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MpSys4 User`s Manual - School of Physics

1. and functions and procedures Example if x lt y print x lt y else print x gt y for i 0 i lt 10 i Microanalytical Research Centre 54 MpSys4 User s Manual print Loading file i load filefi func sinc x return sin x x plot sinc x It will be most useful to use the Skip programming features in macro files and aliases In this way you may reduce long repetitive and complex command sequences to a single macro call See FOR WHILE DO and IF in the Command Reference section below for more information Microanalytical Research Centre 55 MpSys4 User s Manual 7 Brief Command Summary General Commands Exit Terminate the MpSys session returning to command prompt Enkeys List or define function key settings Font Mag display fonts List AAA AU Sel Window commands Mapwindows New reste a new window New Create anew window o Redraw Force a window to redraw itself kaas oe the background colour of a window Setcolor Switch Change the current window to a new window Display a text string inside a window Draw a line inside a window Microanalytical Research Centre 56 MpSys4 User s Manual Data Commands Erase one or more data buffers aa load sorted or unsorted data into a buffer Ges lose a currently running experiment Run a new experiment Start data acquisition Stop data acquisition tune ed a map window to update
2. As event packets are collected MpSys keeps a record of good and bad data words A bad data word will have incorrect bit settings for the station number or identification If we let E be the incoming energy data word for a particular event X be the X scan position data word and Y be the Y scan position data word then an event is bad if E15 14 X13 12 Y13 12 or X15 1 and X14 0 or Y15 0 and Y14 1 Even though bad data words are still recorded in the raw event file both spectra and map images ignore them MpSort can be used to generate sorted data SD and sorted pointer SP files which filter out bad data words Microanalytical Research Centre 65 MpSys4 User s Manual MpSys sorted event data sd sp To improve the speed of reconstruction of spectra from collected data EVT files can be converted into sorted data files SD and sorted pointer files SP Both files must be in the same directory when they are loaded SD files are made up of arrays of events arranged in numerical order not time order as was the case for the event by event file SP files consist of n 32 bit words which act as file pointers to each event within the associated SD file The size of the SP file will always be size MAX_YCHANNELS NUM_OF_STATIONS YPOINTER_SIZE 4 bytes Where by default MAX_YCHANNELS 4096 NUM_OF_STATIONS 4 YPOINTER_SIZE 2 Therefore size 128 kilobytes The sorted data files are created from the event by e
3. Beam Particle type particle_type The type of beam particle used for the experiment This can only be an element from the periodic table MpSys requires this parameter for calibrating RBS spectra Field type restricted text Default value H Beam energy beam_energy The energy of the ion beam used in the experiment MpSys requires this parameter for calibrating RBS spectra Field type positive real number Unit MeV Default value 0 0 Chamber Beam current beam_current The ion beam current detected on the sample This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit A Default value 0 0 Scattering angle scattering_angle The angle as which the RBS detector is placed relative to the incident ion beam hitting the sample If the value is 0 0 then it is regarded as undefined MpSys requires this parameter for calibrating RBS spectra Field type real number Unit degrees Default value 0 0 Vacuum vacuum The vacuum level within the specimen chamber This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit Torr Default value 0 0 Bias voltage bias_voltage Microanalytical Research Centre 45 MpSys4 User s Manual The voltage as which the target specimen holder is biased This parameter is used for information purposes only and is not used by MpSys Field type real number Unit V Def
4. Before calibrating an energy spectrum the experimental parameters must be set in the journal file This may be done by clicking on the journal button La and entering the appropriate parameters in the pull down menus The energy calibration may then be determined from the spectrum of a standard sample by identifying two known points in the spectrum commonly peaks or edges MpSys has two built in data bases One is for RBS spectra and the other is for PIXE spectra If the station corresponding to the spectrum you wish to calibrate is for either of these types of data you can easily use the built in data bases to calibrate the spectrum by just identifying two features in the spectrum that correspond to signals from two different elements MpSys will then identify the correct energy of these two points from the appropriate built in data base and calculate the correct energy calibration If your spectrum does not correspond to either of the built in data bases then the calibration can still be performed by identifying two features in the spectrum for which the energy is known MpSys will then accept the correct energy for these two features and calculate the correct energy spectrum This process is summarised as follows 1 Set experimental parameters using journal file button kal 2 In the sample chamber select your standard sample which should contain two or more known elements Suitable samples are a matter of taste but a quartz screen o
5. Y size micron k N MicroDas Y gain Height 100 Scale Where k is a constant that depends on the beam energy particle and lens system magnification k 1 98 for 3 MeV H ions N is the number of turns on the x scan coils N is the number of turns on the y scan coils MicroDas X gain is the setting of the analogue gain potentiometers on the front of the MicroDas unit for the x direction MicroDas Y gain similarly for the y direction Width is the parameter from the scan category window above Microanalytical Research Centre 18 MpSys4 User s Manual Height similarly Scale similarly Deadtime The deadtime category window requires a full separate manual to discuss the meanings of the deadtime options Experiment Mode Station 1 Timer Resolution 0 00000 Station 2 Station 3 Station 4 Charge Resolution 0 00000 Blanking Under Mode selection of pseudo causes the beam to dwell for additional time at each pixel to compensate for the deadtime of the ADC units and the computer In this way data collected when only a single station is active will be fully deadtime corrected This is the most common mode of operation For the other deadtime modes see the separate manual Microanalytical Research Centre 19 MpSys4 User s Manual Station General MpSys collects data from up to four stations The parameters of the detectors connected to the stations must be entered on the screens under the General category for each s
6. Deadtime Experiment Station 1 Station 2 Station 3 Station 4 Scan Enabled Yes Scan Mode Raster Trigger Clock X Resolution 256 Y Resolution 256 3 7 Scan Width 100 00000 Scan Height 100 00000 Scale 1 0000 Interlace No f count 0 A Dither fi 2 Clock Dam A Events fs OOo Calculate The slots listed on the right panel have the following properties Scan enabled Scan Mode X resolution Y resolution Width Height Allows switching off and on the scan in software MpSys provides two different scan modes Raster is the most commonly used mode In this case the beam commences its scan in the top left corner of the scan area then continues in the horizontal direction to the right dropping to the next scan line when the right edge of the scan region is reached and returning to the left edge There is no flyback Triangle is an alternative mode where the scan covers a fissajous like figure allowing a faster sampling of the scan area compared to the raster mode Sets the number of pixels in the horizontal direction Note that this does not change the scan size it sets the resolution of the scan Sets the number of pixels in the vertical direction Note that this does not change the scan size it sets the resolution of the scan Examples If the scan size is set to 256 um then a X resolution of 256 will set the step size between pixels to 1 um A X resolution of 128 will set the step size betw
7. The options are Save all E Colour Tool Colour Scale Print Colour tool pops up the colour tool window which allows the colour mapping to be changed interactively Colour scale allows the pallette used to display the map files to be changed The list of available colour scales is presented which includes grey scale and alternative colour scales Print allows a selected map or array of maps to be printed Spectra Load allows a new spectrum or set of spectra to be loaded from disk Save saves the current spectrum or spectra in a spectrum file Build is used to recreate the spectra associated with a particular event by event file or sorted data file Microanalytical Research Centre 38 MpSys4 User s Manual 4 Working with Map windows When working with maps as was the situation when working with spectra it is necessary to ensure the map you wish to work with has the focus This will ensure all commands and modifications apply to the correct map window The map window with the current focus is shown by the row of asterisks flanking the name of the map in the title bar To give the map the focus simply left click the mouse on the map area not the frame or title bar Loading Maps Maps can also be loaded from map files in existing map windows Map files have the filename extension map To load a map file into an existing map select the Load menu item in the Map menu of the map window You will s
8. first create a new spectrum window with the new spectrum button I Then the spectrum associated with a particular station may be displayed in the window from the spectrum button on the spectrum window task bar From the pull down menu select the station number of interest then the E x or y spectrum to be displayed In the example shown here an x ray spectrum is displayed The spectrum control buttons on the top right of the task bar 1 have been used to expand the spectrum for a closer look a small range of energies These spectrum control buttons have the following functions gt lt Contract the spectrum so more of the spectrum is visible in the window Expand the spectrum so that a narrower range of the spectrum is visible in the window J al Raise or lower the upper limit of the spectrum to raise or lower the spectrum height El E Move the spectrum to the left or right in the spectrum window Microanalytical Research Centre 23 MpSys4 User s Manual El Access the element selection menu to allow the list of elements associated with the current spectrum to be changed These elements are displayed as arrows at the surface energy for RBS spectra or as x ray lines for x ray spectra The element selection menu allows elements to be listed deleted or extended The use of this feature is discussed following the next section on calibration of an energy spectrum Calibrating an energy spectrum
