WIN-EPRVersion: 921201

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written by

Dr. Herbert Thiele, Jürgen ErstlingBRUKER-FRANZEN Analytik GmbH, Bremen, Germany

Dr. P. Such und Dr. P. HöferBRUKER Analytische Messtechnik GmbH, Rheinstetten, Germany

December 1992

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Contents

Introduction ..............................................................................................................................................................1Hardware Requirements and System Configuration .............................................................................................1Installing WIN-EPR .................................................................................................................................................3

Chapter 1: The BRUKER WIN-EPR SYSTEM ............................................................................................51.1 The File Menu ................................................................................................................................5

Load .............................................................................................................................................6Save as .........................................................................................................................................6Connect .......................................................................................................................................7Status ...........................................................................................................................................8Status Directory .........................................................................................................................9Print ...........................................................................................................................................10Printer Setup .............................................................................................................................10Copy ..........................................................................................................................................10Exit ............................................................................................................................................10

1.2 The WIN-EPR System Menu ........................................................................................................11Spectr. Manipulation ................................................................................................................11Algebra ......................................................................................................................................11Show ..........................................................................................................................................112D-Processing ..........................................................................................................................11Document ..................................................................................................................................11

1.3 The Data Transfer Menu ................................................................................................................12

1.4 The Option Menu ...........................................................................................................................12Colors ........................................................................................................................................12Display Fonts ............................................................................................................................13

1.5 The Help Menu ...............................................................................................................................13About .........................................................................................................................................13

Chapter 2: The Operating Mode -Spectrum Manipulation- ..............................................................152.1 The File Menu ................................................................................................................................16

Load ...........................................................................................................................................16Save as .......................................................................................................................................16Status .........................................................................................................................................17Status Directory .......................................................................................................................17Printer Preview .........................................................................................................................17Print ...........................................................................................................................................18Printer Setup .............................................................................................................................18Copy ..........................................................................................................................................18Exit ............................................................................................................................................18

2.2 The Spectrum Manipulation Menu ...............................................................................................19Filter ..........................................................................................................................................19

Moving Average .........................................................................................................19Polynomial Filter ......................................................................................................19

Resolution Enhancement .........................................................................................................20FFT and inverse FFT .................................................................................................................21

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Phase Correction ..................................................................................................................... 22Interactive .................................................................................................................. 22Manual ........................................................................................................................ 22Return ......................................................................................................................... 22

Window function ..................................................................................................................... 23a. exponential ............................................................................................................. 23b. biexponential ......................................................................................................... 23c. gaussian .................................................................................................................. 23d. hamming ................................................................................................................. 24e. hanning ................................................................................................................... 24f. trapezoidal .............................................................................................................. 24g. rectangle ................................................................................................................ 24h. inv. rectangle ......................................................................................................... 24i. sinebell ................................................................................................................... 25j. sinebell squared ..................................................................................................... 25

inverse FFT ............................................................................................................................... 25Manipulate ................................................................................................................................ 26

Offset Correction ..................................................................................................... 26Flip ............................................................................................................................. 26Calibrate ..................................................................................................................... 26Shift ............................................................................................................................ 26Zero filling ................................................................................................................ 26Reduce ....................................................................................................................... 26Multiplicate ............................................................................................................... 27Logarithm .................................................................................................................. 27Exponential ................................................................................................................ 27Absolute Value .......................................................................................................... 27

Manipulate complex data ........................................................................................................ 27Delete Part ................................................................................................................. 27Swap to complex ....................................................................................................... 27Magnitude Calculation .............................................................................................. 27Power Calculation ..................................................................................................... 27

Integrate .................................................................................................................................... 28Differentiate ............................................................................................................................. 28

Baseline Correction ............................................................................................................. 29Define Points ........................................................................................................................... 30Define Region .......................................................................................................................... 30Functions .................................................................................................................................. 30

Extrapolate ................................................................................................................. 30Two Point ................................................................................................................... 30Point to Point ............................................................................................................ 30Cubic Spline .............................................................................................................. 30Constant ..................................................................................................................... 30Linear ......................................................................................................................... 30Quadratic .................................................................................................................... 30Cubic .......................................................................................................................... 304-th Order .................................................................................................................. 305-th Order .................................................................................................................. 306-th Order .................................................................................................................. 30

Subtract ..................................................................................................................................... 31Replace ..................................................................................................................................... 31Offset Correction .................................................................................................................... 31Real <=> Imaginary ................................................................................................................. 31Return ....................................................................................................................................... 31

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Integrate Region ....................................................................................................................32Define Integrals ........................................................................................................................33Integral Type .............................................................................................................................33Integral modification ...............................................................................................................33

Select ..........................................................................................................................33Normalize ...................................................................................................................33Scaling ........................................................................................................................33Slope + Bias ...............................................................................................................33Erase ...........................................................................................................................33

Automatic Scaling ....................................................................................................................34Delete ........................................................................................................................................34Report ........................................................................................................................................34Return ........................................................................................................................................34

Peak Picking ...........................................................................................................................35Define Region ..........................................................................................................................35Parameter ..................................................................................................................................36Process ......................................................................................................................................36Report ........................................................................................................................................37Return ........................................................................................................................................37

Deconvolution ........................................................................................................................38Define Region ..........................................................................................................................38Automatic Fit ............................................................................................................................38Edit ............................................................................................................................................39Add Peaks ..................................................................................................................................40Delete Peak ...............................................................................................................................40Delete all Peaks ........................................................................................................................40Process ......................................................................................................................................40Show All ....................................................................................................................................40Fit ...............................................................................................................................................40Sum ............................................................................................................................................40Difference .................................................................................................................................40Tick Marks ................................................................................................................................40Report ........................................................................................................................................41Store Fit ....................................................................................................................................41Return ........................................................................................................................................41

WIN-EPR System ....................................................................................................................422D-Display ................................................................................................................................42

2.3 The Parameters Menu ....................................................................................................................43List Parameter ..........................................................................................................................43Change Parameter ....................................................................................................................44Comment ...................................................................................................................................44List Data File ............................................................................................................................44Update Extrema ........................................................................................................................44

2.4 The Display Menu ..........................................................................................................................45Scaling .......................................................................................................................................45

-Times two (keyboard equivalent F5) ......................................................................45-Divide by two (F6) ...................................................................................................45

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-Offset plus (F7) ....................................................................................................... 45-Offset minus (F8) .................................................................................................... 45

Expand ....................................................................................................................................... 46Reset ......................................................................................................................................... 46Split Screen .............................................................................................................................. 46Compare, Restore, Substitute ................................................................................................. 47View .......................................................................................................................................... 47Distance .................................................................................................................................... 48Display ...................................................................................................................................... 49Data Type .................................................................................................................................. 49

2.5 The Options Menu ......................................................................................................................... 50Y-Axis ....................................................................................................................................... 50g-Factor .................................................................................................................................... 50Grid ........................................................................................................................................... 50Annotate .................................................................................................................................... 50Colors ....................................................................................................................................... 50Display Font ............................................................................................................................. 50

2.6 The Help Menu .............................................................................................................................. 50

Chapter 3: The Operating Mode - Algebra- ....................................................................................... 513.1 The File Menu ................................................................................................................................ 52

3.2 The Algebra Menu ......................................................................................................................... 52X-Alignment ............................................................................................................................. 52Interactive X-Align .................................................................................................................. 52Y-Alignment ............................................................................................................................. 53Constant setting ....................................................................................................................... 53Addition .................................................................................................................................... 53Subtraction ............................................................................................................................... 53Multiplication .......................................................................................................................... 53Division .................................................................................................................................... 53WIN-EPR System .................................................................................................................... 53

3.3 The Parameters Menu ................................................................................................................... 54List Parameter .......................................................................................................................... 54Comment .................................................................................................................................. 54List Data File ............................................................................................................................ 54

3.4 The Display Menu .......................................................................................................................... 54Scaling ...................................................................................................................................... 54

-Times two (keyboard equivalent F5) ...................................................................... 54-Divide by two (F6) ................................................................................................... 54-Offset plus (F7) ....................................................................................................... 54-Offset minus (F8) .................................................................................................... 54

Expand ....................................................................................................................................... 54Stacked Plot and Overlay Plot ................................................................................................ 54Reset ......................................................................................................................................... 54View .......................................................................................................................................... 55Display ...................................................................................................................................... 55Data Type .................................................................................................................................. 55

3.5 The Options Menu ......................................................................................................................... 55Y-Axis ....................................................................................................................................... 55g-Factor .................................................................................................................................... 55Grid ........................................................................................................................................... 55Annotate .................................................................................................................................... 55Colors ....................................................................................................................................... 55

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Display Font ..............................................................................................................................55

3.6 The Help Menu ...............................................................................................................................55

Chapter 4: The Operating Mode - Show - ............................................................................................574.1 The File Menu ................................................................................................................................58

4.2 The Show Menu ..............................................................................................................................58Number of Slices .....................................................................................................................58WIN-EPR System ....................................................................................................................58

4.3 The DisplayMenu ...........................................................................................................................59Expand .......................................................................................................................................59Reset ..........................................................................................................................................59Display ......................................................................................................................................59Data Type ..................................................................................................................................59

4.4 The Options Menu ..........................................................................................................................60Y-Axis .......................................................................................................................................60Grid ............................................................................................................................................60Colors ........................................................................................................................................60Display Font ..............................................................................................................................60

4.5 The Help Menu ...............................................................................................................................60

Chapter 5: The Operating Mode -2D Processing- .............................................................................615.1 The File Menu .................................................................................................................................61

Load ...........................................................................................................................................61Save as .......................................................................................................................................61Change to Slice .........................................................................................................................61Save Slice ..................................................................................................................................61Save Projection ........................................................................................................................61Status .........................................................................................................................................61Status Directory .......................................................................................................................61Mix Spectra ...............................................................................................................................622D Algebra ................................................................................................................................63Print ...........................................................................................................................................64Printer Setup .............................................................................................................................64Copy ..........................................................................................................................................64Exit ............................................................................................................................................64

5.2 The 2D-Processing Menu .............................................................................................................65FFT .............................................................................................................................................65Phase Correction ......................................................................................................................66Window Function .....................................................................................................................66Manipulate ................................................................................................................................66

Exchange F1<->F2 ....................................................................................................66Offset Correction ......................................................................................................66Flip ..............................................................................................................................67Calibrate .....................................................................................................................67Shift ............................................................................................................................67Zero filling .................................................................................................................67Reduce ........................................................................................................................68Eliminate ....................................................................................................................68Multiplicate ................................................................................................................68Logarithm ...................................................................................................................68Exponential ................................................................................................................68

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Absolute Value .......................................................................................................... 68Manipulate complex data .......................................................................................... 69Swap to complex ....................................................................................................... 69Magnitude Calculation .............................................................................................. 69Power Calculation ..................................................................................................... 69

Integrate .................................................................................................................................... 69Differentiate ............................................................................................................................. 69

Baseline Correction ............................................................................................................. 70Define Region ........................................................................................................... 70Auto. Subtract ............................................................................................................ 70Auto. Replace ............................................................................................................ 70Extrapolate ................................................................................................................. 70Baseline Functions .................................................................................................... 70Subtract ...................................................................................................................... 70Replace ...................................................................................................................... 70Real<=>Imaginary .................................................................................................... 71Return ......................................................................................................................... 71

Volume Integration ............................................................................................................... 71Define Region ........................................................................................................... 71Duplicate Region ...................................................................................................... 71Report ........................................................................................................................ 71Return ......................................................................................................................... 71

Peak Picking .......................................................................................................................... 72Define Region ........................................................................................................... 72Parameter ................................................................................................................... 72Process ...................................................................................................................... 72Report ........................................................................................................................ 72Return ......................................................................................................................... 72

WIN-EPR System .................................................................................................................... 73

5.3 The Parameters Menu ................................................................................................................... 73List Parameter .......................................................................................................................... 73Change Parameter .................................................................................................................... 73Comment .................................................................................................................................. 73Update Extrema ........................................................................................................................ 73

