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1. Computational effort To use this procedure appropriately it has to be at least as efficient as the highly optimized FFTs To verify this inspect the following equation form N 1 N 1 YO Y SY AUDE DAN A 13 GZ i Then calculate for each i and v effort increases quadratically the latter sums storing them in an extra data array The size of the data array exactly matches the one that would be needed for storing the Fourier Transformation Afterwards you only need the summations for each v v Thus the total effort increases quadratically using the number of the wave numbers and linearly using the number of the sampling points in time A 12 OPUS 3D Bruker Optik GmbH Index Numerics 2D correlation 54 57 58 2D spectrum 54 57 58 3D window 18 19 22 3D window 1 3 32 59 A Absorption intensity 3 12 28 35 36 Add traces 40 Assemble 8 Assemble GC file 35 36 39 Assemble MAP file 35 36 39 B Background color 11 25 C Chemical mapping 66 67 Chromatogram 1 2 16 35 Chromatographic measurement 16 35 Clip data 11 Closure 61 63 Closure concentrations 63 Cluster 24 Cluster list 8 32 Coefficient spectrum 56 Color gradient 11 12 30 Color palette 25 Color scale 4 Component spectrum 61 Compute trace 44 Concentration profile 61 62 63 Concentration trace 44 Constraint tolerance value 63 Constraint value 63 Contour cube 5 Contour level 4 8 11 12 13 28 29 30 Con
2. x 1735 62 x 2861 84 z 1108 95 Z 216 73 ABO Zoom Out Reload Selection Reload All Show Subset Show Trace Extract Spectra Extract Traces Edit Levels Factorize Integrate Index 93 Copy to Clipboard I Autoscale Properties Zoom A Scale All Spectra gt Shift Curve Crosshair gt X Wavenumher Gral Add Anmotatio Sccors Copy Copy All Paste Integrate Properties A kN TA habila Ai E direte b ye lay b d 3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 9800 sl Figure 20 Map Spec Window 3D Plot and the corresponding Spectrum The window type Map Spec also allows the integration of a 3D file using an interactively defined integration area frequency range To define an integration area in the lower spectrum window interactively draw a line across the band of interest while pressing the left mouse button There upon the defined integration area becomes red and the exact integration area limit values are displayed See figure 21 Note If required you can afterwards modify interactively the defined integration area 1 e you can enlarge or narrow down the defined integration area by placing the cursor on an integration area border line and shift it to the left or right while Bruker Optik GmbH OPUS 3D 19 Special Window Types pressing the left mouse button Moreover positio
3. In the Store group field specify how the spectra are extracted and stored Series of single blocks Single blocks are stored in the result files Coadded block All blocks are added to a result file Average block Only the average value is stored If this option is activated the spectra of a cer tain time period or area are averaged The spectra are stored in a result file that contains the average values between the first and the last block New 3D file A small part of a 3D file is extracted and saved as a new 3D file Mapping line A 3D file is generated that corresponds to the section line in mapping data First block only Only the first spectrum is extracted and saved in the result file Last block only Only the last spectrum is extracted and saved in the result file Difference first last The difference spectrum between the first and the last block specified on the Extraction Range page is extracted and saved in the result file Difference last first The difference spectrum between the last and the first block specified on the Extraction Range page is extracted ad saved in the result file lg first last and lg last first The logarithm of the ratio of the two spectra is calculated and saved in the result file In the Jf file already exists group field you have to specify whether the filename is incremented to avoid overwriting an existing file or the process is aborted Activate the corresponding opt
4. OPUS Spectroscopy Software User Manual Version 6 3D gt lt BRUKER de 2006 BRUKER OPTIK GmbH Rudolf Plank Str 27 D 76275 Ettlingen www brukeroptics com All rights reserved No part of this publication may be reproduced or transmitted in any form or by any means including printing photocopying microfilm electronic systems etc without our prior written permission Brand names registered trade marks etc used in this manual even if not explicitly marked as such are not to be considered unprotected by trademarks law They are the property of their respec tive owner The following publication has been worked out with utmost care However Bruker Optik GmbH does not accept any liability for the correctness of the information Bruker Optik GmbH reserves the right to make changes to the products described in this manual without notice This manual is the original documentation for the OPUS spectroscopic software Table of Contents 1 Introduction ia 1 2 Displaying 3D Files xiii 3 2 1 IDE WV AMINO WN e ia EKO TEA aaa tn EK 3 XEL 3D Window DEsigi crecida nos amita oE eik ganga ge 3 2 1 2 Changing the View of the 3D Plot eze gezi zeze eri rr rete 4 2 1 3 Navigating through the DEO 5 2 2 Contour Cube 04 40015 a a Sei 5 2 3 Functions of the 3D Pop up Menu ausa 7 2 4 3D Properties Dialog Window 2s o44442 46 5064 da Ebari gre 9 DAN CID Properties Arra id Ratan Bays Saw E d E Be hee Raa 9 D
5. Open the Signal to Noise Ratio dialog window and drag and drop the 3D file in question into the File s to compute signal to noise field Click on the Fre quency Range tab and specify the frequency range for which the signal to noise ratio is to be calculated After having entered all parameters click on the Calcu late button For detailed information about this function refer to the OPUS Ref erence Manual Bruker Optik GmbH OPUS 3D 53 Peak Picking In case of a 3D file the result of calculating the signal to noise ratio are four traces S N RMS S N PP N RMS and N PE which OPUS stores automat ically in the TRC block You can have the traces displayed both in form of a report and graphically in a 3D plot See chapter 1 In the first case drag and drop the TRC block into a report window In the latter case right click on the 3D window and select in the pop up menu the Properties function As a result OPUS opens the 3D Properties dialog window Click on the Mapping tab select in the Select trace drop down list the corresponding trace and click on the OK button As a result the selected trace is displayed in a different color at a side of the 3D plot 6 4 Peak Picking This function helps you to identify peaks in spectra For detailed information about this function refer to the OPUS Reference Manual In case of a 3D file the result of picking peaks are three traces PP wavenum ber PP absolute intensity and PP widt
6. 0 384 I ymax 0 10 Spacing o1 y Spacing foa y 0 00 ORFS SU Linear Log 0 20 Figure 32 a Complete y Axis divided into b Part of the y Axis divided into Contour Levels Contour Levels 30 OPUS 3D Bruker Optik GmbH Edit Menu Spacing This drop down list allows you to determine the distance between two contour lines and consequently the number of the contour levels The smaller the spac ing value is the more contour levels are inserted and the more detailed the selected color scheme is To implement the settings in the color bar click on the Create button See figure 33a and b x x ok EZE 095 EL Cancel 0 30 Cancel Cancel dei Cancel 0 80 0 75 0 70 0 65 0 60 0 50 Auto contour levels 0 55 Auto contour levels Fiom ETT E ymin bag be ETT ymin 0 40 To 0 984 E ymax 0 35 To EGO IV ymax 0 30 b Spacing fas y 0 25 Spacing 0 05 y 0 20 0 00 GS Linear 2 Log 0 15 GZ Linear a Log 0 10 0 00 Figure 33 a Number of Contour Levels in b Number of Contour Levels in case of a case of a large spacing value small spacing value Linear Log You can choose between either a linear or a logarithmic spacing of the contour lines by activating the corresponding option button To implement the settings in the color bar click on the Create button See figure 34a and b OK OK 0 90 Cancel Cancel 0 80 PO PE 0 70 0 60 0 50 m Auto contour levels m Auto
7. Rotation 120 3 Inclination 45 a x 1735 62 x 2861 EA z 108 95 E Z 216 73 ABO Zoom Out Reload Selection Reload All Show Subset Show Trace Extract Spectra Extract Traces Edit Levels Factorize Integrate Copy to Clipboard Index 393 Properties X Wavenumber cm 1 200 Z Seconds Figure 19 3D Window 18 OPUS 3D Bruker Optik GmbH Displaying 3D Files 2 5 2 Map Spec Window Another useful window type is the Map Spec window which consists of a 3D window and a normal spectrum window See figure 20 The upper subwindow displays only one of the possible plots xyz xy zy or xz at a time by default the xyz plot You can switch between these plots by selecting the desired plot type in the pop up menu The pop up menu of the upper subwindow is identical to the one of the 3D window type For a detailed description of the pop up menu and the 3D Properties dialog window refer to the sections 2 3 and 2 4 For information about the functionality of the 3D window see also section 2 1 The lower subwindow displays the spectrum at the current position of the z axis marker line When you activate the Autoscale check box the spectrum is scaled to its total size For information about the pop up menu functions of this sub window refer to the OPUS Reference Manual v XYZ Plot XY Plot ZY Plot xZ Plot Rotation 120 Inclination 45
8. Thereupon the report window opens showing the integration results in form of a table The results are listed in the upper subwindow in the column of which the title is identical to the defined frequency range 20 OPUS 3D Bruker Optik GmbH Displaying 3D Files f Ele Edit view Window Measure Manipulate Evaluate Display Print Macro Validation Setup Help 38x ARAZ ZERB SESH Sees zee OPUS Browser ax E Display fullaccess ows 1 Operator Defaul E 3d Display full_access ows 2 Operator Dd SE 3d Display full_access ows 3 Operator De E MOA dele ker i 3d Display full_access ows 4 Operator Dd SETAS BIE fullaccess ows 4 Operator Dd Operata ae El ESTE 6 0_3 Betaversior eS Trace Mukiple 1634 63 1565 13 E E 1634 63 1565 13 D 0 1397030912 271993928 1397030912 271993928 0 o 3 3 INoBadFW 458752 458752 o 0 dHFL 0 000000 0 000000 EL 0 000000 0 000000 dHFFL 0 000000 0 000000 EIZA 0 000000 0 000000 FFilterSize 528438 528438 IFilterType 147849219 147849219 dFFP 0 000000 0 000000 du 325 677888 325 677888 dMin 0 000144 0 040039 dMax 0 001292 0 179218 dscF 1 000000 1 000000 dpkafw GO 0 000000 E 9 Report Display full_access ows 5 Operator Default Administrator bx Figure 22 Report with the Integration Results Integration Results To obtain a graphical display of the integ
9. 2100cm and therefore has an opposite sign 0 01 0 00 0 01 2400 2400 p 2200 2000 22 2000 Wavenumber cm Wavenumber cm 1 de 1800 Figure 44 Asynchronous Correlation Spectrum Due to the fact that overlapping spectral regions can be separated these proce dures can be regarded as a high resolution method Polystyrene Film The most prominent field of application for 2D spectroscopy is the analysis of polymer films The usual experimental setup includes a mechanical stretcher and in most cases a polarizer or photoelastic modulator Upon stretching the film the polymer orientates and the degree of order of the main and side chains is increased The induced changes in the absorbance spec trum can mostly be observed by using polarized light Bruker Optik GmbH OPUS 3D A 7 Appendix The two dimensional spectra show the reaction of the different functional groups to the applied mechanical stress The reaction of polystyrene to mechan ical stress is shown in figure 45 and 46 Wavenumber cm 1 1480 1460 1440 1420 Wavenumber cm 1 Figure 45 Synchronous Correlation Spectrum of a Polystyrene Film The synchronous correlation spectrum is dominated by strong cross peaks of the two main bands figure 45 while the asynchronous spectrum figure 46 reveals more detailed information The cross peaks reveal underlying shoulders or overlapping bands The band at the wave number around 1450cm7 has
10. 3D file to which you want to add the trace by dragging and dropping the 3D file from the OPUS browser In the lower Traces field include the traces that you want to add to the 3D file If you want to remove a trace from the Traces field again mark it and press the delete key If the 3D file already contains traces make sure that the new traces have the same number of data points starting point and end point If the 3D file does not contain any traces make sure that the new traces have at least the same number of data points as there are spectra in the 3D file 4 3 Extract Data If you want to process a single spectrum or a trace of a 3D file separately using an OPUS manipulation or evaluation function you have to extract it beforehand Note There are no major differences between extracting a spectrum or a trace from a Chrom file or a Map file Only if you want to calculate the mean value of surface mapping data you have to take the line by line layout of the spectra left to right and top to bottom into account There are two ways of invoking the Extract Data dialog window 1 Select the Extract Data function in the Measure menu 2 Right click on the 3D window and select the Extract Spectra or Extract Traces function from the pop up menu 40 OPUS 3D Bruker Optik GmbH Measure Menu 4 3 1 Select Files In the first case you have to drag and drop the corresponding data block in the File s to extract field The data blo
11. Selection Mapping be Show as lines I Show as highlighting I Show as shading I Show subset x 5 00 z 13 40 x 10 00 Z 6 60 Show b y Show z y Figure 13 3D Properties Selection 14 OPUS 3D Bruker Optik GmbH Displaying 3D Files Show as lines The specified section is indicated by differently colored marker lines For information about the marker lines see also section 2 1 3 Show as highlighting The specified section is displayed in a lighter color Show as shading The specified section is displayed in a darker color Show as subset Only the section defined by X X and Z Z values is displayed by zooming in the plot In this case data are not reloaded Select the Reload Selection function from the pop up menu to display the plot more accurately Show Use these two drop down lists figure 14 to specify the section that is to be dis played The options for the x and z axis of the plot are almost identical The parameters for the X axis are X shows the cross section at position X X shows the cross section at position X X and X shows the cross sections at both positions X and X X X shows the difference between the values for position X and position X X X shows the difference between the values for position X and position X log X X shows the logarithm of the ratio between X and X values log X X shows the logarithm of the ratio between X and
12. The slider enables you to select a certain contour value and in doing so to move in the contour cube through the individual contours Bruker Optik GmbH OPUS 3D 5 Contour Cube Rotation 141 SN 28 00 Inclination 18 3 26 00 24 00 41 67 GEO x 87 50 20 00 be B 130 3D Plot of the e EST selected Layer Redraw zLayers 0 Index 330 Layer 5 2 EK Ea A All E deg 82 Xftioran 0 4120 X Micron Y No Y unit defined Y No Y unit defined r D 20 40 60 80 100 120 O0 20 40 60 80 100 120 X Micron Z Micron Figure 4 Selecting a Layer Rotation 120 3 Inclination 20 3 141 67 x 87 50 E zZ D E 3 Zz e750 3 Redraw Contour Cube zLayers 0 Index 330 Layer All Slider D 4120 X Micron Y No Y unit defined Y No Y unit defined D 20 40 60 80 100 120 0 20 40 60 80 100 120 X Micron Z Micron Figure 5 Contour Cube 6 OPUS 3D Bruker Optik GmbH Displaying 3D Files 2 3 Functions of the 3D Pop up Menu Right click on the 3D window to open the following pop up menu v XYZ Plot xY Plot 2Y Plot XZ Plot Zoom Out Reload Selection Reload All v XYZ Plot xY Plot ZY Plot XZ Plot Zoom Out Reload Selection il Reload 4 Show Subset Show Subset Show Trace Show Trace Extract Spectra Assemble Extract Traces Extract Traces Edit Levels Edit Levels Factorize Factorize Integrate Integra
