse signal after a predetermined dead time interval after each count and is able to retrigger the counting circuit should a pulse pile-up occur.
  • Page 13 pulses are counted more accurately in the case of pile-up and that counting is non- paralyzable.

  • Page 14: Software

    (e.g., a NFS mount) where any program can access them. 4.3.2. Description of the File Structure and Configuration Files on the PILATUS3 Detector Server In the default setup, all necessary data for the use of the PILATUS3 detector system is in the directory /home/det/p2_det. Directory...

  • Page 15: Overview Of Tvx

    TVX contains a user interface and analysis tool suite. TVX communicates over a TCP/IP connection to Camserver. 4.3.4. Configuration Files for TVX In the default setup, all data for the use of the PILATUS3 detector system are in the directory /home/det/p2_det. The following directories are relative to it. Directory...

  • Page 16: Quick Start Guide

    Change to the p2_det directory. All following paths are given relative to this!  cd /home/det/p2_det  Run TVX by typing  ./runtvx After the initialization (~20 s) you should get the following screen: Figure 5. Startup screen after executing ./runtvx User Manual. PILATUS3. Version: V2.1 16/62...
  • Page 17  The command ../runtvx is a shell script which starts the programs Camserver (window on the left side of Figure 5) and TVX (window on the right side of Figure 5) as well as manages all log files.  During startup the detector sets several parameters in the startup scripts (details in 6.1).

  • Page 18: Control The Detector

    Control the Detector 6.1. From the Detector Server The PILATUS3 detector can be controlled from the delivered detector server. Just follow the instructions in the Quick Start Guide (Section 5) to start up the detector. runtvx command is a shell script which starts the actual programs: Camserver and TVX.

  • Page 19: From A Specific Environment

    In the previous section the stand alone operation is shown. However, often there is a need to integrate the detector in an existing environment. The PILATUS3 detector can be easily integrated in any system. To do this, one has to send commands through a socket connection to Camserver. Any client can connect to Camserver via a socket connection, and issue plain text commands.

  • Page 20: Testclients

    41234. Here localhost is the “IP” of the detector and 41234 the by executing telnet localhost port where Camserver is listening to. A basic test client written in C can be found under section15. For more information please contact DECTRIS Ltd. at support@dectris.com. User Manual. PILATUS3. Version: V2.1 20/62...

  • Page 21: How To Use The Pilatus3 Detector Through Camserver

    How to use the PILATUS3 Detector through Camserver Camserver is a completely freestanding program that controls the detector and provides a simple user interface for "atomic" (single function) commands. It is intended to provide a minimal, but fully functional, low level interface to camera hardware.

  • Page 22: Variables

    3 combined exposures. See point 7.3.4 for more details. The usual way is to set all mentioned variables and then execute a command from the section above. User Manual. PILATUS3. Version: V2.1 22/62...

  • Page 23: Image Formats

    7.2. Image formats Due to the high dynamic range of 20 bits (0:1’048’573) of the PILATUS3 detectors, images are stored as 32-bit (signed) integers. These images can be viewed and analyzed with TVX or other image viewers. Many viewers do not support 32-bit TIF files; however, these images may be read in IDL, MATLAB or ALBULA.
  • Page 24 .tif image. The initial header data (this time a .cbf header) is followed by a PILATUS3 section. Exactly as in the .tif format, this section can be extended with additional items (see section 10). Just before the actual compressed data there is additional information for the .cbf format.

  • Page 25: External Triggering

    7.3. External Triggering External triggering can be separated into three different modes:  External Trigger: triggers a predefined series of commands after the detector receives a positive edge.  External Multitrigger: triggers each exposure with an external pulse, but times the exposures using the internal timer.
  • Page 26 The maximum jitter is ~15 ns with an average delay of 177 ns (see Figure 7). Figure 7. Delay and jitter. Orange: enable signal of the detector; Green: trigger. User Manual. PILATUS3. Version: V2.1 26/62...

  • Page 27: External Multi Trigger Mode

    7.3.2. External Multi Trigger Mode External multi trigger mode is started with the command ExtMTrigger imagename.tif where imagename.tif is the name of the images you wish to be taken. The image name will be imagename_00000.tif unless otherwise specified. If NImages >1 the image number will be incremented for each image in the series.

  • Page 28: External Enable Mode

    The image number is only incremented during an exposure series; if you reissue command ExtEnable imagename.tif will start writing images from “imagename_00000.tif” and overwrite existing data. Figure 8. Oscilloscope image of an external enable. Orange: enable signal of the detector; Green: external gate. User Manual. PILATUS3. Version: V2.1 28/62...
  • Page 29 In this example using external enable NImages was set to 3. Because external enable gates the counter directly, it does not rely upon the detector’s internal clock. This means that the Delay between the enable and start of exposure is negligible and mostly given by the rise time of the enable signal provided to the detector.

