1593588 en NIRCal 5.
Imprint Product Identification: Operation Manual, NIRCal 5.5 11593588 en Publication date: 04.2013, Version A BÜCHI Labortechnik AG Meierseggstrasse 40 Postfach CH-9230 Flawil 1 E-Mail: quality@buchi.com BUCHI reserves the right to make changes to the manual as deemed necessary in the interest of experience; especially in respect to structure, illustrations and technical depth. This manual is copyright.
Table of Contents 1 Introduction .................................................................................................................................. 10 1.1....... Introduction to NIR.......................................................................................................... 10 1.1.1 Spectroscopy .................................................................................................................. 10 1.1.2 Chemometrics ................................................
NIRCal 5.5 Software Manual 3.1.6 Principal Component Regression: PCR ......................................................................... 54 3.1.7 Partial Least Squares Regression: PLS ......................................................................... 54 3.2....... Calibration Validation Methods ....................................................................................... 55 3.2.1 Validation Set (VS) .....................................................................................
Table Of Contents 3.18.9 3.18.10 3.18.11 3.18.12 3.18.13 3.18.14 3.18.15 3.18.16 3.18.17 3.18.18 3.18.19 3.18.20 3.18.21 3.18.22 3.18.23 3.18.24 3.18.25 3.18.26 3.18.27 3.18.28 3.18.29 3.18.30 3.18.31 3.18.32 3.18.33 3.18.34 3.18.35 3.18.36 3.18.37 3.18.38 3.18.39 3.18.40 3.18.41 3.18.42 3.18.43 3.18.44 3.18.45 3.18.46 3.18.47 3.18.48 3.18.49 3.18.50 3.18.51 3.18.52 3.18.53 3.18.54 3.18.55 3.18.56 3.18.57 3.18.58 3.18.59 3.18.60 3.18.61 3.18.62 3.18.63 3.18.64 3.18.65 3.18.66 3.18.67 3.18.68 3.18.69 3.18.
NIRCal 5.5 Software Manual 3.18.71 Residuals ...................................................................................................................... 195 3.18.72 Regression Coefficients [1] .......................................................................................... 195 3.18.73 Regression Coefficients / Property Spectra (CLU) ....................................................... 195 3.18.74 Sample ................................................................................
Table Of Contents 3.21.7 Clear Selection ............................................................................................................. 256 3.21.8 Colors ........................................................................................................................... 256 3.21.9 Copy Plot to Clipboard ................................................................................................. 256 3.21.10 Copy Selection To ........................................................
NIRCal 5.5 Software Manual 4.4....... Characteristic absorbance table ................................................................................... 274 5 Software installation .................................................................................................................. 277 5.1....... Software installation ..................................................................................................... 277 5.1.1 Important Notes .................................................
Welcome Dear NIRCal user, NIRCal is recognized as a reliable, comprehensive but also easy to use chemometric software package. It offers a wide variety of tools for method development and optimization. The NIR spectroscopic technology and the range of applications develops continuously, just as new requirements from users and regulatory authorities. NIRCal is designed to fulfill those requirements today and in the future.
NIRCal 5.5 Software Manual 1 Introduction 1.1 Introduction to NIR 1.1.1 Spectroscopy Light is a fast time dependent sequence of electric and magnetic fields propagating in space. Light can be characterised with physical properties, like: frequency: wavelength: wavenumber: velocity of propagation: energy: A summary of the electromagnetic spectrum can be seen in the Picture below. NIR lies between the visible and middle infrared range.
Introduction Beer Law: has just limited validity in the NIR spectroscopy. The application of chemometrics for the evaluation of NIR spectra is a must. Advantages of NIR spectroscopy The relative low degree of absorption coefficient of overtones and combination vibrations causes a low degree of absorbance in the NIR region. Solids have a high degree of reflected light and liquids can be measured for path lengths of several mm. no sample preparation is necessary.
NIRCal 5.5 Software Manual 1.1.3 Cluster calibration Qualitative calibrations are used for identification of different chemical substances and for separation of different qualities of the same substances. The possible applications include identification of: substances with very different chemical characteristics; chemically similar substances; acceptable and rejectable qualities of a given substance. The possible methods are Cluster or SIMCA.
Introduction Figure.1: Solvent spectra (acetone, ethanol, toluene and dichlor-methane), measured through glass cuvettes with measurement option liquid. The slight shifts (light scattering) are not of interest and should be reduced with data pretreatments. Figure.2: Spectra out of figure 1 after data pretreatment (here: 1st derivation) Systematic differences of the four solvents are clear and reproducible For the actual calibration, the Cluster calibration using PCA has been used.
