saxs saxs/waxs waxs data reduction...¾ the time to digital converter (vtdc4) [5] plays a very...

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SAXS

SAXS/WAXS WAXS

DATA REDUCTION

February 15, 2000 E.H.Homan

M.Konijnenburg version 6.0

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Premise

We describe the data acquisition and reduction software for collecting and pre-processing of Small Angle X-ray Scattering (SAXS) and /or Wide Angle X-ray Scattering (WAXS) data for both static and time-resolved measurements performed on the Dubble Collaborative Research Group (CRG) beamline at the ESRF. The software can be used for both isotropic as well as anisotropic scatterers for independent or simultaneously SAXS and WAXS patterns. Dialogue windows allow control of different detector types with no need for the user to edit underlying control parameter files. The data-acquisition program, including the graphical user interfaces, was created by using the high level interpreted language IDL. This language enables straightforward process communication with low-level software, like device servers, and more generally with external data reduction/visualization programs. From the onset of the development we have incorporated requirements expressed by the participants of the canSAS II workshop in Brookhaven and of users of this beamline. The workshop addressed data interchange between software used at different synchrotron and neutron SAS facilities. The data formats BSL/OTOKO, ESRF and ILL and the related data regrouping program suites have been integrated in the same software environment as well as the utilities for conversion between the different formats. The data access routines for the formats SasCIF and NEXUS/HDF have also been added. After initial data reduction data can be automatically converted to the specific templates required by the data entry sections of some commonly used analysis software packages like PDH and GNOM. Els Homan DUBBLE CRG / ESRF, Netherlands Organization for Scientific Research (NWO), c/o. B.P. 220, F-38043 Grenoble Cedex Email: [email protected] Marco Konijnenburg FOM-Institute for Atomic and Molecular Physics, Postbus 41883 NL-1098 SJ Amsterdam Email: [email protected] Wim Bras DUBBLE CRG / ESRF Netherlands Organization for Scientific Research (NWO), c/o. B.P. 220, F-38043 Grenoble Cedex Email: [email protected]

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CONTENTS 1. THE SAXSGUI/WAXSGUI DATA ACQUISITION AND DATA REDUCTION PROGRAM....... 5

2 SAXS........................................................................................................................................................... 6

Communication with the hardware ........................................................................................................ 6 Acquisition system .................................................................................................................................. 6

2.1 GRAPHICAL USER INTERFACE ............................................................................................................... 7 2.2 FILE...................................................................................................................................................... 9

2.2.1. Select OUTPUT directory............................................................................................................. 9 2.2.2. Set OUTPUT filename .................................................................................................................. 9

2.3 SETUP................................................................................................................................................ 10 2.3.1 Timeframe editor ......................................................................................................................... 10 2.3.2 Experiment editor ........................................................................................................................ 11 2.3.3 Detector editor............................................................................................................................. 12

2.4 RUN.................................................................................................................................................... 13 2.4.1 Clear memory .............................................................................................................................. 13 2.4.2 Start ............................................................................................................................................. 14 2.3.3 Stop.............................................................................................................................................. 14 2.3.4 Save ............................................................................................................................................. 14

2.5 TEST................................................................................................................................................... 15 2.6 ONLINE ............................................................................................................................................. 15

2.6.1 Colors .......................................................................................................................................... 15 2.6.2 Online 2D .................................................................................................................................... 15 2.6.3 Online 1D .................................................................................................................................... 17

2.7 UPDATE ............................................................................................................................................... 19

3 WAXS....................................................................................................................................................... 20

Detector mechanics and electronics..................................................................................................... 20 Communication with the hardware ...................................................................................................... 20

3.1 GRAPHICAL USER INTERFACE ............................................................................................................. 21 3.1 FILE.................................................................................................................................................... 22 3.2 SETUP................................................................................................................................................ 23

3.2.1 HV control ................................................................................................................................... 23 3.2.2 MSGC parameters: the detector parameters.............................................................................. 24

3.3. RUN................................................................................................................................................... 25 3.4 ONLINE ............................................................................................................................................. 25

3.4.1 Set display options ....................................................................................................................... 25 3.4.2 Display real/coincidence data ..................................................................................................... 26

3.5 UPDATE ............................................................................................................................................... 28

4 SAXS / WAXS.......................................................................................................................................... 29

SAXS / WAXS Experiments ................................................................................................................... 29

5 DATA REDUCTION .............................................................................................................................. 30

5.1 WINDOW SLOT..................................................................................................................................... 30 5.2 FILE.................................................................................................................................................... 31

5.2.1 Select color table ......................................................................................................................... 31 5.2.1. Select INPUT directory ............................................................................................................. 31

5.3 DISPLAY (BSL/XOTOKO FORMAT ONLY) ............................................................................................ 32 5.3.1 Select data file (bsl/xotoko format only) ...................................................................................... 32 5.3.2. SAXS – 2D .................................................................................................................................. 33 5.3.3. SAXS – 1D .................................................................................................................................. 35 5.3.3. WAXS.......................................................................................................................................... 36 5.3.4. CALIBRATION ........................................................................................................................... 39

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5.3.5. SAXS – 2D (video) ...................................................................................................................... 39 5.3.6. Mirror......................................................................................................................................... 39

5.4 X-AXIS (XOTOKO FORMAT ONLY) ...................................................................................................... 40 5.4.2. Select X-AXIS file (q-axis) .......................................................................................................... 42 5.4.1. Create X-AXIS (q-axis) ............................................................................................................... 43

5.5 2D - DATA ......................................................................................................................................... 43 5.5.1. DIN: Divide and normalise image using a calibration file ........................................................ 44 5.5.2. ADD: Background subtraction ................................................................................................... 47 5.5.3. DIV: Divde by detector response................................................................................................ 48 5.5.4. VER: Perform a vertical integration .......................................................................................... 49 5.5.5. HOR: Perform a horizontal integration ..................................................................................... 50 5.5.6. SEC: Perform a vertical integration........................................................................................... 51

5.6 1D - DATA ......................................................................................................................................... 52 5.6.1. DIN: Divide and normalise image usign a calibration file ........................................................ 52 5.6.2. ADD: Background subtraction ................................................................................................... 52 5.6.3. DIV: Divide by detector response.............................................................................................. 53

5.7 EDF (ESRF DATA FORMAT) ............................................................................................................... 54 5.7.1. EDF – GUI ................................................................................................................................. 54

5.7 CONVERT ......................................................................................................................................... 59 5.7.1 XOTOKO + X-AXIS --> GNOM.................................................................................................. 59 5.7.2 XOTOKO + X-AXIS --> PDH ..................................................................................................... 60 5.7.3 BSL ---> NEXUS ......................................................................................................................... 62 5.7.4 TRANSFORM (Open a binary data file)...................................................................................... 62 5.7.4 EXCEL / Kaleida Graph (Open an ASCII data file).................................................................... 63 5.7.4 FIT2D (Open a BSL data file) ..................................................................................................... 64

5.8 OTHER............................................................................................................................................... 65 5.9 HELP .................................................................................................................................................. 65

6 XOP (X-RAY ORIENTED PROGRAMS)........................................................................................... 66

7 REFERENCES ....................................................................................................................................... 67

APPENDIX A ............................................................................................................................................. 71

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1. The SAXSGUI/WAXSGUI Data Acquisition and Data Reduction Program

This chapter describes the SAXSGUI application for SAXS/WAXS experiments. The program sources are stored inside the directory: /users/dubble/idl on the HP-Unix workstation dubble3. The user interface is written in IDL (software from Research Systems) and comprises a detector interface which consists of some shared libraries written in C. The IDL language is a fourth generation language and it is relatively easy to use. You have to login as: opd26 (password: tonic26) on dubble3, then start the application by typing “saxsgui” or “waxsgui” at your X-terminal. The startup window of the application in both cases (saxsgui / waxsgui) is shown in figure 1.1.

Figure 1-1: Startup window Starting from this window the following operations are possible:

SAXS 1D / SAXS 2D, see chapter 2 WAXS, see chapter 3 SAXS 1D /WAXS and SAXS 2D / WAXS, see chapter 4 Data reduction, see chapter 5 Clear Memory, clear the shared memory, which is created for the online display of the two

dimensional SAXS data. The Data reduction program can run under operations systems: HP, Sun, Sgi and Linux, and is available for SAXS / WAXS - users. This version is realized by using the package XOP [15], see chapter 6.

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2 SAXS This part of the manual describes the control of small-angle X-ray scattering (SAXS) experiment performed with a gas-filled delay –line detector [1,2]. Communication with the hardware The control software runs on a VME crate. There are three levels of software that can be defined (Fig 2-1). On the first (lowest) layer there are the device drivers. The second layer consists of the device servers [9], which use the device drivers. The top level is an application importing a device server and sending commands to it.

Fig 2-1: Communication with the hardware Acquisition system The Figure 2-2 shows the acquisition system hardware architecture. The role of the individual cards is the following:

The Time Frame Generator (TFG) [6,13] is a sequencer, necessary for time resolved measurements. The Multi Channel Scaler (MCS) [7,14] is in the system in order to count the ion chamber signals on

its’ 32 scaler input channel. The Histogramming Controller (VHIST) [4,8] is piping the events coming from a 1D or 2D detector

into an external histogramming memory. The Histogramming Memory (HM) has a capacity of 256. The Time to Digital Converter (VTDC4) [5] plays a very important role in the whole acquisition

system, since it receives signals from the detector and translates time differences from 2 delay lines into digital values which are then available for the VHIST.

The control system of the detector is build using the TACO system [25].

Application (SAXSGUI)

hardware

Operatingsystem

network

Device Server(TFG)

DeviceServer(VTDC4)

Device Server (DLD)

Device Server(VHIST)

Device Server(MCS)

TFGmodule

VHISTmodule

MCSmodule

VTDC4module

HMmodule

VTDCdevicedriver

MCSdevicedriver

VHISTdevicedriver

TFGdevicedriver

software

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Figure 2-2: Hardware architecture of the gas-filled detector acquisition system. 2.1 Graphical User Interface Selection of the “SAXS” button (see Fig 1-1) causes the window in Figure 2-3 to appear.

Figure 2-3: Connection to the detector? Selection of the “Yes” button, will establish the communication with the acquisition servers. If the connection succeeds, the main acquisition window (see Figure 2-4) will appear. In general, the program will start up without any parameters. However, if the default configuration file .saxs_bm26saxs exists in the user’s home directory, the relevant parameters will be automatically loaded into the system. The acquisition window shown in Figure 2-4 consists of two major components:

the menu bar the experiment window

CPUOS9 VTDC4 TFG MCS VHIST HM BIT3

Frame Number

X,Y

ETHERNET

Beamline WorkstationFast Data Link (Bit3)

From X and Y Delay Lines (Cathodes) and from Anode through NIM Discriminator and Delay

VME crate

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By pressing the mouse button whilst the pointer is moving along the menu bar any of the options causes a pull–down menu to appear, very much like a window blind. Moving the pointer down the menu causes each of the menu items to be selected or de-selected in turn. Releasing the mouse button just on one item, e.g. “System configuration”, causes the menu to disappear and the command to be executed. Releasing the mouse outside the menu causes no selection and the menu disappears.

Fig 2-4: Main Window In the lower window slot the following information is given:

Run externally: Used to start an experiment by a trigger. A TTL trigger signal must be connected to the TFG.