9. resized automatically using the F3 key The left and right edges have been set just beyond the first and last channel with non zero counts in the spectrum F4 Expand the spectrum so that the region of the spectrum between markers X0 and X1 is expanded to fill the spectrum window Markers X0 and X1 are set with the left mouse button and the middle mouse button respectively El Spectrum View Calibration Elements 4000 6000 keV pips 853 234 1 3205 73 In the example of this RBS spectrum the markers have been positioned about the interesting region of the spectrum Then F4 is pressed to transform the spectrum window to 2800 El keV pips In this RBS spectrum numerous elements of interest have been identified as selected via the element selection button Microanalytical Research Centre 30 MpSys4 User s Manual Unknown element identification An additional way of adding elements to the element list associated with a spectrum window is to use the identify function to identify the signal from an unknown element To use this function the spectrum must be calibrated See the section on spectrum calibration for more details To identify an unknown element use the mouse to point to the signal from the unknown element In the case of an x ray spectrum this is usually an x ray peak The most intense peak from the element need not be selected In the case of RBS spectra the signal should be the surface energy edge
10. software had to be developed The previous generation of data acquisition system illustrates one solution The system consisted of a dedicated VME crate with its own computer a custom designed and built Fast Data Acquisition Crate FDAC a dedicated workstation to display the data This provided the necessary computer power to collect data from up to four detectors simultaneously while still allowing for FAST specimen scanning with the advantage of a random scan pattern The system was sophisticated expensive to make and maintain but allowed count rates of up to about 5kHz per detector The advent of fast and inexpensive PC s has allowed all this complexity to be eliminated The latest generation of our TQSA data acquisition system the fastest and best yet is also the simplest It consists of a dedicated PC with a National Instruments LabPC card a simple interface unit called MicroDas The PC has sufficient power to simultaneously collect store and display the data from up to four detectors This system is also extremely robust it supports data acquisition rates in excess of 20kHz per detector The key to the new system is the linux operating system This allows for extremely fast and efficient low level code to service the data acquisition needs Linux offers overwhelming advantages for time critical tasks like data acquisition These include the ability of insert efficient low level code into the kernel security in a
11. the shape of the path of the scan Permissible values are raster triangle shape Field type restricted text Default value raster Microanalytical Research Centre 46 MpSys4 User s Manual X resolution scan x_resolution The number of pixels used in producing the x axis scan Field type positive integer number Unit pixels Default value 256 Y resolution scan y_resolution The number of pixels used in producing the y axis scan Field type positive integer number Unit pixels Default value 256 Scan width scan width The physical length of the x axis scan Field type positive real number Unit m Default value 100 0 Scan height scan height The physical length of the y axis scan Field type positive real number Unit m Default value 100 0 Scale scan scale Field type positive real number Default value 1 0 Count scan count The number of complete scans over the specimen A zero setting permits the scanning to continue indefinitely Data acquisition automatically stops once the scan count has been reached Field type positive integer number Default value O Dither scan dither Field type positive integer number Default value 1 Interlace scan interlace Setting this parameter provides a convenient way of getting a fast overview of the specimen when using the raster scan mode A value greater than 1 causes the raster scan to skip scan lines on the first pass On subseq
12. AA UserName Jan C C es Host Name marco ph unimelb edu au DAQ Name MicroDAS Use Test Data ves n General Parameters Printer Name printer_name The UNIX name of the default printer to use for plot and map dumping as well as for printing out log book reports The value will be used as the printer name argument to the UNIX print spool program lpr Example if the printer_name is eon then MpSys will use the command lpr Peon when printing Field type text Default value Ip1 Experiment Parameters General Unique identification number obtained from the operarting system every time an experiment is run This number is system specific so log book files used on other systems may have the same value as existing log book files on that system If the value is O then it is regarded as undefined Field type positive integer number Default value O Run date run_date The date in which the experiment took place When a user begins a run the operating system will automatically put the current date in this field in the format dd mmm yyyy Example 15 March 2001 This parameter is used for information purposes only and is not used by MpSys Microanalytical Research Centre 43 MpSys4 User s Manual Field type text Default value blank Run name run_name The name of the experiment being run This parameter cannot be changed once data acquisition has started Field type text Default value bl
13. For the station parameters the variables all begin with StX where X is a number between 1 and 4 representing one of the four available data acquisition stations The parameter variables can then be loaded with data with the following characterisitics Text any alphanumeric characters and spaces When setting the parameter using the command line interface it is important to enclose the value in double quotes Example set origin Melbourne Australia Restricted text only certain words can be used for this parameter The permissible words will be listed in the parameter description All text entered is case insensitive Yes No only the text words yes or no case insensitive may be used for this parameter Number may be integer positive integer real positive real Unit This is the standard unit for numerical field parameters At present there is no provision for using different units for a given parameter Default Value This is the value assigned to the parameter when MpSys first starts Normally it will be replaced by a setting within the user s default mp file Microanalytical Research Centre 42 MpSys4 User s Manual The parameters found under each of the major sub headings of the journal file window are now described General General Beamline Beam Chamber Specimen Scanning Deadtime Run Name videop1 Station 1 Run ID 5363 a Station 2 Run Date 15 March 2001 Pl Run Time 13 00 Station 3 A
14. Ga Se Sei MPSYS MAP FILES CMAP ee EE ed dree dd ee 10 MPSYS X RAY LINE DATABASE 11 WORKING WITH MPSYS IN A MICROSOFT WINDOWS ENVIRONMENT ssssssssssssesees 70 Microanalytical Research Centre 4 MpSys4 User s Manual 1 Introduction MpSys is control program primarily designed for nuclear microscopy It has the following features Data collection from up to four stations A station usually has a one of the detectors typically employed with a nuclear microprobe connected to it such as an x ray detector or a detector of backscattered particles A scan signal generator for control of the scan of the beam spot over the region of interest on the specimen Provision for tagging each event received in any of the four stations with the corresponding scan coordinates and storing the event in time sequence on disk This is event by event mode of data acquisition Extensive features for manipulation and display of the incoming data stream Most commonly this consists of the display of the energy spectra from each of the four stations together with tuned displays These are intensity maps of the incoming data derived from windows placed in the energy spectra of the four stations One or more tuned displays may be derived from one or more windows placed in each energy spectrum Windows may also be placed in the x and y spectra Extensive features for manipulation and display of the data off line This includes sorting the
15. MPSYS4 Microprobe Data Analysis System User s Manual ommercial Organisation Microanalytical Research Centre School of Physics University of Melbourne VICTORIA 3010 AUSTRALIA Fax 61 0 3 9347 4783 Ph 61 0 3 8344 5376 Email marc physics unimelb edu au Web http www ph unimelb edu au marco January 2002 MpSys4 User s Manual Preface This manual contains an alphabetical listing of help files for all the commands and other command structures in the MpSys data collection and manipulation package Information is provided on syntax for commands as well as detailed information on the Skip programming language incorporated with MpSys Please read the MpSys User s Manual for further information For further technical assistance please contact MARC via the following email address marc physics unimelb edu au Limitation of Liability Micro Analytical Research Centre does not assume any liability arising out of the use of the information contained within this manual This document may contain or reference information and products protected by copyrights or patents and does not convey any license under the patent rights of Micro Analytical Research Centre nor the rights of others Micro Analytical Research Centre will not be liable for any defect in hardware or software or loss or inadequacy of data of any kind or for any direct indirect incidental or consequential damages in connections with or arising out of t
16. NIX shells allow you to put the redirection at the start or the end Example logfile print Loading file file i gt gt logfile load file i gt gt logfile print Done this could be more easily written by grouping the commands logfile print Loading file file i load file i print Done Microanalytical Research Centre 53 MpSys4 User s Manual Online help You may obtain help on any of the Skip features or commands by using the help command UNIX users may want to alias man help Just typing help will print some introductory information then walk you through a series of more detailed topics Example help help print help loops help functions You can obtain help on macros help macroname will print any comments that Skip finds at the start of the macro So if you write macros take the time to put a couple of explanatory comments at the start of your macro files Comments are started by a ff Example loadfiles loads files into the data buffers Usage loadfiles filenames for i 0 i lt 1 i load buffer i file i A programming language Skip is a full programming language for interactive programs The Skip programming language is similar to C or awk Skip provides conditional loops while for and do conditional selection if and else compound commands command list inside curly braces
17. Run name Name of experiment run_name Host name Name of host computer fornhost_ name experiment DAQ name Name of data acquisition system Geteste Microanalytical Research Centre MpSys4 User s Manual Beam line Name Pesoription fetname Pre Feta Beam line name Name of microprobe beam ine beamine name TL Object Diaphragm Diameter of object diaphragm object_diaphragm l e boo m Diameter of aperture diaphragm EE diaphrag kk fm Beam focussed hether a focussed ion beam waslbeam_focussed yesno yes used Beam fen Deag gotramo fer Pai L Particle type ype of beam particle used inparticle_ type experiment Beam energy Energy of beam used inbeam_energy MeV experiment Chamber Name besen etname Type pefaut Beam current lon Beam current detected on thebeam_current C pecimen holder Scattering angle Angle of RBS detector relative to ioniscattering_angle rae beam Vacuum Vacuum level in specimen chamber vacuum Re bn for Bias voltage Voltage that specimen holder isbias_voltage V biased Integrated charge fntegratedchargefe loo Jo Microanalytical Research Centre 61 MpSys4 User s Manual Scanning Name pesempion bam Des faut Enabled ill scanning be used during datascan enabled yesno lyes acquisition Mode Scanmode raster triangle shape bcanmode RI faster X Resolution Number of pixels producing y axisjscan x_resolution l 2 ca 56 pixel 56 n Y Resolution Number of p