13. at least two underlying component bands at the wave numbers around 1451cm and 1455cm as apparently indicated by the corresponding cross peak A 8 OPUS 3D Bruker Optik GmbH Appendix 1480 1460 1440 Wavenumber cm 1 1420 1480 1460 1440 1420 Wavenumber cm 1 Figure 46 Asynchronous Correlation Spectrum of a Polystyrene Film Although this spectrum has been acquired by linearly increasing the stretching force it is important to note that it exhibits all the features being observed by the small amplitude sinusoidal stretching as described in many publications Due to the general correlation algorithm the result is vastly independent of the type of stretching force This is advantageous to these experiments Other Applications All procedures described so far can also be used to gain insight into the depen dence and assignment of bands in the middle and near infrared region The fol lowing example is a three component mixture The spectra of various compositions have been measured in the middle infrared as well as in the near infrared region Then the resulting spectra have been arranged into two differ ent files in exactly the same order The mixtures are composed of an alcohol an ester and a nitrile The resulting correlation coefficient spectrum is shown in figure 47 A detailed explanation of the 2D spectrum would go beyond the scope of this manual Therefore only the most prominent features are
14. block is used for the correction 56 OPUS 3D Bruker Optik GmbH Evaluate Menu Digital Resolution Full All data points are used Limit Only every n data point is used with n being the value you have entered in the Reduction Factor field This option is recommended because the number of data points in the resulting data set increases with the square of the number in the original data set Average The Average mode is not yet implemented 6 5 3 Frequency Range 1st File 2D Correlation x Select Files Method Frequency Range 1st File 2nd File J Use file limits yt r Select Frequencies Get Display Limits gt Starting point 4000 X End point 400 Correlate Cancel Help Figure 57 2D Correlation Dialog Window Frequency Range 1st File Use File Limits When the Use File Limits check box is activated the whole frequency range in the data set is used for the x axis This x axis is the first frequency axis of the 2D spectrum When this check box is not activated x Startpoint and x Endpoint determine the frequency range used for the 2D correlation Interactive Click on this button to specify the frequency range limits for the x axis of the 2D spectrum interactively Get Display Limits When you click on this button the frequency range limits of the currently active display window are taken X Startpoint X Endpoint Specify the frequency range limits for the x axis of the 2
15. factor analysis the evolving factor analysis condenses the under lying information from an evolving system to just one concentration profile and one spectrum for each modeled component This is achieved by applying cer tain constraints non negativity unimodality closure and normalization to the model These constraints help to obtain concentration profiles and component spectra that are very close to the true ones and thus facilitate the interpretation of the analysis results from a chemical point of view Bruker Optik GmbH OPUS 3D 61 Factor Map File To define the constrains for an evolving factor analysis click on the Use the fol lowing constraints for the model tab Factor Map File E x Select Files Options Frequency Range Use the following constraints for the model IV Apply constraints Number of components 0 m Non negativity IV Apply to concentration profiles Method ForceToZero I Apply to spectra Method ForceToZero y M Unimodality IV Apply to concentration profiles Method horizontal E Constraint tolerance Gu IV Apply to spectra Method horizontal y Constraint tolerance 1 Closure Normalization None y Constraint value fi Method Y equal heights Factorize Cancel Help Figure 62 Factor Map File Defining the Constraints for the Model Apply constraints Activate this check box if you want to perform an evolving factor analysis i e a f
16. functions allow you to build 3D files from single spectra The spectra are assembled in the order you have spec ified in the field File s to assemble Note Theoretically you can assemble all single spectra to a Map or GC file no matter of what measurement they originate from But in order to obtain a useful assembled file use only single spectra acquired from one and the same sample at different measurement positions for the assembly of the Map file And assemble only single spectra acquired at the same measurement position over a longer period of time to a GC file 4 1 1 Select Files When you select the Assemble GC File function in the Measure menu the fol lowing dialog window opens Assemble GC File x Select Files Result File Frequency Range Z Axis File s to assemble C OPUS 6 0 Data Extended Demodata MAP BRUKEL tes Data block v Assemble Cancel Help Figure 38 Assemble GC File Dialog Window Select Files Note The Assemble MAP File dialog window is identical to the Assemble GC File dialog window apart from the forth tab that will be discussed in section 4 1 4 and 4 1 5 The first page of the dialog window allows you to select the files containing the single spectra you want to assemble to a GC or Map file You can either drag and drop the files from the OPUS browser or load them using the Load button With the four buttons in the upper right corner of the Fil
17. lt gt um nm Averaging Merge Spectral Ranges Atmospheric Compensation GO Straylight Correction Noise Generation WY Moving mean ZEA Make monotone Figure 51 Manipulate Menu For detailed information about these functions refer to the OPUS Reference Manual Bruker Optik GmbH OPUS 3D 47 Spectrum Subtraction 5 1 Spectrum Subtraction The function Spectrum Subtraction is also applicable to 3D files In the auto matic mode the difference spectra are calculated using multiplication factors which have been determined automatically by a fit using the least squares method These factors are stored separately in the different traces The newly calculated traces are attached to the existing ones 5 2 Spectrum Calculator The Spectrum Calculator is a very flexible spectra manipulation tool that enables you to process 3D files and to calculate complete kinetics Load 3D data blocks into the Spectrum Calculator window by double clicking on the data block or dragging and dropping the data block into the Spectrum Calculator The syntax of the formulas and the calculation methods are identi cal to those for single spectrum files The entered formula is applied to all spec tra in the 3D file i e OPUS processes one spectrum after the other To induce the spectrum calculator to process 3D files the first data block in the formula has to be a 3D block Otherwise you have to modify the formula as fol lows 3D block 3D bloc
18. necessary for an implementation with FFTs Substituting Moda equation 8 into the equation 10 from his article yields Se Im Re Re Im Y v EAE v 0 Y v 0o Y v 0 Y Isa ildo A 7 o0 Recognizing the real part as the cosine transform and the imaginary parts as sine transform the following discrete sums are obtained GO HEIN v2 Sd SO EE purea A ER EAT A 8 N 1 ares y VNOS RIKMA ustua Ao Replacing Aw by and collecting the constant terms in front of the sums and executing the multiplication yields 2 At Gin v OA da KG 2 IV yV2 sin 2nk N cos 2k A 9 cos 2mik N sin 2njk N In the next step you identify N and combine the sine and cosine terms with the help of an additional theorem yielding sin 21rk i j N a NA zal pae ED v2 GE so A AMD BIEN j k N A 10 EK E The innermost sum over k can be calculated analytically yielding Bruker Optik GmbH OPUS 3D A 11 Appendix N ie Site EEI gada Sri N N 2 2 2 SI sin 2m i j k N ee E A 11 KEY 1 cos N with abbreviating i j In the latter part of this equation the sine and cosine terms alternate i e they become zero and make no contribution to the results The first 1 cos term disappears when is even Thus the only contribution to the results arises when is odd In this case the denominator can be replaced by sin yielding 2 _N 1_N 1 o ES A 12 i j with i j being odd
19. selection 10 Remove traces 27 Report 1 20 37 44 52 53 54 60 64 65 68 RGB color model 60 RGB colors 29 RGB trace 60 63 65 66 Rotation 4 9 11 24 S Sample layer 5 Score coefficients 65 Screen resolution 7 11 Select image 16 Select rectangle 16 Select trace 16 Show as highlighting 15 Show as lines 15 Show as shading 15 Show as subset 15 Show subset 7 Show surface 9 Show trace 7 Show wireframe 9 Signal to noise ratio 53 54 Spatial resolution 45 Spatial resolved measurement 1 3 5 36 Spectra matrix 45 Spectral noise 45 Spectrum block 17 Spectrum calculator 48 Spectrum subtraction 48 Spectrum window 19 20 22 Split interferograms 48 Stacked 10 Store cluster 8 T Text color 11 25 Time axis 3 45 Time resolution 48 Time scale 1 Time slice 5 Time resolved measurement 1 3 5 10 35 55 58 Trace 1 2 3 16 27 40 51 52 53 54 68 Transpose 45 Transposed matrix 64 TRC block 1 3 8 20 32 33 41 44 52 53 54 60 64 65 67 68 Two layers 10 U Unimodality 61 63 y Video image 10 13 16 22 Video assisted measurement 10 13 16 22 WwW Wavenumber axis 3 45 Wavenumber scale 11 Z Zoom out 7
20. window page you define the extraction range Extract Data J x Select Files Extraction Range Extraction Mode rom Block fo Beginning of file o Block fi C End of file F Block list I Use block list m Extract Cancel Help Figure 46 Data Extraction Dialog Window Extraction Range When you activate the Block option buttons in the group fields From and To you have to enter the index number of the first and the last spectrum that is to be extracted For information about the index number refer to section 2 1 3 Wen you activate the option buttons Begin of file and End of file all spectra in the 3D file are extracted If activate the Use block list check box only those spectra of which the index number you have entered in the field below are extracted 4 3 3 Extraction Mode On the this dialog window page you define the extraction mode Extract Data d x Select Files Extraction Range Extraction Mode mStore C Series of single blocks Coadded block C Average block C New 3D file Mapping line First block only Last block only Difference first last Difference last first C offirstlast loflast first If file already exists Increment name C Abort Extracted files Do not load C Load Extract Cancel Help Figure 47 Data Extraction Dialog Window Extraction Mode 42 OPUS 3D Bruker Optik GmbH Measure Menu
21. 006 0 010939 3 514510 0 015405 4 686013 0 026647 5 857516 0 012001 7 029019 0 042266 8 200522 0 005272 9 372026 0 030317 Hace 10 543529 0 012848 11 715032 0 029545 12 886535 0 030677 14 056038 0 044549 15 229542 0 026267 16 401045 0 023058 17 572548 0 031265 18 744051 0 012428 19 915554 0 037295 21 087057 0 017227 22 256561 0 038716 272 ANNAA d Figure 1 Report Display of a Trace Trace X Wavenumber cm 1 Figure 2 Graphical Display of a Trace OPUS 3D Bruker Optik GmbH Displaying 3D Files 2 Displaying 3D Files After the completion of a time resolved or spatial resolved measurement the resulting 3D file is displayed in the OPUS browser with the absorbance or trans mittance data block Depending on the kind of measurement the 3D file includes also a TRC block for the traces To load an already existing 3D file use the Load File function in the File menu By default OPUS displays a 3D file in a 3D window See section 2 1 Besides this default window type there are also other special window types for displaying a 3D file See section 2 5 2 1 3D Window When you load a 3D file in OPUS the 3D window opens automatically and the data are displayed as shown in figure 3 The 3D window is the default window type for displaying a 3D file 2 1 1 3D Window Design The 3D window consists of four subwindows Each subwindow displays one type of plot XYZ XY ZY
22. 219 147849219 147849219 dFFP 0 000000 0 000000 0 000000 0 000000 dFLP 325 677888 325 677668 325 6778886 325 677888 dMin 0 000144 0 227386 0 111982 0 378391 dMax 0 001292 4 109604 0 868049 27 402729 dSCF 1 000000 1 000000 1 000000 1 000000 gt dpka_fw 0 000000 0 000000 0 000000 0 000000 x x gil Gia SOAS Display default ows 1 OO 3d Display default ows 2 gt D Report Display default ows 3 BTT Figure 54 Report Window displaying the Integration Results 6 2 Quantitative Analysis Quantitative analysis functions like Quant1 included in OPUS or Quant2 a separate software package are also applicable to 3D files When the required parameters are stored in a method file the quantitative analysis can be applied to the entire 3D file The result of analyzing a 3D file quantitatively is a trace that OPUS stores auto matically in the TRC block The trace name is identical to the name of the Quant method You can have the trace s displayed both in form of a report and graphically in a 3D plot See chapter 1 For detailed information about how to set up a quantitative method refer to the corresponding OPUS manuals For information about Quantl see the OPUS Reference Manual and for information about Quant2 refer to the OPUS QUANT Manual 6 3 Signal to Noise Ratio This function allows the calculation of the signal to noise ratio for a spectrum in a specified frequency range This function is applied to the whole 3D file
23. 38 0 151382 1 869028 8 200522 0 000144 0 254687 0 152004 1 675535 9 372026 0 000192 0 267918 0 155844 1 719149 10 543529 0 000178 0 279533 0 157756 1 771927 11 715032 0 000172 0 296036 0 146735 2 017494 12 886535 0 000180 0 285294 0 156264 1 825720 Display default ows 1 zb 3d Display default ows 2 Data Parameters AB Multiple AB Multiple Data Parameters Trace Multiple Instrument Parameters FT Parameters Sample Parameters Acquisition Parameters Optic Parameters E Contour Method Datafile History 14 058038 0 000180 0 297386 0 167153 1 779125 15 229542 0 000174 0 286765 0 141295 2 029549 16 401045 0 000172 0 268471 0 151704 1 769702 17 572548 0 000195 0 294830 0 154233 1 911595 18 744051 0 000196 0 244790 0 134270 1 823116 19 915554 0 000189 0 227386 0 137834 1 649712 21 087057 0 000178 0 294030 0 151768 1 937365 22 258561 0 000187 0 233495 0 139147 1 678047 E paana PEOR NAA NACEN 7 NOAA Peak 1 Peak2 Peak 1 Peak 2 0 1397030912 271993928 0 1397030912 271993928 0 1397030912 271993928 0 INSR 1397030912 IRun 271993928 INoGoodFw O 0 0 o INoGoodBw 3 3 3 3 INoBadF W 458752 458752 458752 458752 INoBadBw 0 0 0 0 dHFL 0 000000 0 000000 0 000000 0 000000 GUEL 0 000000 0 000000 0 000000 0 000000 dHFFL 0 000000 0 000000 0 000000 0 000000 dLFFL 0 000000 0 000000 0 000000 0 000000 FilterSize 528438 528438 528438 528438 IFilterType 147849219 147849
24. AD Uz ebala lay gop ah het ae Shetek dar ta eo 11 PASS ARR ea Let E EEK a a EAEk E baz gia 14 2A A EAEAN aua 16 245 Mapping Measurements arg coin estes eae dero 16 2 5 Special ELKA AEA 18 ZSL 3D WANdOW Src se bo duta get datoz Edit aa baga ees 18 2 5 2 Map tSpec ea Aa 19 2 5 3 Map Videotspec Window ba e ew aaa dee et 22 2 5 4 Factor 3D Window A sed EAZ Eri a Vea ae 23 3 Edit Men eea Sapient antec bas ee cee wae eae dE EEE 27 3 1 Remove Traces scor A E RR a a a 27 3 2 Contour Levels seu aida neren onan ais 28 3 3 Cluster LIStS pa gietara dr o aaia dad a a badet Pake ugariaren 32 3 3 1 Defining Cluster BEE 32 4 MEET 35 4 1 Assemble GC file Assemble MARS 35 A a A A Pode 36 ALI RE E erida aA baaa EKA 37 ALS Frequency Range ura paw eke de ore a Pe ewes 38 e E Aa EAEN 39 WB Ea ANO 39 4 2 Add Trac s ttn A ham a cates Ord ait gn ge ds at as os Uk aa ela E E 40 4 3 Extract Data quis ZE a el und as de OO e Zee d 40 SEE AP oak hie a ua de ew ane ie i Gbe ta 41 43 2 Extraction Range nia b EO ET dE 42 4 3 3 Extraction Mode ueta kre E dT Gaede gaa 42 4 4 Compute SA 44 4 5 KN EAEE 45 4 6 Bini Era a Si ra ld Era Ee Bae Ca EE are oie Rade Mere a 45 Manipulate Mens 0000ta y ARA EA 47 5 1 Spectrum Subtraction a E A e ibiaren dia 48 5 2 Spectrum Calculator ig slay do ace pore LEI EE 48 5 3 Split Interfero grams ailea ie sete E EA EE E E A A 48 Evaluate Men ui ere eserine eae eae si ee 51 6 1 HBO