Measured %: Showing the done – acquisition time in percentage and in seconds.

#Frames: number of frames: Current frame: the current running frame.

Ion chamber 1: Showing the counts during the acquisition of the first ion chamber.

Ion chamber 2 Showing the counts during the acquisition of the second ion chamber.

Error Memory: Showing the existing of an overflow of the acquisition memory.

Current state: Gives the current state of the main device server (DLD). The possible states are: INITIALISATION, IDLE, RUNNING.

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2.2 FILE The “FILE” pull-down menu allows the following operations:

Select OUTPUT directory Set OUTPUT filename FILENAME info

File information: see appendix A. File information (long): see appendix A. Display LOG file: see appendix A.

PREFERENCES Read preferences: Read a settings file from the directory: /users/opd26/log/saxs. This will update

the following parameters: output directory, output filename, timeframe settings and the resolution settings of the detector.

Write preferences: Save the current settings to a file inside the directory: /users/opd26/log/saxs. Edit preferences: Edit/Display a parameters settings file.

Exit 2.2.1. Select OUTPUT directory The current directory is displayed in the upper window slot (see Figure 2-5) along with its sub-directories in the lower window slot. You can select a directory by clicking with the mouse on a subdirectory. This becomes the current directory and again its sub-directories are listed below it. Click on “..” to move up one level. A new current directory may be entered manually. The “Mkdir” button creates a new directory under the current directory. The “OK” button confirms the selection of a new directory. All files created during measurements will be stored under this directory (be sure you have write access to this directory!).

Fig 2-5: Select OUTPUT directory 2.2.2. Set OUTPUT filename Selection of the “Set OUTPUT filename” menu item causes the window in Figure 2-6 to appear. The prefix for output file names must be chosen out of the 26 alphabet letters. This selects the letter the output filenames shall begin with. This prefix is necessary to create an OTOKO file, mentioned later on in this guide.

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Fig 2-6: Prefix for output file names. 2.3 SETUP The “SETUP” pull down menu allows the following operations:

Timeframe editor Experiment editor Detector editor

It is evident that all settings (System configuration) must be sent to the device servers before an experiment is started. The state of the acquisition server will than change from INITIALISATION into IDLE, and the system is ready to start a measurement. 2.3.1 Timeframe editor Selection of the “Timeframe editor” menu item causes the window in Figure 2-7 to appear. This editor allows the following operations:

Add a timeframe group. Delete a timeframe group. Exit the timeframe editor.

Fig 2-7 Timeframe editor

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A group is defined as a set of frames with identical timing and pulse characteristics. A cycle is defined as a set of groups which make up one lap of an experiment. The maximum number of cycles and the total number of frames depend on the time frame generator. In this case: 4096 cycles and 1024 frames. The main body of the interface is used to describe the timing and pulse characteristics of a particular group of frames. In each group the following fields exist:

Number of frames in the group. Dead Time is defined in seconds. The Dead Time can be set starting from 10 microseconds up to

1023000 seconds. Dead Pause can be set either to 0 or to 1. If the pause bit is set, then the TFG pauses at the beginning of

the frame for which the pause bit is set and continues only after restart (internal or external). Dead Output: used for triggering, for example the fast shutter Life Time is defined in seconds. The Life Time is set in the very same way as the Dead Time. Life Pause: Life Pause can be set either to 0 or to 1. Life Output: used for triggering (see Dead Output).

Fig 2-8a: Experiment Editor, Fig. 2-8b: Detector editor 2.3.2 Experiment editor Selection of the “Experiment Editor” menu item causes the window in Figure 2-8a to appear. The following attributes can be changed:

Number of scalers: The channel scaler card reads the values coming from the voltage-to-frequence conversion card. Generally, the ion chambers (before and after the sample) will measure the counts during the acquisition. Up to 16 channels can be defined.

Number of cycles: The number of cycles corresponds to the number of times that the whole sequence of frames programmed in the timeframe editor is repeated.

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Ion chambers and other read-out parameters What do ion chambers do? By sending an X-ray beam through a gas one partly ionises the gas. If the beam is sent through a space over which a high voltage is applied the ions and electrons move to different plates and generate a current there. If one of the plates is attached to a current amplifier the output of this device is proportional over a wide range with the intensity of the direct beam. This output is then fed into a Voltage to Frequency (VTF) converter. This frequency is ‘readable’ for digital boxes called computers. The software now integrates this frequency over the whole length of time that a single time frame lasts and stores this as a (large) number. The software then writes this to the calibration file. The same can be done with voltages generated by other electronic boxes used in an experiment like for instance a thermocouple read-out or pH meter. If one wants to have a correlation between the large numbers stored in the calibration files and the real measured parameter the user has to calibrate this. The VTF converters can only handle voltages between 0 and 10 Volt, although they can be set to a different, more accurate range of 0-5 and 0-2.5 Volt. If the combination of voltage and length of time frame generates numbers that are too large to be stored in the memory an overflow occurs. How to overcome this problem has to be seen with on a case to case basis. Ion chambers are by no means the only way that a relative beam intensity can be determined. Pin diodes, scattering of foils etc. also can be used. A useful method should satisfy the conditions that it is linear over a wide beam intensity range and not produce unrealistic high background signals in the scattering pattern. Different people have different opinions on the usefulness of different methods. My philosophy is that one should use the method that works, that one likes and that is affordable. Note: - It’s always the users responsibility to make sure that these ion chambers are connected and indeed sampled in the indicated channels.

2.3.3 Detector editor Selection of the “Detector editor” menu item causes the window in Figure 2-8b to appear. The following parameters are defined:

Resolution mode: Select: 0 for half resolution, or 1 for full resolution (see Fig 2-9)

Resolution in X: Possible values are 256, 512 or 1024, 2048 pixels.

Resolution in Y: Possible values are 256, 512 or 1024, 2048 pixels.

Data length: Possible values are 16 or 32 bit.

In case of using the 1D – detector the following settings are advised:

Resolution mode: 0 Resolution in X: 2048 Resolution in Y: 1 Data length: 32 bit

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In case of using the 2D – detector the following settings are advised:

Resolution mode: 0 (half resolution mode) Resolution in X: 512 pixels Resolution in Y: 512 pixels Data length: 32 bit

The result is in an image size of 1 Mbyte per frame.

Fig 2-9: Set resolution mode 2.4 RUN The “RUN” pull-down menu allows the following operations:

Clear memory Start / Restart Stop Save

2.4.1 Clear memory If you are absolutely sure that your data is saved, you can clear the memory. Selecting of the “Clear memory” menu item causes the following actions:

Clearing the acquisition memory Clearing the scaler cards memory on the MCS board.

If you have not explicitly asked to clear the memory, your data will remain there. After the clearing action you can start a new session (Start) or you can reconfigure the system.

1024 x 1024 - Mode:1

512 x 512 - Mode:1 512 x 512 - Mode:0

256 x 256 - Mode:1 256 x 256 - Mode:0

imagedetector

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2.4.2 Start By selecting the “Start” menu data collection will either commence immediately or wait for an external pulse to be applied to the time frame generator. Whichever option is chosen, the status display will be refreshed. The data display update will be suspended at the end of the data collection. The Data collection will start only if the device server is no longer in INITIALISATION mode. The active data collection can be monitored. 2.3.3 Stop Selection of the “Stop” menu item causes the data collection to halt immediately. 2.3.4 Save Selection of the “Save” menu item causes the window in Figure 2-10 to appear.

User Name: Here you can type your name. User comments: Here you type general information about the experiment. Detector info: Filled in automatically by the device server after a measurement. It is showing offset

and timeout of the Time-to-Digital Convert. Measurement Time: Filled in automatically by the device server after each measurement.

Selection of the “Apply” button causes data files to be generated on disk. A data transfer can be stopped, when:

Your login-name is not opd26. There a problems with the network. opd26 has no write access to the current directory.

If the transfer fails check your current directory and try it again. After each measurement the experiment/measurement number will be automatically updated. The data is saved in OTOKO format. This format is used by the programs OTOKO/BSL written at the Daresbury laboratories [18,19]. The OTOKO fileset consists of one header file with the description of the file set and one or more binary files with data in floating point notation. The header file is ASCII written and can be displayed with a simple viewer. The header file states the number of binary files in the file set. The frame size and the number of frames are given in the header for each binary file. A typical data set generated via the GUI will look like:

Xnn000.mdd Header File [ascii] Xnn001.mdd SAXS data [binary] Xnn002.mdd Calibration data [binary] Xnn003.mdd WAXS data [binary]

Where:

X: is the prefix of the output filename nn: is the measurement number mdd: mdd represents the date on which data was recorded, the first digit being the month expressed in

a duodecimal base and the other digits representing the day of the month. Additionally the extra header file xnn.mddlog is created (see appendix A) This additional header file contains the values of some parameters used in the experiment. How to use the program BSL / XOTOKO is explained in chapter 5.4 and 5.5.

Notes: - Always make sure that there is a raw data back-up before starting to process. It’s easy to make errors and UNIX is ruthless in overwriting data files when mistakenly ordered to do so.

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- Once inside the program XOTOKO and BSL are not case sensitive. They are case sensitive with repect to the names of data files that have to be read-in. So the actual files need uppercase names but can be called for, inside the programs, with both upper and lower case names. - XOTOKO can read BSL files and vice versa. - For trouble shooting it is always a good thing to write both the first and second ion chamber readings as well as the ring current in your lab book.

Fig 2-10: Save menu window 2.5 TEST The “TEST” pull down menu allows the following operations:

Stop + Clear Memory Stop + Clear memory + Start

2.6 ONLINE The “ONLINE” pull down menu allows the following operations:

Colors Online 2D Online 1D

2.6.1 Colors Selection of the “Colors” menu item causes the color interface to pop up. It displays the current color table and shows a list of available predefined color tables. Clicking on the name of one color table causes it to be loaded. Other options, such as Gamma correction, stretching etc. can also be applied to the selected color table. 2.6.2 Online 2D Selection of the “Online 2D” menu item causes the SAXS online window shown in Fig 2-11 to pop up.

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The “FILE” pull down menu allows the following operations:

Initialization of the display: this means that all the necessary actions are undertaken for starting monitoring. The 2D data display program dis [17] is started as well. see the user manual of DIS.

Get status: State of the measurement. Exit

The following buttons allow the operations listed in the corresponding lines:

|< monitor the first frame < monitor the previous frame > monitor the next frame >| monitor the last frame Jump Jump to the requested frame (filled in the textfield Jump to frame)

The following text fields show the status of the measurement.

#Frames Total numbers of frames Frame Current frame Display Monitor switch key depending on the state of the measurement.

For example in the INIT state, it is not possible to monitor the data. State Current state.

The communication between the control display written in IDL and the Image Display is realized by using a shared memory [16].

Fig 2-11: SAXS online interface

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The following toggle buttons are defined:

Step by Step (Run Mode) To read an image from the hardware through the BIT3 connection while the experiment is in running - mode, it will takes round 6 seconds for the whole image. By default the online display routine reads the whole image at once. If you select the toggle button “Step by Step”, the image will be read a part of the image.

Pause (Run Mode) If the acquisition is running, every second a new image will be updated. If you select the toggle button “Pause”, the displayed will be paused (until you enable it again).