5.4 The Display Menu .......................................................................................................................... 74Scaling ...................................................................................................................................... 74

-Times two (keyboard equivalent F5) ...................................................................... 74-Divide by two (F6) ................................................................................................... 74-Offset plus (F7) ....................................................................................................... 74-Offset minus (F8) .................................................................................................... 74

Expand ....................................................................................................................................... 75Reset ......................................................................................................................................... 75View .......................................................................................................................................... 75Scan ........................................................................................................................................... 75Distance .................................................................................................................................... 76Mode ......................................................................................................................................... 77

Contour Plot .............................................................................................................. 77Density Plot ............................................................................................................... 77Stacked Plot ............................................................................................................... 78Scan Plot .................................................................................................................... 78Settings ...................................................................................................................... 79

Levels ........................................................................................................................................ 80

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Change all ...................................................................................................................80Change one Level ......................................................................................................81Automatic Levels .......................................................................................................81Intensity Range ..........................................................................................................82Threshold ....................................................................................................................82Color Palette ..............................................................................................................83

Layout ........................................................................................................................................83None ...........................................................................................................................83Skyline Projection .....................................................................................................83Sum Projection ..........................................................................................................83Slice ............................................................................................................................83Slice Numerical .........................................................................................................84

Data Type ..................................................................................................................................84

5.5 The Options Menu ..........................................................................................................................84Axis ............................................................................................................................................84Grid ............................................................................................................................................84Colors ........................................................................................................................................84Display Font ..............................................................................................................................84

5.6 The Help Menu ...............................................................................................................................84

Chapter 6: The Operating Mode -Document - .....................................................................................856.1 The File Menu ................................................................................................................................86

6.2 The Edit Menu ................................................................................................................................86Create ........................................................................................................................................86Delete ........................................................................................................................................86Move ..........................................................................................................................................86Resize ........................................................................................................................................87Fill Text .....................................................................................................................................87Fill Parameter ...........................................................................................................................87Paste ..........................................................................................................................................87Characteristics ..........................................................................................................................87Shift up / Shift down .................................................................................................................88

6.3 The Help Menu ...............................................................................................................................88

Chapter 7: -Data transfer- ...........................................................................................................................897.1 Data transfer using GETEPR.EXE ................................................................................................89

7.2 FTP ..................................................................................................................................................89Installing Schneider&Koch Ethernet interface boards .........................................................89

SK Junior board .........................................................................................................89SK G8 / G16 board ....................................................................................................89

Installing Western Digital interface boards ..........................................................................90Installing FTP Software ...........................................................................................................90

7.3 Data transfer ...................................................................................................................................91Automatic data transfer to PC using FTP/TCPIP - software ................................................91Data transfer between PC and other workstations .................................................................91FTP - Setup ...............................................................................................................................93Get/Send EPR-Files .................................................................................................................94Manual transfer .........................................................................................................................95

7.4 Kermit .............................................................................................................................................96Setup Kermit .............................................................................................................................96Data transfer from OS/9 mainframe to PC ............................................................................96

7.5 Exit ..................................................................................................................................................96

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7.6 Trouble shooting ............................................................................................................................ 97Error messages from GETEPR.EXE ..................................................................................... 97

Appendix .................................................................................................................................................... 99The EPR.INI File .................................................................................................................................... 99The GETEPR.INI File ...........................................................................................................................101The BRUKER.INI File .........................................................................................................................101

IntroductionThe BRUKER WIN-EPR program is written for operators of BRUKER ESP series electron spin resonancespectrometers who do not want to do data treatment on the spectrometer computer but on an external PC.The reasons may be:

• limited measuring time in a workgroup• the wish to perform mathematical manipulations to spectra at your desk• preparing spectra for immediate use with a word processor or DTP program

Looking at its capabilities for data manipulations, WIN-EPR is comparable to the ESP 300 program runningon the ESP 3200 spectrometer computer. As WIN-EPR is a WINDOWS® application MS-DOS® and MS-WINDOWS should be already installed at your personal computer. Most of the commands and options areonly executable using a mouse or a track ball or any other pointing device.

Hardware Requirements and System ConfigurationThe minimum hardware configuration is given in table below

PC-type: PC-ATprocessor: 80386 SX, 80386 DX, i486 SX or i486 DXarithmetic processor: necessary (except i486 DX)RAM: 4 MByte used as extended memorygraphics adapter: VGA (graphics adapter must be supported

by WINDOWS 3.x)interfaces: 2 serial ports (RS 232 C)

1 parallel port (Centronics) Dongle !!!floppy disk: 3 1/2" (1.44 MByte) or 5 1/4" (1.2 MByte)hard disk: 80 MBytepointing device: any WINDOWS supported mouse or track ball

output device: any WINDOWS compatible printer or plotter

The BRUKER WIN-EPR program is a protected software package. You can run it only if a dongle (WIBU-Key) is connected to the parallel port. The dongle is completely transparent for all command sequencesdirected to a printer, which may be connected to the same interface.

The BRUKER WIN-EPR program works also on a computer network system.

The BRUKER WIN-EPR program needs MS-DOS 3.3 (or higher version number) as an operating systemand MS-WINDOWS 3.0 (or higher version number) as an operating system extension. The use ofSMARTDRIVE as a disk cache program is recommended.

The BRUKER WIN-EPR program stores all loaded and manipulated spectra in a temporary directory. Toincrease the execution speed you may place this directory on a RAM-disk, but only if the installed amountof RAM exceeds 4 MByte. The optimal size of the RAM-disk is 2 MByte if you mostly work with 1D-spectra and 4 MByte for 2D-spectra.

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The following frames show some examples for the CONFIG.SYS and AUTOEXEC.BAT file on a computerequipped with 4 MByte RAM, MS-DOS 5.0 and MS-WINDOWS 3.1.

At a PC equipped with 8MByte RAM, DOS 5.0 and WINDOWS 3.1 they may look like these:

AUTOEXEC.BAT

@ECHO OFFPROMPT $p$gPATH=c:\;c:\dos;c:\windows

lh c:\dos\keyb.com gr,437,c:\dos\keyboard.syslh c:\smartdrv.exe c 2048 1024lh c:\dos\share.exelh c:\dos\doskey.com /INSERT

set TMP=c:\tempset TEMP=c:\temp

CONFIG.SYS:

SHELL = COMMAND.COM c:\dos /P /E:800COUNTRY = 049 437 c:\dos\country.sysFILES = 30BUFFERS = 30STACKS = 9,256FCBS = 1,1BREAK = ONDOS = high,umbDEVICE = C:\HIMEM.SYSDEVICE = C:\EMM386.EXE noems...

AUTOEXEC.BAT

@ECHO OFFPROMPT $p$gPATH=c:\;c:\dos;c:\windows

lh c:\dos\keyb.com gr,437,c:\dos\keyboard.syslh c:\smartdrv.exe c 2048 1024lh c:\dos\share.exelh c:\dos\doskey.com /INSERT

set TMP=c:\tempset TEMP=c:\temp

CONFIG.SYS:

SHELL = COMMAND.COM c:\dos /P /E:800COUNTRY = 049 437 c:\dos\country.sysFILES = 30BUFFERS = 30STACKS = 9,256FCBS = 1,1BREAK = ONDOS = high,umbDEVICE = C:\HIMEM.SYSDEVICE = C:\EMM386.EXE noemsDEVICEHIGH=C:\RAMDRIVE.SYS 4096 512 1024 /e...

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Installing WIN-EPRBefore you can start the automatic installation of WIN-EPR you must be sure that MS-WINDOWS 3.x isinstalled and running without problems. If you want WIN-EPR to use a ramdisk for storing it's temporaryfiles the MS-DOS device driver ramdrive.sys must be loaded before the WIN-EPR installation.

The INSTALL.EXE file on the installation disk can either be executed from DOS or from withinWINDOWS. When you start it from DOS the installation program is searching for the WINDOWSdirectory defined by the path command in the autoexec.bat file

The program starts a dialog asking for the device name and the full path to where the program files shouldbe copied. The defaults are C:\EPR. If an earlier version of WIN-EPR can be found on the harddisk, the oldpath is proposed. You may change both before you continue with the automatic installation by clickingInstall or stop it with a click on Exit. If the selected directory doesn't exist, you will be questioned whetherit should be created or not.The next dialog box is asking for two more path names, one to store the example spectra, and another wherethe temporary files should be placed. After copying the program files and the example spectra to theirdestination directories a new program group is generated in which you find the icons for WIN-EPR andGET-EPR.The installation is finished when the initialisation files are created or updated. Now the WIN-EPR programcan be executed by doubleclicking at its icon.

Remember that although the installation can be done without the supplied dongle it is necessary to run thesoftware

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Chapter 1: The BRUKER WIN-EPR SYSTEM

1.1 The File Menu

The File menu contains of the following commands

Load...Save as...Connect...StatusStatus DirectoryPrint...Printer Setup...CopyExit

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Load...The Load... command serves to load one or more spectra files from diskettes or hard disk drives .After clicking Load... a dialog box appears, which allows you to selected the desired spectra.

In the dialog box there are two list boxes to select directory, path and filename . At first the desired path canbe chosen in the left list box, and then by double-clicking a filename the full path is added to the selectedfiles box. Another possibility is to mark a file in the File box and click the Add button. Using the select allbutton adds all available spectra in the actual directory to the selected files box. It is also possible to selectone distinct file more than one time.

To undo a wrong selection mark the file in the selected files box and click the Remove button.

After clicking Ok, all the selected files are copied to a temporary directory and are prepared to be quickaccessible for further manipulations. Because of all the data treatment is done on a copy, the originalmeasured spectra cannot be changed or even be destroyed. Unless you explicitly save the file under thesame name, you can repeat to load one more copy of your original data file.

When you click Cancel or push ESC, the dialog box will be closed without loading the selected files.

Save as...This option is not available here.

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Connect...The Connect... command is used to create a 2D-spectrum file from a series of 1D-spectra. The number of1D-spectra which can be combined is only limited by the computers memory (RAM). If you click theConnect... command, a dialog box is opened which shows on the left side a list of all currently loadedspectra files and on the right side all files which will be combined to one 2D-data set as soon as you clickOk. Using the mouse, you can select the 1D-spectra in the left box. The names are copied to the right boxwhen you click Add ->. They can be cancelled, when you mark them in the right box and then click Remove.

For the combination all the chosen files in their actual state are used according to the position in the rightbox. Note that therefore the 1D-files can also be a variation of one original spectrum, which is processed indifferent ways.

The dialog box can be closed with Cancel respectively with ESC without creating a 2D-spectrum.

When you continue with Ok the Selected Files box will be closed and another dialog box will be shown inwhich you can define parameters which are used for all the combined 1D-spectra.

You can define the horizontal and verticalstarting point, the unit of the axes, and youcan change the extremal values for theintensity of the spectrum. With Ok, the actualsettings are stored in the parameter file forthe 2D-spectrum and the created spectrumappears as a new number in the status line.You can display and manipulate this spectrumusing the program part 2D-Processing .

The reset option changes every parameterback to it's initial value.

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Note: The newly created 2D-spectrum exists only as a file in the temporary directory and will be deleted assoon as you leave the program. If you want to keep it, you have to store it using the Save as... command.

StatusWith the Status command you can toggle the status line to be visible or hidden. A check-mark appears nextto the Status command if the status line is switched to be visible.

The status line is the placed beneath the menus, in which you find a numbered button for every spectrumloaded. There is also a line for a comment string which states the name and the full path of the spectrum filein process. Scroll bars will appear at both sides, if the number of buttons exceed one line. You can use themto scroll in both directions to select a file.

With a single-click with one of the mouse buttons at one of the numbers the name and full path of thecorresponding spectrum file is displayed. The color of the text is black if the spectrum is not visible orcorresponds to the color in which the spectrum is displayed.A double-click at one of the numbers causes the selection of this spectrum. It depends on the currentoperating mode, what happens after.