25. AP Test Spec 0891_GM 1 AB C OPUS 6 0 DatalExtended Demodata MAP Test Spec 0891_GM 1 AB C 1OPUS 6 0 Data Extended Demodata MAP Test Spec 0891_GM 1 AB C OPUS 6 0 DatalExtended Demodata MAP Test Spec 0891_GM 1 A C OPUS 6 0 Data Extended Demodata MAP Test Spec 0955_GM 0 AB C OPUS 6 0 DatalExtended Demodata MAPITestiSpec 0955_GM 0 AB C 1OPUS 6 0 Data eExtended Demodata MAP Test Spec 0955_GM 0 AB C OPUS 6 0 Data Extended DemodatalMAP Test Spec 0955_GM 0 AB C 1OPUS 6 0 Data Extended Demodata MAP Test Spec 0955_GM 0 AB C OPUS 6 01DatalExtended Demodata MAP Test Spec 0955_GM 1 AB C 1OPUS 6 0iDatalExtended Demodata MAP Test Spec 0955_GM 1 AB C OPUS 6 01DatalExtended Demodata MAP Test Spec 0955_GM 1 AB C OPUS 6 0iDatalExtended Demodata MAP Test Spec 0955_GM 1 AB C 1OPUS 6 0 Data Extended Demodata MAP Test Spec 0955_GM 1 AB TAOD tao praami pertza bo E mro lusion Ef 3026_GM 1 1 bas SL Elea kerei Ef 3028_GM 0 1 Arse o o mro kerei Ef 3028_GM 1 1 b do 8o mro lu Ef 3030_GM 0 1 Asael do Bo mo kerei Ef 3030_GM 1 1 sel So Bef mro Isr Ef 3031_GM 0 1 sel do o mro kerei Ef 3031_GM 1 1 Avge Eo blea kerei Ef 3032_GM 0 1 Aae del Be f mro kerei Ef 3032_GM 1 1 bas fo Es mro kerei Ef 3033_GM 0 1 bas SL 8o mro kerei Ef 3033_GM 1 1 Ansel e bl mro kerei Ef 3035_GM 0 1 dosel SL Bo mro kerei Ef 3035_GM 1 1 Ansel Es o mro kerei C OPUS 6 0lDatalExtended Demodata MAP Test Spe
26. Besides the standard evaluation functions described in detail in the OPUS Ref erence Manual there are a number functions especially intended for the evalua tion of 3D files Evaluation functions that yield numerical values as a result will collect the results for all spectra of the 3D file in a trace See chapter 1 The following evaluation functions are applicable to 3D files Evaluate Display Print Macro Ya Curve Eit Integration Quantitative Analysis 1 Setup Quant 1 Method Signal to Noise Ratio Peak Picking Quick Identity Test 14t Quality Test ee Multi Evaluation Setup ZU Multi Evaluation Test GE Quick Compare Setup QC Quick Compare ST statistics 2 Layer Thickness amp Spectrum Search ES Peak Search 2 Information Search S Structure Search bel Initialize Library Yq Store Spectrum in Library Pz Library Editor Ad Library Browser E T T wg Band Assignment Chart Quantitative Analysis 2 Quant 2 Analysis File List Setup Quant 2 Method Calibration Design ke Setup Conformity Test fae Conformity Test BE Identity Test S Setup Identity Test Method HO Cluster Analysis E Cluster Analysis Tes CO CARBON OXygegAnalysis Gz 2D Correlation DMA Factor Map File Chemical Mapping Factor Map File Postrun IES nanan Figure 52 Evaluate Menu Functions relevant to 3D files Bruker Optik GmbH OPUS 3D 51 Integration 6 1 Integration This fun
27. D plot or not See figures 17a and 17b If this check box is deactivated the measurement result is always mapped on a quadratic area independent of the aspect ratio of the actual measurement area Note The scaling is adapted to the actual aspect ratio 2 Centimatgrg Figure 17 a Aspect ratio is kept b Aspect ratio is not kept Bruker Optik GmbH OPUS 3D 17 Special Window Types 2 5 Special Window Types In addition to the standard 3D window for displaying a 3D file there are also a number of other window types 3D Map Spec Map Vid Spec 3d Factor that a relevant to 3D files To open a window of a special type select the New Registered Window function in the Window menu The dialog box shown in figure 18 opens The drop down list includes all available window types Select Registered Window Type E Cancel Figure 18 Selecting a special Window Type 2 5 1 3D Window This window type displays only one of the possible plots xyz xy zy or xz at a time by default the xyz plot You can switch between these plots by selecting the desired plot type in the pop up menu The pop up menu of this window type is identical to the one of the 3D window type For a detailed description of the pop up menu and the 3D Properties dia log window refer to the sections 2 3 and 2 4 For information about the func tionality of the 3D window see also section 2 1 v XYZ Plot XY Plot ZY Plot XZ Plot
28. D spectrum by entering the desired values Bruker Optik GmbH OPUS 3D 57 2D Correlation 6 5 4 2nd Dataset 2D Correlation xx Select Files Method Frequency Range 1st File 2nd File ue r Select 2nd file r Select frequencies Use file limits Get Display Limits Interactive x Starting point 4000 x End point 400 Correlate Cancel Help Figure 58 2D Correlation Dialog Window 2nd Dataset Select 2nd File To correlate two different data sets with each other include a 3D data block into the Select 2nd File field by either double clicking on the data block in the OPUS browser or by dragging and dropping the data block into this field Note Make sure that the second file matches the first file i e the second file also includes a block of multiple absorbance type and that the two data sets match in pairs The pair of data sets can be NIR MIR correlations or originate from polar ization measurements parallel orthogonal The selected files can also be the result of a time resolved measurement or a GC measurement or can be assembled using the corresponding OPUS function Use File Limits When the Use File Limits check box is activated the whole frequency range in the data set is used for the z axis When it is not activated x Startpoint and x Endpoint determine the frequency range used for the 2D correlation Interactive Click on this button to specify the frequency range l
29. The first factor spectrum is the most important one and thus has the high est Eigen value The lower the Eigen value is the more the spectral information decreases and the noise increases 6 6 5 Factorization Theory Assuming that the each spectrum s at a point consists of d data points The spectra at each point are represented by du d2 d3 column vectors which form D data matrix d x s dimension D d d dy d 6 1 When exchanging the rows for the columns in this matrix you obtain DT transposed matrix of s xd dimension Multiply DT transposed matrix by D original matrix to obtain Z covariance matrix Z D D 6 2 A diagonalization and orthogonal transformation of Z produce Eigenvectors and Eigenvalues of Z A 1L Z L 6 3 The column vectors of L matrix s x s dimension are gt 13 Eigenvectors of Z matrix These Eigen vectors are orthonormal i e the following equations are valid for the scalar product of two Eigenvectors IL E 6 4 bl 6 5 A matrix s x s dimension contains A A2 Az A Eigenvalues of Z matrix as the main diagonal all other matrix elements are 0 This means SEE 6 6 D data matrix is factorized by L Eigenvector matrix using multiplication F D L 6 7 F matrix has the same dimensions as D data matrix d x s and includes the vectors of f fo f3 factor spectra as columns Multiplying Fl transposed matrix by F yields 64 OPUS 3D Bruker Optik GmbH Evaluate Me
30. X values mean shows the mean value of the values between X and X integral shows the integral of the values between X and X diagonal shows a cut along the diagonal between position X Z and X Z trace shows a trace which has been calculated previously only for X Cancel Figure 14 Options of the Drop down List Show Bruker Optik GmbH OPUS 3D 15 3D Properties Dialog Window 2 4 4 Chrom Measurements The Chrom tab is only available if the displayed data are the result of a chro matographic measurement using the OPUS CHROM software package At this page you can select the trace chromatogram you want to display The Select X axis trace drop down list contains all variables saved as a trace that can be displayed on the x axis Such a variable can be for example the temperature in a TGA FTIR measurement Select the trace you want to display using the Dis play trace drop down list The selected trace is then displayed in a different color at the side of the cube 3d Properties E 3d Properties Contour Selection Chrom l Select X axis trace 2 Temperature Display trace 0 Gram Schmidt y Figure 15 3D Properties Chrom 2 4 5 Mapping Measurements The Mapping tab is only available if the displayed data are the result of a map ping measurement using the OPUS MAP software package or video assisted measurement using the OPUS VIDEO software package Normally there are seve
31. XZ The size of the subwindows can be changed by moving the border lines with the pressed left mouse button Moreover you can configure the 3D properties of each subwindow independently of the others Figure 3 shows the result of a chromatographic measurement displayed in a 3D window In the top left subwindow all acquired spectra are displayed in a 3D plot In this example the 3D plot consists of three axes the wavenumber axis x axis and the time axis z axis in seconds The y axis shows the absorp tion intensity versus wave number and time The 3D display of the data builds up by lining up all acquired spectra along the time axis Note The physical units of the x axis and z axis depend on the measurement type time resolved or spatial resolved measurement Bruker Optik GmbH OPUS 3D 3 3D Window xyz Plot File Name y 480 xy Plot Rotation 30 b Inclination 20 E xz Plot x firse2 Contour Plot x 2861 84 Editable Ziz e 200 rere ale Contour Level d E Color Scale 2 Index 33 0 T 100020003000 X Wavenumber cm 1 0 04 4 dd kr zy Plot Y Absorbance Units i 4 A N biki Gauz GEA pzta y 0 00 Pride init Tk r T 0 100 200 300 Z Seconds T a T T 1000 2000 3000 X Wavenumber cm 1 Figure 3 3D Window In the right top subwindow the xz plot is displayed Depending on the curre
32. a cluster list see section 3 3 1 The cluster lists are stored in the TRC block To view the result open a Factor 3D window and drag and drop the TRC block in this window For information about this window type refer to section 2 5 4 Integrate This function performs an integration using the frequency range between X and X It is used to integrate peaks and calculate peak heights The applied integra tion method is B For detailed information about integration refer to the OPUS Reference Manual See also section 2 5 2 in this chapter Properties When you select this function the 3D Properties dialog window opens allowing you to customize the appearance of the display For example there are a num ber of options for visualizing the different contour levels For detailed informa tion about this dialog window refer to section 2 4 8 OPUS 3D Bruker Optik GmbH Displaying 3D Files 2 4 3D Properties Dialog Window The 3D Properties dialog window comprises four tabs e 3D Properties e Contour Selection e Mapping or Chrom Note Depending on whether the 3D file is the result of a mapping or chromato graphic measurement the fourth tab is labelled either Mapping or Chrom 2 4 1 3D Properties Rotation and Inclination The parameters Rotation and Inclination refer to the viewing angle of the 3D plot See section 2 1 2 3D Properties q x 3D Properties Contour Selection Mapping Rotation E B Inc
33. actor analysis to which certain constrains are applied Otherwise only a con ventional factor analysis i e without the application of constraints is per formed even if you have defined constraints on this page Number of components Enter the number of the components only if it is known Otherwise use the default value 0 In this case OPUS estimates the number of components from the model during the computation Non negativity This constraint allows only for the presence of positive values You can specify whether this constraint is applied either only to the concentration profiles or only to the spectra or to both by activating the corresponding check box es The available methods algorithms are Force to zero i e negative values in a profile are forced to zero and Fast NNLS fast non negative least squares Note The algorithm Force to zero is the faster one whereas the algorithm Fast NNLS yields more precise results 62 OPUS 3D Bruker Optik GmbH Evaluate Menu Unimodality This constraint allows for the presence of only one maximum peak per profile You can specify whether this constraint is applied either only to the concentra tion profiles or only to the spectra or to both by activating the corresponding check box es The available methods algorithms are vertical horizontal and average The options vertical and horizontal mean that the secondary maxima peaks are cut vertically or horizontally In cas
34. and drag and drop the TRC or AB or TR data block from the OPUS browser in the GC Map file field In the lower field Contour levels the numerical values for the RGB colors of the individual contour levels are displayed Note If you are familiar with the RGB color system you can change the numeri cal values for the contour level colors in this field To adapt the contour levels to your requirements e g specifying the number and the color scheme of the contour levels changing the spacing between the contour lines click on the Interactive button The following dialog window opens ContourEditor i E x Cancel m Auto contour levels From po b ymin To fico b ymax Spacing for Linear Log Create Insert Level TO Delete Level Landscape Color Scheme Monochrome Color Scheme Rainbow Color Scheme Blue Color Scheme Chromatic Color Scheme Figure 31 Contour Editor Window plus the corresponding Pop up Menu To open the pop up menu with the available color schemes and the functions for inserting deleting contour levels right click on the color bar See figure 31 Insert Level This function inserts a new contour line in the color bar at the current cursor position Note You can shift an inserted contour line up or downwards with the pressed left mouse button Delete Level This function deletes an existing contour line To do this place the cursor exactly on the contour line in question and press the r
35. and z axis marker lines If the 3D file is the result of a time resolved mea surement Index value indicates the number of the spectrum at the current posi tion of the z axis marker line To zoom into the graph draw a rectangle around the area you want to enlarge while pressing the left mouse button To reset the plot to its original size dou ble click on the 3D plot 2 2 Contour Cube Normally the 3D file contains the result of only one spatial resolved measure ment In addition to this the OPUS 3D software can also display a 3D file which contains the results of several measurements of these kinds Such a file can be for example the result of time resolved mapping measurement or a mapping measurement of several sample layers The number of the 3D data records in such a file depends on the number of time slices or on the number the sample layers you have measured These 3D data records are stored in TRC block Drag and drop this data block into the 3D window You can display either the 3D plot for one layer sample layer or time slice or the 3D plot for a certain contour value for all layers by selecting either the desired layer or the option A in the Layer drop down list figure 4 In the lat ter case we talk about a contour cube The contour cube displays the data for a selected contour value in a 3D plot The fourth dimension in the contour cube is realized by lying these data of all layers upon each other See figure 5