18. Station 1 Object Diaphragm Station 2 Aperture Diaphragm 1000 000 Beam Focussed Wes Station 3 Station 4 Cancel Beam The next is the Beam category General General Beamline Bean Chamber Specimen Scanning Deadtime Experiment Particle Type H Station Beam Energy 3 00000 Mev Station 2 Station 3 Station 4 Cancel Both the beam particle and the beam energy are required for the elemental identification features of MpSys Microanalytical Research Centre 15 MpSys4 User s Manual Chamber The Chamber category provides slots to enter parameters associated with the charge integration system Experiment Beam Current 0 00000 Station 1 Vacuum Station 2 Bias Voltage Integrated Charge Station 3 Station 4 Specimen Under the Specimen category there are slots for putting information about the curation of the sample General General Beamline Beam Chamber Specimen Scanning Deadtime Experiment Origin Station 1 Composition 2nS Ba Glass Station 2 Station 3 Station 4 Cancel Microanalytical Research Centre 16 MpSys4 User s Manual Scanning The Scanning category is very important because it sets the scan parameters which are sent to the workstation I O card which then provides the scan signal to the scan amplifier This screen can also be accessed through the scan button on the main menu task bar General General Beamline Beam Chamber Specimen Ecanning
19. Sys functions particularly those that deal with elemental identification and energy calibration and so must be set correctly at the start of a run for these functions to perform correctly j The new spectrum button creates a new window on the screen for display of a spectrum The spectrum displayed in the window may be selected by pull down menus on the banner of the spectrum window see more discussion of windows for spectra below The new map button creates a new window on the screen for display of a map or a tuned display The map or tuned display is linked to the desired windows in the energy and x y spectra from a station by the pull down menus on the banner of the map see more discussion of maps below RUNNING STOPPED f data Idm videop2 evt At the end of the row of function buttons is a status bar that shows the current mode of MpSys In this example the scan is stopped and the last run data file has been closed When data collection is in progress this changes to show the status When a run is in progress this is what the task bar looks like In this case the data is going into file videop2 evt RUNNING STARTED Idata Idmvideop2 evt During a run many map and spectrum windows will be on the screen The configuration of these windows is saved in the journal file so that the configuration may be retrieved for future analysis An example is shown on the next page Microanalytical Research Centre 10 MpSys4 Use
20. ank Host name host_name The name of the host computer that is being used for the run This parameter is used for information purposes only and is not used by MpSys Field type text Default value blank DAQ name dag name The name of the data acquisition system that is being used for the run This parameter is used for information purposes only and is not used by MpSys Field type text Default value MicroDAS Beam line Beam line name beamline_name The name of the microprobe beam line used in the experiment This will be laboratory specific This parameter is used for information purposes only and is not used by MpSys Field type text Default value blank Object diaphragm object_diaphragm The diameter of the object diaphragm on the microprobe beam line This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit m Default value 0 0 Aperture diaphragm aperture_diaphragm The diameter of the aperture diaphragm on the microprobe beam line This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit m Default value 0 0 Beam focussed beam_focussed Microanalytical Research Centre 44 MpSys4 User s Manual A boolean statement as to whether a focused on beam was used for the experiment This parameter is used for information purposes only and is not used by MpSys Field type yes no Default value yes
21. anned 28119 square channels 42 91 of total map area 65536 sq ch A Extract stn 2 s r520A The MpSys dialogue screen during the extraction of the two example spectra shown on the previous page Microanalytical Research Centre 36 MpSys4 User s Manual The Main Menu bar Many additional functions of MpSys can be accessed through the main menu on the main MpSys menu screen As with all MpSys functions these functions can also be accessed through the command window by using a MpSys command or through a MpSys macro of MpSys commands also executed through the command window This section provides a brief guide to the functions which can be accessed through the main menu The main menu Experiment Data Journal Maps Spectra Help Each menu item can be clicked on to provide a pull down list of functions Experiment Run _Ctl R These functions control data acquisition and duplicate the functions of the Stat Ctl S menu buttons discussed earlier Run to prepare a new data file to receive Stop Ctl T data Start to start collecting data Stop to stop collecting data Close to close of the data file so that no further data can be collected into it Quit to Close Ctl exit MpSys and return to the unix shell Quit Data Load Ciel The Load menu item allows old data to be reloaded into MpSys The old data pa ee can be in the form of unsorted event by event files evt or as sorted data files Sort sd sp The Sort
22. ating a tuned display or map from windows set in a spectrum Once a run has started and MpSys has begun collecting event by event data to disk it is possible to create a tuned display which is an intensity map of the sample in the scan region obtained from a window or gate placed in the energy spectrum of a particular detector The window may be specified by two methods 1 The first is simply to place markers in the energy spectrum around the signal you wish to map This is done by pointing with the mouse to the left low energy side of the signal and clicking the left mouse button to position marker X0 Then point to the right high energy side of the signal and click the middle mouse button to position marker X1 This method can be used to set the window in any type of spectrum 2 If the necessary experimental parameters have been entered into the journal file and the spectrum corresponds to either an X ray or RBS spectrum it is also possible to specify the window by element In this case the window is automatically positioned about the energy position corresponding to the element energy obtained from the correct data base with a width specified by the energy resolution of the detector specified in the journal file To create the map the procedure is as follows 1 2 Position markers XO and X1 in the spectrum window Create a new map window with the map button or reuse an existing map window by clicking on it O
23. ault value 0 0 Integrated charge integrated_charge This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit C Default value 0 0 Specimen Origin origin A statement as to where the specimen was obtained from for the experiment This parameter is used for information purposes only and is not used by MpSys Field type text Default value blank Composition composition A list of elements and their proportions describing the stoichiometry of the specimen Each element has a proportion value and is separated by a comma for a given layer and each layer is separated by a semi colon Example Cu 2 Ni 1 Au 1 translates to layer 1 having 2 copper atoms per nickel atom and layer 2 being purely made up of gold This parameter is used for information purposes only and is not used by MpSys Field type text Default value blank Scanning The following parameters affect the ion beam scanning hardware of the MicroDAS system They cannot be changed once data acquisition has started See the Beam scanning section in the Data Acquisition chapter for more information about using these parameters Enabled scan enabled A boolean statement as to whether scanning will be used in the next experiment If the value is set to no then data acquisition will take place without the beam being scanned Field type yes no Default value yes Mode scan mode Use this parameter to select
24. ces Example alias pr print alias ssave sort save print Done See ALIAS for more information Macro execution You may also place long sequences of commands in a file Calling this macro file will execute the commands as if you had typed them at the command line Example loadfiles printall Macros may be supplied with arguments on the command line The macros can use these arguments when they are called Example loadfile red data See MACRO for more information Microanalytical Research Centre 52 MpSys4 User s Manual Calculator Skip has a calculator built in The syntax is very similar to the C programming language You may define variables assign values to them and calculate mathematical expressions Skip provides double precision numeric variables string variables and arrays of numbers and strings You can use the Skip programming language to just do some sums for you or you can feed values of variables and expressions to your commands Numeric variables are defined with the real command Example real x y r r sqrt x x y y print Plotting circle of radius r plot circle radius r Input and output redirection You may redirect the input or output of any command or sequence of commands to a file The syntax is very similar to the UNIX shell input output redirection Unfortunately you must place the input output redirection at the start of the command The U
25. ctrum is to be extracted So for example it is possible to extract a spectrum from station 1 from a map derived from a window in station 2 An example is shown in the next spectrum Microanalytical Research Centre 35 MpSys4 User s Manual Spectrum View Calibration 800 600 400 200 2300 2500 2700 2900 El ke Tiny PIPS 3 79186 1 223 152 So this RBS spectrum applies to the same region of interest as the PIXE spectrum in the previous example The extracted spectrum now applies only from the sub region of the scan defined by the shape Therefore less than 100 of the data file has been used to make the extracted spectrum For future normalisation purposes it is essential to keep a record of the percentage of the data that went into the extracted spectrum This number appears in the MpSys dialogue screen as shown in the following example Closed 32 84 of total map area 65536 sq ch MpSys gt extract stn 1 s r520B Spectrum extracted from station number 1 in window map1 events extracted 202216 area scanned 21525 square channels 32 84 of total map area 65536 sq ch MpSys gt shape x MpSys gt extract stn 1 s r520A Spectrum extracted from station number 1 in window mapi events extracted 159563 area scanned 28119 square channels 42 91 of total map area 65536 sq ch MpSys gt extract stn 2 s r520A Spectrum extracted from station number 2 in window mapi events extracted 1626332 area sc