In the 1D- and 2D-Spectrum Manipulation mode, the selected spectrum will be displayed immediatelyafter double-clicking.

In the Algebra mode, a double-click with the left mouse button causes a change of the working file, but adouble-click with the right mouse button chooses a new reference file.

In the Show and Document mode only the appearance of the mouse sign is changed when you double-clickthe left mouse button. You then have to place the spectrum to any position at the screen in order to show it.

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Status DirectoryThe complete contents of the status line is shown in the Status Directory. Besides number, filename andfile size, you can lookup some information from the spectrum's parameter file, such as number of datapoints, date and type of measurement and the comment string.

Here you have the opportunity to delete spectra from the memory, by selecting them with the mouse andusing the Remove command.

Note: The spectrum file will also be erased in the temporary directory, so that all changes during thissession are lost. The spectrum file stored at the harddisk remains as it was before you started the session.

Furthermore you can change the position and number of the spectra in the status line using Move to andCopy to. The left number represents the source, whereas the right number represents the destination. It ispossible to insert an already existing number as a destination. In that case a warning is given stating that thedestination file will be deleted if you continue.

If you leave the Status Directory with Ok, all the changes are kept for further processing. By pressing ESCyou can leave without changing anything.

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PrintThis command cannot be activated here.

Printer Setup...As WIN-EPR is a WINDOWS application it is possible to have several printing devices installed with manysetup options. But only one of them can be the system printer to which all printing jobs are transmitted.Within the Printer Setup... menu you may select the system printer with the mouse and you can choosefrom all the printer specific setup options.

Ok confirms the current selection of the active printer for WIN-EPR, whereas Cancel leaves the dialogbox with no changes.

CopyThis command cannot be activated here.

ExitUsing Exit finishes the WIN-EPR session, without asking you to save you spectra files..

To exit WIN-EPR you can also use the Close command in the system menu or you may push Alt F4.

Note: If you don't want to loose manipulated spectra you have to save them using the save as... command.

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1.2 The WIN-EPR System Menu

The WIN-EPR System menu comprises the following sub menus

Spectr. Manipulation...Algebra...Show...2D -Processing...Document...

These sub menus correspond to the main operating modi, in which the whole program is divided.After selecting one of them the structure of the command list in the main menu is different. Fromevery sub menu you can reach the main menu called 'WIN-EPR-System', but you can also switchdirectly between the operating modi.

Spectr. ManipulationSpectrum Manipulation is the menu in which you can manipulate 1D-spectra. Here you will find allmathematical operations and data treatments, which can be performed with 1D-spectra.

AlgebraIn Algebra you find basic mathematical calculations, such as addition, subtraction, multiplication ordivision of two 1D-spectra.

ShowIn the program part Show you can display or compare up to five different 1D-spectra, but no manipulationscan be performed.

2D-ProcessingIn the 2D-Processing part you can display 2D-spectra, perform two dimensional mathematical operationson 2D-spectra or operations between 1D- and 2D-spectra.

DocumentIn the Document mode you can work, unlike other parts of the program, with 1D- and 2D-spectra as well. Itis used to create more complex printouts, as i.e. several spectra in different frames and to support yougenerating protocols of measurements or documents. Although it is possible to print in all operatingmodes, it is sometimes necessary to have a more flexible output. The Document mode can not replace atext processor or a paint program, but it helps you to create printouts with more flexibility in terms oflayout, thus respecting the specific properties of a EPR-spectrum.

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1.3 The Data Transfer Menu

With the command Data Transfer you call an external WINDOWS application program calledGETEPR.EXE, which offers the transfer of spectra and parameter files from your spectrometer to a PCusing TCP/IP or KERMIT protocol. You will find a more detailed description in Chapter 7: DataTransfer.

1.4 The Option Menu

In the Option menu Colors... and Display Font... sub menus are accessible.

Colors...The WIN-EPR program allows to set colors very individually. After clicking Colors... you can see a dialogbox showing the set of the actual colors for the monitor and the printer/plotter. In the EPR.INI file (in theWINDOWS directory) there is a region [Colors] where the current color setup is stored. Furthermorethere is a region [Palette] in which a number of colors is stored with their names and RGB-values. Thispalette can be edited by an ASCII editor, in order to i.e. change RGB-values or add some more colors. Theinformation of this palette is shown in the lower right box of the Set Colors frame, where it can not bechanged. If you mark one of the here available colors the Color selected field will display it. Click at one ofthe Display, Printer or General colors and it will change.

The color settings for the printer works of course only with devices, which can print colors, such as i.e. HPPaintJet, HP DeskJet 500c or with plotters. All devices with no color ability ignore these settings and printblack and white.

Pressing the Ok button saves the color selection, whereas Cancel leaves the dialog box and keeps thesettings unchanged.

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Display Fonts...This menu is only active if you work with WINDOWS V3.1 (or higher version number). You can select thefonts for the comments at the axes and for the buttons on the screen from a list of available fonts. You canalso choose the size and the attributes of the characters.

You can choose each of the fonts which are installed at your system. The settings are stored in the EPR.INIfile, so that if you start the program another time all text is displayed using that font.

1.5 The Help Menu

The Help menu comprises only the command About...

AboutAbout shows a dialog box displaying copyright information and the version number of the program

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Chapter 2: The Operating Mode -SpectrumManipulation-

In the operating mode Spectrum Manipulation (for 1D-spectra) you will find all operations, which can beperformed with one-dimensional EPR-, ENDOR, FT-EPR spectra.

The Spectr. Manipulation -Menu consists of six main items

FileSpectr.Manip.ParametersDisplayOptionsHelp

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2.1 The File Menu

In the File Menu you will find commands, which control file handling operations (i.e. Load... and Saveas...) and some commands which help you to communicate with external devices (i.e. printer, plotter).

Load...This command loads one or more spectra files and displays them as new number in the status line.For details see Chapter 1: The Bruker WIN-EPR System.

Save as...After manipulating a spectrum you have the possibility to save it under any name on any directory. Whenyou click Save as... a dialog box appears, which lets you choose a filename, a destination directory and theformat under which the spectrum will be saved.

As the format for numbers is different for OS/9 computers and PCs it is not possible to display a file withWIN-EPR format on your spectrometer. Therefore you have to save it in OS/9 format. On the other handyou can read OS/9 files to WIN-EPR, but it takes more time than reading a PC file because each time anautomatic file conversion has to be done. So if you want file compatibility with the spectrometer you haveto use OS/9 format or you select WIN-EPR format in order to save time during the load process.

You can close the dialog box without saving a file, using Cancel or pushing the ESC button.

With Ok respectively ENTER the current file will be saved according to your selection.

If the chosen name is presently used by another file you will see a warning box, giving the opportunity thedecide whether to delete the existing file. By hitting No, the save process will be cancelled and you have toselect another name or another directory.

StatusToggle for the status line

17

For details see Chapter 1: The Bruker WIN-EPR System.

Status DirectoryDisplay of all loaded spectra with extra information from their parameter files.For details see Chapter 1: The Bruker WIN-EPR System.

Printer Preview...The menu item Printer Preview shows how the current spectrum would be printed on the actually installedprinter. This also includes the color attributes, which means if the presently installed printer has no coloroptions no color will be displayed on the screen.

In Printer Preview... mode a new command bar appears with the following items:

Printer Setup offers a collection of all printers, available under WINDOWS. You can choose betweenthem and change some printer specific parameters. When leaving the Printer Setup... menu the display willbe recalculated with the selected parameters and shown on screen.

With the Print command you start the printout of the display.

You can change the color attributes of the spectra in the Colors... menu. A dialog box is opened in whichyou can setup any combination of colors. (Note that the color option works only with plotters and printerswith color abilities.

Clicking Return leaves the Printer Preview... mode and the active spectrum is shown on the monitor.

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PrintThe Print command activates the necessary calculations to prepare the page for printing according to theparameters in the Printer Setup and starts the printer.

A dialog box is shown as long as these calculations are performed and youmay abort them at any time. Then the data are sent either to the printerspooler, where they are stored temporary, or to the printer directly,depending on the options selected in the WINDOWS printer setup.

By using the printer spooler, you can start several print jobs in a short time without having to wait until thesometimes very complex tasks are completed. The printer spooler is a WINDOWS application and includedin the versions V3.x. It is running as a background process.

Printer Setup...Selection and installation of a printer / plotter.For details see Chapter 1: The Bruker WIN-EPR System.

CopyBesides the possibility to use a printer or a plotter as output device, WINDOWS allows to Copy data intothe clipboard. The clipboard is a kind of common platform for all WINDOWS applications to where youcan copy data in one program and from where you can paste data within another program. In this way it ispossible i.e. to get spectra into your word processor without having to care about file import or exportfilters. There are quite a lot of applications which support data exchange using the clipboard. (i.e. MS-Write, MS-WinWord)

ExitTerminates the WIN-EPR session.

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2.2 The Spectrum Manipulation Menu

The Spectrum Manipulation menu contains following items:

Filter...Noisy spectra can be straightened by using a filter function. The Filter... menu offers two differentalgorithms to process your measured data.

In general, you can set the number of convolutionpoints to an arbitrary number between 3 and 15.Using the Moving Average method it is allowed toset n to a number higher than 15, but it must be anodd.

Moving AverageThe Moving Average algorithm calculates thearithmetic mean value from n points

j ii j n

j n

x x n== − −

+ −

∑( )( )/

( )/

/1 2

1 2

xj: jth datapointn: number of convolution points

As the first and the last (n-1)/2 datapoints of the spectrum can not be calculated, they are set to the value ofthe first or the last calculated datapoint.

Polynomial FilterThe Polynomial Filter method corresponds to the Moving Average algorithm, with the difference thateach datapoint is multiplied by a factor, to create a weighted mean value.

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Resolution Enhancement...With the Resolution Enhancement... algorithm you can improve the resolution or the signal to noise ratioof a spectrum using an suitable window function. Here the window function acts on the fourier transform ofa measured spectrum.

In the frame above you see the fourier transformed spectrum below the original spectrum. After selectingthe appropriate window function (i.e. exponential ) you have to multiply the fourier transformed spectrumwith it. The result, after reverse fourier transformation gives a straight noiseless spectrum shown above theoriginal. Now you can change interactively the parameters of the window function until the result fulfils allneeds. It is also possible to select another window function, when you click the Function button.Ok terminates this process and you will see the result as a new spectrum on screen. If you push Cancel, theprocess will be interrupted and no changes will be made to the original spectrum.

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FFT and inverse FFTFFT is the abbreviation for Fast Fourier Transform(Depending on the status of the spectrum, only one of the commands is selectable).

For the FFT algorithm used here, it is absolutely necessary to have a spectrum with (2n) datapoints. If this isnot the case an automatic Zerofilling will be performed, which fills up the spectrum with zeroes until thenext power of two is reached.

The FFT is commonly used to transform a time domain signal into the frequency domain, whereas theinverse FFT transforms the other way around. But you can also transform field sweep spectra using FFT, inorder to use its ability to convert inherent frequencies to amplitudes, then manipulate them and perform thereverse transformation. For this kind of digital filter you will find a collection of so called windowfunctions from which you may select a suitable one (see Window Function and ResolutionEnhancement).