36. ange Z Axis 7 Use file limits r Select frequencies Interactive Get Display Limits Starting point 4000 X End point 400 Assemble Cancel Help Figure 41 Assemble GC File Dialog Window Frequency Range If the Use file limits check box is activated the frequency range of the first spec trum in the list of the selected files see figure 38 are adopted If this check box is deactivated you can specify the limits of the frequency range either interac tively or by entering the wanted values in the X Starting point and X End point fields Clicking on the nteractive button opens the Select Frequency Range s window in which you can set interactively the frequency range limits using the mouse cursor When you click on the Get Display Limits button the frequency range limits of the currently active display are adopted 38 OPUS 3D Bruker Optik GmbH Measure Menu 41 4 Z Axis Define the z axis range by entering appropriate values in the Z Starting point and Z End point fields and select an appropriate time unit for the z axis from the drop down list A linear trace will be added to the result file The intensity scale of this trace will be defined by the start and endpoint of the z axis Assemble GC File x Select Files Result File Frequency Range Z Axis r Select 2 Range Z Starting point o Z End point b Assemble Figure 42 Assemble GC File Dialog Windo
37. binning field selected the wanted number of spectra arrayed in a matrix 2 x 2 4x4 or 8 x 8 and click on the Binning button See figure 50 CO i xl Select File s File s for binning m Parameters Array of spectra to be averaged 2x2 y Reducing resolution of 3D files all nxn spectra will be replaced by an average spectrum Cancel Help Figure 50 Binning Select File s 46 OPUS 3D Bruker Optik GmbH Manipulate Menu Manipulate Menu There are a number of manipulation functions in OPUS that can be applied to a 3D file as well See figure 51 You only have to drag and drop the 3D data block instead of the single spectrum data block into the corresponding dialog box Afterwards when executing the selected manipulation function all spectra included in a 3D file are manipulated automatically at once The following manipulation functions are applicable to 3D files Manipulate Evaluate Display Print Baseline Correction Spectrum Subtraction 4B lt gt TR Conversion Straight Line Generation Spectrum Calculator Cut Normalization Make Compatible Convert Spectra Smooth Functions relevant to 3D files Derivative Frequency Calibration Raman Correction Black Body Interferogram to Spectrum Inverse FT Post Zerofilling Fourier Self Deconyolution Symmetric FT Kramers Kronig Transformation Split Interferograms Spectrum From Interferograms tim Extrapolation TE Jem
38. button The file list report is stored in a LIST data block which is attached to the result file To display the report right click on the LIST data block and select the only available pop up menu item Show Report As a result the OPUS report window opens displaying the file list report The report contains the following information path name and spectrum type block of all files used for a GC or MAP file assembly See figure 40 If one file cannot be loaded you can either replace it with 0 or abort the process by checking the corresponding option button Jf result file exists you can either increment the name e g WORK 0 gt WORK 1 or abort the process by check ing the corresponding option button Bruker Optik GmbH OPUS 3D 37 Assemble GC file Assemble MAP file PF File Edit view Window Measure Manipulate Evaluate Display Print Macro Validation Setup Help 8x GROS ZE EBL SR ESM Semmes eee KS E OPUS Browser ax E C OPUS 6 0 DatalExtended Demodata E AB FileList Filelist C OPUS 6 DlDatalExtended Demodata MAP Test Spec 0891_GM 0 AB C OPUS 6 0 DatalExtended Demodata MAPITestiSpec 0891_GM 0 AB C 1OPUS 6 0 Data Extended Demodata MAP Test Spec 0891_GM 0 AB C 1OPUS 6 0 DatalExtended DemodatalMAP Test Spec 0891_GM 0 AB C 1OPUS 6 0 Data eExtended Demodata MAP Test Spec 0891_GM 0 AB GORE 6 0 Data Extended Demodata MAP Test Spec 0891_GM 1 AB C 1OPUS 6 0 Data Extended Demodata M
39. c 0891_GM 0 C OPUS 6 0iDatalExtended Demodata MAP Test Spec 0891_GM O AB C 1OPUS 6 0 Data Extended Demodata MAP Test Spec 0891_GM 0 AB C OPUS 6 0 Data Extended Demodata MAP Test Spec 0891_GM 0 AB C 1OPUS 6 0 Data Extended Demodata MAP Test Spec 0891_GM 0 AB C OPUS 6 0 Data Extended Demodata MAP Test Spec 0891_GM 1 AB C 1OPUS 6 0 Data Extended Demodata MAP Test Spec 0891_GM 1 AB GORE 6 0 Data Extended Demodata MAP Test Spec 0891_GM 1 A Bar CHJOPUS 6 0 DatalExtended DemadatalMAP Test Spec 0891_GM 1 AB mr en a LIST Block C OPUS 6 0 DatalExtended Demodata MAP Test Spec 0891_GM 1 AB es rt OC C OPUS 6 0 DatalExtended Demodata MAP Test Spec 0955_GM 0 AB GL 3037_GM 1 1 C OPUS 6 0iDatalExtended DemodatalMAP Test Spec 0955_GM 0 AB C OPUS 6 0 DatalExtended Demodata MAPITestiSpec 0955_GM 0 AB C OPUS 6 0 DatalExtended Demodata MAPITestiSpec 0955_GM 0 AB C OPUS 6 0 DatalExtended Demodata MAP Test Spec 0955_GM 0 AB C OPUS 6 01DatalExtended Demodata MAP Test Spec 0955_GM 1 AB C 1OPUS 6 0 Data Extended Demodata MAP Test Spec 0955_GM 1 A C OPUS 6 01DatalExtended Demodata MAP Test Spec 0955_GM 1 AB C OPUS 6 0 Data Extended Demodata MAP Test Spec 0955_GM 1 A C OPUS 6 DiDatalExtended Demadata MAP TestiSpec 0955_GM 1 AB E Figure 40 File List Report 4 1 3 Frequency Range On this dialog window page you specify the frequency range for the result file See figure 41 Assemble GC File x Select Files Result File Frequency R
40. ck type depends on whether a spectrum or a trace is to be extracted Note In a 3D file the single spectra are stored in the AB or TR data block and the traces are in the TRC block In the second case the right data block is already included in the File s to extract field depending on which of the two pop up menu functions you have selected Extract Data x Select Files Extraction Range Extraction Mode File s to extract Save to Path CA0PUS 6 0 DATASEXTENDED DEMOD Change Path File name EXTRACTO Increment extension C Increment filename Extract Cancel Help Figure 45 Extract Data Dialog Window Select Files In the Path field define the target path for the files containing the extracted spectra or traces If you want to save them under another path than the one sug gested click on the Change Path button The standard Select Path dialog box opens in which you can specify the target path for them In the File Name field enter the desired file name In case of extracting several spectra or traces the name for all newly generated files is the same it is the file name you have entered Therefore you have to specify whether the extension 1 2 A etc or the filename extractl 0 extract2 0 extract3 0 etc is to be incremented by clicking on the corresponding option button Bruker Optik GmbH OPUS 3D 41 Extract Data 4 3 2 Extraction Range On the this dialog
41. contour levels 0 40 From fo 204 IV ymin From 204 ymin 0 30 do To 0 984 Y ymax To b ymax 0 10 Spacing o1 y Spacing E y 0 00 Linear C Log Linear Log 0 10 0 10 0 20 Figure 34 a Linear Spacing b Logarithmic Spacing After having defined the contour levels according to your needs click on the OK button Bruker Optik GmbH OPUS 3D 31 Cluster Lists 3 3 Cluster Lists This function enables you to store a cluster list which either you have defined before in the 3D window see the following subsection 3 3 1 or you have gen erated by entering a list of spectrum numbers in the Cluster lists field See figure 35 Cluster Lists 3 x Select Files 1231 GA r GC Map file a dee CAOPUS 6 0 Data Extended Demodatas MAF 4 b Cluster lists 299 300 301 302 303 304 305 306 307 308 309 310 31 Figure 35 Storing Cluster Lists In case the 3D file is already loaded in OPUS the file is already included in the GC Map file field when this dialog window opens Otherwise load the 3D file and drag and drop the TRC or AB or TR data block from the OPUS browser in the GC Map file field In the lower field Cluster lists the pixel numbers of the previously defined clusters i e the clusters you have defined in the xz plot of the 3D window see figure 36 are displayed automatically as well 3 3 1 Defining Cluster Lists Drag and drop the TRC block of the 3D file in the 3D
42. ction enables the integration of bands and the calculation of the band height or the integral The OPUS software offers 18 different integration modes Select in the Evaluate menu the Integration function As a result OPUS opens the Integration dialog window You can either load an existing integration method by clicking on the Load Integration Method button or set up a new one by clicking on the Setup Method button In the latter case the Setup Integration Method dialog window opens in which you specify the integration area fre quency range and the integration mode After having entered all parameters click on the Store Method button The selected parameters are stored in a method file For detailed information on how to set up an integration method refer to the OPUS Reference Manual Now start the integration by clicking on the Integrate button The result of integrating a 3D file is a trace that OPUS stores automatically in a TRC block As you can determine several integration areas several traces can be calculated in one run The trace name is identical to the peak name you have entered in the Label field You can have the trace s displayed both in form of a report and graphically in a 3D plot See chapter 1 In the first case drag and drop the TRC block into a report window In the latter case right click on the 3D window and select in the pop up menu the Properties function As a result OPUS opens the 3D Properties dialog windo
43. d automatically in the Define subset field Bruker Optik GmbH OPUS 3D 59 Factor Map File 6 6 2 Options Factor Map File xj Use the following constraints for the model Select Files Options Frequency Range r Save factors C No keep spectra Yes save all C Upto 0 Factor indices for RGB trace Red fo Green fo Blue fo Factorize Cancel Help Figure 60 Factor Map File Dialog Window Options Save Factors There are three options for saving the factors No keep spectra When this option button is activated only the loadings are saved in the TRC block In this case only the original spectra are kept and the calculated factor spectra are not saved Y es save all When this option button is activated all factor spectra are saved in the 3D block In this case the original spectra are overwritten and the loadings are saved in the TRC block Up to When this option button is activated you have to specify the number of factor spectra that are to be saved These factor spectra are saved in the 4B block In this case the original spectra are overwritten and the loadings are saved in the TRC block Factor indices for RGB trace This function provides the opportunity to display three loadings as a color image using the RGB color model Enter the number of the respective loadings in the entry fields Red Green or Blue These three loadings are combined into one image In the cours
44. deviations of this condition 1 e slight variation of the total concentration in the system are allowed If the system is not closed the application of the constraint Normalization 1s recommended Two normalization methods are available the spectra can be normalized either to equal height or to equal length Note If no closure or normalization is applied to the model the scale indetermi nacies may occur during the ALS optimization After having defined all parameters start the factorization by clicking on the Factorize button The result of factorizing a Map file are several traces the RGB trace the singular values trace and the loading traces which are stored automatically in the TRC block You can have the trace s displayed both in 1 ALS Alternating least squares procedure Bruker Optik GmbH OPUS 3D 63 Factor Map File form of a report and graphically in a 3D plot See chapter 1 In the first case drag and drop the TRC block into a report window In the latter case right click on the 3D window and select in the pop up menu the Properties function As a result OPUS opens the 3D Properties dialog window Click on the Mapping tab select in the Select trace drop down list the corresponding trace and click on the OK button As a result the selected trace is displayed in a different color at a side of the 3D plot Note The factor spectra are sorted according to the Eigen values Eigen value sin gular value
45. discussed In the wave number range between 3100 and 3500cm as well as between 6100 and 7000cm a diagonal peak can be observed This peak represents the correlation of the OH stretching region in the middle infrared and the corresponding first overtone in the near infrared Bruker Optik GmbH OPUS 3D A 9 Appendix 8000 7000 6000 Wavenumber cm 1 5000 1000 2000 3000 Wavenumber cm 1 Figure 47 Correlation Coefficient Spectrum of a Three Component Mixture The varying alcohol concentrations within the mixtures lead to changes in the spectra Generally the highest peaks arise if the bands are not distorted by other absorbencies as shown in figure 47 This fact can be useful for the evaluation of near infrared spectra when the highest peaks are assigned to frequency regions Another example for a peak at its overtone can be seen around 2250 4400cm where the CN vibration reaches its overtone OPUS 3D Bruker Optik GmbH Appendix Mathematical Appendix The following explanation is mainly intended for the specialist and provides the mathematical details for the special implementation of the asynchronous corre lation spectrum without using the Fourier Transformation As you have to deal with discretely sampled data it is advisable to make a tran sition from the integral representation to discrete sums Furthermore the fol lowing mathematical treatment is restricted to equidistant sampling positions equally
46. e combined with each other so called hyphenated techniques e g GC IR or TG IR measurements using the OPUS CHROM software package and e spatial resolved mapping measurements with OPUS MAP or OPUS VIDEO software package and spatial resolved surface map ping measurements using the FPA detector and the OPUS FPA soft ware package Note For information about how to perform such a measurement refer to the cor responding OPUS manual Additionally OPUS 3D enables the extraction of single spectra from a 3D file in order to further process the extracted single spectrum spectra separately For information about how to extract spectra refer to section 4 3 The other way round this software package also enables the assembly of a 3D file using single spectra See section 4 1 All spectra acquired during a time or spatial resolved measurement are stored in a 3D file and displayed by default in a 3D window See section 2 1 This kind of data representation enables the visualization of spectral changes against time e g in case of a chromatographic measurement or against space e g in case of a mapping measurement Moreover additional information e g chro matograms time scale or position on the sample surface are stored in the 3D file as well Afterwards when you further process a 3D file e g integrate or factorize a 3D file the result is stored in a TRC block which is appended to the 3D file This data block contains the t
47. e corresponding entry field In addition you can specify the fre quency range for the bands and a weighting factor i e the relative intensity of a band within the specified frequency range Chemical Mapping y x Select Files User defined method Name of functional group fu ser defined Bands Weighting from to D exclude 4000 400 fi 4000 400 fi sooo feo gn Calculate Cancel Help Figure 65 Chemical Mapping User defined Method After having entered all required parameters click on the Calculate button The result of a chemical mapping calculation is a trace which is stored automat ically in the TRC block The trace name is identical to the name of the func tional group you have selected or entered when specifying the calculation Bruker Optik GmbH OPUS 3D 67 Chemical Mapping parameters You can have the trace s displayed both in form of a report and graphically in a 3D plot See chapter 1 In the first case drag and drop the TRC block into a report window In the latter case right click on the 3D window and select in the pop up menu the Properties function As a result OPUS opens the 3D Properties dialog window Click on the Mapping tab select in the Select trace drop down list the corresponding trace and click on the OK button As a result the selected trace is displayed in a different color at a side of the 3D plot 68 OPUS 3D Bruker Optik GmbH Ap