Follow run (Run Mode) After selection of the “Follow run”-button, the current running frame will be displayed automatically.

Quick read (Idle Mode) To read an image from the hardware through the BIT3 connection, while the experiment is in idle- mode, it will takes round 2.5 seconds for the whole image. This function can be enabled by selection of the “Quick Read” – toggle button.

2.6.3 Online 1D Selection of the “Online 1D” menu item causes the SAXS-online window shown in Figure 2-12 to popup. The “FILE” pull-down menu allows the following operations:

Initialization of the display: this means that all the necessary actions are undertaken for starting monitoring.

Get status: State of the measurement. Exit

The “PLOT” pull-down menu allows the following operations:

Set display options: Different display options such as: logarithm scale, limits, single frame / multiple frames.

Xplot: see the user manual of XPLOT. The following buttons (around the plot-area) allow the following operations: Frames:


Plot:

< move x 10 units to the left > move x 10 units to the right Full Full screen Replot Replot the diagram


#Frames Total numbers of frames Frame Current frame Display Monitor switch key depending on the state of the measurement.

For example in the INIT state, it is not possible to monitor the data. State Current state.

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Fig 2-12: SAXS online/offline interface

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2.7 Update The version 7.6 has the following updates: The interface is split up: File

Select OUTPUT directory Filename info File information File information (long)

Display LOG file Data Reduction Exit

Setup Time Frame Generator Run Clear memory Start Stop Fetch Set OUTPUT directory Save data Save data [From,To] Online Sleep Select Color Table Online 1D Advanced New USER setup Select OUTPUT directory Preferences Hardware Setup Use default parameters Experiment editor Detector editor System configuration Test Stop + Clear memory Stop + Clear memory + Start Help

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3 WAXS This part of the manual describes the controlling of an experiment using a microstrip gas chamber (MSGC) detector. The detector is referred to as MSGC. Detector mechanics and electronics Explaining the interface itself, it is necessary to have some idea about how the detector operates. The WAXS detector main part is a box with a gas mixture in which electrons are freed by incoming X-rays. These electrons drift to anodes where they are collected. When the charge that is built up by the electrons on a channel (anode) exceeds a certain threshold, a counter register is increased. When the electron cloud is large, enough to build up a charge on two anodes, another mechanism comes into play. The counter register belonging to the two anodes are increased and at the same time a third is increased. This counter is said to be a coincidence (virtual) channel. Which is then subtracted by software from its neighbouring real (physical) channels, thus doubling the resolution. In total there are 1024 physical channels and 1024 virtual channels. There is also a facility to read sixteen general-purpose input channels. One of these channels could be for instance the read-out of an ion chamber or sample temperature. These readings are converted into frequency signals and passed over to the type of counters used for the other channels. All the counters are 12 bit wide and are being read out every 0,5 ms. The values are added until a certain period has expired and the result is a 32 bit word for each channel. A header is added on the top and the result is called a frame. The header describes the frame number and the counter register how many times the counter has been read out. The detector also has some options that can be set, like threshold levels, a test mode etc. Communication with the hardware The WAXS detector is connected to a VME crate. The control software runs on this crate. There are three levels of software that can be defined. On the first (lowest) layer are the device drivers [11]. The second layer consists of device servers [12], which use the device drivers. The top level is an application that imports the device servers and executes commands on them. The three layers and the corresponding hardware are shown in figure 3-1.

Network

OS9 Device driver(ipmsgcdrv)

OS9 Device driver(tframe) OS9 Device driver (vhqdrv)

Device Server (Msgc)

Application (WAXSGui)

Hardware

OperatingSystem

Device Server(Tfg)

Software

MSGC IP ModuleTime FrameGenerator

VME Module

High Voltage VME Module

High Voltage VME Module

FIG 3-1 : Communication layer structure.

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The device driver for the time frame generator has been written by the Daresbury Laboratory. The remaining drivers and the device server for the detector are the result of an in-house development. Most software functionality of the WAXSGUI [10] is shared with the SAXSGUI, therefore in stead of repeating the same text, a large use of references is made in the following. 3.1 Graphical User Interface After establishing of the communication with the acquisition servers (see chapter 2.1), the main acquisition window (see Figure 3-2) will appear.

Fig 3-2: WAXS interface In the upper window slot the following information is given: Frames:

<< monitor the first frame < monitor the previous frame > monitor the next frame >> monitor the last frame State Get the current state of the main device server. The following states are

defined: PAUSED, ERROR, INIT, IDLE and RUNNING. Get Getting a frame from the acquistion memory, and transfer the data to the

WAXSGUI.

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In the lower window slot the following information is given: Plot:

< move x 10 units to the left > move x 10 units to the right Full Full screen Replot Replot the diagram + Zoom in - Zoom out

In the left window slot the following information is given:

Time duration: Showing the done – acquisition time in percentage and in seconds. #Frames: Number of frames. Current frame: The current running frame. Start time: The start time of the acquisition. End time: The end time of the acquisition. Rate: Rate of the part currently viewed Total Rate: Total rate of the complete frame Scan Treshold: A test field for testing different treshold-values.

3.1 FILE The “FILE” pull-down menu allows the following operations:

Select OUTPUT directory, see chapter 2.2.1 Set OUTPUT filename, see 2.2.2 FILENAME info

File information: see appendix A. File information (long): see appendix A.

Exit

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3.2 SETUP The “SETUP” pull down menu allows the following operations:

Timeframe editor, see chapter 2.3.1 HV control MSGC parameters

It is evident that all settings (System configuration) must be sent to the device servers before an experiment is started. It is essential to know what has to be done during an experiment. A description of all the required steps follows. The first step is to set the timing (see Timeframe editor). This must be done with respect to the restrictions of the hardware. The options of the detector can be set: the threshold levels (MSGC parameters and HV control). When the initialization is done, the device server is ready to start with a measurement. A measurement is started by selecting the internal or external start function. When one of the two functions is selected, the detector is reset and the preferences of the user are sent to the detector. 3.2.1 HV control The detector has two high voltage modules, each equipped with two independent output channels. Only three of these channels are actually used by the detector. The high voltage is needed to drive the electrons to the anodes. The high voltage object class has three encapsulated HV objects Each object controls a HV source. The sources have several options. All the settings are displayed in a window (Fig. 3-3), together with the current output voltages and currents.

Fig. 3-3: HV Control

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It can be seen from Figure 3-3 that there are three kinds of parameters:

Dynamic parameters. These parameters are the current settings of the module. They cannot be directly changed by software.

Set parameters, these are input parameters. Static parameters, hardware defined.

3.2.2 MSGC parameters: the detector parameters For setting the detector parameters a separate window is available. The window (Fig 3-4) consists of an area in which 16 thresholds can be set. Each threshold is used for a group of scalers and can be set separately. It is possible to add an offset value to all thresholds using the bottom slot of the window. Filling in negative values to subtract.

Fig 3-4: MSGC parameters

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3.3. RUN The “RUN” pull-down menu allows the following operations:

Start / Restart, see chapter 2.4.2 Stop, see chapter 2.4.3 Save, see chapter 2.4.4

3.4 ONLINE The “ONLINE” pull down menu allows the following operations:

Set display options Display real/coincidence data Run XPLOT [15], see the user manual of XPLOT

3.4.1 Set display options Selection of the “Set display options” menu item causes the window in Figure 3-5 to appear.

Fig 3-5: Set display options

Fig 3-6. Single frame mode. Fig 3-7 . Multiple frames mode.

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Here follows a list of the options implemented and their function.

Logarithmic Y-axis: setting this option causes the Y-axis to be displayed in logarithmic scale. Use the minimum and maximum values: setting this option causes the minimum and maximum values

to be used while plotting the data. Data points below the minimum or above the maximum will be left out of the plot. Minimum and maximum for the real and virtual channels can be set separately.

Auto-display incoming frames: when set, any new incoming frame will be displayed directly. Select channel number range: normally the full detector is shown. It is however possible to see only a

part of the detector. The chosen range can be entered either by typing or by selecting a region pressing a mouse button at the beginning of the selection and moving the pointer to the end of the selection and then release the button.

It is possible to view multiple frames in one window. The user can select a range of frames to be displayed. The program returns automatically to the single frame mode, when only one frame is active. An example of both modes is shown in Figure 3-6 and 3-7.

3.4.2 Display real/coincidence data At present, only one real manipulation routine is implemented. This routine is the coincidence compensation. As mentioned before there are 1024 physical and 1024 virtual (or coincidence) channels. The counters belonging to the virtual channels register one event when both neighbouring physical channels are activated at the same time. To compensate this double counting for the virtual counts are subtracted from the counts registered by the neighbouring physical channels. Table I describes the operation done by the routine. On each line the channel number is stated first. All the real channels have even numbers whereas the odd numbers are assigned to the virtual channels. The calculation is straightforward. The only problems are at the edges of the array. At the top of the array only one virtual channel has to be subtracted. At the bottom of the array the last element that needs to be calculated is the element with index 2046. To be more specific:

S0000 = S0000 - S0001 (physical) S0001 = S0001 (virtual) S0002 = S0002 - S0003 - S0001 (physical) S0003 = S0003 (virtual) S0004 = S0004 - S0005 - S0003 (physical) S0005 = S0005 (virtual) S0006 = S0006 - S0007 - S0005 (physical) : : : : S2044 = S2044 - S2045 - S2043 (physical) S2045 = S2045 (virtual) S2046 = S2046 - S2047 - S2045 (physical) S2047 = 0 No useful information

Table I: Compensation of coincidence data Selection of the “Display real/coincidence data” menu item causes the window in Figure 3-8 to appear.

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Fig 3-8: Display real/coincidence data Here follows a list of the options implemented and their function.

Compensate for coincidence: when this option is set the virtual channels are subtracted from the real channels.

Show GPIM data: when set, a window pops up with the GPIM data displayed. Equal scale for coincidence: when set, the coincidence window uses the same scale as the real

channels. Separate coincidence: setting this option causes the real and virtual channels to be shown in separate

windows. Compensate dead channels. The compensation of dead channels is done by reading the file :

$IDL_PATH/detector/dead.channels. This file contains dead channels and the channel number for compensations.

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3.5 Update The version 7.6 has the following updates: The interface is split up: File

Select OUTPUT directory Filename info File information File information (long)

Display LOG file Data Reduction Exit

Setup Time Frame Generator Run Clear memory Start Stop Fetch Set OUTPUT directory Save data Online Sleep Set display options Compensate channels Run Xplot Advanced New USER setup Select OUTPUT directory Preferences Hardware Setup Use default parameters HV control MSGC parameters System configuration Test Scan Treshold Help

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4 SAXS / WAXS

This part of the manual describes the controlling of a SAXS/WAXS – measurements. SAXS / WAXS Experiments In this case the SAXS Time Frame Generator triggers the WAXS detector and synchronizes SAXS and WAXS measurements. For WAXS experiments only it is the WAXS Time Frame Generator which triggers the WAXS detector to start an experiment. Figure 4-1 shows the acquisition window for SAXS / WAXS measurements.

Fig 4-1: SAXS / WAXS interface This interface is a combination of the SAXS and WAXS interfaces, so no further explanation is needed. See chapter 2 and/or 3.