The FFT can act on real and complex data, but the results are not interchangeable. Usually a real spectrumhas to be transformed, using a real FFT algorithm and a complex spectrum has to transformed with complexFFT. The program automatically distinguishes between real and complex data input, and selects theappropriate routine. In both cases the result of the transformation is a complex spectrum. Sometimes it canhave advantages to use the complex FFT for a real signal. For that reason you have to add an imaginary part,which is filled up with zeroes. This can be done by using the command Swap to Complex in the sub menuManipulate complex data.

upper spectrum: measured spectrum FID.SPC lower spectrum: corresponding FT-Magnitudespectrum

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Phase CorrectionThe Phase Correction is an operation, which can only be performed with complex data sets, usually withspectra, which are the fourier transform of an FT-EPR time domain signal. FT-EPR spectra can have twosources of phase errors:A frequency independent and a frequency proportional phase error. Therefore you must have a phasecorrection routine of 0 th and 1st order. The 0th order correction corresponds to a rotation of the referencephase of the quadrature detected time domain signal, and is in principle no true phase error in that sense.The linear phase error is a result of the spectrometer dead time and is proportional to the frequency of thedetected signal and the dead time of the detection. To process a linear phase correction the frequency andthe phase difference of two datapoints have to be known. The values have to be defined in the correspondingfields in the dialog box, that the frequency dependent factor for the Phase correction can be calculated.This can be done in the Interactive part of the menu.

InteractiveIf you invoke the interactive phase correction you will see a dialogbox to define the phase parameters. For the 0th order correction,you have to set the correct phase (i.e. absorption) for one line ofthe spectrum using the level bar at the right side of the box. Definethis value by Fix Position (this defines also the first value for the1st order correction). Now the shape of the pointer changes to avertical line, which has to be placed at the center (i.e. top) of thebefore phase optimised line and then fixed by pushing the rightmouse button. This position of the spectrum is now marked with anarrow. Now you change to PH 2 and repeat the same procedurewith another line of the spectrum, to define the second value andthen switch to 1. Order. You can change the phase differencebetween these two points by a multiple of 360°, using the + or -key next to the Diff. field. The Range+ and Range- change thesensitivity of the level bar at the right side of the dialog box.

Hints:If you define position1 in the spectrum to the left of position2, the phase of position2 has to be rotatednegative compared to the phase of position1.

If you know the precise dead time of the detection system you can shift the time domain signal before FFTto the right. You know the time resolution of the measured spectrum, so you can calculate how manydatapoints you have to add at the left side (This can be done in Spectrum Manipulation mode with thecommand Shift in the Manipulate menu). After FFT, only a 0th order correction may be necessary.

ManualUsing the manual phase correction, only the parameters for the 0th order and 1st order have to be inserted inthe corresponding fields. When pushing Ok the corrected spectrum will be displayed after leaving the phasecorrection menu.

Ph0: Phase parameter 0th order.Ph1: Phase parameter 1st order.

Return

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Return terminates Phase Correction and returns to Spectr. Manipulation. All changes of the spectrumphase, which are performed interactively are confirmed and the new spectrum appears in the manipulationmenu.

Window functionUsually spectra are multiplied by Window functions in order to get a weighted spectrum (i.e. incombination with FFT). This manipulation results in a change with respect to the amplitude properties.Clicking this item opens a dialog box, where you have the choice of quite a collection of differentfunctions:

You can select a type of function just by clicking to the text with the mouse. In the frame Display mode,one can choose what will be displayed during the interactive manipulation. Pushing Ok leads back to thespectrum, but a small dialog box is also visible, which allows to define the function parametersinteractively.

Description of the window functions:

a. exponentialexponential function:

LB: line width [0,10]

Maximum: 1.00

b. biexponentialdouble-exponential function:

LB: line width + position of maximum ]0,10]GB: amplitude of maximum ]0, 1]

Maximum: 1.00 - 10.0

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c. gaussianGaussian - function

LB: line width [-10, 0[GB: position of maximum [ 0, 1]

Maximum: 1.00

d. hammingHamming function:

max: decay of the function to minimum ] 0, 3 ]

Maximum: 1.00 - 10.0

e. hanningHanning function:

max: decay of the function to minimum ] 0, 3 ]

Maximum: 1.00 - 10.0

f. trapezoidaltrapezoidal function:

TM1: left corner of trapeze [ 0 , TM2 [TM2: right corner of trapeze ] TM1, 1 ]

Maximum: 1.00

g. rectanglerectangular function:

RM1: left corner of rectangle [ 0 , RM2 [RM2: right corner of rectangle ] RM1, 1 ]

Maximum: 1.00

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h. inv. rectangleinverse rectangular function:

RM1: left corner of rectangle [ 0 , RM2 [RM2: right corner of rectangle ] RM1, 1 ]

Maximum: 1.00

i. sinebellsinebell function:

SSB: phase parameter [ 0, 30]SBO: decay to zero ] 0, 1 ]

Maximum: 1.00

j. sinebell squaredsquared sinebell function:

SSB: phase parameter [0,30]SBO: decay to zero ]0,1]

Maximum: 1.00

inverse FFTInverse Fourier Transform: see FFT.

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Manipulate

Several data processing operations are collected under the menu item Manipulate.

Offset CorrectionAfter activating the Offset Correction a horizontal line appears in the spectrum frame, which representsthe new level for zero signal. This line can be move by the mouse. Pressing the right mouse key confirmsthe selected level.You can cancel this operation by pushing SHIFT + ESC simultaneously.

FlipFlip inverts the order of datapoints. The datapoints and the comment for the ticks at the x-axis will be savedin reversed order.

Calibrate...To change the x-axis of the spectrum you can use the Calibratecommand. A vertical line can be set to the datapoint in the spectrum,which should be defined by a new value. After pushing the rightmouse button a small window will be displayed, which indicates thepresent x-value, and offers the possibility to change it.

Shift...Using the Shift command adds or subtracts a desired number ofdatapoints to the beginning of the actual spectrum. This results inshifting the spectrum right or left. The absolute number of datapointsis kept constant. If some points (zeroes) are added to the beginning,the same number of points will be discarded at the end of thespectrum. If some points are deleted at the beginning, the same numberof zeroes are added to the end.

Zerofilling...Fills up a spectrum with zeroes until the number of datapoints reaches the power of two, which you candefine in the Zerofilling dialog box. The number of datapoints may vary between 23 and 219. If the definednumber of datapoints is smaller than the actual one, the difference will be discarded at the end of thespectrum. In case of a complex spectrum, the zerofilling acts on both, the real and the imaginary part.

Reduce...This command reduces also the number of datapoints of the actualspectrum. Only every nth datapoint is kept, the rest is discarded. (wheren represents a small natural number)

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Multiplicate...A factor, by which the whole spectrum will be multiplied, can be defined in a dialog box.

LogarithmCalculates the natural logarithm of the intensity values.

ExponentialReverses the results calculated by the natural logarithm of the intensity values. This function works only ifall intensity values are smaller than 70.

Absolute ValueCalculates an absolute value spectrum. Within this calculation the absolute value of the real part and theimaginary part of a spectrum are treated independently.

Manipulate complex data

Following items are executable in the Manipulate complex data menu.

Delete PartDeletes either the real part or the imaginary part of a complex spectrum and treats the rest as a newactive spectrum.

Swap to complexThis command creates a complex spectrum by adding a zero filled imaginary part to the real spectrum.

Magnitude Calculation

iy y yi i= +2 2Re( ) Im( )

yi : ith datapoint

Power Calculation

iy y yi i= +

2 2Re( ) Im( )

yi : ith datapoint

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IntegrateClicking the Integrate command integrates the complete spectrum. In case of a complex spectrum, theIntegrate command acts on both parts. This operation is also available if you press the function key F2. Ifyou only want to integrate certain lines in the spectrum, use the Integrate Region command, which isdescribed below.

DifferentiateThis command is used to Differentiate a spectrum. In case of a complex spectrum the Differentiatecommand acts on both parts

Note:Although Integrate and Differentiate are inverse functions, it can happen that after proceeding several timesback and forth, the spectra look very distorted. This is related to rounding errors within calculations usingfloating point variables.

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Baseline Correction

This menu item replaces Spectrum Manipulation by a new menu, which contains commands and optionsto define baselines and correct the spectra using these baselines.

The Baseline Correction menu contains the following eight items:

Define PointsDefine RegionFunctionsSubtractReplaceOffset Correctionreal <==> imaginReturn

To define a baseline of a spectrum you can process as follows: At first you mark the datapoints or regions,which should be used for the calculation. Then you select a suitable function type from a list of availablefunctions. These functions can roughly be separated in two groups:

• functions, only defined in a few points (two Point, Point to Point and Cubic Spline)• and polynoms.

When the baseline is calculated it can be subtracted from the original spectrum using the Subtractcommand, or the original spectrum can be replaced part by part with the baseline function, using Replace.

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Define PointsSelecting Define Points allows to choose up to 50 characteristic datapoints for the baseline calculation.They can be marked with the left mouse button. If you click the right mouse button the selection of the lastdefined datapoint will be cancelled. For the calculation it does not matter in which order the points aredefined.

Define RegionIf you don't want to characterise the baseline function by single datapoints, you can also Define Regions.All points in the defined areas are used for the calculation procedure. After clicking Define Region youmay define the beginning of one region with the left mouse button. Two vertical lines appear, from whichthe first is fixed to the defined starting point, whereas the second changes its position according to themovement of the mouse. The end point of the region has to be defined again with the left mouse key. Nowthe cursor jumps again to the left line and a correction of the starting point is possible. If you push the rightmouse button, the region is defined and changes its color. You may cancel the selection of the last regionby hitting again the right mouse button. If you continue in this way, you are able to define up to ten regionsin every spectrum. The defining procedure is terminated by SHIFT + ESC . If all regions are set, you maychoose a suitable model function for the baseline, which will then adapt its parameters according theselection of datapoints or regions.

FunctionsThe menu item Functions opens another pop up menu, which shows a list of model functions.

extrapolateWith extrapolate you can choose between calculating the baseline only in the defined regions orextrapolate it for the whole spectrum..

two PointOnly the first and the last defined datapoint will be connected by a straight line. All others are ignored forthe calculation. (This command is not available, if you work with defined regions.)

Point to PointThe defined datapoints will be connected by straight lines. (This command is not available, if you work withdefined regions.)

Cubic SplineThis option connects the marked datapoints with 3rd order functions (cubic splines). Another boundarycondition for the calculation is, that these functions are steady at the position of the datapoints. The resultbaseline leads through every defined point.

Here, you see the collection of available polynoms:ConstantLinearQuadraticCubic4-th Order5-th Order6-th Order

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All marked points or regions are used to calculate a nth order regression factor. These functions do notnecessarily touch all the defined points, because they are only a least square fit of a function through themarked points.

SubtractThis menu item is active only, when a baseline function has been calculated. Then the difference of theactual spectrum and the baseline function is shown on the display. The calculation is only temporary, whichmeans that you still can change the model function and/or define other characteristic datapoints and getdifferent results. The baseline will be subtracted permanently when you leave Baseline Function bypushing Return.

ReplaceThe marked region of the spectrum will be replaced by the baseline function. In general it is of no sense touse Replace, if Extrapolate is active.

Offset CorrectionGives the possibility to perform an Offset Correction.(see item Manipulate in the Spectrum Manipulation menu for details!)

real <=> imaginToggles between real and imaginary part of a complex spectrum. The baseline correction can be performedindividually for each part or the marked datapoints respectively regions can be used in common.

ReturnTerminates the Baseline Correction and leads back to the Spectr. Manipulation menu. The correctedspectrum is shown on the display in the case that Subtract or Replace was active. Otherwise no changesare made to the spectrum.

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Integrate Region

The operating mode Integrate Region serves to calculate 1st or 2nd order integrals over a predefinedregion. The items of the Spectrum Manipulation menu change to the integration menu.

The Integration menu consists of the following items:

Define IntegralsIntegral typeIntegral modificationautomatic ScalingDeleteReport...Return

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Define IntegralsBefore you can calculate the integral of spectrum parts, you have to define the regions. After clickingDefine Integrals you may define the beginning of one region with the left mouse button. Two vertical linesappear, from which the first is fixed to the defined starting point, whereas the second changes its positionaccording to the movement of the mouse. The end point of the region has to be defined again with the leftmouse key. Now the cursor jumps again to the left line and a correction of the starting point is possible. Ifyou push the right mouse button, the region is defined, the integral and the normalised area are calculated.You have to define the region for the integration from left to right. It is not possible to define overlappingregions.