26. current spectra marker positions for station X Station X Elements Create map using a specified element from a calibrated spectra Modify map parameter Create a map from a map file Save a map to a map file Rename a map Display map parameters Clear a map Close a map window If the map is a tuned display which has been generated on line then the tune menu applies Station X Markers Create a tuned map using current spectra marker positions forl Station X Elements Create a tuned map using a specified element from a calibrated spectra Extracting spectra from Maps One of the most powerful features of MpSys is the ability to extract spectra from regions of interest within the scan This allows detailed analysis of features within the scan region The fact that the entire run is stored in the event by event file means that the region of interest need not be specified in advance and new regions of interest can be applied to the scan region an any time after the run has concluded To extract a spectrum from a region of interest within the scan area follow these steps 1 Create a map which shows the region of interest 2 Use the mouse to start drawing an outline of the region of interest called a shape on the map This is done by pointing the perimeter of the region of interest and clicking the left mouse button two clicks will be necessary if the map window does not have the current focus A line now follows the
27. data into energy and position order for rapid extraction of maps A map is the off line equivalent of a tuned display MpSys collects data into the event by event file for the duration of a run The user determines the duration of a run which is typically for a time long enough to collect statistically significant spectra from the region of interest within the scan The diagram below shows the typical experimental set up for the use of MpSys to collect data The energy signals from any of the four detectors E Ez Es Ex is interfaced to MpSys via a MicroDas unit and a data acquisition card in the linux workstation Scan coils E detector gt ampir H anc aico 4 gt aaa gt mu Laast gt MpSys x y Data acquisition system with MpSys Microanalytical Research Centre 5 MpSys4 User s Manual From experiment MpSys MpSys command macro Videoip evt Video1p img Video1p mp Event by event Spectra of energy Journal file of data file x and y for all MpSys in time order stations commands Files created by MpSys following a run with example file names for run videop1 At the conclusion of a run MpSys closes the files associated with the run As shown in the above diagram these are the event by event data file extension evt the energy x and y spectra associated with each station concatenated into one file extension img and the MpSys command macro extension mp
28. e scan will commence and data will start appearing in windows It is now not possible to change the scan parameters although they can be reviewed at any time during the run by pushing the scan button The run may be stopped and started at any time with all data going into the same file Note that the scan will recommence from the start each time the start button is pressed Microanalytical Research Centre 9 MpSys4 User s Manual e The stop button causes the data collection to stop along with the scan but does not close the file being used to store the new data This means that the run can be restarted by pressing the start button The close button is used at the conclusion of the run to close the file used to store the ata and stop the data collection process The system will now be ready for a new run o mi The scan button allows access to the scan menu If there is no run in progress this menu can be used to change the scan parameters If there is a run in progress the apply button is missing and the menu may only be used to review the current scan parameters The scan menu is discussed in more detail below The journal button allows access to the journal file that holds all of the experimental parameters of the run This includes the beam energy and particle details about the present specimen and the operating parameters of the system hardware for future reference Some of these experimental parameters affect other Mp
29. earch Centre 40 MpSys4 User s Manual Using the colour tool To invoke the colour tool you select the Colour Tool menu item in the Maps menu of the main window Command Line window on the MpSys main menu can also be used to invoke the colour tool ctool The colour tool is used to interactively change the mapping between the colour scale and the intensity of the map Clicking on the right mouse button adds a handle to the colour line the left mouse button can then be used to drag the line to change the mapping Clicking on the middle mouse button clears the handle Microanalytical Research Centre 41 MpSys4 User s Manual 5 Journal file options MpSys 3 provides a means for experimental parameter information to be recorded with actual experiment data obtained during a run When the user loads a previous collected data set the associated journal file will also load A warning is given if no journal file found Normal use of Mpsys involves the use of a journal file The purpose of this section is to discuss the MpSys journal file parameters in detail These parameters may be accessed by the users and incorporated into MpSys macros that employ the Skip programming language In the discussion to follow each parameter is listed and it characteristics described The paragraph describing each parameter has a boxed header To the right hand side of each parameter name is the MpSys parameter variable which is used by the set command
30. ecereseseceresesesersseseserssesesereseseseresesesesesesesereseseserere 39 LOADING MAPS tg oct Ee Ree E dee Eeer Ee AE telde 39 SAVING MAPS EE 39 PRINTING MAPS ie ee EA ASSEN i 39 CLEARING MAPS deed A0 CLOSING MAP WINDOW Sanear edd ee IAE RIOR Sav dee Eed dd 40 MANIPULATING MAP COLOUR tcs 40 General Paramete Si E 43 Experiment EE 43 STALLION Parameter SAA aia 48 THE SKP LANGUAGE 0 ans dancer dies 52 COMMAND ALIASING MACRO EXECUTION RE CALCULATOR A laa INPUT AND OUTPUT REDIRECTION 3 vssececsscusesscreviesee eg d er dee ee deed etica ooer eeki 53 ONLINE HELP teca 54 A PROGRAMMING LANGUAGE cit aia ii 54 BRIEF COMMAND SUMMARY cscssssssssssssssssesesereseseseresesesersseseseresesesersseseserssesesereseseseresesesereseseserere 56 GENERAL COMMANDS bass 56 WINDOW COMMANDS inicio 56 DATA COMMAND Sl eee 57 IR Reie CH RR E 57 SPECTRA COMMANDS eer AEE REETA ASSEN 58 MAP COMMAND Silices ee eene dei 59 PILE SYSTEM COMMANDS leegen 59 JOURNAL PARAMETER SUMMARY e sessessesesseoseoscoscossossossossoseoseoscoscossossossesecsecseosooscossossossossosseseosees 60 GENERAL PARAMETERS sde See A e de 60 Microanalytical Research Centre 3 MpSys4 User s Manual EXPERIMENT PARAMETER Std desdseees 60 A aS PE TSS SC OSE A BP EEE AE E ST 60 eme duer eelere ia oi Scanning Deadtime STATION PARAMETERS GONE EEN MPSYS RAW EVENT DATA E Di ade MPSYS SORTED EVENT DATA SD SP MPSYS SPECTRA FILES IMO a
31. ee a file loading dialog box appear allowing you to select which map file to load The map file will automatically be displayed in the map window and the window name will change to the map file name without the extension Command line interface load m lt filename gt load m window map1 lt filename gt See section 9 for information about the format of an MpSys map file Saving Maps Maps can be saved as MpSys map files JPG files TIF files or ASCII text files To save a map select the Save menu item in the Map menu of a map window and then select which file format you want to save the map as The file formats will be one of MAP ASCII JPG or TIF The map is automatically saved in the format specified using the map name as the filename If the operation is successful the message saving map lt name gt as lt name gt lt extension gt in the current directory will be displayed Where name is the name of the map window and mn o extension is one of map asc jpg or tif If the operation could not be performed then you will see the error message save could not save map as file lt operating system reason gt Command line interface save m lt filename gt Printing Maps Any map window may be printed on a postscript printer dump type map windows cul rb101_si Microanalytical Research Centre 39 MpSys4 User s Manual The optional argument cls may also be u
32. een pixels to 2 um The width parameter sets the width of the scan area Values of the width parameter less than 100 will proportionately narrow the scan width The height parameter sets the height of the scan area Values of the height parameter less than 100 will proportionately compress the scan height Microanalytical Research Centre 17 MpSys4 User s Manual Scale The scale parameter allows fine control of the entire scan size Count The count parameter is uses when it is desired to produce just a precise integral number of passes over the scan region If count is zero the scan continues rastering indefinitely Example Setting the count to 2 will cause the beam to raster to the bottom of the scan area then raster back to the top whereupon it will stop Dither The dither parameter causes the rastering to skip an integral number of rasters on the first pass on the return pass the missing rasters are gradually filled in This option is useful is it is desired to pass quickly over a region to check if the scan region is on the correct place Interlace Setting interlace to no causes the scan to raster uniformly from top to bottom and return With interlace set to yes the scan does every second raster on the way down on the return the missed rasters are filled in Trigger Advance of the scan from pixel to pixel is triggered by several methods Clock advances the scan after an elapsed time A slot for entering the desired dwell ti
33. ering Angle Filter 120 micron Be Elements Si k Cu k Fe K Au 1 Ca K 41 K Microanalytical Research Centre 21 MpSys4 User s Manual Station E Calibration The E Calibration screen allows the energy calibration for the detector to be reviewed The best way of determining the energy calibration for the detector is via the procedure discussed in the next section of this manual Experiment Calibrated Station Parameter A Station 2 Parameter B Parameter C X Axis Label Normalise on charge No Station 3 Station 4 The energy calibration applied to the data is shown in this window E keV Channel number a keV ch b keV c Channel number 2 Station X Calibration The calibration screen for the X and Y axes are very similar to that for the energy spectrum Microanalytical Research Centre 22 MpSys4 User s Manual Working with a spectrum in a spectrum window When working with spectra it is necessary to ensure the spectrum you wish to work with has the focus This will ensure all commands and modifications apply to the correct spectrum The spectrum with the current focus is shown by the row of astericks flanking the name of the spectrum in the title bar To give the spectrum the focus simply left click the mouse on the spectrum area not the frame or title bar Spectrum control buttons E 10 14 E2 keV Ultra Legge 1 49496 1 16 1048 To display a spectrum on the screen