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5 DATA REDUCTION For data reduction of SAXS data the software packages BSL and XOTOKO are available, both being developed in Daresbury by Geoff Mant. The predecessor of XOTOKO is OTOKO which was developed by Michel Koch at EMBL Hamburg. The routines inside the data reduction interface, act as a macro on BSL and XOTOKO. This part of the manual describes the data reduction of the SAXS/WAXS data.

Fig 5-1: Data reduction interface The main window shown in Figure 5-1 consists of two major components:

the menu bar the display / conversion window

By pressing the mouse button whilst the pointer is moving along the menu bar any of the options causes a pull–down menu to appear, very much like a window blind. Moving the pointer down the menu causes each of the menu items to be selected or de-selected in turn. Releasing the mouse button just on one item, e.g. “System configuration”, causes the menu to disappear and the command to be executed. Releasing the mouse outside the menu causes no selection and the menu disappears. 5.1 Window slot In the first window slot the following buttons are defined:

Use Xplot: The SAXS 1D data can be displayed in two different ways. The first possibility is to display the data in a similar way as the acquisition or inside the program XOP [15].

Use script (toggle button), Two different versions of the program BSL and XOTOKO can be used. The programs bsl_script and xotoko_script are specially developed for working with scripts as input. Selection of this toggle button results in the use of the programs bsl_script and xotoko_script instead of bsl and xotoko.

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Swap endian (toggle button), When performing binary I/O (Reading a data file, converting a datafile to another format, etc.), all multi-byte data has its byte ordering swapped. This is useful when accessing files also used by another system with byte ordering different than that of the acquisition host.

Display + Load data file (toggle button): When performing a 1D/2D BSL/XOTOKO-script (defined under the pull-down menu “1D DATA” or “2D DATA”) the selected data file will automatically be displayed.

Load data file (toggle button): When performing a 1D/2D BSL/XOTOKO-script (defined under the pull-down menu “1D DATA” or “2D DATA”) the selected data file will be automatically be loaded.

In the second window slot the following buttons are defined:

Data file: In order to display or to convert a XOTOKO / BSL file the file must be selected, this function is also defined under the pull-down menu “DISPLAY”.

X-axis file: selection of a x-axis file for a XOTOKO data file, this function is also defined under the pull-down menu “X-AXIS”.

Create: generate an x-axis calibration file for a XOTOKO data file, this function is also defined under the pull-down menu “X-AXIS”.

SAXS 2D: display SAXS – 2D data, this function is also defined under the pull-down menu

“DISPLAY”. SAXS 1D: display SAXS – 1D data, this function is also defined under the pull-down menu

“DISPLAY”. WAXS: display WAXS data, this function is also defined under the pull-down menu “DISPLAY”.

The right window slot describes the conversion from BSL/XOTOKO into other formats, also defined under the pull-down menu “CONVERT”. 5.2 FILE The “FILE” pull-down menu allows the following operations:

Select color table Select INPUT directory FILENAME info

File information: see appendix A. File information (long): see appendix A. Display LOG file: see appendix A.

Exit 5.2.1 Select color table Selection of the “Select color table” menu item causes the color interface to pop up. It displays the current color table and shows a list of available predefined color tables. Clicking on the name of one color table causes it to be loaded. Other options, such as Gamma correction, stretching etc. can also be applied to the selected color table. 5.2.1. Select INPUT directory The current directory is displayed in the upper window slot (see Figure 5-2) along with its sub-directories in the lower window slot. You can select a directory by clicking with the mouse on a subdirectory. This becomes the current directory and again its sub-directories are listed below it. Click on “..” to move up one level. A new current directory may be entered manually. The “Mkdir” button creates a new directory under the current directory. The “OK” button confirms the selection of a new directory.

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Fig 5-2: Select INPUT directory

5.3 DISPLAY (bsl/xotoko format only) The “DISPLAY” pull-down menu allows the following operations:

Select Data file, select a SAXS/WAXS data file (BSL – format only) SAXS –2D, display a two-dimensional SAXS data file. SAXS –1D, display a one-dimensional SAXS data file. WAXS, display a one-dimensional WAXS data file. CALIBRATION, display the calibration data, such as ion chambers. SAXS – 2D (video), display a two-dimensional SAXS data file, in video-mode Mirror, mirror a set of data.

5.3.1 Select data file (bsl/xotoko format only) Selection of the “Data file” button item causes the window in Figure 5-3 to appear.

Fig. 5.3 Selection of a XOTOKO / BSL Data file. (a = Image Viewer, b = WAXS 1D data, c = SAXS 2D data.

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The files in the current selected directory (see chapter 5.3) are displayed in the lower window slot. You can select a file by clicking with the mouse on a filename. This becomes the selected file, automatically one or more windows appears (see Fig. 5.3b and 5.3c). From the current selected XOTOKO/BSL file the first frame from the SAXS and WAXS data will be displayed (when exists). Only XOTOKO / BSL files can be selected. If you want to select the current data file, click on the “Select” button, in order to confirm the selection of a data file.

Fig 5-4: Data reduction interface after selection of a data file. The middle upper window slot is showing the information of the selected datafile. In this example (Fig 5-4) we loaded the datafile:A30000.C02, and this file consists of a three calabration frame and three saxs frames (2 dimension). 5.3.2. SAXS – 2D After the selection of a file (“DISPLAY”,”Select Data file”) it is possible to display the two dimensional SAXS data. Selection of the “SAXS 2D” menu item causes the SAXS offline window shown in Fig 5-5a to pop up. The following buttons allow the operations listed in the corresponding lines:

|< monitor the first frame < monitor the previous frame > monitor the next frame >| monitor the last frame Jump Jump to the requested frame (filled in the textfield Jump to frame) Read The new frame will not be automatically loaded (after |<,<,>,>|,Jump), but must be

manually loaded by this button.

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#Frames Total numbers of frames Display Frame Current frame in display Display Monitor switch key depending on the state of the measurement.

For example in the INIT state, it is not possible to monitor the data.

Fig 5-5: two dimensional SAXS data display (a =Main window, b =Print Window / PS, c = PS - window) The “FILE” pull down menu allows the following operations:

Print Window / PS: Selection of the “Print Window / PS” menu item causes a graphical window to pop up (Fig 5-5b). It is displaying the current selected frame. Selection of the “PostScript Output” menu item causes a configuration window for the PostScript printer to popup (Fig 5-5c).

Write GIF: the current displayed frame will be converted to a GIF – file (with the extension .gif). Write TIFF: the current displayed frame will be converted to a TIFF-file (with the extension: .tiff) Write JPG: the current displayed frame will be converted to a JPG-file (with the extension: .jpg) Open image display: opens the image display program (see chapter 2.6.2). The communication

between the control display written in IDL and the Image Display is realized by using a shared memory [16].

The “EDIT” pull down menu allows the following operation:

Select color table: Selection of the “Select color table” menu item causes the color interface to pop up. It displays the current color table and shows a list of available predefined color tables. Clicking on the name of one color table causes it to be loaded. Other options, such as Gamma correction, stretching etc. can also be applied to the selected color table.

The “DISPLAY” pull down menu allows the following operations:

Horizontal Display (scroll Y): Selection of this function item causes a graphical window to pop up. The interface is similar as the interface for one dimensional data (see chapter 5.3.3), but in this the program is scrolling through the Y values in stead of scrolling through the frames.

Vertical Display (scroll X): Selection of this function item causes a graphical window to pop up. The interface is similar as the interface for one dimensional data (see chapter 5.3.3), but in this the program is scrolling through the X values in stead of scrolling through the frames.

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The “BSL” pull down menu allows the following operations:

SEC: Perform a sector integration. After the integration is succeed, a new window is displaying the SAXS one dimensional data.

HOR: Perform a horizontal integration. After the integration is succeed, a new window is displaying the SAXS one dimensional data.

VER: Perform a vertical integration. After the integration is succeed, a new window is displaying the SAXS one dimensional data.

5.3.3. SAXS – 1D After the selection of a file (“DISPLAY”,”Select Data file”) it is possible to display the one dimensional SAXS data. Selection of the “SAXS 1D” menu item causes the SAXS offline window shown in Fig 5-6a or Fig 5-6b to pop up.

Fig 5-6: one dimensional SAXS data display (a=SAXSGUI display, b= XOP) The SAXS 1D data can be displayed in two different ways. The first possibility is to display the data in a similar way as the acquisition or inside the program XOP [15]. This is performed by the “Use Xplot” – toggle button in the main – window. This manual is describing the selection of the normal display. (Fig 5-6a) The “PLOT” pull-down menu allows the following operations:

Set display options: Different display options such as: logarithm scale, limits, single frame / multiple frames.

The following buttons (around the plot-area) allow the following operations: Frames:


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Plot: < move x 10 units to the left > move x 10 units to the right Full Full screen Replot Replot the diagram


#Frames Total numbers of frames Frame Current frame

5.3.3. WAXS

Fig 5-7: one dimensional WAXS data display (Graphical User Interface) After the selection of a file (“DISPLAY”,”Select Data file”) it is possible to display the two dimensional SAXS data. Selection of the “WAXS 1D” menu item causes the WAXS offline window shown in Fig 5-7 to pop up. The “PLOT” pull down menu allows the following operations:

Set display options Display real/coincidence data

The “CALIBRATION” pull down menu allows the following operation:

Display (current) frame. A new window is pop-up containing the current frame in floating –values. 5.3.3.1 Set display options Selection of the “Set display options” menu item causes the window in Figure 5-8 to appear.

37

Here follows a list of the options implemented and their function.

Logarithmic Y-axis: setting this option causes the Y-axis to be displayed in logarithmic scale. Use the minimum and maximum values: setting this option causes the minimum and maximum values

to be used while plotting the data. Data points below the minimum or above the maximum will be left out of the plot. Minimum and maximum for the real and virtual channels can be set separately.

Auto-display incoming frames: when set, any new incoming frame will be displayed directly. Select channel number range: normally the full detector is shown. It is however possible to see only a

part of the detector. The chosen range can be entered either by typing or by selecting a region pressing a mouse button at the beginning of the selection and moving the pointer to the end of the selection and then release the button.

It is possible to view multiple frames in one window. The user can select a range of frames to be displayed. The program returns automatically to the single frame mode, when only one frame is active. An example of both modes is shown in Figure 5-9 and 5-10.

Fig 5-8: Set display options

Fig 5-9. Single frame mode. Fig 5-10 . Multiple frames mode.

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5.3.3.2 Display real/coincidence data At present, only one real manipulation routine is implemented. This routine is the coincidence compensation. As mentioned before there are 1024 physical and 1024 virtual (or coincidence) channels. The counters belonging to the virtual channels register one event when both neighbouring physical channels are activated at the same time. To compensate this double counting for the virtual counts are subtracted from the counts registered by the neighbouring physical channels. Table II describes the operation done by the routine. On each line the channel number is stated first. All the real channels have even numbers whereas the odd numbers are assigned to the virtual channels. The calculation is straightforward. The only problems are at the edges of the array. At the top of the array only one virtual channel has to be subtracted. At the bottom of the array the last element that needs to be calculated is the element with index 2046. To be more specific:

S0000 = S0000 - S0001 (physical) S0001 = S0001 (virtual) S0002 = S0002 - S0003 - S0001 (physical) S0003 = S0003 (virtual) S0004 = S0004 - S0005 - S0003 (physical) S0005 = S0005 (virtual) S0006 = S0006 - S0007 - S0005 (physical) : : : : S2044 = S2044 - S2045 - S2043 (physical) S2045 = S2045 (virtual) S2046 = S2046 - S2047 - S2045 (physical) S2047 = 0 No useful information

Table II: Compensation of coincidence data Selection of the “Display real/coincidence data” menu item causes the window in Figure 5-11 to appear.