  • Page 30: Multiple Exposure Mode

    It is necessary to provide 6 pulses or positive edges to achieve a successful readout (only a single pulse is required for the ExtTrigger mode). Figure 10. Oscilloscope image of the multiple exposure mode. Orange: enable signal of the detector; Green: external gate. User Manual. PILATUS3. Version: V2.1 30/62...

  • Page 31: Trimming The Detector

    Trimming the Detector 8.1. Principle PILATUS detectors possess an adjustable energy threshold which has to be set due to the working principle of the detector. This threshold is controlled by the comparator voltage of the detector chip. Furthermore, the threshold of every pixel can be individually trimmed with six trim bits (6-bit DACs) which allow 2 = 64 different values.

  • Page 32: Set The Threshold With More Control

    50% of the incoming energy, it is necessary to specify the correct energy as a parameter in the SetThreshold command for an adequate flat field. User Manual. PILATUS3. Version: V2.1 32/62...
  • Page 33 Command Description SetThreshold [energy Allows to set the threshold energy as well the incoming energy_value] [[gain] threshold] energy for an optimized flat fields Usage: SetThreshold [energy energy_value] [[gain] threshold] 1. if parameters are omitted, the current settings are shown 2. if energy (with an energy_value) is given, energy_value is recorded as incident energy, else incident energy is assumed to be 2x the threshold energy.

  • Page 34: Bad Pixel Mask And Module Gaps

    In TVX: pixlfill 1 17 126 17 126 The coordinates are given twice because it is also possible to define a box which will be filled with the first value after the pixlfill command. User Manual. PILATUS3. Version: V2.1 34/62...

  • Page 35: Make A New Bad Pixel Mask From An Uniform Illumination

    9.1.2. Make a new Bad Pixel Mask from an Uniform Illumination If you expose the detector with a flat field you can use this image to create a new mask with TVX by defining upper and lower limits. Pixels in the detector that are either dead, too noisy or behave in a non-desirable manner can be masked out.

  • Page 36: Flag The Module Gaps

    9.2. Flag the Module Gaps On the PILATUS3 the gaps between the modules can be filled either with 0 or with -1. Which number will be filled in is controlled by the Camserver command called GapFill (see Camserver command at section 14).

  • Page 37: Adjust Crystallography Parameters

    The parameter 'CBF_template_file' gives the full path to the template. Note that the CBF template may be used to set variables even when TIF images are to be written. MXsettings CBF_template_file 0 can be used to turn off this setting. More information can be found in the cbf specification available from www.dectris.com.

  • Page 38: Flat Field Image

    This is because the flatfield-corrected image will be rounded to the nearest integer and saved as data type integer. User Manual. PILATUS3. Version: V2.1 38/62...

  • Page 39: How To Use The Pilatus3 Detector Through Tvx

    12. How to Use the PILATUS3 Detector through TVX TVX is a powerful tool for data acquisition and analysis. This section describes only the most commonly used commands in TVX. All commands are case-insensitive; however, filenames are case-sensitive. An ‘object’ in TVX may be an image or a graph. Many commands, such as move, will work on objects of either kind.
  • Page 40 D…destination image. Type… Char, Short, Int, Float define DEFINE name="instruction1; instruction2;.." Defines user symbol name and value. E.g. define tpict="zpict; move imt=im3" defines symbol tpict as a comination of ‘zpict’, and the built-in move instruction. User Manual. PILATUS3. Version: V2.1 40/62...
  • Page 41 CaptureIM filename Capture the default image to filename captures a displayed image (and its zoom) as a .ppm (portable pixmap) file, including coloration and contrast adjustments. CaptureGR filename Capture the default graph to filename Captures a displayed graph (and its zoom) as a .ppm (portable pixmap) file.

  • Page 42: Description Of The Image Display

    Moreover, it is possible to display the image in different color schemes. This image display will automatically show up after you execute the expose macro in TVX. Figure 11. Image display from TVX User Manual. PILATUS3. Version: V2.1 42/62...
  • Page 43 Display tool Description (sliders) Define the color and the contrast of the image. For every value of a pixel a color from a lookup table will be displayed. With the two left sliders the cut off for the low and high values can be set. Values outside this range are displayed with the same color.
  • Page 44 Useful for crystallographic images. Several test images and graphs are included in the system. Try the following: imagepath examples 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. PILATUS3. Version: V2.1 44/62...
  • Page 45 Example: Butterfly selection tool This selection tool is useful for straight line integrations (densitometer traces) and for integrating small angle scattering patterns from either a line or a point X-ray source. Figure 12. Example of a the butterfly selection tool The size and position can be adjusted directly with the mouse or by typing the values directly into the boxes.

  • Page 46: Analysis Commands

    3 (or 7) numeric parameters must be specified. In the integral mode, the integral is written to 'hist[n+1].dat'. if the name is specified, it is appended with "_i" for the integral. See also 'histset' User Manual. PILATUS3. Version: V2.1 46/62...
  • Page 47 Command Description Print statistics from the current box selection tool on the image. Alternatively, specifiy image name and box coordinates on the command line. Usage: box [IM] [x1 y1 x2 y2] If IM is not given, the default IM is used. [x1 y1 x2 y2] are the coordinates of box to be examined.