Integral typeYou can select between single and double integration. The predefined integrals will be automaticallyrecalculated and immediately shown on the display.

Integral modificationYou can select distinct integrals in order to modify them individually:

SelectThe select mode has to be switch on, to choose an integral for further modifications. You then just have toclick to the integral with the mouse cursor and a colored horizontal bar will appear above the x-axis,indicating that this integral can now be manipulated individually.

NormaliseThe selected integral is used for the normalisation. If you define thenormalisation factor to a desired value, all the other integrals will berecalculated compared to the new result for the area of the selectedintegral.

ScalingThe Scaling command toggles the scaling options either to be available for the spectrum or for theintegrals. If it is switched on, the sizing options act on the integrals. The offset control works for all theintegrals in common, whereas the scaling factor only affects the active integral. The scaling factor isdisplayed individually for each integral at the upper border of the screen.

Slope + Bias...

By activating Slope + Bias, an automatic linear baselinecorrection will be performed for the selected integral. Thecurrent values for slope and bias are shown in a dialog box.They can be change independently from each other with thelevel bars next to them. These parameters describe a linearfunction which is added to the selected integral. Everychange causes an automatic actualisation of the displayedintegral and its calculated area.

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EraseDeletes the selected integral.Automatic ScalingThe Automatic Scaling options ensures that every integral can be fully displayed. It looks for the largestintegral, and scales the others accordingly.

DeleteDeletes all regions and integrals.

ReportSelecting Report brings up a dialog box, which contains a list of important characteristics for all theintegrals.

Important parameters are starting and ending point of the integral, as well as the integral value and anormalised integral value. This list can be printed as ASCII table and can be copied to the clipboard.Furthermore you can save the list as text file on the disk.

The integral values (SI for single integration and DI for double integration) are calculated as follows:

kSI a f ii n

m

k

k

( ) ( )==∑ respectively

kDI aj n

af i

i n

j

k k

( ) ( )== =∑ ∑

wherea = nk, ...., mkf(i) = datapoints

The last column contains the normalised integral value. The normalisation constant N is calculatedaccording to:

Nconversion time recievergain Anzahl der Datenpunkte

sweep width=

* * ( - )

1

ReturnTerminates Integration and leads back to the Spectrum Manipulation menu.

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Peak Picking

The operating mode Peak Picking helps to identify peak positions.

The Spectrum Manipulation menu changes to the Peak Picking menu with the following options:

Define RegionParameter...ProcessReport...Return

Define RegionIf you don't want to look for all peak positions in the spectrum, you have to define regions where you wantto search. You can mark up to ten different regions. If you do not mark a region, the routine searches thewhole spectrum. After clicking Define Region, you may define the beginning of one region with the leftmouse button. Two vertical lines appear, from which the first is fixed to the defined starting point, whereasthe second changes its position according to the movement of the mouse. The end point of the region has tobe defined again with the left mouse key. Now the cursor jumps again to the left line and a correction of thestarting point is possible. If you push the right mouse button, the region is defined, and a colored bar isshowing its borders. You can cancel the selection, if you press SHIFT + ESC simultaneously. By pushingagain the left mouse button, the procedure can be repeated for another region. If you want to cancel the lastmarked region, push the right mouse key once more.

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Parameter...

The Parameter... command helps to setupthe parameters for the peak pickingroutine.

The Peak Constant PC is a meter for thesensitivity of the search algorithm..

In the Peaks Sign field, you can decidewhether to look only for positive (default)or only for negative or for peaks with bothsigns.

Intensity Range lets you define aintensity level, where MI is the minimumintensity (in percent) and MAXI is themaximum intensity of a signal to berecognized as a peak.

Regions of Interest are the probably already defined regions. It is possible to change the settings manually,by adding or replacing starting and ending points in the appropriate fields and confirming them by clickingInsert. Remove deletes an existing region.

In the parameter frame Application you may decide, whether the current settings are only applied for thecurrent spectrum (local ) or are kept for a whole series of spectra (global ) i.e. in order to compare peakintensities.

The Process button saves the parameter setup and starts the search algorithm.Cancel ignores all changes and leaves the Parameter... list.

ProcessAs already seen in the Parameter... menu the Process command starts the algorithm, using the actualsearch parameters.

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Report...

Presents a dialog box with a list of some information about the found peaks.:

where:

Nr. is the actual number of the peak

Data Point is the number of the datapoint with maximum value

Value is the value of the x-axis corresponding to the maximum

Intensity is the peak intensity in the maximum

You can Print , Copy or Save this list. Pushing Ok terminates the peak Report... .

ReturnTerminates the Peak Picking sub menu and returns to Spectrum Manipulation.

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Deconvolution

The Deconvolution menu comprises the following commands:

Define Regionautomatic Fit...Edit...add PeaksDelete PeakDelete all PeaksProcessShow allFitSumDifferenceTick marksReport...Store Fit...Return

Define RegionIf you want to apply the deconvolution only to a part of the spectrum, you have to define the correspondingregions. If no regions are marked, deconvolution acts on the whole spectrum. (for details how to defineregions see Integrate Region or Peak Picking)

automatic Fit...

For the automatic search of then main peaks in a markedregion, it is only necessary toselect a Fit Type and thedesired Number of peaks n.By giving the commandProcess a search algorithm isstarted.

Fit Type: You can define to use either a Lorentzian or a Gaussian line shapes as a fit function.The number of peaks can be varied from 1 to 40.

Instead of typing the Number of peaks you can use the search algorithm of the peak picking routine, if youinsert a number above 0.0 (i.e. 3.0) as a Peak Constant. Then all peaks found by the peak picking routinewill be fitted and the value in the field Number of peaks will be ignored.

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Edit...

In the box, which appears when you execute the Edit... command, all peaks are listed with their specificparameters. If you click on a line with the left mouse button, this line will appear in the editor and theparameters can be changed individually.

Start and End defines the region where the fit should be performedCenter tells the position of the maximum on the x-axisWidth refers to the width of the Lorentzian/Gaussian lineHeight is the amplitude of the line.

In this parameter fields you normally insert approximate values, but you can also type the correct values(i.e. known from the literature) and then exclude these values from the fit procedure with the commandsFix Position, Fix Width, and Fix Height.

The line type is indicated in a small frame below the Start field:

L: LorentzianG: GaussianE: Exponential function

Now you can Insert the new peak into the list. If you want to replace an existing peak, you first have toDelete the old one, before you can Insert another.

When all settings are completed you can start the fit algorithm with Process. The predefined settings areused as a first approximation, and will change during several iterations, except if a certain parameter isFixed.

40

add PeaksWhen you click the add peaks command, you have the choice between Gaussian, Lorentzian orExponential line shapes. As soon as you select one of them the cursor of the mouse changes its shape to apeak of the chosen line shape. As you move the mouse, the amplitude and the position on the x-axis changescontinuously. In that way you can set an additional peak to the desired position, change its amplitude, and bypressing SHIFT and moving the mouse simultaneously, you can also set the line width. You accept theparameters by pressing the left mouse key, and these values are transferred to the peak list. The keycombination SHIFT + ESC cancels the manipulations on one peak, but all the previous defined peaks arekept. By pushing the right mouse key you invoke the calculation with the new peak parameters.

Delete PeakIn order to delete a peak you can either go to the edit menu, as described above, or you can select the menuitem Delete Peak and use the mouse for that purpose. Clicking Delete Peak changes the mouse cursor to avertical line and by pressing the left mouse button each peak which is hit by that line is erased. The rightmouse button forces a recalculation of the left over peaks. The Delete Peak command is left by thecombination SHIFT + ESC.

Delete all PeaksDeletes all calculated and all added peaks.

ProcessThe Process command invokes the deconvolution algorithm and displays the results on screen..

The next five menu items control the appearance of the spectrum and the peaks on the monitor. All activeoptions have a check mark next to their name. If an active options selected again the check mark disappearsand the option is not active any more.

Show allShows all fit peaks, the sum of all peaks, and the difference of spectrum and ticks.

FitShows all fit peaks. The color of the peaks varies according to the defined color table.

SumAll peaks are added, and the result is displayed.

DifferenceAll peaks are added, and the result is subtracted from the spectrum. The difference is shown on the screen.

Tick marksEach peak is marked with an ongoing number.

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Report...

List of all peaks with their specific parameters.The list can be Printed, Copied to the clipboard, or Saved on the harddisk.

Store Fit...Stores the results of the fit procedure on the harddisk. Depending on the options for the display, the storedspectrum is the sum of all peaks, or the difference between the sum of all peaks and the original spectrum.

You can select a new path and a new name under which the file should be stored. Again you have thepossibility to use WIN-EPR Format or OS/9 Format (for details see Chapter 2.1). With Ok you confirmthe save process, with Cancel you discard it.If you try to save a file under an existing name you will receive a warning message.

If you want to overwrite type Yes, if not type No to cancel.

ReturnTerminates the Deconvolution sub menu and leaves to the Spectrum Manipulation menu.

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WIN-EPR SystemTerminates the 1D Spectrum Manipulation Menu and returns to the WIN-EPR System. From there you canreach the following operating modes : Algebra, Show, 2D Processing and Document.

2D-DisplayIf you have left the 2D-Processing Part for any reason directly to the 1D- Processing Menu (i.e. to lookmore careful to one slice of a 2D-spectrum), you can use the command 2D-Display or alternately F1 to goback.

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2.3 The Parameters Menu

In the Parameters menu you will find the following items:

List Parameter...Change Parameter...Comment...List Data File...Update Extrema

List Parameter...Shows a list of all important entries of the parameter file, which belongs to a measured spectrum.Depending on the file type, different parameters are listed.

If you want to have a look at all available parameters, you may use the View full list... command. This willopen another frame, in which you will find a list box with all entries in the parameter file.With the Ok command you can close the list.

44

Change ParameterThe scaling parameters for the x- or the y-axisof a spectrum can be adjusted in the dialog boxChange Parameter. The wake up parametersare read from the parameter file, which belongsto the actual spectrum. Any changes are storedto the parameter file when you press Ok. WithCancel all changes are neglected and the boxdisappears. Before you leave the dialog box,you can also recall the original parameters,using reset.

Comment...Offers the possibility to edit the comment string from a spectrum's parameter file.

List Data File...Creates an ASCII table for all datapoints of a spectrum. It can happen with larger spectra, that the entriesstop after approximately 2000 points, due to the memory limitation of 64 KByte for each list box.

You can Print, Copy the list to the clipboard or Save it as an ASCII file on the harddisk.

Update ExtremaRecalculates extremal values of the actual spectrum, and displays full size on the screen.

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2.4 The Display Menu

The Display Menu contains following items:

ScalingExpand...ResetSplit ScreenCompareRestoreSubstituteView...Distance...DisplayData Type

ScalingThe display of the spectrum can be scaled in a wide range. The sub menu Scaling offers following options:

-Times two (keyboard equivalent F5)enlarges display by the factor of 2

-Divide by two (F6)reduces display by the factor of 2

-Offset plus (F7)shifts up the spectrum.

-Offset minus (F8)shifts down the spectrum

Using the keyboard equivalents (function keys F5 to F8) allows quick access to the often used scalingcommands.

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Expand...A dialog box shows the starting and the ending value of the active spectrum as well as the maximum andminimum intensity. These parameters can be changed manually to any value, even if a new parameter islarger than the spectrum size. With this option it is possible to display part of a spectrum very precisely, i.e.in order to compare it with another one.

A click at the reset button causes the program to read the original values from the parameter file on disk.

ResetDisplay of the spectrum full size.

Split ScreenThe Split Screen command divides the display in two parts. In the upper part you can see the overallspectrum, whereas in the lower part you can see an enlarged section. The region shown in the lower displayis marked in the upper spectrum. If you choose a different section in the overall spectrum with the mouse, itwill be shown in the lower display.