48. e of the factorization among other traces also a RGB trace is calcu lated and stored automatically in the TRC block You can have the RGB trace displayed both in form of a report and graphically in a 3D plot See chapter 1 60 OPUS 3D Bruker Optik GmbH Evaluate Menu 6 6 3 Frequency Range Factor Map File xj Use the following constraints for the model Select Files Options Frequency Range rte I Use file limits E y Select frequencies Interactive Get Display Limits X Starting point 4000 End point 400 Factorize Cancel Help Figure 61 Factor Map File Dialog Window Frequency Range Use File Limits When the Use file limits check box is activated the whole frequency range in the data set is used When this check box is deactivated x starting point and x end point determine the frequency range used for the factorization of the Map file Interactive Click on this button to specify the frequency range limits interactively Get Display Limits When you click on this button the frequency range limits of the currently active display window is taken X Starting point X End point Specify the frequency range limits manually by entering the desired values in these entry fields 6 6 4 Use the following Constraints for the Model This function allows also the study of so called evolving systems in which a sample is modulated by a variable e g time temperature or pH In contrast to a conventional
49. e of the option average the sec ondary maxima are corrected by using the average values The constraint tolerance value defines how strictly the constraint is to be applied A value of 1 means that no deviation from the unimodality constraint is allowed If the constraint tolerance value is higher than 1 slight deviations from the unimodality are allowed Note A constraint tolerance value of 1 05 for example means that secondary maxima exceeding the neighboring value by less than 5 are allowed i e that in decreasing slopes of the main peak a particular point can increase by maximum 5 of the previous value before the unimodality constraint is applied Note For systems with low to medium noise levels use values between 1 0 and 1 1 Closure Normalization In the group field Closure Normalization you can select either the constraint Closure Concentrations or Normalize Spectra or None of the two constraints The selection of the constraint depends on the reaction system to be analyzed The constraint Closure means the fulfilment of a mass balance condition in reaction based systems i e the sum of the sample concentration is a known constant value The Constraint value indicates the tolerance limit of this constraint Equal con dition constraint value 1 forces the sum of the concentrations in the closed system to equal exactly to the total concentration at each stage of the process A constraint value of gt 1 allows for some
50. e s to assemble group field you can delete files Delete button sort them in the right order EAI Move Up or Move Down arrows or insert a new file by typing its name in the line after clicking on the 2 New button 36 OPUS 3D Bruker Optik GmbH Measure Menu Note that all selected files have to contain spectra of the same type e g absorp tion spectra If there are several data blocks to choose from select the appropri ate one from the Data block drop down list 4 1 2 Result File On the Result File page you specify the path and the file name for the result file i e the assembled GC or Map file See figure 39 Assemble GC File E x Select Files Result File Frequency Range Z Axis m Path jc OPUS E O4DATAMEXTENDED D Change Path File name 34 1 l Generate filelist report Yes C No M Ifa file cannot be loaded e Replace with 0 C Abort If result file exists Increment name C Abort Assemble Cancel Help Figure 39 Assemble GC File Dialog Window Result File If you want to save the result file under another path than the one suggested click on the Change Path button The standard Select Path dialog box opens in which you can specify the target path for the result file In the File Name group field enter the desired file name Moreover you can specify whether a file list report is to be generated or not by activating the corresponding option
51. ed Factor Map File Postrun a xi Select File File to process gabe C OPUS E O Data Extended Demodata MAP WAFER O 1 Factors for RGB trace Red Loading 4 y Green Loading 5 y Loading 6 y Loading 6 Loading 7 Loading 8 Loading 9 Loading 10 Loading 11 Loading 12 Loading 13 Loading 14 x Execute Figure 63 Factor Map File Postrun Dialog Window 6 8 Chemical Mapping This function allows you to calculate the trace for a functional group e g alco hols you are interested in 6 8 1 Select Files Drag and drop the spectra data block AB or TR of the 3D file in question from the OPUS browser into the File s for chemical mapping field The Functional group drop down list contains already a number of functional groups but you can also generate a chemical mapping for a user defined func tional group In this case select the option User defined 66 OPUS 3D Bruker Optik GmbH Evaluate Menu Chemical Mapping xj Select Files User defined method m File s for chemical mapping Functional group User defined pea ire Figure 64 Chemical Mapping Select Files 6 8 2 User defined Method If you have selected a provided functional group from the Functional group drop down list you need not switch to User defined method page Otherwise click on the User defined method tab and enter the name of your functional group into th
52. esolved Spectroscopy External Stress Temperature Dependence Depth Profiling Concentration Dependence They evaluation methods can be applied to various experimental set ups because of their universal procedure They have only one thing in common that is a change in the absorbance spectra has to be induced Then the 2D spectra reflect the spectral response to this influence or perturbation You can also evaluate data sets assembled from different samples e g samples with various compounds containing one specific group and side chains of vari able length This kind of evaluation would reveal the influence of the side chain Correlating two Data Sets The evaluation methods previously discussed use the two resulting frequency ranges that are taken from the same data set For other applications it might be interesting to examine the correlations between corresponding spectra in the middle and near IR range For this purpose the values for the different fre quency ranges can be stored in two separate data sets Make sure that the spectra of each pair match e g if the first spectrum in the first data set corresponds to a certain point in time the first spectrum in the second data set has to be recorded at exactly the same point in time Additionally these data sets can contain pairs of different states of the various measurements Therefore the correlation of the following states is possible Different polarization orientat
53. file In this case you obtain a 3D file in which influence of the pure substance s has been eliminated Compute Trace xj Select Files r Principal file for trace computation H File s with pure component spectra Subtract cect lr Figure 48 Trace Computation Select Files Then click on the Compute button The calculated trace s is are stored auto matically in the TRC block The number of calculated traces depends on the number of files with the pure component spectra you have included in this dia log window The trace names are identical to the file names of the used pure component spectra You can have the trace s displayed both in form of a report and graphically in a 3D plot See chapter 1 In the first case drag and drop the TRC block into a report window In the latter case right click on the 3D window and select in the pop up menu the Properties function As a result OPUS opens the 3D Properties dialog window Click on the Mapping tab select in the Select trace drop down list the corresponding trace and click on the OK button As a result the selected trace is displayed in a different color at a side of the 3D plot 44 OPUS 3D Bruker Optik GmbH Measure Menu 4 5 Transpose This function allows you to transpose the X and the Z coordinates e g the time axis and the wavenumber axis Use this function if you want to apply a manip ulation function e g smooth to the time ax
54. h which OPUS stores automatically in the TRC block You can have the traces displayed both in form of a report and graphically in a 3D plot See chapter 1 In the first case drag and drop the TRC block into a report window In the latter case right click on the 3D window and select in the pop up menu the Properties function As a result OPUS opens the 3D Properties dialog window Click on the Mapping tab select in the Select trace drop down list the corresponding trace and click on the OK button As a result the selected trace is displayed in a different color at a side of the 3D plot 6 5 2D Correlation The two dimensional methods are analogous to methods commonly used in nuclear magnetic resonance NMR spectroscopy In 2D IR spectroscopy a 2D spectrum is defined by two independent wave number scales The 2D spectrum is calculated by a correlation analysis which is based on IR signal variations These variations are generated by an external per turbation of the sample The origin of the spectral change may be kinetic or imposed as a periodic mechanical strain The following description does not cover all features of this procedure It just gives you some useful hints It will become obvious that these methods are not limited to dichroic measurements of periodically stressed polymers apparently 1 S N RMS Signal to Noise Root Mean Square 2 S N PP Signal to Noise Peak to Peak 3 N RMS Noise Root Mean Square 4 N PP No
55. he arrow cur sor on one of the four upper corners of the plot As a result the arrow cursor transforms into a hand cursor While pressing the left mouse button rotate the 3D plot into the desired perspective OPUS 3D Bruker Optik GmbH Displaying 3D Files 2 1 3 Navigating through the 3D Plot The 3D plot displays marker lines which define a cross section along the x axis and the z axis Changing the values in the X and Z entry fields moves the marker lines along the respective axis A marker line can also be moved interactively by placing the arrow cursor on the small cone at either end of the marker line As a result the arrow cursor transforms into hand cursor While pressing the left mouse button drag the marker line to the desired position For each of the two axes you can activate a second marker line X and Z by clicking with the right mouse button on the desired plot and selecting in the pop up menu the Properties function In the 3D Properties dialog window click on the Selection tab and select in the two drop down lists labelled Show the options X and X and Z and Z The procedure for moving these marker lines is analogous to the one of the marker lines X and Z The area between the four marker lines can be highlighted as described in section 2 4 3 In case the 3D file is the result of a spatial resolved measurement the Index value indicates the number of the spectrum at the current intersection point of the x
56. i oer ele tee wha ee eee od are ada 52 6 2 Quanttanve Analysis eio Sek a eae E agata era 53 6 3 eU aA aA RO sida Hew od ah eee R le Mees 53 6 4 Peak aa eai 54 6 5 SARR Sas BA REA 54 65 1 Select FUES i sicko tet see et Zier En Me OR eS 55 6 520 Method rs D dizi zibilari eai podia HO obs 56 6 5 3 Frequency Range 1st File arteari gt eten burn nr pez gra 57 654 2nd Dataset ca eae ie dai Dates ate dagite 58 6 6 Factor Map File apenes EE EEE Gra E A d gaitze He 59 6 6 1 Select Piles ni ne d wae II 59 6 60 27 OPTOMA Aiete aoa Yelle t 60 6 6 3 Frequency Range 5 Ek ce ow seg da eee 61 6 6 4 Use the following Constraints for the Model 61 6 6 5 Factorization Theory suis iaa a o aed 64 6 7 Factor Map Fil EO a e aratu ace eh d oe kw tr de Zia 65 6 8 Chemical Mapping as ein aces oia geituta pet Leia edi eiz 66 Oo Select Piles aa biat wae Ghd Eba Se bi arkara 66 6 8 2 User defined Method da Zn gt atenta Pk nae GE biot Gura 67 Appendix EAEE A 1 Theoretical OREOAK ia A 1 HABANA eu A 11 Introduction 1 Introduction The OPUS 3D software package provides functions for displaying editing manipulating and evaluating three dimensional spectral data so called 3D files 3D files are the result of e time resolved rapid scan or step scan measurements e g with the Rapid Scan TRS function of the OPUS basic package or measure ments using the OPUS STEP software package e measurements at which two different techniques ar
57. ight mouse button to open the pop up menu If the cursor is not positioned on a contour line this function is grayed out Bruker Optik GmbH OPUS 3D 29 Contour Levels Landscape Color Scheme This color scheme visualizes the different contour levels by a color gradient ranging from blue via green yellow to orange red Monochrome Color Scheme This color scheme visualizes the different contour levels on the basis of a gray scale Rainbow Color Scheme This color scheme visualizes the different contour levels by a rainbow like color gradient Blue Color Scheme This color scheme visualizes the different contour levels by a color gradient ranging from dark blue to light blue Chromatic Color Scheme This color scheme visualizes the different contour levels on the basis of the color temperature scale ranging from black via red and yellow to white From to For the division into contour levels you can define either the complete y axis range by activating the ymin and ymax check boxes or only a part of the y axis by deactivating these check boxes and entering the desired y values To implement the settings in the color bar click on the Create button See figure 32a and b x x OK DK 0 90 0 900 Cancel Cancel 0 80 E EEE 0 800 0 70 0 700 0 60 0 600 0 50 0 500 0 40 0 400 0 30 r Auto contour levels From fo 30 I ymin m Auto contour levels From fo 204 IV ymin E To 0 984 ESTO To
58. imits for the x axis of the 2D spectrum interactively Get Display Limits When you click on this button the frequency range limits of the currently active display window are taken X Startpoint X Endpoint Specify the frequency range limits for the z axis of the 2D spectrum by entering the desired values 58 OPUS 3D Bruker Optik GmbH Evaluate Menu 6 6 Factor Map File There are two ways of invoking the Factor Map File dialog window 1 Select the Factor Map File function in the Evaluate menu or 2 Right click on the 3D window and select the Factorize function from the pop up menu As a result OPUS opens the following dialog window Factor Map File xj Use the following constraints for the model Select Files Options Frequency Range File s to factorize Define subset ei Factorize Cancel Help Figure 59 Factor Map File Dialog Window Select Files 6 6 1 Select Files Include the desired Map file in the File s to factorize field of the Factor Map File dialog window by either dragging and dropping the spectrum data block in this field or by double clicking on this data block in the OPUS browser In order to restrict the whole mapping area to the area of interest you can define a subset using the marker lines in the 3D window For detailed information about the marker lines refer to section 2 1 3 The index numbers of the spectra within the defined subset are displaye