Fig 5-11: Display real/coincidence data Here follows a list of the options implemented and their function.

Compensate for coincidence: when this option is set the virtual channels are subtracted from the real channels.

Show GPIM data: when set, a window pops up with the GPIM data displayed. Equal scale for coincidence: when set, the coincidence window uses the same scale as the real

channels.

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Separate coincidence: setting this option causes the real and virtual channels to be shown in separate windows.

Compensate dead channels. The compensation of dead channels is done by reading the file : $IDL_PATH/detector/dead.channels. This file contains dead channels and the channel number for compensations.

5.3.4. CALIBRATION Selection of the “CALIBRATION” menu item causes the window in Figure 5-12 to appear, containing the calibration values, sorted by frame number.

Fig 5-12: Calibration values Fig 5-13: SAXS-2D (video) 5.3.5. SAXS – 2D (video) Selection of the “SAXS – 2D (video)” menu item causes the window in Figure 5-13 to appear, displaying all the frames in video mode. 5.3.6. Mirror Selection of the “Mirror” menu item will mirror the image (only possible with one dimensional images). The grapical user interface is executing the command: “.MIR” under XOTOKO. This function is relevant for converting one dimensional data into PDH and GNOM format (see chapter 5.7).

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5.4 X-AXIS (xotoko format only) The “DISPLAY” pull-down menu allows the following operations:

Select X-AXIS file, select a X-AXIS data file (XOTOKO – format only). Create X-AXIS, create a X-AXIS file. Display X-AXIS, display the selected X-AXIS file (same structure as SAXS-1D display).

q-axis calibration procedure using BSL and XOTOKO The most cumbersome case is when the a pattern has to be calibrated that is obtained with a two dimensional pattern. This procedure is outlined below. Step 1 Display the pattern that needs to be calibrated (.DIS) and determine the thresholds that are necessary to bring out the diffraction features that one is interested in but especially make sure that the beamstop is properly displayed.

1

512

5121

pixel

pixel

Figure 1 Step 2 Perform a .VER procedure over the indicated strip with cursor selection option. Note down the values over which the integration procedure is performed. Then repeat the .VER but now making sure that the integration is performed over the full pixel range 1-512 in the horizontal direction. (This often does not happen when using the cursor option). Safe file.

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1

512

5121

pixel

pixel

Figure 2 Step 3 Perform a .HOR procedure over the indicated strip with cursor selection option. Note down the values over which the integration procedure is performed. Then repeat the .HOR but now making sure that the integration is performed over the full pixel range 1-512 in the vertical direction. Safe file.

1

512

5121

pixel

pixel

Figure 3 Now you have two files readable in XOTOKO. Repeat step 2 and 3 with the pattern of a calibration sample. This can be a rat tail pattern or a silver behenate sample. When reducing data obtained with a 1-dimensional detector the preceding steps can not be performed and one only has to follow the rest of the procedure. Start up XOTOKO. Display the first rat tail file (.PLO with diamond option and possibly zooming in to enlarge specific ranges) and determine which pixel number corresponds to which q-value of the rat tail peak. If one needs a more accurate determination one can take all these pairs of values and perform a linear regression on these pairs. Now one has a function which correlates pixel number with q-value. With the function .XAX one can create a file which correlates the pixel number with the correct q-values. All the options in XOTOKO in which this axis can be used are preceded with an *. So the function *PLO asks for the x-axis file and then for the intensity file and displays this function. This q-axis file can be used for the actual data.

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Some examples of calibration patterns

1000

104

105

106

107

0 0.05 0.1 0.15 0.2 0.25

Calibration of SAXS detector using oriented hydrated collagen fibres (rat tail tendon)

primary spacing 672 ± 5 Å

Inte

nsity

1

2

3

q ( Å-1)

4

5

6 78

9

10 11 12

14 20 2115 17 18

d-value of n th order diffraction peakd = 672 / n (Å)

q-value of n th order diffraction peakq = n x (2 π / 672) (Å -1)

The wet rat tail pattern is one of the most used patterns for low angle calibrations since the peaks are quite sharp and the diffraction orders easily recognisable. The peaks 1, 3, 5, 9, 12 and 20, 21, 22 are relatively strong.

5.4.2. Select X-AXIS file (q-axis) Selection of the “Select X-AXIS file” button item causes the window in Figure 5-14 to appear.

Fig. 5.14 Selection of a XOTOKO file with X-AXIS data. The files in the current selected directory (see chapter 5.5) are displayed in the lower window slot. You can select a file by clicking with the mouse on a filename. This becomes the selected file. If you want to select the current data file, click on the “Select” button, in order to confirm the selection of a data file.

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5.4.1. Create X-AXIS (q-axis) This button is only used, when you did select a one dimension SAXS file (“DISPLAY”,”Select Datafile”). The raw SAXS 1D data in an XOTOKO fileset, doesn’t have an q-axis. In order to convert this SAXS file into GNOM or PDH it is necessary to have an q-axis. Given the channel numbers and q values of 2 positions, it is possible to generate an x-axis calibration file using .XAX command in XOTOKO. It is conventional to use the same output file number for the data file and its associated .xax file.

Fig. 5.15 Interface to create an X-axis file. Selection of the “Create X-AXIS” button causes the window in Figure 5-15 to appear.

The following fields are defined:

First and last channels of output Channel number and q-value. Channel number and q-value.

5.5 2D - DATA The “2D - DATA” pull-down menu allows the following operations:

BSL: This function spawns a child process to execute the program BSL. DIN, a script for using the BSL command “DIN” ADD, a script for using the BSL command “ADD” DIV, a script for using the BSL command “DIV” VER, a script for using the BSL command “VER” HOR, a script for using the BSL command “HOR” SEC, a script for using the BSL command “SEC”

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5.5.1. DIN: Divide and normalise image using a calibration file

Normalisation with 1D and 2D detectors using ion chambers (XOTOKO) We assume that the time-integrated ionisation chamber readings are stored in the first two channels of the calibration file Ann002.ext. (Always check this) Now use the procedure .DIN, both in BSL and XOTOKO. This first asks for the calibration file. Answer Ann002.ext. Then it asks for the frame. Answer 2 for the second ion chamber. Then it asks for the data frame. Answer Ann000.ext. Asks data or calibration. Reply data. Asks for output file. Answer Ann00).DIN. This is now the same file as before but all the pixels in all the time frames are divided by the corresponding ionisation chamber readings.

Normalisation with 2D detectors and semi-transparent beamstop (XOTOKO) When using area detectors a more accurate way to determine the transmitted intensity is by using the detector and a semi transparent beamstop. An enlarged part of the pattern is shown below in the first figure. With the routines .VER and .HOR and using XOTOKO one can determine the extent of the beam profile in pixel values. Then define a box around the beam profile and make sure that the whole beam is included. See the second figure.

Back into BSL. Use the routine .INT. This gives the options of using cursor selection or defining the pixels. Use the latter option. Give output file the name Xnn000.NOR. This is a one dimensional XOTOKO file that contains the integrated value over the beam profile of all time frames. Then use option .DIN. Asked for calibration file reply Xnn000.NOR. Calibration or data? Reply data. Asked for data file. Reply Ann000.EXT. Asked for output. Reply Ann000.DIN. Ready.

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Selection of the “DIN” button causes the window in Figure 5-16 to appear.

Fig 5-16: DIN Script Interface The following fields are defined:

Calibration files: The name of the calibration file (headername). Input files 2: The name of the raw data file (headername) INPUT[1]:[first,last,step]-Frame (Calibration file)

In this case 2, in order to normalise on the second ion – chamber. INPUT[2]:[first,last,step]-Frame (Raw data file)

Definition of the used frames. First frame, last frame and incremental frame-value. INPUT[2]:[x1 x2 y1 y2] – matrix (Raw data file – maxtrix)

Selection of the matrix- area (mostly x1=1, x2=512, y1=1, y2=512) Select all frames (toggle button)

This button is overrouling the selection of the number of frames. Selection of this toggle button performs a normalisation of all the frames inside the choosen file(s). This functions is very useful in case to normalise all files with different number of frames.

The following buttons are defined:

File 1 & 2: Selection of the (two) data files. The first input file is the calibration file. The second input file is the data file. It is possible to select these files, by selection the common header file.

Run: Running the script using BSL. If the button “Use Script” (main window) is selected than the script will run using bsl_script, ontherwise the script will run using bsl. The user has the possibility to run the script in background, otherwise the progam will wait.

Exit

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Filename [A-Z]* (under “Select”). Selection of more filenames. Selection of the “Filename [A-Z]*” button causes the window in Figure 5-17 to appear.

Fig 5-17: Select all filenames [a-z]*

The prefix for output file names must be chosen out of the 26 alphabet letters. Secondly the data extensions (see chapter 2.3.4) must be typed in. All files under the directory (“FILE”,”Select INPUT directory”) with the mask [LETTER]??00.[EXTENSION], will be selected.

Files with mask (under “Select”): Selection of more filenames. Selection of the “Files with mask” button causes the window in Figure 5-18 to appear.

Fig 5-18: Select all files with mask All files under the directory (“FILE”,”Select INPUT directory”) with the mask typed in by the user, will be selected.

Range of files (under “Select”): Selection of more filenames. Selection of the “Range of files*”

button causes the window in Figure 5-19 to appear.

Fig 5-19: Select range of files

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.DIN: Devide and normalise image using a calibration file (inside BSL) *Enter instruction: .din Calibration file(s) Enter filename (X99999.xxx[/]) or <ctrl-D>: A30000.C02 Enter [1] positional, [2] calibration data or aux [3] [1]: 2 Total number of frames: 6 Enter first and last frame, increment or <ctrl-D>: 2 Memory 2 first and last frame 2 2 incr 0 Enter filename (X99999.xxx[/]) or <ctrl-D>: A30000.C02 Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 3 Enter first and last frame, increment or <ctrl-D>: 1 3 1 Memory 1 first and last frame 1 3 incr 1 Enter first & last pixels and first & last rasters or <CTRL-D> [1, 512,1, 512]: Using normalisation value 3030686. Enter output filename [Xnn000.xxx]: A30000.DIN Enter first header: Enter second header: Using normalisation value 3647718. Using normalisation value 4006602.

