Dectris PILATUS 1M User manual

USER MANUAL
PILATUS Detector Systems
Version 1.2

I
Table of Contents
1Document History.....................................................................................4
1.1 Changes............................................................................................4
2How to use this manual.............................................................................5
2.1 Address and support..........................................................................5
2.2 Explanation of symbols......................................................................5
2.3 Definitions of terms............................................................................6
3Warnings...................................................................................................7
4System Description...................................................................................8
4.1 Overview............................................................................................8
4.2 Principle.............................................................................................8
5Software..................................................................................................11
5.1.1 Overview of TVX.......................................................................12
5.1.2 Overview of Camserver............................................................13
6Getting started........................................................................................13
7How to operate the system.....................................................................14
7.1 Login to the computer......................................................................14
7.2 Connect to a network.......................................................................14
8How to use TVX......................................................................................16
8.1 Description of the directories...........................................................16
8.2 Main commands..............................................................................17
8.3 Description of the image display......................................................21
8.4 Image formats..................................................................................25
8.5 Analysis commands.........................................................................25
8.6 Mask files.........................................................................................27
8.7 User defined commands..................................................................28
8.8 Glossary files...................................................................................29
8.9 Various commands..........................................................................29
9How to use Camserver ...........................................................................30
9.1 Main commands..............................................................................30
9.2 Variables..........................................................................................31
9.3 Exposure series...............................................................................32
9.4 Integration into other systems..........................................................32
9.4.1 Steps to bring up a PILATUS detector in a new environment:..33
10 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
10.5 Adjusting the analog amplifier manually ..........................................43
10.6 Loading trim files and setting the threshold automatically................45
11 Creating a flat field correction image...................................................47
11.1 Using the flat field correction image.................................................48
12 Factory Calibration and Correction......................................................49
13 External Triggering..............................................................................51
13.1 Command list...................................................................................51
13.2 External Trigger mode.....................................................................52

II
13.3 External Multi Trigger mode.............................................................54
13.4 External Enable mode .....................................................................54
13.5 Multiple Exposure mode..................................................................56
14 Appendix.............................................................................................57
14.1 Table of figures................................................................................57

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1 Document History
Actual document
Version Date status prepared checked released
1.2 6.2.2009 In Work PS
1.1 Changes
Version Date Changes
1.1 31.08.2007 Various improvements
1.2 06.02.2009 Various improvements

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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. Read it thoroughly.
2.1 Address and support
DECTRIS Ltd.
Neuenhoferstrasse 107
Switzerland
Phone: [phone]
Fax: + 41 56 500 21 01
Email: [email protected]
Should you have questions concerning the system or its use, please contact
us via phone, mail or fax.
2.2 Explanation of symbols
Symbol Description
Important or helpful notice
Caution. Please follow the instruction carefully to prevent
equipment damage or personal injury.
DC-current
AC-current
Ground

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2.3 Definitions of terms
Term Description
MCB Module control board
DCB Detector control board
BCB Bank control board
DAC Digital to Analog Converter

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3 Warnings
Please read these warnings before operating the detector
•Before turning the power supply on, check the supply voltage with the
label on the power supply. Using the improper mains voltage will
destroy the power supply and damage the detector.
•Power down the detector system before connecting or disconnecting
any cable.
•Make sure the cables are connected and properly secured.
•Avoid pressure or tension on the cables.
•The air intakes and outlet for the detector fan should not be obstructed.
•The detector system should have enough space for proper ventilation.
Operating the detector outside the specified ambient conditions could
damage the system
•Do not touch the entrance window of the detector.
•The detector is not specified to withstand direct beam at a synchrotron.
Such exposure will damage the exposed pixels.
•Replace the protective cover when the detector is not in use.
•On powering up the detector, the ammeter on the power supply should
show a current of approximately 2 A. In operation the ammeter should
not exceed a current of about 3 A. (where applicable)
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.
DO NOT UPDATE THE OS OR THE KERNEL

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Data
PC
Detector PILATUS
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
Figure 1 Overview of the PILATUS detector system setup.
4.2 Principle
DECTRIS X-ray detector systems operate in "single photon counting" mode
and are based on the newly developed CMOS hybrid pixel technology. The
main difference with respect to existing detectors is that the x-rays are directly
transformed into electric charge (Figure 2) and processed in the CMOS
readout chips. This new design has no dark current or readout noise, a high
dynamic range of 1'000'000 (20 bits), a read out time of less than 3 ms, a
framing rate of over 200 images/s and an excellent point spread function of <
1 pixel. The quantum efficiency of the 0.32 mm thick silicon sensor is optimal
for experiments in the energy range from 3-12 keV; however the detectors can
be used for energies of up to 30keV or more. The counting rate is more than
2x10
6
/s/pixel, enough to perform many experiments using the high flux of
modern synchrotron light sources.

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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. This connection process is called ‘bump-bonding’.
Figure 3 The detector module, the basic element of all DECTRIS detector systems

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The great advantage of this approach is that standard technologies are used
for both the silicon sensor and the CMOS readout chips, which guarantees
highest quality. Both processes are optimized separately, as the best silicon
substrates for X-ray detection and for high-speed/high-quality electronics are
very different. Moreover, the small size of the pixel and of the interconnection
results in a very low capacitance, which has the beneficial effect of reducing
the noise and power consumption of the pixel readout electronics.
X-ray data collection can be improved with detectors operating in single
photon counting mode. A hybrid pixel which features single photon counting
comprises a preamplifier, which amplifies the charge generated in the sensor
by the incoming X-ray, and a discriminator, which produces a digital signal if
the incoming charge exceeds a pre-defined threshold. The discriminator feeds
a 20 bit counter, which then leads to completely digital storage and noiseless
readout of the number of detected X-rays in each pixel (Figure 4)
Global
Tresh
6 Bit Latch
+ DAC
CS
Amp
Comp
Bump
Pad
DOUTAOUT
Rowsel Pixsel
Pixsel
Pixsel
Pixsel
Colsel
-
+
CAL
1.6fF
20 bit
Counter
Pixsel Pixsel
&
PILATUS II Pixel Cell
DCLK
ENA
Pulse
Shaper
DIN
φ
1
-
Gen
φ
2
CNT/RO
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
2
. The
readout chips are wire-bonded to the mounting bracket with its readout control
electronics and forms the complete module (Figure 3).