NIRCal 5.5 Software Manual Figure 3: After transformation with the PCA, the spectra appear as points assorted in clusters, which are well separated from each other. * In case of many different categories (properties) more than three delineation axes are required to show all important differences. It is not necessarily the case, that the first three axes are the most important ones.
Introduction Important: For the choice of the reference samples, all components of the mixture (and eventually varying parameters like temperature) must be considered, even components not being calibrated. For complex compositions, like foodstuffs, the requested amount of samples might be quite high. The choice of calibration samples must be carried out very carefully.
NIRCal 5.5 Software Manual An incorrect distribution of the samples with two separated concentration ranges should be avoided. Either an independent calibration should be generated for each range or additional samples, covering the missing range, should be measured. For reference measurement, the probe and reference material need to be absolutely clean. This is valid for the measurement of calibration spectra as well as for the measurement of application spectra.
Introduction The choice of parameters and calculation methods can be done automatically by using the Calibration Wizard. Figure 2: For the review of a quantitative calibration the prediction values according to equation [1] are compared with the reference values. In an ideal case, the corresponding points are lying on the 45° calibration curve through the zero point both for the calibration and validation samples.
NIRCal 5.5 Software Manual In case spectra breaking ranks, show clearly deviating Scores and Residuals (Graphics / Spectra / Residuals), these spectra are real outlier and should be eliminated from the calibration / validation. In case there are big differences between the reference values and the predicted values, but the Scores of the referring spectra do not have particular deviations with high probability, the Outliers appear because of false reference value.
Introduction NOTE To be able to take full profit from all the possibilities of the NIRCal chemometric software, a Buchi training is highly recommended. 1.2.2 Starting NIRCal Windows 7: Start / All Programs / BUCHI / NIRSolutions /NIRCal Windows 8: Write “NIRCAl” in the main screen and navigate to programs Icon: To use NIRCal Log On with User name and Password. User rights and setup is managed with the NIRWare Suite "Security Designer".
NIRCal 5.5 Software Manual 1.2.3 NIRCal Project NIRCal stores the imported spectra and their properties , which belong together in a project.
Introduction Explanation of the symbols (right window): Spectra belonging to the C-Set Spectra belonging to the V-Set Spectra in unused Set = U-Set (these spectra are not used for calibration nor for the validation of a calibration Spectra in C- and V-Set at the same time. Overlapping is not allowed. Red color indicates selection. These spectra for example can be assigned to the user set and be plotted separately. 1.2.5 Properties Overview All properties in this project can be seen here.
NIRCal 5.5 Software Manual Min/Max represents the calibration range for quantitative properties. For qualitative properties Min/Max is shown as 0/1. 1.2.6 Calibration Validation Methods To be able to judge the performance of a calibration a set of independent validation samples is necessary. Validation Set (VS) Normally all spectra within a project are divided into 2 sets with a suggested ratio of 2/3 to 1/3. The two sets should be completely independent from each other.
Introduction Calibration Inputs are the measured spectra with their properties and with the reference values together with the calibration data selection. Outputs are the calibration for the properties together with the validation for the validation set (V-Set) spectra or the result of Cross Validation (CV). Application Inputs are the calibration and a measured spectrum. Outputs are the predicted property value(s), calibration limits or hitlist; spectral residuals. 1.2.
NIRCal 5.5 Software Manual 1.2.9 Matrices Overview The matrices shown here depend on the selected calibration and validation method. Items marked with a yellow pen can be edited by pressing F2 or a double click. 1.2.10 Data Raw data like spectra and property values are loaded from the NIRWare Database. Spectra and property values, loaded from the database, are not modifiable in NIRCal anymore. Pretreatments never change the original spectra. These data are stored in a NIRCal Project.
Introduction It is not possible to import data from NIRCal 4 ".ncf" format, because ncf-files do not include spectral data. It is important to take care of the compatibility of the spectra from different instruments! Link: Convert and Import..in NIRWare DB. 1.2.11 Selections Data selections are needed to group the data before the calculation of a calibration. For each calibration the selections can be different. Calibration method selection Choose the method according to the target of the application.
NIRCal 5.5 Software Manual Select spectra for the calibration (Calibration Spectra = C-Set) and for the validation of the calibration (Validation Spectra = V-Set). The C-Set will be used for the calculation of the calibration, the V-Set is used as an internal test of the calibration. The same spectra should not be defined as C-Set and V-Set Spectra at the same time.