34. es the highlighted element from the list The add button pops up a new window where the name of the element can be specified by either typing in the chemical element symbol or Ge H A Pl selecting the periodic table and clicking on the desired element k Shell A Apply Cancel Microanalytical Research Centre MpSys4 User s Manual Resizing spectra A complete 8k channel MpSys energy spectrum typically has the interesting part compressed into a relatively small number of channels So the full spectrum needs to be expanded KR Spectrum View Calibration Elements 2000 1000 T T 5000 15000 25000 03295 822 El keV pips 27360 8 132765616 This example shows the situation where a 1 k channel RBS spectrum appears in the first eighth of a full energy spectrum The next example shows the spectrum expanded by the F3 special function key ei Spectrum View Calibration Elements 4000 E El ke pips 5565 13 1 5860 95 This shows that in addition to the use of the spectrum control buttons on the task bar described in the previous section it is also possible to resize the spectrum via mouse functions and the special function keys on the keyboard The special function keys are F3 Perform an automatic spectrum resize to expand the non zero channels in the spectrum into the spectrum window In the above RBS spectrum the spectrum has Microanalytical Research Centre 29 MpSys4 User s Manual been
35. hape the energy spectrum for the region of interest 5 Further processing of the energy spectra from roi s with other software packages e g nufit RUMP GUPIXE etc Lu Video1p evt E Event by event GC data file ai in time order Video1p sd Video1p sp Video1p map Video1pA img Sorted data file Sorted pointer Intensity map Energy Events sorted file for sorted from window spectrum from into position order data file in energy spectrum roi in map Each step in this process is described in more detail in the following sections of this manual Microanalytical Research Centre 7 MpSys4 User s Manual 2 Starting MpSys MpSys is started from the command line prompt of a Unix X window On some systems an icon on the desktop may be used to invoke MpSys Several arguments may be added to the command to modify the characteristics of MpSys when it starts Most users will simply type mpsys at the Unix command line praxis dnj ldata dnj runl mpsys Below is the full command line specification for running MpSys mpsys login_macro display dname fontc namel fontl name2 fonte name3 font name4 fg fcolor bg bcolor bd bdcolor geom geom The MpSys macro file login_macro will be executed first if it exists It will be searched for in HOME macros If a macro is not specified the default login macro login mp will be executed if it is found dname is the name of the X Windows display address you want to use for d
36. he performance or use of any of its products The foregoing limitation of liability shall be equally applicable to any service provided by Micro Analytical Research Centre Note No part of this publication may be reproduced stored in a retrieval system or transmitted in any form or by any means electronic mechanical photocopying or otherwise without the prior written permission of MARC Manual Version 1 0 Manual Date January 2002 Microanalytical Research Centre 1 MpSys4 User s Manual 2002 Microanalytical Research Centre Microanalytical Research Centre MpSys4 User s Manual Table of Contents 1 2 INTRODUCTION ege ee En ere ere 5 STARTING MPSYS ee eg 8 ON LINE HELENE ARERR Osa 8 LAOS YAA o A A 9 THE FUNCTION BUTTON Sesso a e ost est eveesaevceststteseessbev esse erties Sesh dE EE Eed ica 9 EXAMPLE DESK TOP nasa 11 STARTING A RUN A ii 12 SETTING THE EXPERIMENTAL PARAMETERS IN THE JOURNAL PUP 13 WORKING WITH A SPECTRUM IN A SPECTRUM WINDOW cccsssssssseessessescesessesscoecsscssessessecaesaesaeeaeeaeeenes 23 KT 23 Calibrating ARNES DEAN is Elemental a Using the element selection button Resizing pecht Unknown element identification secccsesesesesesereresesereeseeseseseseseseseseseseaeseseaeaeaeseaeaeaeaes GENERATING A TUNED DISPLAY OR MAP FROM WINDOWS SET IN A SPECTRUM EXTRACTING SPECTRA FROM MAPS THE MAIN MENU BAR ec tite WORKING WITH MAP WINDOWG cscsccscssscssscssss
37. he top buttons w Select value e The left button Element allows the chemical symbol for the element to be selected SE e The right button Value allows the correct energy Element Zn A Pl of the signal to be entered by hand in the value box With the Element option and the station set to X ray app Cancal it is possible to choose the chemical symbol corresponding to the marked signal by typing directly into the box In the example shown here the element has been typed into the element box and the relevant x ray line for the element has been selected from the Shell window Of course not all elements have all K L and M lines likewise some elements have entries in the data base for more than one x ray line Only the most intense x ray line for the selected shell for the element may be used for calibration purposes See further discussion of the data base below Instead of typing the element chemical symbol it is possible to click on the periodic table button a and select the element from the pop up periodic table The remainder of the calibration is as before 9 With the first element marked MpSys marks the element and is now ready to receive a second marked element So steps 6 to 8 must be repeated for additional elements When the additional elements are marked they appear in the uncalibrated spectrum EES EE Spectrum View Calibration Elements fol Al t e gt 2 z 8 7 Cy pee Sr K E2 channels U
38. isplaying all MpSys windows An example address could be marc physics unimelb edu au 0 0 name commands text font name name labels text font name name exponents font name name4 general text font name fcolor foreground colour of X Windows bcolor background colour of X Windows bdcolor border colour of X Windows geom allows you to specify initial size and position of commands window where geometry is given as width x height x y in pixels On line Help The help files are also available on line while using MpSys and are accessed by typing help lt topic gt Where lt topic gt is the capitalised topic name in the following listing Please remember however to type the topic name in lower case letters to be compatible with MpSys and the UNIX operating system under which MpSys runs Microanalytical Research Centre 8 MpSys4 User s Manual 3 MpSys Quick Start This section provides a brief introduction to MpSys and describes how to perform the most common application the collection and display of images and spectra After starting MpSys from the unix command prompt the main MpSys window appears Experiment Data Journal Maps Spectra Welcome to MPSYS Microprobe data acquisition and analysis system Version 4 Revision A3 Copyright 1997 2001 Microanalytical Research Centre MARC with contributions by Arthur Sakellariou and Andrew Bettiol Microanalytical Research Centre Emaili marc physics unimelb edu au School of Physic
39. ixels producing caian resolton Je e ke Can Scan width Physical length of xaxis scan __oan width ong scan height Physical length of y axis scan Lean height Ra A 00 0 Sale kommscio Be fo Count Number of complete scans overiscan count l pecimen Dither O y dwe ee Interlace Scan every alternate scan line can interlace yesno O EES Trigger ype of trigger source for creatingjscan trigger RT clock cans Clock Dwell time used for clock scaniscan clock R 1000 0 e mode Events Number of external events used toscan events 1 advance the scan in external or data scan modes Deadtime Description Setname be Beta Mode for deadtime detection deadtine mode RT none ull pseudo or none n deadtime charge_resolut l ion ill beam blanking be usedideadtime blanking yesno jno hen obtaining deadtime information Microanalytical Research Centre 62 MpSys4 User s Manual Station parameters General S Detector name kidetectoname Detector type b eeer ype Radiation detected A radiation _detect eA EE SE dista E EE Coarse gain stX coarse_gain Fine gain b nn Bias voltage bg voltage pe JL er LI Elements b aemege Microanalytical Research Centre MpSys4 User s Manual 9 File Formats MpSys raw event data evt The MpSys event by event file extension evt is the standard raw data file generated when collecting data It is a se
40. ltra Legge 443 1 511 Microanalytical Research Centre 25 MpSys4 User s Manual 10 With two or more elements marked the calibration can now be calculated and applied to the spectrum This is done from the calibration option on the task bar of the spectrum window Select calibrate on the pull down menu 11 Now the calibration is applied to the spectrum and the caption on the horizontal axis changes as an indication that the spectrum is now calibrated In addition the actual values of the calibration can be seen in the relevant slots in the journal menu accessed by the journal file button d El Spectrum View Calibration Elements 7 10 14 18 E2 kel Ultra Legge 18 9219 1 20 0344 12 Once the calibration has been applied the new calibration must be saved in the journal file associated with the run This is done from the pull down menu associated with journal on the main menu If the calibration has been done during a run then the close command or button click automatically saves the calibration in the journal file Once the spectrum is calibrated the list of elements associated with the station will be displayed See the discussion of spectrum windows for more information Microanalytical Research Centre 26 MpSys4 User s Manual Element labels For RBS and x ray type detectors it is possible to label the position of element signals in the corresponding spectrum This feature only works of the correct experi
41. m windows if the calibrated parameter is yes Field type text Default value keV X calibration label stX x_cal_label Y calibration label stX y_cal_label Label used for the x axis of X and Y windows if the calibrated parameter is yes Field type text Default value Microns Normalise on charge stX norm_on_charge A boolean statement to determine whether to normalise the y axis of energy spectra for this station Normalisation occurs by dividing the y axis counts by the total integrated charge also a parameter Field type yes no Default value no Microanalytical Research Centre 51 MpSys4 User s Manual 6 The Skip Language Skip stands for Simple Kommand Interface Package Skip is a powerful command processing and programming language It is written to be used as an interface between the user s keyboard and interactive programs Beginning users will find the command aliasing and calculator useful More advanced users and programmers may use the full programming language available Skip is programmed using a syntax quite similar to C and awk Programmers will find that Skip interfaces easily to most pre existing programs You can easily add a great deal of power and flexibility to your interactive programs by adding Skip to the front end of your command processor Command aliasing You may reduce the amount of typing you do by defining aliases for common command sequen