59. ion button In the Extracted files group field you have to specify whether the files with the extracted spectra are only saved on the hard disk and not loaded into OPUS or saved and loaded at the same time Activate the corresponding option button Note When extracting chromatograms the name of the integration method is saved as the parameter for labelling the y axis In the print out this name will be plotted with the y axis Bruker Optik GmbH OPUS 3D 43 Compute Trace 4 4 Compute Trace This function allows the computation of a concentration trace for certain sub stance On the basis of the concentration trace you can find out at which point in time during a chemical reaction a certain substance has been produced at which concentration For this kind of trace computation a single spectrum of the pure substance in question is required Drag and drop the 3D file containing the spectral information about the chemi cal reaction progress into the Principal file for trace computation field and the file with the single spectrum of the pure substance in question into the lower field Note You can drag and drop also several single spectrum files in the lower field In doing so for each substance of which a single spectrum file is included a con centration trace is calculated When you activate the Subtract check box the spectrum of the pure substance scaled with the computed factor is subtracted from the spectra of the 3D
60. ions Two solvents Two spectral ranges Bruker Optik GmbH OPUS 3D A 3 Appendix Simulated Band Shapes In this section only simple examples will be discussed For detailed information on general properties of 2D correlation spectra refer to the relevant literature One of the most frequent band shapes is the Lorentzian curve If such a band is modulated by a cosinusoidal perturbation a dynamic spectrum results as shown in figure 40 If two bands of a synchronous correlation spectrum exhibit the same cosine like variation a symmetric cross peak will emerge figure 41 0 06 0 04 0 02 0 00 0 02 8 0 04 Minutes 0 06 1800 1900 Wavenumber cm 1 2200 Figure 40 Lorentzian Band with Cosine Oscillation OPUS 3D Bruker Optik GmbH Appendix 1600 2000 Wavenumber cm 1 2200 2200 Wavenumber cm 1 1600 Figure 41 Symmetric Crosspeak for two Bands having the same Time Dependence If you interpret the peaks of a synchronous spectrum bear in mind that the same kind of peak can also arise if both bands remain constant over the given time period Therefore these static components must be eliminated from the data set In case of an asynchronous correlation the 2D spectrum of two bands varying in phase has to be zero If one band is oscillating in a cosine curve while the other band is 90 out of phase a cross peak arises from the asynchronous corre lation as shown in figure 41 Fig
61. is instead of the wave number axis for example Drag and drop the 3D in question file into the File s to transpose field and click on the Transpose button Before the transposition the 3D file contains n spectra with m data points After the transposition the 3D file will have the dimension m spectra x n data points x Select Files m File s to transpose O sakez C SOPUS 6 0 Data Extended Demodata MAP ea mo Figure 49 Transpose Select Files 4 6 Binning This function allows you to improve the data quality of a 3D file generated using a FPA detector later The FPA detector is a multi element detector i e the detector consists of a matrix with 64 x 64 or 128 x 128 detector elements In contrast to a single ele ment detector e g MCT detector the FPA detector acquires simultaneously as many spectra as the detector has elements The result of one single measure ment is a spectra matrix analogous to the detector element matrix The function Binning calculates the average spectrum of n x n spectra arrayed in a matrix and replaces them by the calculated average spectrum The entire spectra matrix is processed in this way This measure reduces the spectral noise and consequently improves the data quality But however it reduces also the spatial resolution 1 Focal Plane Array Detector Bruker Optik GmbH OPUS 3D 45 Binning Drag and drop the 3D file in question into the File s for
62. ise Peak to Peak 54 OPUS 3D Bruker Optik GmbH Evaluate Menu the most frequently published application Other applications combine mid IR and near IR data for example This kind of application can be used for recog nizing pairs of bands belonging together or for assigning bands to each other The Appendix provides mathematical background information as well as theo retical and experimental examples to illustrate possible applications of these methods 6 5 1 Select Files Select in the Evaluate menu the 2D Correlation function As a result OPUS opens the 2D Correlation dialog window 2D Correlation x Select Files Method Frequency Range 1st File 2nd File KO File s for 2D Correlation Correlate Cancel Help Figure 55 2D Correlation Dialog Window Select Files Include one or more files in the File s for 2D Correlation entry field by either double clicking on the desired file s in the OPUS browser or dragging and dropping it them into the entry field To delete a file mark it and press the Delete key The selected files can either be the result of a time resolved mea surement or a GC measurement or can be assembled using the corresponding OPUS function The resulting two dimensional spectrum will be stored in the original file which then is marked as being modified and will be displayed in the OPUS browser as a Chrom data block Bruker Optik GmbH OPUS 3D 55 2D Correlati
63. k actual formula During the calculation a loop is carried out and the formula is applied to every single spectrum in the 3D block The calculation results for all spectra are stored in a new 3D block You can also combine single spectrum files with 3D files in a formula In doing so all spectra included in a 3D file can be divided by one single spectrum e g the reference spectrum for example You can for example also multiply two 3D blocks by each other in pairs In this case the single spectrum in each 3D block is calculated according to the loop number Therefore all subsequent 3D data blocks must have the same number of spectra as the first 3D data block 5 3 Split Interferograms This function allows the splitting of a double sided forward backward acquired interferogram into four single sided interferograms This measure improves the time resolution 48 OPUS 3D Bruker Optik GmbH Manipulate Menu You can apply this function only to interferograms provided that they have been acquired in the Double Sided Forward Backward mode This condition applies to both single spectrum files and 3D files To set this measurement parameter click in the Measurement dialog window on the Acquisition tab and select the option Double Sided Forward Backward in the Acquisition Mode drop down list Bruker Optik GmbH OPUS 3D 49 Split Interferograms 50 OPUS 3D Bruker Optik GmbH Evaluate Menu Evaluate Menu
64. lination 20 E Show surface Show wireframe Stacked No image Contourmap Video image I Two layers ba Show box Y OpenGL fonts 1234567890 Text Color Background Color I Clip data T Flip X axis Minimum DO Maximum fii92 Cancel Help Figure 7 3D Properties Dialog Window Show surface This option is the default way of displaying 3D data The data points on the grid are linked together by polygons and form a continuous surface See figure 8a Show wireframe This option links the data points together using a grid The display becomes more transparent as illustrated in figure 8b Stacked In case of data resulting from a time resolved measurement this option displays the single spectra one after the other without cross linking them as illustrated in figure 8c Bruker Optik GmbH OPUS 3D 9 3D Properties Dialog Window Figure 8 a Surface b Wireframe c Stacked Display No image This option is the default setting with no image displayed below the 3D plot See figure 9a Contour map This option projects a contour plot below the 3D plot See figure 9b Video image In case the displayed file originates from a video assisted measurement a video image of the sample can be displayed below the 3D plot provided that the video image has been saved in the same file as the spectra Normally this video image is scaled in such a way that the spectral points
65. n cluster In other words they represent a three dimensional space in which with great probability are the great majority of the data points belonging to a cluster When you click on a data point a tiptool appears displaying the number of the cluster to which the data point in question belongs Series the index number of the data point within a certain cluster Point and the spectrum number of the data point in question See figure 27 SA v EE T Point 3 Spectrum 484 pc2 00 7 Figure 27 Display of the Results with hidden Ellipsoids 24 OPUS 3D Bruker Optik GmbH Displaying 3D Files The drop down lists Factor X Factor Y and Factor Z allow you to specify which of the calculated factors are to be used for spanning the three dimen sional factor space 3D plot By selecting the desired factor numbers for the 3D diagram axes you can display the result in a three dimensional space depending on the calculated factor Text color When you click on this button you can define the text color i e color of the plot axes and axis labelling using a color palette The number sequence below the button is displayed in the currently selected text color Background color When you click on this button you can define the background color of the 3D plot using a color palette The background of the number sequence is displayed in the currently selected background color 1 The terms Fact
66. n uses a gray scale to visualize the different contour levels Activate this option button for black and white printers or monochrome display units Chromatic This option uses the color temperature scale ranging from black via red and yellow to white to visualize the different contour levels None The whole 3D plot is displayed in one color by default in blue No color splitting Normally the negative absorption intensity values are displayed in blue and the positive ones in green yellow and red In case the vast majority of these values is negative activate this check box in order to make more colors e g green and yellow available in the negative absorption intensity range This improves the visualization of different negative absorption intensity values Contours This drop down list allows you to determine the distance between two contour lines and indirectly the number of the contour levels See also section 3 2 Note The smaller the value is the more contour levels are added and the more detailed the selected color scheme is To find the optimal value for your data you have to proceed empirically 12 OPUS 3D Bruker Optik GmbH Displaying 3D Files Method Depending on the plot type xyz or xz plot there are different methods for visualizing the contour levels xyz Plot xz plot Stepped color gradient 1 Contour colors Stepped color gradient 2 Contour lines Smooth color gradient Colo
67. namics Automatic Accessory Recognition Extract Data Add Traces Assemble GC File Assemble MAP File lt t Functions relevant to 3D files Compute Trace Transpose Binning EE Control Process g Setup Process al Convert Process ZN Sample Wheel Measurement tas Opus LAB Figure 37 Measure Menu 4 1 Assemble GC file Assemble MAP file GC files and MAP files belong to the category 3D file A GC file is the result of time resolved measurement e g a chromatographic measurement using the OPUS CHROM software This file contains all spectra which have been acquired during a predefined time interval Besides frequency and absorption intensity a third dimension namely the time is included Thus a chromato gram trace represents the change in absorption intensity within a certain fre quency range during a certain time interval Bruker Optik GmbH OPUS 3D 35 Assemble GC file Assemble MAP file A MAP file is the result of a spatial resolved mapping measurement i e the sample surface has been scanned In this case the spectra are acquired at the predefined positions on the sample surface using the OPUS MAP or OPUS VIDEO package The data of a Map file give information about the changes in the absorption intensity within a certain sample surface area The xz dimension of the 3D plot corresponds with the measured sample surface area The Assemble GC File and Assemble MAP File
68. nding drop down lists Red Green and Blue and execute this function See figure 63 Note The drop down lists contain all loadings which have been calculated in the course of the factorization you have performed before The result of this function is a new RGB trace which is stored automatically in the TRC block You can have the trace displayed both in form of a report and graphically in a 3D plot See chapter 1 In the first case drag and drop the TRC block into a report window In the latter case right click on the 3D window and select in the pop up menu the Properties function As a result Bruker Optik GmbH OPUS 3D 65 Chemical Mapping OPUS opens the 3D Properties dialog window Click on the Mapping tab select in the Select trace drop down list the corresponding trace and click on the OK button As a result the selected trace is displayed in a different color at a side of the 3D plot Note Do not confuse the newly calculated RGB trace with the RGB trace which is the result of the factorization The newly calculated RGB trace is the last entry in the drop down list Select trace Note You can repeat this function as many times as you like using each time a new assignment Each time a new RGB trace is calculated and stored in the TRC block As the previous RGB trace is not overwritten do not confuse them The order of the traces in the Select trace drop down list corresponds to the order of the functions you have perform
69. nge the display properties of the 3D view right click on the Factor 3D window and select the only item Properties of the pop up menu As a result the following dialog window opens View properties x Display Options Rotation E Inclination fie b Show box MV Show points IV Show axes IV Show ellipsoides Factor x fi y Text Color Factor Y 2 gt Background Color Factor Z 3 zi 1234567890 Cancel Apply Help Figure 26 View Properties Dialog Window Bruker Optik GmbH OPUS 3D 23 Special Window Types You can change the view perspective of the 3D plot either by entering the desired values directly in the fields Rotation and or Inclination and clicking on the OK button or interactively In the latter case position the arrow cursor on one of the cube corners As a result the arrow cursor transforms into a hand cur sor While pressing the left mouse button rotate the 3D plot into the desired view Moreover you can hide the points the ellipsoids the axes and or the box cube by deactivating the corresponding check box es In case the Show axis check box is deactivated the axis labelling is not displayed whereas in case the Show box check box is deactivated the cube disappears but the axis labelling is dis played Figure 27 shows the 3D plot displaying only the data points in a three dimen sional factor space the ellipsoids are hidden Note The ellipsoids represent a confidence interval of a certai
70. ning the cursor on the defined integration area allows you to shift the whole integration area to the left or right in the same way See also the OPUS Reference Manual chapter Evaluate sec tion Integration Then right click in the spectrum window lower subwindow and select in the pop up menu the function Integrate See figure 21 Thereupon OPUS calcu lates the integral for all spectra included in the 3D file using the frequency range you have defined before Note The applied integration method is B For detailed information refer to the OPUS Reference Manual chapter Evaluate section Integration Rotation 30 a Inclination 20 3 Xx 1735 62 x 2861 84 z 299 90 Z 303 42 ABO ATOI Index 93 I Autoscale Zoom Scale All Spectra Defi n ed l n te Shift Curve A g ration Area Crosshair gt 0 0100 0 0000 4 e 2400 ESSN 00 2000 1900 1800 1700 1600 1500 1400 1300 Properties Figure 21 Defining the Integration Area and starting the Integration The result of integrating a 3D file is a trace which is stored in the TRC block There are two ways of viewing the result e displaying the calculation results in form of a report as shown in figure 22 and e displaying the trace in the 3D plot as shown in figure 23 To display the result in form of a report right click on the TRC block in the OPUS browser and click on the appearing pop up menu item Show Report