Introduction Blow Up Parameter: The allowable limits are calculated with a default blow up limit. These limits can be adjusted by the user: for quantitative calibrations the scores and residual blow up limits; for qualitative calibrations the scores, residual and radii blow up limits and the radii calculation formula.
NIRCal 5.5 Software Manual The plots can show different selections, while the selection plotted is always visible on the subtitle. The use of modern rendering techniques, such as Anti-Aliasing and Alpha-Blending (new hardware accelerated features of newer graphic cards), allows to eliminate jagged edges and stair-stepped lines. NIRCal applies these features to improve the graphical performance. Anti-Aliasing (hotkey: a) eliminates jagged edges and stair-stepped lines.
Introduction 1.2.13 Protocols The term "protocol" in NIRCal means report. Calibration Protocol The calibration protocol is an important validation document, which contains all information about a calibration, like the user specific data selection and the results of the chemometrical calculations applied for the C- and V-Set spectra in the project. The calibration protocol is stored within the calibration.
2 Tutorials 2.1 Qualitative 2.1.1 Qualitative Tutorial Qualitative calibrations are used for identification of different chemical substances and for separation of different qualities of the same substances. Either Cluster or SIMCA method can be used for identification, both using Principal Component Analysis PCA. The Cluster method is explained first. For detailed explanation to the method see Link : Cluster (CLU) and Link : SIMCA 2.1.
NIRCal 5.5 Software Manual NOTE Loop 1 to Loop 3 represent the sequence for optimising a calibration. After each change in the selection, the calculation and principal component selection should be repeated. 2.1.3 Selecting the Calibration Method The calculation method can be selected in the Menubar: [Calibration / Method / CLU Cluster] or by clicking the icon 2.1.
Tutorials Suggested selection: use all measured wavenumber in the first calculation, otherwise see Loop 2. Link Wavelength selection 2.1.6 Selecting the Calibration Properties The calibration properties are the substances to be identified in the application. The mathematical algorithm of PCA will be applied for the selected properties. Normally all qualitative properties that must appear in the calibration model must be selected. Suggested selection: select all properties.
NIRCal 5.5 Software Manual 2.1.10 Secondary Principal Components The secondary or calibration PCs are used for the separation of the different substances and are responsible for the tolerance radii calculation. The number of secondary PCs is limited by the number of primary PCs. Recommended graphics for the selection: 2- and 3-D Scores plots, Scores against Spectra and Property Box Radii. These plots are part of the Overview-Plot.
Tutorials 2.1.13 SIMCA It is possible to transfer a cluster calibration into several SIMCA calibrations. See Transform Cluster to SIMCA. This tool creates for all C-Set properties one SIMCA calibration, the name of the calibration is "SIMCA + calibrated property name". 2.2 Quantitative 2.2.1 Quantitative Tutorial Quantitative calibrations are used for the determination of different concentrations or physical parameters.
NIRCal 5.5 Software Manual NOTE Loop 1 to Loop 3 represent the sequence for optimising a calibration. After each change in the selection, the calculation and principal component selection should be repeated. 2.2.3 Selecting the Calibration Method For the quantitative calibration, basically two calculation methods are available: Principal Component Regression (PCR) consists of a Principal Component Analysis (PCA) with subsequent MLR.
Tutorials Suggested wavenumber range for NIRFlex N-500 with measuring options -1 Solids and Liquids: 4'000-10'000 cm ; -1 Fiber Optics: 4'500-10'000 cm . -1 Solids with Tablet Accessory: 6'000-11'520 cm . The calibration wavelengths define the spectrum range where the mathematical algorithms is applied. Suggested selection: use all measured wavenumber in the first calculation, otherwise see Loop 2. Link Wavelength selection 2.2.
NIRCal 5.5 Software Manual 2.2.9 Primary Principal Components Primary principal components are the PCs, which are used for reconstruction of the spectra. They determine the residual value. The more primary PCs used, the smaller the allowed residual of the calibration. Recommended graphics for primary PCs selection: X-PRESS function, Loadings graphic; Spectra Residuum plots. Suggested selection: avoid overfitting, do not use too many primary PCs.
Tutorials After several calibration optimizations and running the automatic calibration wizard, there will be several calibrations in the project. Sort the calibrations with a click on the Name, Q-Value or e.g. SEP. NOTE Keep only the best calibration and delete all others. 2.2.12 Save Calibration - Lifecycle Save the project and the calibrations to the database. Only approved calibrations according to Lifecycle will be available in the NIRWare Application Designer.