42. me is provided It is best to use a dwell time greater than 1000 ms if magnetic scanning is used This will prevent eddy currents in the beam tube from causing double imaging of edges in the scan region Charge advances the scan after a set number of charge counts have been counted A slot for entering the desired number of charge counts is provided An appropriate charge digitiser unit is required to be connected to the charge input on the rear of the MicroDas interface unit A suitable unit would have a sensitivity of at least 10 Coulombs pulse Charge mode is the most common mode of operation of the system External advances the scan after a set number of external events have been counted from the external input of the MicroDas unit In other respects the operation of the External mode is similar to the Charge mode Events advances the scan after a set number of energy events have been counted This mode is typically used with IBIC experiments where the sample can be expected to produce an IBIC signal at every pixel of the scan In an IBIC experiment the contrast in the image is provided by variations in the energy of the signal not in the intensity of the signal This mode is also appropriate for STIM CSTIM experiments Note that only a single station should be in use for this mode to work correctly The true scan size of the beam on the sample will be given by the following formula X size micron k N MicroDas X gain Width 100 Scale
43. mental parameters have already been set in the journal file and the energy spectrum is calibrated As discussed in the previous sections elements are associated with a spectrum using the element selection menu The x ray line labels In an x ray spectrum the x ray lines for a selected element are drawn as a mini intensity histogram For elements with more than one x ray line corresponding to decays to the selected shell the K lines L lines or M lines the x ray lines are drawn with a length proportional to the intensity of the line The following example shows this Spectrum View Calibration Elements 18 18 7511 1 20 0344 RBS surface energy labels In a RBS spectrum the elements are identified by arrows drawn at the surface energy for each element selected AAA A BERGBEEEL 1 1500 El keV pips 3170 98 134668 The element selection button is discussed in the next section Microanalytical Research Centre 27 MpSys4 User s Manual Using the element selection button The element selection button allows the user to select the elements to have their signals labeled in the spectrum For this feature to work correctly the essential experimental parameters must already have been set in the journal file Clicking on the element selection El button pops up the list of elements associated with the spectrum Clicking on add allows a new element to be added to the list Clicking on delete delet
44. menu item runs MpSort for sorting event by event files and producing the sorted data files Journal This menu provides access to the journal file As discussed earlier the journal file is a macro i e a list of MpSys commands that holds the experimental parameters associated with a run show Save Show provides access to the journal editing screens allowing experimental data to be loaded and reviewed See the section titled Setting the experimental parameters in the journal file earlier in this manual for a detailed discussion of the journal file save as default Print Save is used to save the journal file after any changes have been made after the run has commenced So if you make changes or corrections to the journal file such as corrections to the energy calibration or changes to the experimental parameters it is important to click on Save to save changes Save as default is used to save the current journal file as the default journal file This will be used to configure MpSys when it is first started from the Unix shell Print is used to print the parameters of the journal file for future reference Microanalytical Research Centre 37 MpSys4 User s Manual Maps Build using elements allows all the maps associated with the present data to be recreated from the lists of elements associated with each station Build using elements Save All allows all the current maps to be saved
45. mouse pointer anchored on this starting point 3 Continue moving the mouse around the region to point to the perimeter of the region of interest while clicking with the left mouse button This will draw a continuous line around the perimeter of the region of interes 4 Complete the line around the perimeter of the region of interest to conclude drawing the shape by clicking the middle mouse button 5 If you make a mistake type the command shape x in the MpSys command window This will clear the shape and allow you to start again Microanalytical Research Centre 34 MpSys4 User s Manual 6 Extract the spectrum from the shape with the extract command typed in the MpSys command window See the documentation on the extract command in the command section of this manual 7 Example extract s stn 2 videop1A This command will extract a spectrum into a new window videop1A from the detector of station 2 stn 2 while also shading s the shape to confirm the region from which the spectrum has been extracted This shows the appearance of the map after the spectrum has been extracted fal SEN pe LJ Map Tune Extract The white rectangle is the shaded shape The extracted spectrum appears in a new window that pops up when the extract is complete as shown here 1 10 03441062 E2 ke SitLi gt 6 67516 1 50 7814 Note that is not necessary to draw the shape in a map window derived from the same detector from which the spe
46. multi user environment extreme robustness no blue screen of death or general protection fault common under Windows After two years experience with the new system and sales to several other laboratories worldwide the new system has shown its qualities very well But still some users prefer a Windows environment instead of the less user friendly unix environment There can be no doubt that Windows offers many advantages except for data acquisition Fortunately MicroDas can be seamlessly integrated with a Windows environment This is accomplished by using a second Windows equipped computer to control MicroDas All the second computer requires is a X server program such as the excellent DEC product eXcursion running under Win3 1 Win95 Win98 WinNT or later Microanalytical Research Centre 70 MpSys4 User s Manual An icon on the Windows machine desktop invokes MpSys on the linux machine and pops up the MpSys graphical user interface The data disk on the unix machine is mapped to a network drive on the Windows machine The user does not even know they are running a process on a unix machine All functions of the power of the unix system are provided with the convenience of the Windows environment With this way of running MpSys the user has the convenience of being able to control the data acquisition system from ANY suitably equipped Windows PC In the laboratory in the office at home overseas Also advanced users can
47. n the task bar of the map window click on the type of map appropriate for the present state of the system e Map if you are in the process of analysing data off line e Tune if you are collecting data and wish to see the map appear as the data is collected Map Tune H A From the resulting pop up window click on the station number for the selected detector Choose from markers or element to select the desired window method If element was selected a new pop up window allows the element to be selected The map specification process is now complete a yellow bar will appear in the energy spectrum labeled with the name of the map Microanalytical Research Centre 32 MpSys4 User s Manual Spectrum View Calibration Elements 6 10 5 10 4 10 3 10 2 10 1 10 0 10 10 18 03146098 E2 keW Ultra Legge 1 49496 1 16 1048 In this example element windows have been selected for Si S K Ba L Fe Ni Zn K Sr and Y K Marker windows were specified for Zn K and Y K Two of the resulting maps are shown here ir SN Map Tune Extract f i j 1 f Other map features The menu on the map task bar gives access to a number of different possible map operations as well as a convenient way of regenerating the map from new spectrum windows This table summarises the sub menus of the map menu Microanalytical Research Centre 33 MpSys4 User s Manual Station X Markers Create map using
48. of the unknown element With the mouse pointing to the unknown signal type I for Identify on the keyboard The case does not matter MpSys will then search the appropriate data base for the unknown element with the energy closest to the identified signal The energy separation between the identified signal and the data base entry will be shown in a list of possible elements In the case of the x ray data base the relative intensity of each line will also be listed The number of possible elements in the list depends on the energy resolution of the relevent detector for the station corresponding to the energy spectrum The energy resolution is entered as part of the journal file discussed elsewhere A detector with a poor energy resolution will produce a longer list of possible elements For example typing with the mouse positioned on the Fe K alpha x ray line in the energy spectrum below on this page produces the pop up window shown opposite 0 0536 1 0000 Clearly the most intense x ray lines in this list have the best chance of being the unknown line In this example the most likely unknown line is indeed Fe so this has been slected with a mouse click The line is highlighted Clicking on Ok will then cause the Fe x ray lines to be plotted on the spectrum see below al po videopt plots NES CODO 10 0 1 28333 E2 keV Ultra Legge 18 7511 1 20 0344 Microanalytical Research Centre 31 MpSys4 User s Manual Gener
49. or the various detectors in use These parameters will be stored with each run Click on the run button Ka to prepare the system for data collection At this time the general data window from the journal file also appears to allow you to confirm or change any of the run parameters Click on the start button e to start data acquisition and logging of the data to disk Once the system is running it is not possible to change the scan parameters If it is necessary to change the scan parameters it is best to start a new run In some circumstances rare if may be necessary to change the scan parameters during a run which can be done by stopping S the run changing the parameters then starting the run once again At the conclusion of the run stop the data acquisition by clicking the stop button EI then clicking the close button to close off data acquisition into the data file Further runs may be done by returning to step 4 Microanalytical Research Centre 12 MpSys4 User s Manual Setting the experimental parameters in the journal file Prior to collecting any data the experimental parameters need to be loaded into the journal file This is necessary because MpSys uses some of these parameters to display elemental information calculate energy calibrations or simply because it is good practice to keep a detailed record of the experimental parameters with each data file for future reference The journal file is accessed from the jo