5.5.2. ADD: Background subtraction

Background subtraction Use XOTOKO for 1-D data and BSL for 2-D data. The rest of the procedure is the same. Assume data to be in Ann000.DIN and background in Azz000.DIN. The background can be either a time frame series of the same length as the data or a single frame. Use routine .ADD. First reply Ann000.DIN then reply Azz000.DIN. The weight of the files should be 1 and -1 respectively. Output file Ann000.SUB. Ready. Off course this does not always work perfectly and sometimes one has to subtract less background to prevent the high q-values from dropping below zero. If this is much more than 95% then something is wrong and one has to trouble shoot. What the cause is one has to determine on a case to case basis.1

Selection of the “ADD” button causes the interface window for performing the background subtraction. This interface is almost the same as the interface for the “DIN” – function (chapter 5.5.1), so no further explanation is needed. ADD: Background subtraction (inside BSL)

*Enter instruction: .add Enter filename (X99999.xxx[/]) or <ctrl-D>: A30000.DIN Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 3 Enter first and last frame, increment or <ctrl-D>: 1 3 1 Memory 1 first and last frame 1 3 incr 1 Enter filename (X99999.xxx[/]) or <ctrl-D>: B00000.918 Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Memory 1 first and last frame 1 1 incr 0 Do you want the same constants for all for all spectra [Y/N] [Y]: Y Do you want to zero negative values (Y/N) [N]: N Enter weights of first & second spectrum [1.0,1.0]: 1.0 -1.0 Enter output filename [Xnn000.xxx]: A30000.ADD

1 Copied from the station manual BM26b

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Enter first header: Enter second header:

5.5.3. DIV: Divde by detector response

Division by detector response Most detectors don’t have a uniform pixel sensitivity. To compensate for this effect one has to divide the background subtracted patterns by a detector response or, alternatively named, flood field pattern. This detector response ideally should be taken with the same X-ray energy as the scattering patterns since detectors have a different response to different energies. However, if the energy difference is not too large one can use a radioactive source to obtain the flood field. This source should be placed at such a distance from the detector so that the detector is more or less uniformly illuminated and should have the same or, preferably, better statistics than the scattering patterns. Let’s give this file the name Dnn000. EXT. Then the following mathematical procedure should be followed:

Is ( x ,y , t ) = Isnb ( x, y, t )

D( x, y )

In which Isnb is the normalised and background subtracted series of time frames and Is the series of time frames that one would like to obtain. In practice use routine .DIV. Asked for data file. Reply Ann000.SUB. Asked for division file Dnn000.EXT. One can give weights to the different files. This doesn’t change anything but one should always use the same values over all the different experiments since otherwise they are not comparable anymore. Quite often giving weights is useful since the division by the ion chamber readings lead to small numbers per pixel and the subsequent subtraction and divisions make these numbers even smaller. Personally I find values between 1 and 105 more easy to deal with than values between 1 and 10-5. But that is a personal taste. Close to the beamstop, or any other step function like feature, this method can break down unless one uses very low count rates. Detectors simply don’t like step functions.

Selection of the “DIV” button causes the interface window for performing the division by the detector response. This interface is almost the same as the interface for the “DIN” – function (chapter 5.5.1), so no further explanation is needed.

DIV: Divide by detector response (inside BSL)

*Enter instruction: .div Enter filename (X99999.xxx[/]) or <ctrl-D>: A30000.ADD Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 3 Enter first and last frame, increment or <ctrl-D>: 1 3 1 Memory 1 first and last frame 1 3 incr 1 Enter filename (X99999.xxx[/]) or <ctrl-D>: D00000.918 Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Memory 1 first and last frame 1 1 incr 0 Do you want the same constants for all for all spectra [Y/N] [Y]: Do you want to zero negative values (Y/N) [N]: Enter weights of first & second spectrum [1.0,1.0]: Enter output filename [Xnn000.xxx]: A30000.DIV Enter first header: Enter second header:

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5.5.4. VER: Perform a vertical integration Selection of the “VER” button causes the interface window for performing a vertical integration. This interface is almost the same as the interface for the “DIN” – function (chapter 5.5.1), so no further explanation is needed. VER: Perform a vertical integration (inside BSL), see Fig. 5-20

*Enter instruction: .ver Enter filename (X99999.xxx[/]) or <ctrl-D>: A30000.DIN Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 3 Enter first and last frame, increment or <ctrl-D>: 1 3 1 Memory 1 first and last frame 1 3 incr 1 Do you want to use cursor selection [Y/N] [N]: n Enter first & last pixels and first & last rasters or <CTRL-D> [1, 512,1, 512]: 1 512 300 400 Do you want to include mirrored section [Y/N] [N]: Do you want to display plot [Y/N] [Y]: n Enter output filename [Xnn000.xxx]: A30000.VER Enter first header: Enter second header :

Definition of raster and pixel used in BSL and XOTOKO: First & last pixels = X1 and X2 First & last rasters = Y1 and Y2

1

512

5121

pixel

pixel

Fig 5-20: Vertical integration

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5.5.5. HOR: Perform a horizontal integration Selection of the “HOR” button causes the interface window for performing a horizontal integration. This interface is almost the same as the interface for the “DIN” – function (chapter 5.5.1), so no further explanation is needed. HOR: Perform a horizontal integration (inside BSL), see Fig 5-21

*Enter instruction: .hor Enter filename (X99999.xxx[/]) or <ctrl-D>: A30000.DIN Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 3 Enter first and last frame, increment or <ctrl-D>: 1 3 1 Memory 1 first and last frame 1 3 incr 1 Do you want to use cursor selection [Y/N] [N]: n Enter first & last pixels and first & last rasters or <CTRL-D> [1, 512,1, 512]: 240 280 1 512 Do you want to include mirrored section [Y/N] [N]: Do you want to display plot [Y/N] [Y]: n Enter output filename [Xnn000.xxx]: A30000.HOR Enter first header: Enter second header: Enter filename (X99999.xxx[/]) or <ctrl-D>:

1

512

5121

pixel

pixel

Fig 5-21: Horizontal integration

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5.5.6. SEC: Perform a vertical integration

Selection of the “SEC” button causes the interface window for performing a sector integration. This interface is almost the same as the interface for the “DIN” – function (chapter 5.5.1), so no further explanation is needed. SEC: Perform a vertical integration (inside BSL), see Fig 5-22

*Enter instruction: .sec Enter filename (X99999.xxx[/]) or <ctrl-D>: A30000.DIN Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 3 Enter first and last frame, increment or <ctrl-D>: 1 3 1 Memory 1 first and last frame 1 3 incr 1 Do you want fixed centre, starting & final angles, radius & width [Y/N] [N]: y Enter (x,y) coordinates of centre, start angle, final angle, radius and width [ 256, 256, 0, 360, 128, 64]: 256 256 60 120 10 210 Average the integrated data [y/n] [y]: Do you want to include mirrored section [Y/N] [Y]: n Enter output filename [Xnn000.xxx]: A30000.SEC Enter first header: Enter second header:

Fig 5-22: Sector integration

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5.6 1D - DATA The “1D - DATA” pull-down menu allows the following operations:

XOTOKO: This function spawns a child process to execute the program XOTOKO. DIN, a script for using the XOTOKO command “DIN” ADD, a script for using the XOTOKO command “ADD” DIV, a script for using the XOTOKO command “DIV”

5.6.1. DIN: Divide and normalise image usign a calibration file Selection of the “DIN” button causes the interface window for performing a normalization using a calibration file. This interface is almost the same as the interface for the “DIN” – function (chapter 5.5.1), so no further explanation is needed. All channels in the ith frame of the input sequence are divided by the value of the constant in the ith channel of the calibration file. .DIN: Divide and normalise image usign a calibration file (inside XOTOKO)

*Enter instruction: .din Calibration file(s) Enter filename (X99999.xxx[/]) or <ctrl-D>: A85000.220 Enter [1] positional, [2] calibration data or aux [3] [1]: 2 Total number of frames: 6 Enter first and last frame, increment or <ctrl-D>: 2 Memory 2 first and last frame 2 2 incr 0 Enter filename (X99999.xxx[/]) or <ctrl-D>: A85000.220 Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 24 Enter first and last frame, increment or <ctrl-D>: 1 24 1 Memory 1 first and last frame 1 24 incr 1 Enter first and last channels of output [1,2048]: Enter output filename [Xnn000.xxx]: A85000.DIN Enter first header: Enter second header:

5.6.2. ADD: Background subtraction

Selection of the “ADD” button causes the interface window for performing background subtraction. This interface is almost the same as the interface for the “DIN” – function (chapter 5.5.1), so no further explanation is needed.

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ADD: Background subtraction (inside XOTOKO) *Enter instruction: .add Enter filename (X99999.xxx[/]) or <ctrl-D>: A85000.DIN Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 24 Enter first and last frame, increment or <ctrl-D>: 1 24 1 Memory 1 first and last frame 1 24 incr 1 Enter filename (X99999.xxx[/]) or <ctrl-D>: B00000.218 Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Memory 1 first and last frame 1 1 incr 0 Do you want the same constants for all for all spectra [Y/N] [Y]: Enter weights of first & second spectrum [1.0,1.0]: 1.0 -1.0 Enter output filename [Xnn000.xxx]: A85000.ADD Enter first header: Enter second header:

5.6.3. DIV: Divide by detector response

Selection of the “DIV” button causes the interface window for performing a division by detector response. This interface is almost the same as the interface for the “DIN” – function (chapter 5.5.1), so no further explanation is needed. DIV: Divide by detector response

*Enter instruction: .div Enter filename (X99999.xxx[/]) or <ctrl-D>: A85000.220 Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Total number of frames: 24 Enter first and last frame, increment or <ctrl-D>: 1 24 1 Memory 1 first and last frame 1 24 incr 1 Enter filename (X99999.xxx[/]) or <ctrl-D>: D00000.218 Enter [1] positional, [2] calibration data or aux [3] [1]: 1 Memory 1 first and last frame 1 1 incr 0 Do you want the same constants for all for all spectra [Y/N] [Y]: Enter weights of first & second spectrum [1.0,1.0]: Enter output filename [Xnn000.xxx]: A85000.DIV Enter first header: Enter second header:

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5.7 EDF (ESRF Data Format) The “EDF” pull-down menu allows the following operations:

EDF – GUI, a graphical user interface for data reduction using the EDF format [27] EDF data reduction programs, a list of “EDF” – commands.

Before explaining the graphical user interface for the EDF Data File Format. It is necessary to give a small introduction to this file format. This File Format is developed at the ESRF. The data file has a logical structure, which is described as follow: a Global Header Section that describes the properties belonging to all data within the file and a number of Data Blocks, each with it’s own Header Section that describes properties local to this particular Data Section, these local values will displace any global value in the Global Header Section. 5.7.1. EDF – GUI Fig. 5-23 displays the main window of the EDF sub-menu. Pressing the different buttons in the window causes the parameter entry sub-window to appear on the screen (see next sections). The template in each sub-window varies according to the program to be executed. The buttons in this window are non-exclusive. More than one button can be pressed at the same time, indicating that as many programs shall be run. All variables are assigned a default value. Once their values are set, they can be stored in a user defined file by clicking on the ‘Save’ button of the window. The ‘Load’ button serves the purpose of loading the parameter settings previously saved. With the ‘Done’ button one quits the interface, whereas via the ‘RUN’ button one executes the selected programs. Fig 23b displays the data file selection window.

Fig 5-23a EDF – Graphical User Interface Fig 5-23b Read a EDF-file

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5.7.1.1. saxs_normn Fig. 5-24a shows the ‘saxs_normn’ main window. The related program performs the normalization of an image sequence to absolute intensities by using a flat field image (‘Flatfield’). The buttons ‘Done’, ‘Help’ and ‘Run’ work in the same way as described before. By clicking on the ‘Browse’ buttons the window in Fig. 5-23b is popped up and any of the EDF files present in the current directory can be selected. In the ‘Scaler Monitor’ entry field the user defines the number of the scaler module providing the experimental parameter values needed for a correct normalization (default = 1). Fig. 2b shows the ‘options’ window which is a child of the ‘saxs_normn’ main window, obtained by clicking on the ‘Options’ button of the ‘saxs_normn’ main window: i1cen and i1cen2 are the x and y coordinates of the image center (in pixels), respectively opix1 and opix2 are the detector pixel dimensions in x- and y-direction, respectively i1fst and i1lst are the first and last frame number, respectively, to be processed.