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Compare, Restore, SubstituteLike in the Split screen mode, the display in the Compare mode is divided in two sections. But this time,the upper window contains a original spectrum, whereas the lower window can contain the same spectrumafter performing some manipulations i.e. filtering, integrating or baseline correction. In the lower frameyou see the result and you may look at it very detailed and decide whether the data treatment was successful.If necessary you can Restore the original to the lower window, or if the result spectrum is satisfying youcan Substitute the original by the manipulated spectrum.

COMPARE -Mode: upper frame: original spectrum lower frame: filtered with 13-point movingaverage

On the other hand it is also possible to keep a reference spectrum in the upper frame and compare this withother files selected from the status line. But then the reference spectrum can not be manipulated.Furthermore you have to be careful using the Restore command, because then the reference spectrum willreplace the spectrum in the lower frame which is lost. There will be no warning!

View...Displays a small box which contains information about the number,the x-axis position and the intensity of the datapoint, which iscurrently hit by the mouse cursor. Additionally, the exact positionin the spectrum will be marked with a small red arrow.

The box disappears as soon as you select again the menu item View, or if you double-click at the minus inthe upper left corner.

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Distance...Like using the View command, a small box appears, which contains information about the current cursorposition. But this time the mouse cursor changes to a vertical line in the spectrum.

This line can be fixed to a desired x-axis position by pressing the left mouse button. Then a second verticalline will appear and the window shows the difference between the fixed line and the current cursor position.

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If you press again the left mouse button, you may change the position of the reference line. The Distancewindow can be submitted if you select the Distance command once more, or if you double-click at theupper left corner of the window.

DisplayIn the Display sub menu you can select how the spectrum data are shown on the screen. There are severaloptions:

-Line: datapoints are connected through straight lines (default)

-Point: datapoints are displayed as points

-Cross: each point is marked with a cross(this option can additionally be selected with Line or Point)

-Histogram: each datapoint is displayed as a thin bar to the zero line

The active options are signed with a check mark.

Data TypeThere are complex spectra, which means besides the real part they also have an imaginary part. Normallyonly the real part of a spectrum is displayed, but sometimes it is also interesting to see the imaginary part(i.e. quadrature detected signals). Therefore you can select which Data Type should be shown in the screen.Of course, you can only switch to the imaginary part if it exists.The option complex causes the display to be split into two sections. In the upper frame you can see the realpart, whereas the lower frame contains the imaginary part of the spectrum. Manipulations can only be donein the upper windows.The active option is signed with a check mark

Display of the complex spectrum ECHO: upper frame: real part lower frame: imaginarypart

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2.5 The Options Menu

Y-AxisToggles the y-axis comments

g-FactorToggles the conventional x-axis to a g-factor axis

GridToggles the grid

Annotate...Introducing additional text frames to the spectrum

In a dialog box you can choose, whether a free definableText, the actual value of the x-Coordinate or theIntensity of the cursor position should be displayed.Text has to be entered into the Annotation text line. Afurther option is the orientation of the annotations. It canbe horizontal or vertical . After closing the box with Ok,you are back in the spectrum display and you can positionthe annotations using the mouse. When the final positionis reached, push the right mouse button to fix theannotation box. You can continue adding more text boxesto the spectrum.

Annotations are only temporary. They will not be saved together with the spectrum. All text windows aredeleted when you select Annotate and then leave with Cancel.

Colors...Selection of color options for display and printouts.

Display Font...Selection of font used for the axes comments.

For details about Colors... and display Fonts... see The Options Menu in Chapter 1!

2.6 The Help Menu

About shows a dialog box displaying copyright information and the version number of the program.

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Chapter 3: The Operating Mode -Algebra-

In the operating mode Algebra, you will find all kinds of manipulation, which can be done with two 1D-spectra. You will have a reference spectrum and a work spectrum which can be combined by algebraicoperations, like addition, subtraction, multiplication and division. Furthermore it is possible to multiply thework spectrum by a constant factor and add an offset to it.

The algebra screen is divided into two frames, where the upper one holds the reference spectrum and thework spectrum, and the lower frame shows the result of the algebraic operation. After wake up the upperwindow contains the first and the second spectrum of the status line, whereas the lower window is empty.You can select any spectrum for reference by a double-click with the right mouse button at the desirednumber in the status line. To choose the second spectrum, you have to use the same procedure with the leftmouse button. The spectra are shown on the same x-axis, so that in general they have not the same start andend values. As soon as you define an algebraic operation, the result is shown in the lower window. Theadditive constant and the multiplicative constant, which can be defined in the Constant setting... box arealso taken in account.

Default values: 0.0 for the additive constant1.0 for the multiplicative constant

The Algebra menu consists of the following main items:

FileAlgebraParametersDisplayOptionsHelp

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3.1 The File Menu

In the File menu you will find the following list of commands:

Load... loads one or more spectra to the status line

Save as... saves the result spectrum on the floppy disk or the harddisk

Status toggles the status line

Status Directory shows the names of all loaded spectra with additionalinformation from the parameter file.

Printer Preview displays a preview of the current page to print

Print starts the printer

Printer Setup setup and configuration of the printer

Copy copies the actual screen to the clipboard

Exit. Terminates the WIN-EPR session

For details see Chapter 1!

3.2 The Algebra Menu

Following items are contained in the Algebra menu:

X-AlignmentThe X-Alignment command allows to shift the work spectrum with respect to the reference spectrum onthe x-axis. Therefore you have to mark a desired point in the reference spectrum with the left mouse buttonand then connect it to a point in the work spectrum. After pushing the right mouse button both points willbe aligned.

Interactive X-AlignFor the same purpose, you may also use the Interactive X-Align command. This offers the possibility toshift the work spectrum interactively, using a level bar, which is displayed in a dialog box. The X-Offset(number of datapoints) is displayed in the same box, so you can control the shift procedure more precisely.If this number is negative it means that the work spectrum has been shifted to the left, a positive valuestands for a shift to the right.

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Y-AlignmentWith the Y-Alignment command you can adjust the intensities of the two spectra. When clicking thiscommand, the mouse cursor in the upper spectrum changes to a vertical line. With this line you can select aposition in the reference spectrum, to which the intensity of the work spectrum should be aligned. If youpush the right mouse button the calculation starts, and the work spectrum will be manipulated until theamplitudes at the chosen position are identical.

Constant settingThe general formula, which describes the algebraic operation between two spectra is given by:

result = reference [operation] (const * work spectrum + offset)

The multiplicative constant and the offset can be defined in the Constant setting dialog box.

If an operation in the Algebra menu is selected, you willsee a result spectrum in the lower frame. Then you can alsoset the additive and the multiplicative constant. You may doit either , by typing the desired values into the appropriatefields, or you can do it interactively by moving the levelbars next to this fields. The result spectrum will berecalculated immediately and shown on the screen.

If there is no result spectrum you can only define theseconstants in the corresponding fields. They will be taken inaccount for all further algebraic operations.

Here you find a list of all available algebraic operations:

Additionresult = reference + work spectrum.

Subtractionresult = reference - work spectrum.

Multiplicationresult = reference * work spectrum.

Divisionresult = reference / work spectrum.

The result spectrum is shown in the lower display. Using Save as... this spectrum can be saved on disk ortransferred to the operating mode Spectrum Manipulation, where it is treated like any other spectrum.But then you have to remember that it is only stored temporarily in RAM and will be lost, as soon as youleave for the WIN-EPR System or terminate the WIN-EPR session.

WIN-EPR SystemTerminates the Algebra Menu, and leads back to the WIN-EPR System.

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3.3 The Parameters MenuThe Parameter Menu shows all the parameters of the result spectrum.

List ParameterShows all important entries of the parameter file of the result spectrum.

CommentOffers the possibility to edit the comment string in the parameter file

List Data FileShows the intensities of the datapoints in the result spectrum.

For details see The Parameters Menu in Chapter 2!

3.4 The Display MenuAll operations in the Display Menu act only on the appearance of the spectra on the screen. You cannotperform permanent manipulations.

ScalingThe display of the spectrum can be scaled in quite a wide range. The sub menu Scaling offers the followingoptions:

-Times two (keyboard equivalent F5)enlarges display by the factor of 2

-Divide by two (F6)reduces display by the factor of 2

-Offset plus (F7)shifts up the spectrum

-Offset minus (F8)shifts down the spectrum

ExpandA dialog box shows the starting and the ending values of the active spectra as well as their maximum andminimum intensities. These parameters can be changed manually. Furthermore you can add a x-offset of thework spectrum compared to the reference spectrum in physical units.

Stacked Plot and Overlay PlotUsually the reference and the work spectra are displayed as a so called Stacked Plot, which meansseparately one under another in the upper frame. But it is also possible to see them in the so called OverlayPlot. The active option is signed with a check mark.

ResetDisplays the spectrum in full size.

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ViewDisplays a small box which contains information about the number, the x-axis position and the intensity ofthe datapoint, which is currently hit by the mouse cursor. Additionally, the exact position in the spectrumwill be marked with a small red arrow.

DisplayIn the Display sub menu you can select how the spectrum data are shown on the screen. There are severaloptions:

-Line: datapoints are connected through straight lines (default)

-Point: datapoints are displayed as points

-Cross: each point is marked with a cross(this option can additionally be selected with Line or Point)

-Histogram: each datapoint is displayed as a thin bar to the zero line

The active options are signed with a check mark.

Data TypeYou can select whether the real part or the imaginary part of a complex spectrum is shown.

3.5 The Options Menu

Y-AxisToggles the y-axis comments

g-FactorToggles the conventional x-axis to a g-factor axis

GridToggles the grid

Annotate...Introducing additional text frames to the spectrum

Colors...Selection of color options for display and printouts.

Display Font...Selection of font used for the axes comments.

For details about Colors... and display Fonts... see The Options Menu in chapter 1 or chapter 2!

3.6 The Help Menu

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About shows a dialog box, displaying copyright information and the version number of the program

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Chapter 4: The Operating Mode - Show -

In the program part Show you can display or compare up to five different 1D spectra, but no manipulationscan be performed.

The Show menu consists of five main items:

FileShowDisplayOptionsHelp

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4.1 The File Menu

In the File menu you will find the following list of commands:

Load... loads one or more spectra to the status line

Save as... saves the result spectrum on the floppy disk or the harddisk

Status toggles the status line

Status Directory shows the names of all loaded spectra with additionalinformation from the parameter file.

Printer Preview displays a preview of the current page to print

Print starts the printer

Printer Setup setup and configuration of the printer

Copy copies the actual screen to the clipboard

Exit. Terminates the WIN-EPR session

For details see The File Menu in chapter 1!

4.2 The Show Menu

In the Show menu you will find the following commands:

Number of SlicesIn this box you can insert the number of spectra you want to show. You can choose the value between 2 and5. After starting the Show all windows contain the first spectrum in the status line. To select another one,you may double-click (left mouse key) the desired number in the status line and then move the mousecursor over a spectrum frame. Pressing again the left mouse button will display your selection in the frameunder the mouse cursor.

WIN-EPR SystemTerminates the Show Menu, and leads back to the WIN-EPR System.

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4.3 The Display Menu

In the Display Menu you will find the following options:

ExpandDepending on the chosen number of spectra, a dialog box shows the starting and the ending values of allspectra as well as their maximum and minimum intensities. These parameters can be changed manually.Using these options allow to display each desired section of the spectra very precise.

Clicking on reset forces to read the default parameters from the parameter files.

ResetReplaces the chosen sections by the overall spectra. If you only want to reset a single spectrum, use theright mouse button and click on it.

DisplayIn the Display sub menu you can select how the spectrum data are shown on the screen. There are severaloptions:

-Line: datapoints are connected through straight lines (default)

-Point: datapoints are displayed as points

-Cross: each point is marked with a cross(this option can additionally be selected with Line or Point)

-Histogram: each datapoint is displayed as a thin bar to the zero line

The active options are signed with a check mark.