50. or this station MpSys requires this parameter for displaying elements on energy spectrum windows as well as producing element maps Field type positive real number Unit keV Default value 0 0 Shaping time stX shaping_time This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit s Default value 0 0 Coarse gain stX coarse_gain The coarse gain setting on a spectrum amplifier module used to amplify the detector signal Microanalytical Research Centre 49 MpSys4 User s Manual This parameter is used for information purposes only and is not used by MpSys Field type positive real number Default value 0 0 Fine gain stX fine_gain The course gain setting on a spectrum amplifier module used to amplify the detector signal This parameter is used for information purposes only and is not used by MpSys Field type positive real number Default value 0 0 Bias voltage stX bias_voltage The voltage required to bias the detector for this station This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit V Default value 0 0 Filter stX filter This parameter is used for information purposes only and is not used by MpSys Field type text Default value blank Elements stX elements The elements that have been selected for displaying in the energy spectrum window for this station Field type text Default val
51. quentially created file which is made up of event packets that are appended to the file as data is collected Each event packet consists of three 16 bit data words representing e the energy level of the event e the X scan position at the time the event was collected e the Y scan position at the time the event was collected Included within each data word are two data bits describing which of the four data acquisition stations the event was collected with 15 015 015 0 Energy data word lt 8192 channels gt 15 14 13 12 0 Bits 0 12 make up the actual energy value which comprises a maximum of 8192 channels Bit 13 is reserved Bits 14 and 15 describe which station was used in collecting the event and the conversion table is shown below SO S1 Station 0 0 1 1 1 2 2 0 3 1 1 4 X data word lt 4096 channels gt ope To se 15 14 13 12 11 0 Bits 0 11 make up the actual X scan position value which comprises of a maximum of 4096 channels Bits 12 and 13 describe the station number similarly to how the energy data word describes it above Bits 14 and 15 identify the data word as an X data word as opposed to a Y data word This information is used by MpSys for error checking Microanalytical Research Centre 64 MpSys4 User s Manual Y data word lt 4096 channels gt COCO CA CIN pe 15 14 13 12 11 0 This word is the similar to the X data word except bits 14 and 15 are swapped Determining bad data words
52. r a fragment of old SSB detector silicon substrate with thin gold layer are suitable 3 Expose sample to the beam and collect an energy spectrum from all active stations by following the sequence new run SS start O wait stop E and close 4 A spectrum similar to this example PIXE from an Al Sr sample will appear Notice that this is an uncalibrated spectrum because the horizontal axis is in units of channels a nO gt gt gt gt EN Spectrum View Calibration Elements DR Hebbian 300 500 E2 channels Ultra Legge 442 1 511 24 MpSys4 User s Manual 5 If necessary clear the old energy calibration by clicking on calibration on the task bar of the spectrum window and select uncalibrate 6 Use the mouse to point to the first signal in the spectrum that corresponds to a known element in the standard sample In this case the large peak on the left is known to correspond to aluminium Al It is not necessary to click on the mouse buttons at this stage but this can be useful to provide a visual confirmation of the feature selected 7 With the mouse pointing at the known signal type M on the key board either upper or lower case is fine Be careful not to move the mouse while you do this 8 Now MpSys asks for the element that corresponds to the marked signal with a new pop up window This window allows the correct energy associated with the marked signal to be identified There are two options vap selected by t
53. r s Manual Example desk top This shows an example desk top configured by the user and stored in the journal file for future reference omea 1 Me Fer scent cop SOOM eit pet krit rat Zeg whi Journal Lrirrg is zm tone T w acroe thet en It zg cad wr ted cece File vangist GIZADI verte e gt M I wan N Aen Eet Lie tr maen TE rg do eol Jeet detal ce E charts Abr e eis It shows a typical configuration of MpSys for data collection on two stations showing spectrum and map windows Microanalytical Research Centre 11 MpSys4 User s Manual Starting a run The simplest way to start a run f Login to the data acquisition work station then set the directory to the local data area creating a new subdirectory for the current project if required Start MpSys from the command prompt If you have run before or if there is a system default journal file a series of spectrum windows will appear on the screen and the starting values of many parameters in the journal file will be loaded at this time If you have not run before create as many spectra and map windows as you like from the spectrum and map buttons Use the pull down menus on the task bar for the spectrum windows to connect them to the energy windows of the stations connected to detectors Click on the journal button ka to set the present experimental parameters such as the beam energy beam particle and parameters f
54. rch Centre 13 MpSys4 User s Manual Run Time The time of the run User Name The login name of the user Host Name The name of the workstation used to collect the data DaQ Name The name of the data acquisition system used to collect the data This is to distinguish the system from earlier versions of the hardware used with MpSys Experiment Joumal Window General General Beamline Beam Chamber Specimen Scanning Deadtime Run Name videop1 Station 1 Run ID 5363 Ss Station 2 Run Date 15 March 2001 Run Time 13 00 User Name Station 3 Station4 HostName marco ph unimelb edu au DAG Name MicroDAS Use Test Data The use test data window is used to connect MpSys to a file in the current directory called testdata evt for off line collection of data This is useful for demonstration or diagnostic purposes This reveals the sub categories of the Experiment category For use of some of the built in features of MpSys for elemental identification in spectra it is essential that the information in these sub categories be set correctly The parameters associated with the elemental identification features are enclosed in a box in the discussion to follow Microanalytical Research Centre 14 MpSys4 User s Manual Beam Line The first is Beam Line which holds parameters associated with the beam line itself General General Beamiine Beam Chamber Specimen Scanning Deadtime Experiment Beam line name
55. rea Energy Resolution The energy resolution of the detector Used in the automatic elemental mapping feature to set the width of the window placed in the energy spectrum about the element signal Shaping time The shaping time used on the spectroscopy amplifier for the detector Microanalytical Research Centre 20 MpSys4 User s Manual Coarse Gain Fine Gain Bias Voltage Scattering Angle The coarse gain used by the spectroscopy amplifier for the detector Similarly for the fine gain The detector bias voltage The angle between the straight through direction of the incident beam and the centre line of the detector in degrees In this convention the beam approaches the sample from a scattering angle of 180 Backscattering detectors therefore have scattering angles between 90 and 180 Filter Elements The name of any filter used over the front of the detector The list of elements associated with the station that will have their signals labeled on the energy spectrum These elements are set using the element selection menu button El on the task bar associated with a spectrum window A second example of the general category is shown here for an X ray detector Experiment Enabled Station 1 Detector Name Ultra Legge Station 2 Detector Type X Ray Radiation Detected Station 3 Station 4 Active Area Specimen Distance Energy Resolution Shaping Time Coarse Gain Fine Gain Bias Voltage Scatt
56. s Phone 61 3 9344 5433 University of Melbourne Fax 61 3 9347 4783 Parkville Australia 3052 Buffer sizes exyt50000 xy5t 50000 txy 2048 Last built Feb 8 2002 11 16 17 Loaded journal information in home 1dm macros default mp Mpsys gt This window gives quick access to all of the most frequently used MpSys functions The window may be resized by clicking and dragging on the corners MpSys can be controlled by two methods using this window The most convenient method is by use of the function buttons and the pull down menus from the task bar Advanced functions can be accessed from the command prompt window at the bottom of this window This provides access to the full power of the Skip command language embedded within MpSys and allows users to run macros of stored MpSys commands The function buttons Reading from left to right the function buttons are arranged the same sequence used to start a run A The run button prepares MpSys for a new run All data areas are cleared and the system is initialized ready to start the collection of data which will be stored in a new file At the same time the scanning menu appears to confirm the file name for the new data and allow any last minute changes to the scan parameters Note that the scan parameters cannot be changed after the run has started Once these parameters have been set the run is ready to Start E The start button causes the data collection to start Th
57. sed to specifiy the colour scale file to use when converting the map images into postscript This is important when printing maps on a black and white printer as the printer will try to approximate its own grey scales if a colour postscipt image is supplied Example for printing on a grey scale printer dump type map windows cul rb101_si cls grey Clearing Maps A map window originally used to display a tuned map during a run cannot be reused to display a map generated from sorted data unless it is cleared first Either use the command window and the command clear Or click on the map option on the task bar of the map window itself Closing Map windows To close a map window you can either 1 Select the close menu item in the map menu 2 Use the kill lt window name gt command Manipulating map colours The colour scale The colour scale used by all maps can be changed to possibly improve contrast and enhance important map features It can be changed by loading a new colour scale into memory or by manipulating in real time the colour tool To load a new colour scale either use the command line clscale lt colour scale filename gt or use the Maps option of the task bar of the MpSys main menu Note that the colour scale applies to all maps displayed on the screen It is not possible to individually change the colour scale of maps Grey scale colour scale Default spec colour scale Microanalytical Res
58. sitive integer number Default value 1 Charge resolution deadtime charge_resolution Field type positive integer number Default value 1 Blanking deadtime blanking Field type yes no Default value no Station Parameters General Enabled stX enabled A boolean statement as to whether this station is being used for data acquisition Field type yes no Default value no Microanalytical Research Centre 48 MpSys4 User s Manual Detector name stX detector_name The name of the detector associated with this station This parameter is used for information purposes only and is not used by MpSys Field type text Default value blank Detector type stX detector_type The type of detector used for this station Permissible values are x ray ros other Field type restricted text Default value x ray Radiation detected stX radiation_detected This parameter is used for information purposes only and is not used by MpSys Field type text Default value blank Active area stX active_area This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit mm2 Default value 0 0 Specimen distrance stX specimen_distance This parameter is used for information purposes only and is not used by MpSys Field type positive real number Unit mm Default value 0 0 Energy resolution stX energy_resolution The energy resolution of the detector used f