Fig 5-24: normalization interface 5.7.1.2. saxs_add Fig. 5-25a shows the ‘saxs_add’ main window. The related program adds two image sequences, or, more generally performs the linear combination of two sequences of images illustrated in the header line of the window. The buttons ‘Done’, ‘Help’ and ‘Run’ work in the same way as described before. By clicking on the ‘Browse’ buttons the window in Fig. 5-23b pops up and any of the EDF files in the current directory can be selected. The data entry fields are self-explanatory. Fig. 5-25b shows the ‘options’ window which is a child of the ‘saxs_add’ main window, obtained by clicking on the ‘Options’ button of the ‘saxs_add’ main window: i1inc is the increment of the input frame sequences the meaning of i1con, i2con and ofac is perspicuous odum is the dummy value of each image (e.g. odum = -1 sets the output dummy value to –1)

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Fig 5-25: Add – interface 5.7.1.3. saxs_sub

Fig 5-26: SUB – interface Fig. 26a shows the ‘saxs_sub’ main window. The related program subtracts two image sequences, or, more generally performs the linear combination of two sequences of images illustrated in the header line of the window. The buttons ‘Done’, ‘Help’ and ‘Run’ work in the same way as described before. By clicking on the ‘Browse’ buttons the window in Fig. 5-23b pops up and any of the EDF files in the current directory can be selected. The data entry fields are the same as saxs_add. Fig. 5-26b shows the ‘options’ window which is a child of the ‘saxs_sub’ main window, obtained by clicking on the ‘Options’ button of the ‘saxs_sub’ main window. saxs_sub uses the same parameters as saxs_add and differs from it just only by the sign of the factor fac2.

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5.7.1.4. saxs_angle Fig. 5-27a shows the ‘saxs_angle’ main window. The related program transforms data from cartesian (qx,qy) coordinates into polar (qr,qθ) coordinates by pixel interpolation and azimuthal averaging. The buttons ‘Done’, ‘Help’ and ‘Run’ work in the same way as described before. By clicking on the ‘Browse’ buttons the window in Fig. 5-23b pops up and any of the EDF files in the current directory can be selected. Fig. 5-27b shows the ‘options’ window which is a child of the ‘saxs_angle’ main window, obtained by clicking on the ‘Options’ button of the ‘saxs_angle’ main window: rsys defines the reference system. saxs_angle uses by default the real reference system (offset, pixel size) r0 is the minimum radius [pixel]. The default is 0.0 a0 is the azimuthal start angle [deg]. The default is 0.0 odim1 is the radial interval [pixel]. The default value corresponds to 1 pixel odim2 is the azimuthal interval [deg]. The default is 1.0 deg

Fig 5-27: ANGLE– interface 5.7.1.5. saxs_row Fig. 5-28 shows the ‘saxs_row’ main window. The related program carries out the projection of a horizontal band in a sequence of images onto one single row (qr). The projection extends from row number ‘Row1’ to row number ‘Row2’ (s. the corresponding entry fields in the window). The output row is written to a line of the output image. The buttons ‘Done’, ‘Help’ and ‘Run’ work in the same way as described before. By clicking on the ‘Browse’ button the window in Fig. 5-23b pops up and any of the EDF files in the current directory can be selected. This window has no child window.

Fig 5-28: ROW– interface

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5.7.1.4. saxs_col Fig. 5-29 shows the ‘saxs_col’ main window. The related program carries out the projection of a vertical band in a sequence of images onto one single column (qθ). The projection extends from column number ‘Column1’ to column number ‘Column2’ (s. the corresponding entry fields in the window). The output column is swapped to a line and written out in the output image. The buttons ‘Done’, ‘Help’ and ‘Run’ work in the same way as described before. By clicking on the ‘Browse’ button the window in Fig. 5-23b pops up and any of the EDF files in the current directory can be selected. This window has no child window.

Fig 5-29:COL– interface 5.7.1.4. saxs_ascii Fig. 5-30 shows the ‘saxs_ascii’ main window. The related program transforms an EDF binary file into an ASCII format file. The buttons ‘Done’, ‘Help’ and ‘Run’ work in the same way as described before. By clicking on the ‘Browse’ button the window in Fig. 5-23b pops up and any of the EDF files in the current directory can be selected. The following parameters can be set by the user: rsys defines the reference system. saxs_ascii uses by default the saxs reference system. swap enables/disables swap of rows and lines This window has no child window

Fig 5-30:ASCII– interface

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5.7 CONVERT The “CONVERT” pull-down menu allows the following operations:

XOTOKO + X-AXIS --> GNOM XOTOKO + X-AXIS --> PDH XOTOKO ---> ASCII: This function spawns a child process to execute the program reconv2 [26], to

convert a XOTOKO data file into ASCII. The program otcon can be used to convert an ASCII Data File into BSL.

BSL ---> NEXUS BSL ---> EDF: This function spawns a child process to execute the program binary2saxs [27], to

convert a BSL data file into EDF. BSL ---> ILL

EDF ---> BSL: This function spawns a child process to execute the program saxs2bsl [27], to convert a

EDF data file into BSL

RAW DATA ---> BSL: Some conversions from “raw” – acquisition data into BSL

SWAP BSL / XOTOKO: This function reverses the byte ordering of the binary saxs data. It can make “big endian” number “litte endian” and vica versa. Conversion of the file A0000.208 (header) and A0001.208 (binary) results in the following files: A0000.208, A0001.208.org and A00001.208.

We tried to offer the most common conversions from one data format into the other. If you would like to have another conversion, let me know. 5.7.1 XOTOKO + X-AXIS --> GNOM Before describing the conversion into the data format GNOM [20], it is necessary to explain the structure of this data format. Table III is displaying a small part of a gnom data file. A gnom data file normally has the extension .DAT. The file is readable ASCII. The first n lines (where n is undefined) are used for comments. GNOM automatically recognize the real data. There exists three data columns, the first data column are the q-values, the second columns are the I(q) scattering intensity at q and the third column (which is not necessary !) are the error margins. comment 1 ... comment n-1 comment n .5000E-02 .3317E+06 .1637E+05 .6000E-02 .3075E+06 .1598E+05 .7000E-02 .3064E+06 .1553E+05 Table III: GNOM – data file After selection of the datafile (“DISPLAY”,”Select data file”) and the X-axis file (“X-AXIS”, ”Select X-axis”) it is possible to create a GNOM data file, just by selection of the “GNOM” button. The graphical user interface is creating a GNOM – file without error margins (just two columns of data) Selection of the “GNOM” button causes the following windows to appear sequential Fig 5-31 a,b

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Fig 5-31: GNOM – interface windows After the selection of the wanted frame number, the graphical user interface displays the data before it creates the GNOM Data file. When the original XOTOKO data file has the name: A0000.208. The GNOM Data file that will be created has the name: A0000.DAT. 5.7.2 XOTOKO + X-AXIS --> PDH Before describing the conversion into the data format PDH [21]. It is necessary to explain this data format. Table IV is displaying the first part of a PDH Data File Format. 15% P94 40°C, ES=60, 2K, 5x15000s, 28.-29.11.97 SAXS 400 0 0 0 0 0 0 0 1.500000E+02 2.160000E+01 2.500000E-01 1.000000E+00 1.540000E-01 4.000000E+01 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 1.236000E-02 1.189373E+01 -1.000000E+00 1.854000E-02 2.961453E+01 -1.000000E+00 2.472000E-02 3.615193E+01 -1.000000E+00 3.090000E-02 3.748373E+01 -1.000000E+00 3.708000E-02 2.479953E+01 -1.000000E+00 4.326000E-02 1.483060E+01 -1.000000E+00 4.944000E-02 1.067407E+01 -1.000000E+00 5.562000E-02 8.924200E+00 -1.000000E+00 6.180000E-02 7.949867E+00 -1.000000E+00 6.798000E-02 7.383533E+00 -1.000000E+00 Table IV: PDH – data format The PDH Data File Format consists of the following lines: Line 1: ASCII string up to 80 characters, Format (A80) not interpreted, used for problem description. Line 2: Keywords, Format (16(A4,1X)), sequence of characters to define type of experiment.

KW1 : SAXS defines small angle x-ray data

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All other keywords are unused and free for your special use. Line 3: Integer Constants I(1) - I(8), Format (8(I9,1X)) I(1): Number of data points in this file

All other constants are unused and free for your special use. Line 4: Real Constants R(1) - R(10), Format (10(E14.6,1X)) R(1): Concentration [mg/mL]

R(2): for SAXS data: distance sample to detector [cm] R(3): for SAXS data: Gamma, ratio Kβ to Kα radiation

R(4): normalization factor, default: 1.0 R(5): wavelength [nm] Line 5: R(6): temperature [°C]

All other constants are unused and free for your special use. Line 6 – Line I(1)+6: data lines, x, y, sigma, Format (3(E14.6,1X))

x: q-value y: I(q) scattering intensity at q

sigma : sigma(q) standard deviation of I(q) (if unknown use sigma(q)=-1 like in the case of exact functions)

Additional lines are possible and free for your special use. Selection of the “PDH” button causes the following windows to appear sequential Fig 5-32 a,b,c.

Fig 5-32 a,b,c : PDH interface windows After the selection of the wanted frame number (Fig 5-32b) and the external data information (Fig 5-32a), the graphical user interface displays the data (Fig 5-32c) before it creates the PDH Data file. The third column is created by using counter statistics error bars. When the original XOTOKO data file has the name: A0000.208. The PDH Data file that will be created has the name: A0000.PRI.

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5.7.3 BSL ---> NEXUS Nexus is based on the Hierararchical Data Format (HDF). This data format is a multi-object file format that facilitates the transfer of various types of data between machines and operating systems. HDF is a product of the National Center for Supercomputing Applications (NCSA). HDF is designed to be flexible, portable, self-describing and easily extensible for future enhancements or compatibility with other standard formats. Selection of the “BSL --> NEXUS” button causes the creating of a Nexus data file. When the original XOTOKO/BSL data file has the name: A0000.208. The Nexus data file will have the name: A0000.HDF. 5.7.4 TRANSFORM (Open a binary data file) In this chapter we describes how to open a BSL/XOTOKO data file in the commercial program TRANSFORM [31] which is running under Windows, see Fig 5-33.

Fig 5-33: Transform In the most commercial packages it is possible to open a binary data file. In this case select directly the Binary data file (for example: A00001.920: SAXS Binary data file). Secondly fill in the size of the data file (for example: 512 x 512) and the Data Type. The BSL binary data file format is: IEEE Float. Don’t forget to swap the byte order, in case the data is produced on a machine with different endian Format. TRANSFORM also has the possible to open a Nexus data file.

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5.7.4 EXCEL / Kaleida Graph (Open an ASCII data file) In this chapter we describes how to open a ASCII data file in the commercial program EXCEL.