Data TypeYou can select whether the real part or the imaginary part of a complex spectrum is shown. This selectionholds for all displayed spectra.

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4.4 The Options Menu

Y-AxisToggles the y-axis comments

GridToggles the grid

Colors...Selection of color options for display and printouts.

Display Font...Selection of font used for the axes comments.

For details about Colors... and display Fonts... see The Options Menu in chapter 1 or chapter 2!

4.5 The Help Menu

About shows a dialog box, displaying copyright information and the version number of the program.

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Chapter 5: The operating mode -2D Processing-

5.1 The File Menu

The File menu contains the following commands:

Load...The Load... command serves to load one or more spectra files into the status line.

Save as...Saving of result spectra to diskette or hard disk.

Change to SliceThis menu item is active if the display mode is set to Scan Plot, or if the additional display of data slices inmenu Display : Scan : Row/Columns is activated(either rows or columns). It is possible then to copy thecurrent displayed slice temporarily within the menu item Change to Slice. The operational mode isswitched immediately from the 2D processing to the 1D processing mode (Spectrum Manipulation) and theslice (row/column) may be processed here. The data slice is handled as an independent data set and has noinfluence on the 2D data set. The extracted slice can not be inserted into the 2D spectrum again.The F1 function key transfers a data slice from 2D spectrum to the 1D processing program part.

Save SliceSave Slice is similar to Change to Slice and is available only within the Scan Plot or, when therow/column display is active. The displayed slice is copied temporarily into the status line and is availableas a 1D data set from the 1D processing program part (Spectrum Manipulation). Save Slice can be used bypressing SHIFT+F1.

Save ProjectionThe menu item is divided into F1-Domain und F2-Domain.The current projection in F1 direction or F2 direction may be copied temporarily into the status line andcan be used for further manipulations within the program part Spectr. Manipulation.

StatusEnables/disables the status line.

Status DirectoryDisplay of currently loaded spectra and additional information from the parameter file.

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Mix SpectraIt is possible to create a new 2D spectrum from the real and imaginary part of two differing spectra of equalsizes.

The left-hand list box contains the data sets for selecting the real part of the newly created spectrum. Eitherthe real or the imaginary part of the data sets may be selected. The right-hand list box contains data sets forselecting the imaginary part of the newly created spectrum. Either the real or imaginary part should bechosen. Any combination is possible as long as both parts have same data point sizes. After the selectionhas been made, path and file names have to be specified in the lower part of the dialog box. Creategenerates new 2D spectrum. The new spectrum is stored on hard disk and additionally loaded into the statusline. It thus is immediately available for further processing.

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2D AlgebraWithin the menu of 2D-Algebra, a 2D spectrum can be connected with a 1D, or another 2D spectrum.

The reference data set is a 2D spectrum to which a second 2D spectrum or a 1D data set may be added orsubtracted. A constant multiplication factor can be added to the operation. In addition, an offset value in F1or F2 direction can be defined. If a 1D spectrum is connected to a 2D file, the direction in which the 1Dfile should be calculated (F1 or F2) should be defined. The path and the file name of the resulting spectrumhas to be specified in the lower part of the dialog box. Calculate starts the calculation and the result isstored on disk and is also copied into the status line. The calculation is interrupted by pressing Cancel,when the dialog box disappears.

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PrintPrints the currently loaded spectrum in the display mode shown. After clicking the menu item, define theprint size in the dialog box.

Three options are available:

Full page uses optimum paper size forprint output.

Square defines a 2D print output withequal axis length.

Variable Size defines the size of the printoutput to the nearest millimeter.

In addition, Level-Information contains information about the intensity values of the 2D spectrum.

Pressing Ok starts the printer. The print dialog box appears when the print procedure is finished.

Printer SetupSelection and configuration of a printer.

CopyCopy of the display into the clipboard.

ExitUsing Exit finishes the WIN-EPR session without asking you to save your spectra files

A detailed description of some menu points are found in Chapter 1 and 2.

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Chapter 6: The Operating Mode - Document

In the Document mode you can work, unlike other parts of the program, with 1D- and 2D-spectra as well. Itis used to create more complex printouts, as i.e. several spectra in different frames and to support yougenerating protocols of measurements or documents. Although it is possible to print in all operatingmodes, it is sometimes necessary to have a more flexible output. The Document mode can not replace atext processor or a paint program, but it helps you to create printouts with more flexibility in terms oflayout, thus respecting the specific properties of a EPR-spectrum.

After starting the Document mode, you see a blank sheet of paper on the screen. You may fill it up withframes containing spectra, parameter lists, bitmap images or text and you can arrange them on the screen asyou like. When you select a spectrum in the status line (double-click with the left mouse button), it will fillyour work sheet. If you want to add more spectra or other possible items, you have to Create a new frame,in which the selected item will be placed as before. After that you can freely Move the frame across thework sheet. Furthermore there are options like Resize , Edit and Delete a frame.

According to the actual task, the mouse cursor changes its appearance as follows:

Represents the lower right, or the upper left corner of a new frame. As long as thesesigns can be seen, you can vary the size of the frame interactively.

A spectrum is selected and can be filled in an existing frame or fill the entire work sheet.

With this marker you select an existing frame, which should contain parameters.

If you click to a frame with this cursor, you can add text to it.

Shifts the spectrum which lies under the cursor, when you press the left mouse buttonand move the mouse simultaneously.

Deletes the frame which lies under the marker.

Displays the frame characteristics.

Changes the order, in which several frames are overlaid.

and

and

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6.1 The File Menu

In the File menu you will find the following list of commands:

Load Spectrum loads one or more spectra to the status line

Status toggles the status line

Status Directory shows the names of all loaded spectra with additionalinformation from the parameter file.

Printer Preview displays a preview of the current page to print

Print starts the printer

Printer Setup setup and configuration of the printer

Copy copies the actual screen to the clipboard

WIN-EPR System leaves for the WIN-EPR System menu

Exit terminates the WIN-EPR session

For details see The File Menu in chapter 1!

6.2 The Edit Menu

All the commands you need to create a complex work sheet are hidden in the Edit menu.

CreateA command to Create a new frame, which can contain spectra, parameters, text or graphics. First you haveto fix the upper left corner by pushing the left mouse button, then you do the same for the lower rightcorner. Pushing the right mouse key creates the adjusted frame.

DeleteDeletes the frame, which lies under the cursor, and its contents. The program remains in Delete mode untilyou give another instruction or you press the right mouse button.

MoveThe Move command allows to change the position of a frame on the work sheet. Therefore you have tomove the cursor over the desired frame, and keep the left mouse button pushed, until you reach the frame'sdestination. When you release the button, the frame is fixed to the new position but the program stays in theMove mode. You can leave by pressing the right mouse key.

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ResizeIf you want to change the dimensions of a frame, you may use the Resize instruction. As soon as you pressthe left mouse key over the selected frame the cursor changes its shape and you may change the size of thisframe interactively by moving the mouse. The dimensions are fixed if you release the key, but you are stillin the Resize mode. Terminate with the right mouse button.

Fill TextThe cursor changes its shape to a 'T', which is the sign for the Text mode. If you select an existing framewith that cursor (use the left mouse key), a dialog box is opened in which you can edit the old text or, ifthere was no text before you may start a new text. Remember that a frame can only contain one item, whichmeans, if you accidentally insert a spectrum to a text frame you will loose that text and there will be nowarning.

Fill ParameterAnalog to Fill Text, the Fill Parameter mode offers the possibility to insert entries from a parameter fileinto a frame. The parameter file belongs to the full size spectrum. By clicking at the desired parameters,they will be transferred to the text box, and when you leave that dialog box the selected parameters willappear in the frame.

PasteIf there is a text, a metafile or a bitmap in the clipboard, you can use the Paste command, to copy it to anexisting frame. Just shift the mouse cursor over the frame and press the left mouse button. The Pastecommand is disabled, if the clipboard contains other kinds of information.

CharacteristicsThe dimensions and the appearance of an existing frame can be looked up and varied if you use theCharacteristics instruction. You select the desired frame, by moving the question mark to it and push theleft mouse key. A dialog box will appear, in which you can change several frame specific parameters.

In the dialog boxes for all kindsof frames you have thepossibility to select the frame'sPosition and Size with respectto the upper left corner of thework sheet.Furthermore you can selectLayout attributes for theframe, and whether the Axes ofa spectrum are to be displayed.If the frame contains a 2D-spectrum you can also choosebetween several Displaymodes.

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As a further option you can select the size of a spectrum in the frame by inserting numbers in theappropriate fields for the Spectrum Size . If the window contains text, you may define the maximumhorizontal and vertical number of characters instead of the frame size.

Shift up / Shift down:This instructions changes the display order of overlapping windows. To bring a desired frame to the top, usethe Shift up command, to hide a frame under another use the Shift down command. These commands areonly sensible if the frames are not transparent!

6.3 The Help Menu

About shows a dialog box, displaying copyright information and the version number of the program.

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Chapter 7: Data Transfer

This chapter contains information about the data transfer between different computer systems, usingdifferent transfer possibilities

Options are: EthernetKermit

7.1 Data transfer using GETEPR.EXE

GETEPR.EXE was developed to simplify the data transfer between OS/9 computers and PCs. The programsupports data transfer via Ethernet (using FTP) and the serial port (using KERMIT).

By starting GETEPR.EXE (the program resides in the directory you specified during the installation of theWIN-EPR system) the display shows a status line with three main menus, which are FTP , Kermit and Exit.You will find detailed information about these pull-down menus in the following chapters.

7.1 Ethernet

It is assumed that all drivers and net programs are stored in the directory C:\TCPIP. If you use an otherdirectory, substitute TCPIP by the directory you use.

Installing Schneider&Koch Ethernet interface boardsSK Junior boardBefore installing your Ethernet card note the number of the base address of your card (i.e. d000 - labelledon one chip) and the number of the interrupt. These details are required for the use of the ethernet card! Addthe following lines in your AUTOEXEC.BAT file:

C:\TCTIP\SKTCPJUNC:\TCPIP\IPxxxxC:\TCPIP\ETHDRV

Substitute xxxx with the number of your IP-driver.

SK G8 / G16 boardAdd the following lines in your AUTOEXEC.BAT file, i.e.:

C:\TCPIP\SKDRV -bc8 -i5C:\TCPIP\IPDRVC:\TCPIP\ETHDRV

-bc8 is the memory address-i5 is the interrupt of the ethernet boardConsult the manual of your ethernet board and drivers for more details!

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Installing Western Digital interface boardsThere are several drivers available for Western Digital boards.The command for the driver might look as follows:

C:\TCPIP\8003PKDR.EXE /B:300 /R:CC00 /I:5

or:

C:\TCPIP\WD8003E.COM 0x60 0x5 0x280 0xcc00

Consult the manual of your ethernet board and drivers for more details!.

Installing FTP SoftwareCopy all the ethernet software into a sub directory (i.e. C.\TCPIP]. Add the following lines in yourCONFIG.SYS file:

DEVICE=C:\TCPIP\IFCUST.SYSDEVICE=C:\TCPIP\IPCUST.SYS

Expand the environment variable PATH in the AUTOEXEC.BAT file by the name of the directory where theTCPIP software resides or copy FTP.EXE into your WINDOWS directory. The driver ETHDRV.EXE is amemory resident program and requires about 80 KB of memory. To free this memory enter the followingcommand:

C:\TCPIP\INET.EXE UNLOAD

Then adapt the device driver to your ethernet card: install the address of your PC by the followingcommand:

C:\TCPIP\IFCONFIG C:\TCPIP\IFCUST.SYS 192.9.200.26

Define the name of the host table (the file, which contains all the names and addresses of the availablehosts), i.e.:

IPCONFIG C:\TCPIP\IPCUST.SYS HOSTTABLE C:\TCPIP\HOSTS

The file C:\TCPIP\HOSTS might look like the following:

192.9.200.1 OS/9192.9.200.26 PC_1192.9.200.28 PC_2192.9.200.36 Unix_computer192.9.200.45 new_PC

Finally modify the file /h0/ISP/ETC/hosts on the OS/9 in the same way.