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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.
Figure 5 Normal operation with TVX and Camserver on one computer.
But it is also possible, to operate the detector without TVX and access
Camserver directly via a socket connection from another PC.
Figure 6 Operation with TVX and Camserver on separate computers.

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5.1.1 Overview of TVX
TVX is a free, open source, data acquisition and control software suite tailored
to X-ray science. TVX is an attempt to provide a flexible user interface that is
easily adapted to control a broad range of 2-D X-ray detectors as well as a
powerful collection of analysis tools.
TVX operates by distributing the tasks of data analysis and hardware control
between two separate programs. The first program, which is most often
referred to as TVX, contains the user interface and analysis tool suite. The
other, which is referred to as the Camserver, is responsible for controlling the
hardware of the specific data acquisition system. These two programs
communicate over a TCP/IP connection, as shown in Figure 5, and thus do
not need to run on the same machine, or even under the same operating
system; see Figure 6.
Figure 7 TVX communication scheme
Camserver bundles all of the details of the hardware control into a C program
which can be ported across computer platforms. An added benefit of this
model is that it allows the experimenters to do their analysis wherever and
whenever it is most convenient from them, be it at the beam line while the
data are being taken or back at their home institution or corporation.
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.

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5.1.2 Overview of Camserver
Camserver is a freestanding program that controls an x-ray camera and
provides a simple user interface for "atomic" (single function) commands. It is
intended to provide a spartan, but fully functional, low level interface to
camera hardware.
On invocation, the program 'camserver' takes a single command-line
argument, the path to its resource file, by default called 'camrc'. Camserver
will also use the same path to open its debugging file, 'camdbg.out'.
A major function of camserver is to accept socket connections from a high
level controller (e.g., 'tvx'), which can provide high level services to this or
other cameras. The interface is a simple text-based message passing system.
Images - the ultimate product of a working area x-ray detector - do not pass
thru the socket interface, but are written to a configurable location (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.

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7 How to operate the system
Before you turn on the system, make sure you have read this manual, the
technical specification and connected the detector accordingly.
7.1 Login to the computer
Turn on the PC.
Log in procedure:
User:
PW:
Root PW:
7.2 Connect to a network
The IP address of the detector is identical to the IP address of the PC where
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.

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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.

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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
correct Detector specifications
docs User manual, technical specification
graphs Graphs are stored by default in this directory
images Images are stored by default in this directory
programs Program code for TVX and Camserver

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8.2 Main commands
TVX is a powerful tool for data acquisition and analysis and has a complete
description of all commands, which can be accessed through the help
command.
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. Objects may combined with
standard arithmetic operators (+, -, *, /, +=, etc.), logical operators (<, >, <=,
>=, |, ||, &, &&) 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.

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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.

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Command or Macro Description
menu Shows all commands
It is divided in 4 parts:
•TVX reserved words
•TVX defined commands
•Macros, saved in default.gl or typed by the user
•Variables
help command -or-
man command Shows the help text for the command. Help help is a
good way to start. Help “gr*” will show all commands
beginning with ‘gr’; the quotes are required, else the
system takes ‘*’ to mean multiplication.
ESC-button Stop a running task and return to the TVX line
interpreter
CTRL-C Full reset of TVX
cam k stops the running Camserver processes
rbd Read Back Detector.
Self test of the digital part of the detector. Sends a
digital pattern to each pixel, reads it out and displays
the image.
Use this command always after a startup.
Every pixel should show 1000 counts.
calibdet Self test of the detector.
Sends 100 calibrate pulses to the analog part of the
detector, reads back the recorded values as an image
and displays the result. Every pixel should show 100
counts.
Use this command always after a startup.
Should the pixels not show 100 counts in the absence
of radiation, repeat the command. If the image is
black, type setdac, then repeat the command. In case
this tests fails, turn the power supply off, close the
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

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Command or Macro Description
path for images. The imagepath command also sets
the autoname to the new path.
grafpath path Display or change the default path for graphs. The
keyword 'grafpath' can be used in expressions as
[grafpath]
exp filename Make an exposure. If filename is not given, TVX uses
the next automatic filename. The files created are
saved in the directory specified in imagepath.
expose exposure time
(in seconds)
expose 1: makes an image with an exposure time of 1
sec.
shortest exposure time: > 1 us, 0.000’001.
Shows the exposed image immediately on completion.
Exposem
exposure time continuous camera mode without saving images.
Takes images until any key is pressed. The last image
is stored in temp.tif
disp filename Display an image. Opens up to 3 windows for
successive invocations.
disp1 filename Displays an image reusing the last window. Useful in
loops.
graf fn1[fn2[ fn3]] Graph up to 3 graphs in a window
show variable -or-
show string Shows the content of a variable or a string
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.
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.
connect [ip_address] Connect the socket connection from TVX to the
Camserver at [ip_address]
disconnect Disconnect the socket connection from TVX to