  • Page 48: Mask Files

    Set pixels in IM to value using the current box (coordinates) as a template. This permits you to manually alter a mask image based on observations different image. Alternatively, the box coordinates can be specified as described in section 9.1.1. User Manual. PILATUS3. Version: V2.1 48/62...

  • Page 49: User Defined Commands

    If the command deleteallobjs is used after you have loaded a mask image your maskimg will be reset; of course, the stored image is untouched. 12.4. User defined commands TVX supports complex C-like commands in the command line. Example: To display a series of images as a movie: format 2;...

  • Page 50: Glossary Files

     move corr.tif=[mean]/corr_image_float.tif If the image_00001.tif was an appropriate “flat” image (see section 11 for details) the 5 lines create a proper correction image (corr.tif) which can be used for flat field correction. User Manual. PILATUS3. Version: V2.1 50/62...

  • Page 51: Factory Calibration And Correction

    (as it is the case at some synchrotrons) and a high precision at high count rates is required, specific rate correction factors can be requested from Dectris. The rate correction can be optionally turned off in the control software (e.g. triggering on short single X-ray bursts).

  • Page 52: Camserver Commands

    NExpFrame prior to of last image execution (see Multiple Exposure Mode 7.3.4). The time from arming the system until the arrival of the first User Manual. PILATUS3. Version: V2.1 52/62...
  • Page 53 Command Arguments Description Socket Socket (unit) connection connection [default return return text values] code trigger is unlimited. Use 'K' transmitted over the socket connection to interrupt this state. ExtEnable file_base_name + Make an exposure or an exposure series using an external at the start: 15 at start: Starting externally file extension...
  • Page 54 Shutter_time, CBF_template_file Not settable with mx_settings, but provided to templates from detector settings: Timestamp, Exposure_period, Exposure_time, Count_cutoff, Compression_type, X_dimension, Y_dimension SetCu Command to trim the detector optimal for usage with OK /tmp/setthreshold.cmd Copper radiation User Manual. PILATUS3. Version: V2.1 54/62...
  • Page 55 Command Arguments Description Socket Socket (unit) connection connection [default return return text values] code SetMo Command to trim the detector optimal for usage with OK /tmp/setthreshold.cmd Molybdenum radiation SetCr Command to trim the detector optimal for usage with OK /tmp/setthreshold.cmd Chromium radiation SetFe Command to trim the detector optimal for usage with Iron...
  • Page 56 Filename must be a full pathname. If filename is not given, the current setting is shown. If filename is '0' or "off", the pixel flagging function is turned off. The maximum number of bad pixels is 9000; the flag User Manual. PILATUS3. Version: V2.1 56/62...
  • Page 57 Command Arguments Description Socket Socket (unit) connection connection [default return return text values] code value is -2. LdFlatField Filename (text) Load the flat-field correction file none or pathname [none] Filename must be a full pathname. File must be a 32-bit floating-point TIF image.
  • Page 58 Show the number of 1 KB blocks available on ImgPath. 1K blocks available ExpEnd Return the filename with which the exposure ended. full path name of last image CamSetup Report camera setup. Camera definition: Camera name: Camera state: Target file: User Manual. PILATUS3. Version: V2.1 58/62...
  • Page 59 Command Arguments Description Socket Socket (unit) connection connection [default return return text values] code Time left: Last image: Master PID is: Controlling PID is: Exposure time: Last completed image: Shutter is: Telemetry Report camera telemetry. Image format: and additional camera messages Version Print the TVX/Camserver version.
  • Page 60 5. The format is also constrained by the requested number of images. 2 … Automatically set by the trimming command (e.g. SetCu). 3 … Set by any trimming command (e.g. SetCu) to the default value /home/det/p2_det/config/cam_data/ratecorrection/Continuous. User Manual. PILATUS3. Version: V2.1 60/62...

  • Page 61: Camserver Test Client

    = htons((unsigned short) port); s_addr.sin_addr = *(struct in_addr*) hostent->h_addr; // Connect to socket if (connect(s, (struct sockaddr *) &s_addr, sizeof(s_addr)) < 0) return; printf("\n***** Command line socket interface for camserver *****\n\n"); printf("Type 'exit' to quit\n"); User Manual. PILATUS3. Version: V2.1 61/62...
  • Page 62 // Data from socket else if (FD_ISSET(s, &rfd)) { // Read from socket if (read(s, buffer, BUFSIZE)==0) { printf("server not existing anymore, exiting...\n"); break; printf("%s\n",buffer); bzero(buffer, sizeof(buffer)); close(s); return 0; User Manual. PILATUS3. Version: V2.1 62/62...

This manual is also suitable for:

Pilatus3 6mPilatus3 2mPilatus3 1mPilatus3 300kPilatus3 300k-wPilatus3 200k

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