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7.3 Data transfer

Automatic data transfer to PC using FTP/TCPIP - softwareSoftware requirements:for an automatic data transfer you need the program FTP.EXE. It must be able to process the followingcommands (i.e. Schneider & Koch):

### take filename (take batch file filename)### image (do not convert the data)### mkdir (create a directory on host)### get file_host file_PC (get file_host from host and store the file as file_PC on the local PC)### put file_PC file_host (Send the file file_PC from local PC and store the file as file_host onhost)### exit (terminate FTP.EXE)

Data transfer between PC and other workstationsIf your host is not a OS/9 system and the directory structure is not known (see FTP-Setup-Copyparameters), you must specify the directory structure of your host in GETEPR.INI: Return to DOS and startthe program FTP.EXE, enter host name, user name and password and login to your host. Then enter thecommand:

dir / C:\HOSTDIR

The host directory will be transferred to the PC and stored as C:\HOSTDIR. The following information isrequired for a correct use of the host directory under WINDOWS:

### distinguishing characteristic of a directory### distinguishing characteristic of a filename### position of these characteristics### position of filenames

A (OS/9) host directory might look like this:

Directory of . 09:28:51Owner Last modified Attribute Sector Bytes Name

0.0 90/10/16 1774 d-ewrewr 1AA5 736 C0.0 90/10/14 2009 d-ewrewr A3 5152 CMDS0.0 90/10/16 1709 d-ewrewr 1B11 2176 DEFS0.0 90/01/11 1104 d-ewrewr D977 192 FORCE0.0 90/06/29 1137 d-ewrewr D97D 256 GPIB0.0 90/01/15 1813 ------wr 172AB 63300 OS9Boot0.0 90/01/15 1402 ------wr 8E7C 65134 OS9Boot.OK0.0 89/11/17 1025 ------wr 19E 61602 OS9Boot.h00.0 90/08/13 1220 ------wr 180F8 63154 OldBoot0.0 90/01/22 1328 d-ewrewr 19BC3 256 PCM0.0 90/09/03 1039 d-ewrewr F336 64 PLSPOOL0.0 89/11/09 1821 ------wr 2E2 3117 Readme0.0 90/10/26 1427 d-ewrewr 1FFF 1344 S0.0 90/09/03 1039 d-ewrewr F33F 64 SPOOL0.0 90/10/16 1226 d-ewrewr 299 608 SYS0.0 90/09/06 1434 d-ewrewr 2337 288 SYSMODS0.0 90/10/26 1622 d-ewrewr 27F4 1440 T0.0 90/10/01 1918 d-ewrewr 18A8C 448 TE0.0 90/10/14 1849 ------wr 2F9 39 init.graph

After loading this file into a text editor (i.e. NOTEPAD.EXE) you will see that directories are defined by a"d" in column 23 and normal files are defined by a "-" in column 23. The name of a directory or file is foundat column 46 to 57 (or at column 46 to the end of line).

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Define these parameters in GETEPR.INI in the following way:

### [host-...] name of the host (i.e.. [host-OS9])### chardirectory: distinguishing characteristic of a directory### posdirectory: column of chardirectory### charfile: distinguishing characteristic of a filename### posfile: column of charfile### filenamestart: first column of filename### filenameend: last column of filename### ignorefile: ignore filename

GETEPR.INI file i.e.:

[kermit]Path= ; Kermit-directory for MSKERMIT.EXEName= ; Name of Kermit-program

[FTP]Path= ; TCPIP-directory for FTP.EXE, TNVT.EXE etc.Name= ; Name of FTP-program

[Parameter]hostfile=c:\tcpip\hosts ; Name of hosttable

[host-os9]chardirectory=dcharfile=-posdirectory=27posfile=27filenamestart=54filenameend=70ignorefile=----

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FTP - Setup

Use Setup... to define standard parameter. The directory parameter are important for the correct display ofa received directory. First select the desired host. The current values for the selected host are shown in thedialog box. You can change the values using the corresponding edit box (for details see chapter Datatransfer between PC and other workstations).

If you do not know the directory structure of your host , click the button Copy Parameter. There areseveral known directory structures shown (i.e. SUN OS, OS/9 and PC directory formats.

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Get/Send EPR-FilesSelect Get... and select the desired host. The available hosts are listed in a box. Selecting a host which isnot specified in GETEPR.INI initiates the use of default parameters.

Specify the following parameters:

### Host: desired host### User: user name (i.e.: guest)### Password: password### Path: the selected path (on the host) will be used for data transfer### File type: select the file types to be displayed in the list box (Spectra or All Files)### Get File: the file to transfer

Define the desired host, user and password and click to the button Get host directory. This activatesFTP.EXE and displays the host directory in a list box. Now you can change directories and select files fromthe host the same way you do on your local PC

Filenames longer than eight characters will be truncated to eight characters.

Selecting the Ok button will start the transfer. In the same way data can be transferred from the PC to thehost.

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Manual transfer

To start manual transfer select the menu item Run FTP... . If the parameters hostname, user and passwordare already defined, FTP.EXE will start and login to the host.

The following commands are available (selection):

• fcd change foreign directory (i.e. fcd /h0/USR/JME)• lcd change local directory (i.e. lcd C:\EPR\DATA)• iget host-file PC-file transfer file host-file from host to local PC and save this file as PC-file.• iget transfers a file without any modification of the data set (i.e. iget

kin4.par)• iput PC-file host-file: transfer file PC-file from local PC to host and save this file as

host-file.### exit terminate FTP.EXE.

Use Run TNVT... to start TNVT.EXE or Run FTPSRV to have your PC act as FTP server.

For more information see your TCPIP manual.

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7.4 KermitGETEPR.EXE requires a PC-Kermit version , which is able to handle the following commands(i.e. MS-Kermit Version 2.31):

### take### cwd### remote host mkdir### get### send name1 name2### finish

Setup Kermit

Select Setup... to define parameters for the data transfer (speed, port, host, flow and parity). Parametersspecified here will be stored in GETEPR.INI

Data transfer from OS/9 mainframe to PCSelect Run Kermit, enter the command con to connect to your OS/9 and login. Start Kermit on your OS/9,define speed and file type (binary) (for more details see your Kermit manual) and enter the servercommand. Now escape back to your local PC by Control-C or Alt 29-C (press the Alt key and enter 29 onthe numerical key pad, then enter C). Enter exit to terminate Kermit on your PC, select Get..., specify thedesired local directory and specify the file to receive.

Note: Filenames longer than eight characters will be truncated to eight characters.

7.5 ExitExit to WINDOWS

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7.6 Trouble shootingIf the default data from GETEPR.INI isn't accepted, ensure that GETEPR.INI resides in your WINDOWSdirectory and delete all other existing GETEPR.INI files

Error messages from GETEPR.EXE

Error opening FTP.EXE:

### Reason: FTP.EXE not found### Remedy: define in GETEPR.INI after entry [ftp] the parameter Path= and Name=.

Specify the directory where your FTP software resides, i.e.[ftp]Path=D:\TCPIPName=FTP.EXE

### Reason: number of buffers and/or files in CONFIG.SYS too small### Remedy: enlarge values for buffers (i.e. 20) and/or files (i.e. 30) and restart your computer

Error opening MSKERMIT.EXE:

### Reason: MSKERMIT.EXE not found### Remedy: define in GETEPR.INI after entry [Kermit] the parameter Path= and Name=.

Specify the directory where your Kermit software resides i.e.[Kermit]Path=D:\DFUEName=MSKERMIT.EXE

Error opening TNVT.EXE: see FTP.EXE

Error opening FTPSRV.EXE: see FTP.EXE

Error opening command file ...!

### Reason: unable to create a file, perhaps no space on hard- or RAM-disk### Remedy: delete some unwanted files

Error writing file!

### Reason: unable to write a file, perhaps no space on hard- or RAM-disk### Remedy: delete some unwanted files

Error message from TNVT.EXE: usage ....!

### Reason: required keyboard driver not found### Remedy: specify the complete path name for the driver in the AUTOEXEC.BAT file i.e.:

SET h19_keymap=C:\TCPIP\GERMAN.MAP

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Appendix

The EPR.INI File

The WIN-EPR.EXE program needs the EPR.INI file when it should be executed. In this initialisation file,which must reside in the WINDOWS directory, all the definitions concerning path, fonts, colors and otheruseful information is stored. This file is created during the installation procedure but every time youterminate a WIN-EPR session, the program automatically stores some parameters in it. If you want tochange this file, you have to follow the below given rules, otherwise the program can be corrupted.

An initialisation file is divided in several sections. Each section start with a title, which is set in [brackets].After the title you find a list of all options. The general format is option = text. There are no restrictions,concerning the order of the sections and options.

Entries displayed in italics can be changed, whereas bold entries have to be kept. If there are various valuesfor one option, the default is underlined.

[Directories] directory definitions for programs and dataepr= C:\EPR\ WINEPR.EXE directorydata=C:\EPR\DATA\ last used data directorytemp=C:\TEMP\ directory for temporary files

It is very important, that the here defined directories are existing!

[device] installed printerprinter= name, driver name, interfacei.e. printer=HP LaserJet IIP,HPPCL, LPT1:

[Settings] miscellaneous settingslogo=yes Bruker logo at printouts: yes/no.sound=no support of a sound card : yes/no.

[Axis-font] font setting for the axes commentsFace=Arial font nameHeight=12 height of characters in pointsWidth=5 width of characters in pointsWeight=400 weight of characters: 400: normal, 600: bold; 200: thin

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[Colors] color settingscol1d=255 255 0 yellow color of the 1.-level (for monitor)col2d=255 0 0 red color of the 2.-levelcol3d=0 255 0 green color of the 3.-levelcol4d=0 255 255 turquoise color of the 4.-levelcol5d=255 0 255 violet color of the 5.-levelcol6d=0 0 255 blue color of the 6.-levelcol7d=255 0 0 red color of the 7.-levelcol8d=0 255 0 green color of the 8.-levelcol1p=0 0 255 blue color of the 1.-level (for printer/plotter-output)col2p=255 0 0 red color of the 2.-levelcol3p=0 255 0 green color of the 3.-levelcol4p=0 255 255 turquoise color of the 4.-levelnumbers=255 255 255 white color of the annotationsbar=255 0 0 red color of the region marksbckgrnd=0 0 0 black color of the spectrum backgroundmain=0 255 255 turquoise background color of the main window (default: turquoise)

[Palette] palette for the color selection1=0 0 0 black2=255 255 255 white3=255 0 0 red4=0 255 0 green5=0 0 255 blue6=255 255 0 yellow7=0 255 255 turquoise8=255 0 255 violet9=127 127 127 grey

You can add more colors, using the following form:n= R G B-value name of color

[MainWindow] position and size of the main windowLeft=15Top=1Right=616Bottom=394

[ViewWindow] position and size of the viewcursor windowLeft= 423Top= 46Right=195Bottom=99

Further window positions:[Win1] and [Win2]

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The GETEPR.INI File

The GETEPR.INI file is created by the data transfer utility program GETEPR.EXE. For details see chapter7: Data Transfer

The BRUKER.INI FileAdditionally, the BRUKER.INI is created, which is meant to harmonise the execution of several BRUKERWINDOWS-applications

[WINEPR] information about WIN-EPRProgPath=C:\EPR\ path definition for WIN-EPR.EXEProgName=WINEPR.EXE filename of the executable fileWinName=WIN2EPR internal name for the WINDOWS-frameWinGroup=WIN-EPR name of the group file

[GETEPR] information about GET-EPRProgPath=C:\EPR\ path definition for GETEPR.EXEProgName=GETEPR.EXE filename of the executable fileWinName=GETEPR internal name for the WINDOWS-frameWinGroup=WIN-EPR name of the group file