Fig. 5-34: EXCEL: Open ASCII data file The Gnom data file format and the PDH data file format described in chapter 5.72. and 5.7.3 are ASCII. We load these files into EXCEL, by selection of the button “FILE”/”OPEN”. After selection of the data file (Fig 5-34a), EXCEL is asked the exact layout of the data file (Fig 5-34b). The first lines in a Gnom or PDH data file must be skipped (Start import at row). The file origin is Windows (ANSI).

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In the same way it is possible to read an ASCII File Format into Kaleida Graph (Fig 3-35)

Fig 3-35: Kaleida Graph 5.7.4 FIT2D (Open a BSL data file) It is possible to read a BSL data file into FIT2D [32], following the following recipes:

Click on: “KEYBOARD INTERFACE” COMMANDS Main menu: ENTER COMMAND [INPUT DATA]: <ENTER> FILE FORMAT [GAS 2-D DETECTOR (ESRF)] :bsl INPUT FILE NAME [no_data.dat]: B26000.226 INFO: Data-set ("memory") 1 contains 1 image(s) of 512 x 512 pixels INFO: Data-set ("memory") 2 contains 1 image(s) of 1 x 6 pixels DATA-SET ("MEMORY") NUMBER (Range: 1 to 2) [1]:1 1 IMAGE NUMBER (Range: 1 to 1) [1]: 1 Main menu: ENTER COMMAND [IMAGE]: <ENTER>

Click on: “SAXS/GISAXS” Click on: INPUT Select file <select filename, (header)> Unknown format, click on: BSL/OTOKO DATA-SET ("MEMORY") NUMBER (Range: 1 to 2) [1]:1 1 , OK IMAGE NUMBER (Range: 1 to 1) [1]: 1 , OK

Fig 3-36: Fit2d

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5.8 OTHER The “OTHER” pull-down menu allows the following operations:

NEXUS editor: This function spawns a child process to execute the program HDFLook [28] PDH: This function spawns a child process to execute the program pdh [21] GNOM: This function spawns a child process to execute the program gnom [20] SASCIF-Translator: This function spawns a child process to execute the program sascif [29] Image Display: This function spawns a child process to execute the program dis/onze [17]

It is possible to open a EDF data file into the program dis. XV: This function spawns a child process to execute the program xv. [30]

The software developed at the Daresbury laboratories under the name CCP13 suite [31] are very useful. The following programs are available (for most UNIX systems):

CONV : File format conversion

CORFUNC : Correlation function analysis program suite

FD2BSL : Conversion of LSQINT output files to BSL format

FDSCALE : Scaling and merging of integrated intensities

FIT : 1-D curve and peak fitting

FIX : Preliminary processing of fibre diffraction patterns

FTOREC : Remapping of diffraction patterns into reciprocal space

LSQINT : 2-D background subtraction and peak fitting

SAMPLE : Fourier-Bessel smoothing of data

XCONV: File format conversion (Graphical User Interface)

XFIT : 1-D curve and peak fitting (Graphical User Interface)

XFIX : Preliminary processing of fibre diffraction patterns (Graphical User Interface) 5.9 HELP The “HELP” pull-down menu allows the viewing of the following manuals: gnom, dis (Image Display), EDF-Format, XOTOKO and BSL.

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6 XOP (X-ray Oriented Programs)

XOP is a widget based interface written in IDL, which drives different programs that calculates the synchrotron radiation source spectra (bending magnet, wigglers and undulators) and the reflection and transmission characteristics of optical elements as : mirror, filters, flat crystals, bent perfect crystals and multilayers. XOP runs under most Unix machines and Windows (95 and NT). It is possible to add routines (or packages) to XOP, by using “XOP extension”. "XOP extension" is a software package which is not part of the XOP standard distribution, but it can be installed optionally and run under the XOP interface. The inclusion of these "extensions" is completely coherent with the principal goal of XOP of providing a common front-end for a wide variety of computer programs useful for x-ray applications. The graphical user interface for SAXS (described in chapter 5) is available as extension under XOP.

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7 References 1. Dr. W.Bras, Requirements for SAXS/WAXS data acquisition system, 1997 2. Dr. W.Bras Schematic description of SAXS/WAXS experiment, February 1997 3. Dr. W.Bras Beamline manual SAXS 4. F. Sever, VVhist OS-9 Device Driver Users' Guide,

5. M. Mohan, Vtdc4 Device Server User's Guide, DSUG/xxx, 6. P. Blanc-Gras, F. Sever, Tfg Device Server User's Guide, DSUG/112,

7. P. Blanc-Gras, F. Sever, Mcs Device Server User's Guide, DSUG/113, 8. P. Blanc-Gras, F. Sever, VVhist Device Server User's Guide, DSUG/114,

9. F. Sever, Dld Device Server Users' Guide, DSUG/159. 10. M.Konijnenburg, WAXSGui, A graphical user interface for the wide angle x-ray

scattering detector, April 1999 11. M.Konijnenburg, WAXS detector, Device drivers and device server for the wide

angle x-ray scattering detector, June 1999 12. A.Götz, Device Server Programmer’s Manual, June 1996 13. Daresbury Laboratory Technical Manual "EC740 Time Frame Generator". 14. Daresbury Laboratory Technical Manual "EC738, 32 Channel Scaler". 15. ESRF, XOP,

http://www.esrf.fr/computing/scientific/xop/ Developed by:

Manual Sanchez del Rio European Synchrotron Radiation Facility BP 220; F-38043 Grenoble Cedex 9, France Email: [email protected] 16. ESRF, Shared memory routines,

http://www.esrf.fr/computing/bliss/online/shared/idl/idl1.html

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17. ESRF, Dis,

http://www.esrf.fr/computing/bliss/gui/dis/ Developed by:

Gilles Berruyer European Synchrotron Radiation Facility BP 220; F-38043 Grenoble Cedex 9, France Email: [email protected] 18. Daresbury Laboratory, BSL,

http://srs.dl.ac.uk/ncd/computing/manual.bsl.html#RTFToC1 Developed by:

G. Mant CLRC Daresbury Laboratory

Keckwick Lane Daresbury, Warrington, WA4 4AD, UK

Email: [email protected] 19. Daresbury Laboratory, XOTOKO,

http://srs.dl.ac.uk/ncd/computing/manual.otoko.html Developed by:

G. Mant

20. EMBL, Hamburg, GNOM, http://srs.dl.ac.uk/ncd/computing/manual.gnom.html#Manual Developed by:

Dmitri I Svergun Hamburg Outstation, EMBL c/o DESY Notkestrasse 85 D-22603 Hamburg, Germany

Email: [email protected] 21. O.Glatter, PDH

Developed by: O. Glatter Institue fuer Physikalische Chemie

Karl Franzens Universitaet Graz Heinrichstr. 38 A-8010 Graz, Oesterreich

22. EMBL Hamburg, SAXS programs, http://www.embl-hamburg.de/ExternalInfo/Research/Sax/index.html Developed by:

Dmitri I Svergun

69

23. canSAXS – workshop,

http://www.ill.fr/lss/canSAS/main.html 24. NEXUS : HDF Data Format,

Neutron & X-ray Data http://lns00.psi.ch/Nexus/

25. TACO,

http://www.esrf.fr/computing/cs/taco/whatis.html 26. RECONV2

Conversion from a BSL data file into an ASCII data file Contact person:

M.Shotton CLRC Daresbury Laboratory

Keckwick Lane Daresbury, Warrington, WA4 4AD, UK

Email: [email protected]

27. ESRF, EDF-Format, http://www.esrf.fr/computing/bliss/gui/dis/ Developed by:

P.Boesecke European Synchrotron Radiation Facility

BP 220; F-38043 Grenoble Cedex 9, France Email: [email protected]

28. NEXUS/HDF - browser

http://lns00.psi.ch/Nexus/Nexus_utils.html

29. SASCIF-Translator Developed by:

Dmitri I Svergun 30. xv

Developed by: John Bradley Email: [email protected]

31. TRANSFORM

Copyright: Fortner Research

70

32. FIT2D

http://www.esrf.fr/computing/expg/subgroups/data_analysis/FIT2D Developed by:

A. Hammersley European Synchrotron Radiation Facility

BP 220; F-38043 Grenoble Cedex 9, France Email: [email protected] 33. OTCON

Conversion from an ASCII data file into a BSL data file http://srs.dl.ac.uk/ncd/computing/manual.otcon.html#RTFToC1 Contact person:

M.Shotton 34. CCP13 Suite

http://wserv1.dl.ac.uk/SRS/CCP13/software.html Contact person:

M.Shotton

71

APPENDIX A This appendix is showing the following files:

E.NDX: An index file with is created for the measurements saved under the letter E. It is showing the acquisition time and date, the filename, and the user comment.

E.NDX2: An index file with is created for the measurents saved unter the letter E. It is showing some acquisitions parameters.

E0.922LOG: A log file of the measurement : E00000.922 Example: E.NDX ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; E00000.922:Wed Sep 22 09:49:17 1999 Ag-behenate ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; E01000.922:Wed Sep 22 10:15:42 1999 rattail ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; E02000.922:Wed Sep 22 10:27:03 1999 rattail no Al foils ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

Example: E.NDX2 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; Path: inhouse/data/external/eindhoven Headerfile: E00000.922 Headers: Wed Sep 22 09:49:17 1999 Ag-behenate # Binary files: 2 Filename: E00001.922 Type: 1 Data dimension: 2D Indicators: 512, 512, 1, 0, 0, 0, 0, 0, 0, 1 Filename: E00002.922 Type: 2 Data dimension: 1D Indicators: 1, 6, 1, 0, 0, 0, 0, 0, 0, 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; Path: inhouse/data/external/eindhoven Headerfile: E01000.922 Headers: Wed Sep 22 10:15:42 1999 rattail # Binary files: 2 Filename: E01001.922 Type: 1 Data dimension: 2D Indicators: 512, 512, 1, 0, 0, 0, 0, 0, 0, 1 Filename: E01002.922 Type: 2 Data dimension: 1D Indicators: 1, 6, 1, 0, 0, 0, 0, 0, 0, 0 Example: E0.922LOG

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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; SAXS - EXPERIMENT (NO WAXS) ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; USED-PARAMETERS ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; D26 #USER-NAME Eindhoven #USER-COMMENT Ag-behenate #REMOTE-DIR inhouse/data/external/eindhoven #LOCAL-DIR /users/opd26/data/inhouse/data/external/eindhoven #PREFIX-FILENAME E #FILENR 0 #SAXS:RESOLUTION X 512 #SAXS:RESOLUTION Y 512 #SAXS:RESOLUTION MODE [0=half mode, 1=full mode] 0 #SAXS:DATALENGTH 32 #FRAMES 1 1 0.0010000000 0 0 300.0000000000 0 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; USER-INFO ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; #TDC-INFO TDC res (ps): 0 TDC offset (ns): 254 TDC timeout (ns): 295 #ADDITIONAL INFO ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; END OF LOG-FILE ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; Example: E00000.922 Wed Sep 22 09:49:17 1999 Ag-behenate 512 512 1 0 0 0 0 0 0 1 E00001.922 1 6 1 0 0 0 0 0 0 0 E00002.922

saxs saxs/waxs waxs data reduction...¾ the time to digital converter (vtdc4) [5] plays a very...

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