59. still unleash the power of unix for their projects The total cost of all the hardware and software required for the complete system is less than the cost of the VME crate alone in the previous generation data acquisition system End of Manual Microanalytical Research Centre 71
60. tation The detector parameters are required for the MpSys element identification features to work correctly This screen shows the General category for station 1 The screen is the same for the other three stations A Experiment Jounal Window ii General General E Calibration X Calibration Y Calibration Experiment Enabled Yes Station 1 Detector Name pips Station 2 Detector Type RES Radiation Detected 0 00000 Station 3 lt Active Area 50 00000 mm2 Station 4 specimen Distance 0 00000 mm Energy Resolution 12 00000 key Shaping Time 0 50000 us Coarse Gain H 00 F Fine Gain fi gt Bias Voltage 50 00000 y Scattering Angle 145 0000 deg Filter None Elements Ag Sik In LO k C k u l Cu Cancel The parameters for the general category for the detector connected to station have the following attributes Enabled This slot allows the station to be disabled in software feature not implemented in MpSys version 3 1 Detector Name The name of the detector can be entered in this slot This name will be used to label the axes of the E X and Y spectra associated with this station Detector Type Selects from rbs X ray or other This sets the data base to be used for elemental identification features Radn Detected Not used Active Area The area of the detector facing the sample Specimen Dist The distance of the detector from the sample Used to calculate the solid angle of the detector from its active a
61. th 2 bytes H Map height 2 bytes Each map intensity datum is 4 bytes Microanalytical Research Centre 68 MpSys4 User s Manual 10 MpSys X ray line database This matrix shows the number of x ray lines in the MpSys data base for each element pom ct fin ic be efe u bo Ly Cl Lee foa In Sn fs ls rete ES El majete rr fia mel Le fos fte fra 2 2 2 2 2 2 Ar 2 2 K 2 2 Ca 2 4 Sc 2 4 Ti 2 3 V 2 4 Sa SCHEER ES rl Ear En E pe je os leis ar fa ee 2 ES m fel Ea E jou 2 Fae Microanalytical Research Centre 69 MpSys4 User s Manual 11 Working with MpSys in a Microsoft Windows environment Based on a MARCO Technical Report October 1998 Many of our collaborators ask us if a PC version of the MpSys data acquisition system is available Surprisingly the answer is yes This section explains how this is done First a little history Over the past 15 years the MARC laboratory employed a wide variety of different computers to perform data acquisition and analysis The concept of Total Quantitative Scanning Analysis TASA pioneered by George Legge was implemented on each computer in a program we always called MpSys This was not always an easy task With each generation of computer the task never became easier as demande for more graphics intensive facilities became ever greater To meet the demands of TASA specialised hardware and
62. ue blank Calibration Energy Calibrated stX calibrated_e X Calibrated stX calibrated_x Y Calibrated stX calibrated_y A boolean statement as to whether the spectrum associated with this station has been calibrated or not MpSys reads this parameter every time it draws or redraws a spectrum window If the value is yes then MpSys uses the parameters below to rescale the x axis Warning manually setting this value to yes without properly setting the actual calibration parameters will cause unpredictable rescaling of the x axis of the spectrum for this station Field type yes no Default value no Energy calibration a stX energy_cal_a Energy calibration b stX energy_cal_b Energy calibration c stX energy_cal_c Microanalytical Research Centre 50 MpSys4 User s Manual These are the parameters used for calibrating the energy spectrum for this station Field type real number Default value 0 0 X calibration a stX x_cal_a X calibration b stX x_cal_b X calibration c stX x_cal_c These are the parameters used for calibrating the X spectrum for this station Field type real number Default value 0 0 Y calibration a stX y_cal_a Y calibration b stX y_cal_b Y calibration c stX y_cal_c These are the parameters used for calibrating the Y spectrum for this station Field type real number Default value 0 0 Energy calibration label stX energy_cal_label Label used for the x axis of energy spectru
63. uent passes the scan fills in the skipped scan lines A scan is complete when all skipped scan lines are filled in This parameter is only used if the scan mode parameter is set to raster Field type yes no Default value no Trigger scan trigger Microanalytical Research Centre 47 MpSys4 User s Manual This parameter determines the trigger source use for creating the scan steps For internal triggering use the clock value To trigger on incoming data use the data value and to trigger on incoming charge use the charge value Permissible values are clock data charge Field type restricted text Default value clock Clock scan clock The dwell time for each scan step when the trigger is set to clock A figure less than 1000 can lead to eddy current ghosting when magnetic scanning coils are used Field type positive real number Unit s Default value 1000 0 Events scan events The number of external events to receive in the Event counter input at the back of the MicroDAS unit or data events before advancing the scan position This parameter is only used if the scan trigger setting is external or data Field type positive integer number Default value 1 Deadtime Mode deadtime mode Permissible values are none full pseudo Field type restricted text Default value none Timer resolution deadtime timer_resolution Field type po
64. urnal file button e on the main window This causes this pop up window to appear LPR Printer Name nt Experiment Station 1 station 2 station 3 Station 4 In the left hand panel are the categories within the journal file that hold the experimental and other parameters associated with the run They appear like the directories in a file manager and may be expanded by clicking on the category headings in the list The expanded list of parameters associated with each category appears in the right panel Experiment Clicking on the Experiment category pops up the same window Under Experiment appear the parameters associated with the individual run In the example shown above you can see the parameters in the General category These are Run Name The name of the run and contains the file stem used to generate the file names for the event by event data file the spectra file and the journal file In the example shown these would be videop1 evt videop1 img and videop1 mp If you select a Run Name with an embedded number MpSys will automatically increment this number for subsequent runs So in this example MpSys will choose video2p as the next Run Name Run ID A global run identification number that is stored in a system area and incremented each time any user starts a new run on the workstation This allows each run to be uniquely identified if the user reuses old run names Run Date The date of the run Microanalytical Resea
65. vet files with the command mpsort lt event by event file stem gt MpSys will read sorted data files to produce maps etc Microanalytical Research Centre 66 MpSys4 User s Manual MpSys spectra files img This file contains spectra information for Energy and X and Y beam scan positions for four data collection stations It consist of 4 byte words representing an event count inside a given Energy X or Y channel The size of the IMG file is NUM_STATIONS NUM_ENERGY_CHANNELS 4 bytes NUM_STATIONS NUM_X_CHANNELS 4 bytes NUM_STATIONS NUM_Y_CHANNELS 4 bytes 4 8192 4 4 4096 4 4 4096 4 256 kilobytes The file is structured as follows Energy X Y Station 1 Station 4 Station 1 Station 4 Station 1 Station 4 0 8192 0 8192 O 4096 O 4096 0 4096 O 4096 MpSys 2 X allowed use of simplified IMG files which had only enough spectrum information for one station as well as for one of Energy X or Y MpSys 3 encourages use of the complete IMG file for all four stations as there is no means of telling within a simplified IMG file exactly what station the spectrum was collected on Microanalytical Research Centre 67 MpSys4 User s Manual MpSys Map files map Mpsys MAP files are binary data files containing energy intensity information over a scanned region The structure of the MAP file is shown below Bytes 1 1 2 2 W H 4 X Future expansion unused in MpSys 2 X W Map wid
66. which holds all the experimental parameters associated with the run This macro is used to reconfigure MpSys to the parameters associated with the run in the future This combination of event by event data and the MpSys command macro means that the entire experiment can be replayed off line and no data associated with the experiment is discarded After the run has concluded the event by event file may be sorted and the data redisplayed in a variety of formats Some of the possibilities are illustrated in the following diagram Data Set Data Display y E z e Image Y y x Energy Spectrum Y y D Ee 7 x Line Scan y E RBS Tomography Microanalytical Research Centre 6 MpSys4 User s Manual The typical steps tp data processing wth MpSys is illustrated in the following diagram The steps may be summarised as 1 Run MpSys and collect data from an experiment Data collected into an event by event file evt and an associated file of containing the energy x and y spectra from each station img 2 Sort the event by event file to produce a sorted data file sd and its associated sorted pointers file sp 3 Load the sorted data file into MpSys and create maps from energy windows set in the energy spectrum map 4 Draw shapes in a map to define a region of interest roi on the sample Extract from the s
67. while data is being collected Microanalytical Research Centre 57 MpSys4 User s Manual Spectra Commands Gemen o oo Comet 1 bow o A AAA Expand Extract Co ee Load AAA Right Save Show Display elements in a spectrum Showrange Spectrum Create a spectrum within a plot window sum eure all counts within a specified range in a spectrum a Uncalibrate Uncalibrate a spectrum Unzoom Microanalytical Research Centre MpSys4 User s Manual Map Commands Petz eet a new colour scale into memory Co Display the colour tool for adjusting map window colours Load a map file into a map window Ctoo Load Map Create a map within a map window hape S Save a map to a map file S Shape ede and manipulate shapes inside a map window File system commands E d i the current directory Directory listing Microanalytical Research Centre 59 MpSys4 User s Manual 8 Journal parameter summary Field types are given by T Text RT Restricted text Integer number R Real number I Positive integer number R Positive real number YN Yes or No Default settings of mean that the setting is blank General parameters Name pese pion bam De Defaut Printer Name ee of printer for dumping windows Experiment parameters General Name pesempion Bet name Des faut Run ID GEN identification for current datarun_id l Run date pateotexperiment mee t Ho

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