71. nt position of the marker lines the corresponding xy plot is displayed above the xz plot and the corresponding zy plot is displayed on the right of the xz plot Note The xy plot above the xz plot is identical to the plot in the left lower sub window and the zy plot right to the xz plot is identical to the plot in right lower subwindow In addition the right upper subwindow includes an editable contour level color scale Right clicking on the color scale opens a pop up menu which is identical to the one shown in figure 31 For a detailed description see chapter 3 section 3 2 Double clicking on the color scale opens a color palette which allows you to define the color of a contour level individually Moreover you can change the spacing of the contour levels by placing the cursor on a contour line and moving it up or downwards while pressing the left mouse button 2 1 2 Changing the View of the 3D Plot At the left side of the 3D window there are several entry fields See figure 3 The entry fields Rotation and Inclination enable you to change the perspective of the 3D plot These values can be changed by using the up and down arrow buttons next to the entry fields or the corresponding arrow keys of the PC key board or by entering the desired values directly In the latter case the plot will only be updated if you click on the Redraw button or any other element e g the graph To change the view of the 3D plot interactively position t
72. ntensity is defined as ie a Se Yv o Y v 0 do D v v2 i v v2 A 3 0 Bruker Optik GmbH OPUS 3D A 1 Appendix with v v and Y v v being the synchronous and asynchronous cor relation spectra respectively and T being the duration of the whole measure ment According to Noda the synchronous spectrum can be calculated as follows T 2 Pev f piru t vy de A 4 T 2 For discretely sampled data the synchronous spectrum can be expressed by the following sum 1 Nil N 1 N li d P v v2 SA yi v y v At SE y V1 yi v2 A 5 i For the asynchronous spectrum Noda does not provide a comparable equation Therefore we have derived an evaluation method for this kind of spectrum without using Fourier Transformations See Mathematical Appendix Note that in equation A 5 all references to measurement time or sampling times are eliminated The correlation intensity is only a function of two series of measured absorbance values Therefore this way of calculating a 2D spectrum can be applied to any measurements series However this does not imply that correlation spectra do not depend on the type of measurement as the experiment is always reflected in the resulting spectrum If you interpret the resulting cross peaks you have to keep in mind that these peaks arise according to the various experiments i e in a time resolved experi ment a cross peak will be observed for bands
73. nu F F D L x D L L D D L L Z L A 6 8 The elements of FTF quadratic matrix s x s dimension are the scalar products which can be created in pairs together with factor spectra The 6 8 equation causes the factor spectra to be orthogonal to each other fS 0 ei 6 9 Ji i 6 10 The vector norm of a factor spectrum is equal to the square root of the corresponding Eigen value Using L orthogonality D data matrix can be as follows T T D D 1 D L L F L 6 11 The spectra at a point are represented as linear combinations of the factor spectra and the coefficients are contained in the columns of L matrix Based on the equation 6 11 the following applies for the first spectrum at a point T T T T di Lii fit Lai hth ht t Lsi hs 6 12 The score coefficients are the coordinates of the spectra at a point in the factor spectra system Any u spectrum can be represented as linear combination of the factor spectra u F k e 6 13 The unknown k column vector corresponds to the column elements of L matrix E error spectrum is the difference between the u spectrum and recon structed spectrum 6 7 Factor Map File Postrun In case you have already factorized a Map file this function allows you to assign later other factors loadings to the RGB colors See also subsection 6 6 2 Drag and drop the TRC block of Map file in question into the File to process field Select the desired loadings factors in the correspo
74. of the 3D plot lie exactly above the corresponding points in the video image See figure 9c Figure 9 a No Image b Contour Map c Video Image Two layers If the file contains more data points than the screen can display the data are compressed as described above in section Reload Selection In this case there are two layers which represent the upper and lower limit of the data Activate this check box if you want to display the second lower data layer Show box When you activate this check box the 3D plot is displayed as a cube Other wise only the three axes are displayed 10 OPUS 3D Bruker Optik GmbH Displaying 3D Files OpenGL fonts This check box allows you to determine the font for the axis labels and num bers You can either use the screen font or format the text in OpenGL fonts The latter option yields better results at a higher screen resolution whereas the screen font is advisable at a lower screen resolution Text color When you click on this button you can define the text color using a color pal ette The number sequence to the left of the button is displayed in the currently selected text color Background color When you click on this button you can define the background color of the 3D plot using a color palette The background of the number sequence is displayed in the currently selected background color Clip data When you activate this check box you can specify the display limit
75. on 6 5 2 Method 2D Correlation xi Select Files Method Frequency Range 1st File 2nd File r Correlation mode Squared Correlation y Fhase angle cutoff fo 001 Correction reference None First C Average Last Digital resolution Full C Limit Average Reduction factor fi 0 Correlate Cancel Help Figure 56 2D Correlation Dialog Window Method Correlation Mode The Correlation Mode drop down list contains all options for calculating a 2D spectrum The following correlation modes are available Asynchron The asynchronous correlation spectrum is calculated Synchron The synchronous correlation spectrum is calculated Correlation The correlation coefficient spectrum is calculated Squared Correlation The square of the correlation coefficient is calculated Regression The slope of the regression line is calculated Phase Angle The phase angle between the two frequencies is calculated directly Phase Angle Cutoff Enter a cutoff value to exclude unreliable phase angle values Correction Reference Especially in case of a synchronous correlation the result is impaired by con stant terms You can compensate for these terms by subtracting a reference spectrum None No correction Data is used as it is First The first spectrum in the block is used for the correction Average The average of all spectra is used for the correction Last The last spectrum in the
76. or and Principle Component PC are synonymous Bruker Optik GmbH OPUS 3D 25 Special Window Types 26 OPUS 3D Bruker Optik GmbH Edit Menu Edit Menu Apart from the standard editing functions described in the OPUS Reference Manual there are also functions in the Edit menu intended especially for edit ing 3D files The following figure shows these functions im Q View Window Measure Manip Edit Parameter z gt y Replay Attach video Image SZ E Remove Traces z d 2 Add Information as z E Setup Information Mask Import Structure Edit Create Structure Functions relevant to 3D files Attach Structure Convert 3 D Jcamp Create Spectrum Fr Contour Levels mt IND GS gt amp fl Setup Filelist E 7 Fd Cluster Lists 4 d Copy Paste E p Ek Paste Special Copy To Image File Insert New Object Figure 28 Edit Menu 3 1 Remove Traces To remove individual traces select in the Edit menu the Remove Traces func tion As a result the Remove Traces dialog window opens Drag and drop the trace data block from the OPUS browser in the File to remove traces from field All traces included in the 3D file in question are displayed automatically in the Select traces to remove field See figure 29 You can select either one trace several traces separately or a block of traces To select several traces separately left click on the traces you want to remo
77. pendix Appendix Theoretical Background Essentially the 2D correlation procedures are based on two articles I Noda Generalized Two Dimensional Correlation Method Applicable to Infrared Raman and Other Types of Spectroscopy Appl Spectrosc 47 1993 1329 13306 F E Barton II D S Himmelsbach J H Duckworth M J Smith Two Dimensional Vibrational Spectroscopy Correlation of Mid and Near Infrared Regions Appl Spectrosc 46 1992 420 429 Although there are time resolved spectroscopic changes there will be no depen dence on the individual sampling times in the end because the time reference cancels out as shown in the following equations Thus the 2D correlation can also be applied to other sets of data and other experiments Synchronous Asynchronous In this case the starting point is what Noda calls a dynamic spectrum a func tion y v of absorbance values for a given wavenumber range over a certain time period Using Fourier Transformation in this case the domains are the time frequency pair in contrast to the wave number retardation pair frequently used in FTIR yields the following equation Yvo y v Detetdt Yv 0 Y v 0 A 1 Only for real numbers of y v t e g absorbance the inverse Fourier Transfor mation yields Y 1 0 y v detiodt Y v oJriY wo A 2 with Y v 0 being the conjugate values of the normal complex FT The complex two dimensional correlation i
78. r blending Stepped color gradient 3 Contour lines and colors Video No contours For xyz plot there are different methods for calculating the color gradation They use different algorithms and therefore yield different results Find out empirically the method that suits your needs best When the 3D file results from a video assisted measurement and the video image is stored in the 3D file OPUS can project the video image on the 3D plot See figure 11 To do this activate at the Contour page the option button None and select in the Method drop down list the option Video YING Yatnit cel Figure 11 3D Plot with the Video Image projected on the 3D plot In case of the xz plot the available methods visualize the contour levels in dif ferent ways The following figure shows some examples color blending col ors lines and lines plus colors for a two dimensional contour plot Bruker Optik GmbH OPUS 3D 13 3D Properties Dialog Window Centimeters Centimeters 45 1 0 05 0 0 45 1 0 0 5 0 0 Centimeters Centimeters Centimeters Centimeters 1 0 0 5 0 0 Centimeters Centimeters Figure 12 XZ Plot displayed in different Contour Modes 2 4 3 Selection At this page of the 3D Properties dialog window you can specify a section on the xz dimension and highlight it in different ways The section is defined by the X X and Z Z values 3D Properties b xj 3D Properties Contour
79. race s calculated for the used function Note In case of OPUS functions that yield numerical values as result the result is stored in a trace The trace contains the calculated numerical values for all spectra of the 3D file in question You can have the calculated trace s displayed both in form of a report figure 1 and graphically in a 3D plot figure 2 In the latter case the trace is displayed in a different color at a side of the 3D plot Each spectrum in the trace of a 3D file is represented by one data point Bruker Optik GmbH OPUS 3D 1 A special kind of trace is the chromatogram which is generated as the result of a chromatographic measurement using the OPUS CHROM software package A chromatogramm shows the integral intensity changes at a certain frequency or in a given frequency range against the time The trace shown in figure and 2 is the result of an integration Note In case the 3D file has been integrated in the Map Spec window as described in section 2 5 2 the trace name is identical to the frequency range you have defined for the integration If however the 3D file has been integrated using the Integration function of the Evaluate menu the trace name is identical to the peak name you have entered in the Label field See also section 6 1 D OPUS 6 0_3 Betaversior Seconds 1634 63 1565 137 Trace Multiple 0 000000 0 031229 Trace Name 1 171503 0 034209 2 343
80. ral traces and video images stored in one file so you can select which trace image rectangle and spectrum block you want to display See figure 16 Select trace This drop down list includes all traces which have been calculated and stored in the 3D file in question A trace can be for example the RGB values of an image to generate a false color plot Select the trace you want to display Select image This drop down list includes all video images you have acquired and stored in the 3D file in question Select the video image you want to display Select rectangle This drop down list includes all rectangular areas that have been scanned during video assisted measurement Select the rectangular area you want to view 16 OPUS 3D Bruker Optik GmbH Displaying 3D Files 3D Properties x 3D Properties Contour Selection Mapping Select trace 0 T Select image v Select rectangle fi Spectrum block y IV Keep aspect ratio Cancel Apply Help Figure 16 3D Properties Dialog Box Mapping Spectrum block Usually a mapping file is displayed as a trace data block In combination with the Extract function or the Map Spec window you can use associated 3D blocks If there are several associated 3D blocks you can select one from this list Keep aspect ratio In case of a mapping measurement you can specify whether the aspect ratio of the actual measurement area is to be maintained in the 3
81. ration result right click in the upper subwindow 3D plot and select in the pop up menu the Properties function Click in the 3D Properties dialog window on the Chrom tab and select in the Display trace drop down list the corresponding the trace Note The name of the integration trace is identical to frequency range used for the integration Then click on the OK button Thereupon the integration trace is displayed in a different color at a side of the 3D plot See figure 23 AB D Rotation feo 3 Inclination 20 x fi 735 62 4 x 2861 DA z 108 95 Z 216 73 Index I Autoscale Z Saconds X Wavenumber cm 1 4000 3500 3000 2500 2000 1500 1000 500 Figure 23 Graphical Display of the Integration Result in Form of a Trace Integration Trace Bruker Optik GmbH OPUS 3D 21 Special Window Types 2 5 3 Map Video Spec Window The Map Video Spec window consists of three subwindows two 3D windows and a normal spectrum window See figure 24 In case the loaded 3D file results from a video assisted mapping measurement and a video image has been acquired and stored in the 3D file the left upper subwindow by default displays the video image The functionality of this sub window however is identical to the one of the normal 3D window i e you can switch between the different plots The right upper subwindow is also a normal 3D window By default the xz plot conto
82. red To assign a different color to the individual rectangles you have to reselect them sev eral times Then right click on the xz plot select in the pop up menu the Store Clusters function and store the selected clusters as described in the above section 3 3 To display the results in a three dimensional factor space open a Factor 3D window and drag and drop the TRC block into the window For detailed infor mation see section 2 5 4 Bruker Optik GmbH OPUS 3D 33 Cluster Lists 34 OPUS 3D Bruker Optik GmbH Measure Menu Measure Menu Apart from the standard measurement functions described in the OPUS Refer ence Manual there are also other functions in the Measure menu intended espe cially for processing 3D files provided you have installed and registered the corresponding optional software packages The following figure shows the functions that are relevant only to 3D file Measure Manipulate Evaluate Display Print dk Advanced Measurement Setup Measurement Parameters Routine Measurement Repeated Measurements Rapid Scan Time Resolved Measurement Direct Command Entry Optic Setup and Service Optics Diagnostics Temperature Control E Motorized Stage Control BROAN d EO E Video Assisted Measurement TE Time Resolved Step Scan I Chromatography T t Step Scan Modulation 3 Interleaved Time Resolved Measurement ml EPA Step Scan wi Continuous Scan FPA Measurement B Protein Dy
83. s for the y axis Enter a minimum and a maximum value in the corresponding fields This option is useful if you want to look at smaller bands in the presence of larger more dominant bands Flip X axis When you activate this check box you can flip the x axis to get the standard increasing wave number scale To manipulate the other axes use the Rotation and Inclination parameters 2 4 2 Contour This page of the 3D Properties dialog window allows you to subdivide the absorption intensities into several contour levels For the visualization of the different contour levels there are several color gradients and methods available Standard By default the different contour levels are visualized by a color gradient rang ing from blue via green yellow to orange red Rainbow The different contour levels are visualized by a rainbow like color gradient Blue The different contour levels are visualized by a color gradient ranging from dark blue to light blue Bruker Optik GmbH OPUS 3D 11 3D Properties Dialog Window 3D Properties xj 3D Properties Contour selection Mapping Standard C Black and white C Rainbow Chromatic C Blue None Stored table I No colour splitting Contours 10 v Method Smooth color gradient ba Figure 10 3D Properties Contour Stored table This option uses the color gradient specified using the Edit level function See also section 3 2 Black and white This optio
84. te Copy to Clipboard Copy to Clipboard Properties Properties Figure 6 Pop up Menu of the 3D Window Depending on the type of spectrum loaded 3D spectrum or single spectra the pop up menu is slightly different In case you have loaded a 3D file the pop up menu contains the function Extract Spectra However if you have loaded single spectra there will be the function Assemble Note After having factorized a Map file the Factorize function is substituted for the Store Clusters function XYZ Plot This option displays the data in the 3D plot XY Plot ZY Plot XZ Plot These options display the data in the corresponding 2D plots Zoom out Use this function to undo a magnification and reset the plot to its original size Reload Selection In case a file contains more data points than a monitor with the normal screen resolution can display the spectra in the 3D plot are displayed at a lower resolu tion to match the screen resolution of the monitor To display a smaller region of the plot more accurately i e at a higher resolution define an area using the X X Z and Z markers and select the Reload Selection function Show Subset Only the area defined by X X and Z Z values is displayed by zooming in the plot In this case the data are not reloaded Select the Reload Selection function from the pop up menu to display the plot more accurately Show Trace Displays latest calculated trace Br
85. tour line 8 29 31 Contour map 10 Contour plot 4 10 13 22 Contour value 5 Correction reference 56 Correlating two data sets 3 Correlation coefficient 56 Correlation mode 56 Correlation spectrum 56 Covariance matrix 64 D Data matrix 64 65 Digital resolution 57 E Edit levels 8 Eigenvalues 64 Eigenvector 64 Ellipsoid 24 Evolving factor analysis 61 62 Evolving system 61 Extract data 40 Extract spectra 8 40 Extract traces 8 40 Extraction mode 42 Extraction range 42 F Factor 8 25 60 65 Factor 3D window 8 23 Factor space 23 25 33 Factor spectrum 64 65 Factorization 23 32 60 64 Factorize 32 59 File list report 37 Flip X axis 11 FPA detector 45 Functional group 66 67 G GC file 35 36 37 I Inclination 4 9 11 24 Index number 59 Index value 5 Integrate 8 Integration 2 19 52 Integration area 19 52 Integration method 8 20 52 Integration trace 21 K Keep aspect ratio 17 L LIST data block 37 Loading 60 65 M Map file 8 35 36 37 63 65 Map Spec window 2 17 19 Map Video Spec window 22 Mapping measurement 5 16 36 Marker line 5 19 59 Mass balance condition 63 N No image 10 Non negativity 61 62 Normalization 61 63 Normalize spectra 63 O OpenGL fonts 11 P Peak picking 54 Phase angle 56 Phase angle cutoff 56 Pure component spectrum 44 Q Quantitative analysis 53 R Reduction factor 57 Regression line 56 Reload all 8 Reload
86. uker Optik GmbH OPUS 3D Functions of the 3D Pop up Menu Reload all To display the whole 3D plot at a high resolution after having enlarged an area select this function Extract Spectra This function extracts single spectra from the 3D block If you select Extract Spectra the Data Extraction dialog box opens which is described in detail in the section 4 3 Assemble If you have loaded several single spectra use this function to assemble the loaded single spectra to a 3D file Extract Traces This function extracts a single trace from the 3D block If you select Extract Traces the Data Extraction dialog box opens which is described in detail in the section 4 3 Edit Levels Use this function to specify the number of contour levels the spacing between two contour lines and the color of the several contour levels This function is identical to the function Contour Levels in the Edit menu For detailed informa tion refer to section 3 2 Factorize Use this function to condense the characteristic information of a spectral data set This is accomplished by factorizing the data set This function is identical to the Factor Map File function in the Evaluate menu See section 6 6 Store Cluster After you have factorized a Map file the function Factorize in the pop up menu is substituted for the function Store Cluster This function allows you to store cluster lists you have defined before For information about how to define
87. ur plot is displayed For information about the pop up menu and the functionality of the 3D window see sections 2 1 2 3 and 2 4 The lower subwindow displays the spectrum at the given intersection point of the x and z axis marker lines For information about the pop up menu functions of this subwindow refer to the OPUS Reference Manual 5 00 4 50 4 00 27200 3 50 3 00 2 50 2 00 1 50 1 00 49200 49100 49150 X Micron Rotation fa 20 Inclination as x 4913511 x 49192 18 Ze 2 2707593 Z 27179 20 Figure 24 Map Video Spectrum Window 3600 3250 3000 2750 1600 00 1500 00 1400 00 1300 00 1200 00 1100 00 1000 00 300 00 800 00 700 00 600 00 500 00 400 00 300 00 200 00 Z Micron pe 49100 49150 49200 X Micron 500 1500 1000 750 1250 2500 2250 2000 1750 22 OPUS 3D Bruker Optik GmbH Displaying 3D Files 2 5 4 Factor 3D Window This special window type is intended for displaying the results of a factorization in a three dimensional factor space See figure 25 Open a Factor 3d window and drag and drop the trace data block containing the cluster list s into this window For information about how to define clusters and store a cluster list refer to section 3 3 PC3 Py Display default ows 1 OO 3d Display default ows 2 Figure 25 Factor 3D Window To cha
88. ure 42 shows a more complex example Two large bands are modulated by a cosine function and a small band in the middle shows a sinusoidal variation and thus is out of phase Bruker Optik GmbH OPUS 3D A 5 Appendix 2 1600 E 2000 ei Lo Wavenumber cm 1 2400 Figure 42 Variation of Two Large and One Small Band The variation of the smaller band one tenth in the middle of the two large bands can hardly be seen in the original data Synchronous correlation yields a 2D spectrum as shown in figure 43 As expected four peaks are observed one for each pair of the two large bands 1800 2000 2200 Wavenumber cm 1 2400 2400 2200 2000 1800 Wavenumber cm 1 Figure 43 Synchronous Correlation Spectrum OPUS 3D Bruker Optik GmbH Appendix However the correlation with the small band is obtained by means of the asyn chronous spectrum that has two peak pairs Their positions indicate that the two main bands correlate with the band of a third component The position of this band is exactly between the two main bands The 2D contour of the two main bands and the third small band is antisymmet ric One peak pair has positive values and the other negative ones This gives an indication of the band sequence The band at 2100cm occurs before the band at 2050cm if the original data are the result of a time resolved measurement However it is obvious that the band at 2050cm occurs after the band at
89. ve while pressing the CTRL key To mark a block of traces select the first trace of the block by clicking on it then select the last trace of the block by left clicking on it while pressing the Shift key After having selected the traces click on the Remove Traces button Bruker Optik GmbH OPUS 3D 27 Contour Levels Remove Traces x Remove Traces m File to remove traces from bekei C OPUS 6 DiDatalExtended Demodata MAP WAFER O 1 m Select traces to remove Loadina 12 E Remove Traces E Cancel Help Figure 29 Remove Traces 3 2 Contour Levels This function enables you to subdivide the y axis absorption intensity into several levels so called contour levels and to visualize them by a color scheme There are two ways of invoking the Contour Levels dialog window 1 Select the Contour Levels function in the Edit menu 2 Right click on the 3D window and select the Edit Levels function from the pop up menu Contour Levels Y x Select Files aE bea m GC Map file adrei CADPUS 6 01 Data Extended Demodata MAP 4 A Contour levels O 6356992 0 2 1895841536 0 4 1090492160 0 6 16 Interactive cora toe Figure 30 Contour Levels 28 OPUS 3D Bruker Optik GmbH Edit Menu In case the 3D file is already loaded in OPUS the file is already included in the GC Map file field when this dialog window opens Otherwise load the 3D file
90. w Z Axis 4 1 5 Raster As already mentioned the Assemble MAP File dialog window is identical to the Assemble GC File dialog window apart from the forth tab In case the Assemble GC File dialog window this tab is labeled Z Axis whereas in case of the Assemble MAP File dialog window this tab is named Raster See figure 43 x Select Files Result File Frequency Range Raster D dikan X Points ha Delta x fi 0 Y Points I DeltaY fi 0 Unit Milimeters ei pe le Figure 43 Assemble MAP File Dialog Window Raster Define a raster by entering appropriate values in the X Points and Y Points fields i e the number of points in x direction or y direction and in the Delta X and Delta Y fields i e the distance between two points Select an appropriate length unit for the x axis and the y axis from the corresponding drop down list Bruker Optik GmbH OPUS 3D 39 Add Traces 4 2 Add Traces This function enables you to add traces to an existing 3D file Use this function if you want to add traces you have extracted before in order to preprocessed them separately Choose Add Traces from the Measure menu The following window opens x Select Files GC Map file Adee C OPUS 6 0 DataExtended Demodata MAP 4 b Traces O eehee C OPUS 6 0 DataExtended Demodata MAP Add Cancel Help Figure 44 Add Traces Dialog Window In the upper GC Map file field include the
91. w Click on the Mapping tab select in the Select trace drop down list the corresponding trace and click on the OK button As a result the selected trace is displayed in a different color at a side of the 3D plot In case of a 3D file you can also calculate the quotient oftwo peaks To do this set up an integration method as described in the OPUS Reference Manual chapter Evaluate section Integration The only thing however you have to pay attention to is When you enter the name of the second peak in the Label field do not forget to enter a hash sign after the peak name See figure 53 Label Peak24 Number of Areas 2 Figure 53 Setup Integration Method Dialog Box Detail Figure 54 shows the result of such an integration in form of a report In the two subwindows there is a column with the title Name of the first Peak Name of the second Peak e g Peak 1 Peak 2 52 OPUS 3D Bruker Optik GmbH Evaluate Menu ZTO Ele Edit View Window Measure Manipulate Evaluate Display Print Macro Validation Setup Help vas dB KZ ZE b SG RAR RSM Sees z wee WS Gis EZEZ OPUS Browser ax Peaki Peak2__ Peak 1 Peak2 0 000154 0 254577 0 145682 1 747486 1 171503 0 000165 0 270147 0 152999 1 765678 2 343006 0 000158 0 280563 0 151208 1 855474 3 514510 0 000167 0 327875 0 151334 2 166561 4 686013 0 000182 0 308685 0 160731 1 920505 5 857516 0 000175 0 293231 0 151606 1 934163 7 029019 0 000169 0 2829
92. window Right click on the 3D window and select in the pop up menu the function Factorize After OPUS has accomplished the factorization right click on the xz plot of the 3D window and select in the pop up menu the function Properties Activate on the Properties page the option button Pixelimage Then click on the Mapping tab and select in the Select trace drop down list the option x RGB with x being the number of the trace As a result the xz plot is displayed as a pixel image 1 This function is identical to the Store Clusters function in the pop up menu In the pop up menu this function is not available until the Map file has been factorized 32 OPUS 3D Bruker Optik GmbH Edit Menu Rotation feo Inclination E 3 x 34 27 x 36 41 E Zz 4 28 a Z 6 43 WAFER O 12000000 00 11000000 00 10000000 00 _ xz Plot 3000000 00 8000000 00 7000000 00 6000000 00 5000000 00 4000000 00 3000000 00 2000000 00 1000000 00 Index 74 1004 Eb Y No Y unit defined E GO O O E GO GO E Ge EA I ZO j Y No Y unit defined 20 0 7 T 7 T 7 D 10 20 30 40 50 X Millimeters T T r r A 10 20 30 40 5 Z Millimeters Figure 36 Defining Clusters Select the area of interest by drawing a rectangle around it See figure 36 You can draw as many rectangles as you like Note At first all rectangles are displayed in the same color by default
93. with similar kinetics while for an external force the 2D spectrum indicates similar response to the stress Correlation Another approach is based upon Barton s article For a given data set the 2D correlation coefficients are calculated for all wave number combinations using the following equation ny ur EE JII vilva 1 1 1 A 6 E ut ardie urt eri with n being the number of spectra or value pairs y v being the absorbance values for the first wave number and uda being the absorbance values for the second wave number The square of the correlation coefficients can also be calculated default setting to improve the evaluation of the resulting spectra because any correlation pos itive or negative will yield values close to 1 while areas with poor correlation exhibit coefficients around 0 OPUS 3D Bruker Optik GmbH Appendix Regression The correlation coefficient sign indicates what kind of correlation you deal with Positive peaks in the 2D correlation plot indicate that the changes appear in the same direction whereas negative peaks indicate that one band increases while the corresponding band decreases For further quantitative evaluations you can calculate the regression coefficient If a correlation already exists this value the slope of the regression line indi cates that one band increases e g five times faster than the other etc Experiment Types Possible applications are Time R

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