3 Chemometrics 3.1 Calibration Methods 3.1.1 Principal Component Analysis: PCA Principal Component Analysis is a mathematical, statistical evaluation of a large amount of chemical data. In this case the chemical data are the measured NIR spectra. PCA is made for two reasons: - to reduces the data amount without loosing necessary information. Noise is truncated by the number of primary PCs; - to evaluate the measured spectrum automatically after creating a calibration.
NIRCal 5.5 Software Manual A reduction of the dimensions is performed when the number of PC's (i) is not higher than 1.501. Through this type of data reduction it is impossible to lose information. With today's powerful computers, the prime object is no longer the reduction of the data volume. Today, the main goal of PCA is to find and automatically evaluate characteristics of identity, quality and quantity in the spectra.
Chemometrics Scores: v in Weightings of each PC after the pretreated spectrum has been transformed into the cluster. A score is the portion of a PC used for the reconstruction of the original spectrum. Each spectrum has different and up to max. i scores. Residuum: R n (k) The difference between the pretreated spectrum and the reconstructed spectrum is the residuum spectrum. When the residuum is summed across the wavelength, a number is obtained, the Residual.
NIRCal 5.5 Software Manual For 100 spectra with1501 data points the following data reduction is obtained with 15 PCs: 100 x 1.501 ==> 1.501 + [15x1.501] + [100x 15] + 100 150.100 ==> 1.501 + [22.515] + [1.500] + 100 Example for a Principal Component Analysis: 4 different acetone qualities: without and with 0.3 %; 0.7 % and 1.0 % added water. There are only 3 PCs necessary to reconstruct the spectra. The scores according to PC 1 and PC 2 are repeatable. The residuum spectra have only noise character.
Chemometrics The scores can be represented in two- or three-dimensional PC plots. Each number represents a spectrum, v in its score. Here, the scores of the spectra 1, 2 and 3 of the PCs 1 and 2 are graphically represented. Each spectrum with "i" PCs will also have "i" scores. The closer together the points in the plot, the "more similar" the spectra. It is now possible to break down an unknown spectrum with regard to these two PCs, i.e. to determine the scores. If this spectrum is located, e.g.
NIRCal 5.5 Software Manual The Büchi NIRCal software package only works with the normalised distances, the user can not see the result without it. 3.1.2 Cluster: CLU Goal: to identify different chemical substances using the PCA and as a result to get a well separated cluster area in the scores plot for each substance. The clusters are created according the selected secondary PCs.
Chemometrics Additional tool: The Score Disorder values show how effectively a particular PC separates different properties (substances) from each other. By scanning the score values in one direction of a PC and counting the changes between the membership of A or B the disorder value is achieved. If a PC completely separates all calibration properties, the disorder values is the [number of calibration properties - 1]. PCs with small disorder values are possible calibration PCs.
NIRCal 5.5 Software Manual Formula 2 If generally small tolerances are required, Formula 2 can be used: min. of or or r = R1*0.499 (0.499: to avoid overlapping) r = R3 * Pre Blow Up * f r = R4*0.5*Pre Blow Up * f The smallest of the three possible values for the radius “r” is used. The pre Blow Up factor is 5, this is an empirically evaluated value. The default Radii Blow Up f = 1, this value can be adapted by the user. In general it should be increased to get connected spheres.
Chemometrics Distance The distance to the next calibration spectra should be smaller, than the tolerance ring radius of the neighboring calibration spectrum. In this case the distance criterion is OK, the spectrum is in a cluster. Property Residuum zero means, all spectra are in the correct cluster. Here only a value of 0 is acceptable. Property Residuum +1 means, that a spectrum is outside the cluster: it is not identified.
NIRCal 5.5 Software Manual NOTE Switching the "Mean centering after Pretreatment" OFF, the first principal component represent almost the mean value spectrum. This is suggested for only one property in the calibration, which is always the case for SIMCA. SIMCA can also be created without a transformation from a cluster calibration.
Chemometrics SIMCA Overview Plot The Overview plot is automatically opened after the SIMCA calculation is finished. Each calibration has the name: SIMCA + substance name (property name) selected for the calibration. The Overview plot contains the following plots: 1 2 3 4 5 Plot name Pretreated Spectra scores against PCs scores vs. scores spectra residual residuals vs.
NIRCal 5.5 Software Manual PC (Factor) Selection Wizard Primary PC selection: Test 1.5 : C-Set X-PRESS Slope Ratio Highest test w(i+1) = ( y(i) - y(i+1) ) / ( y(i+1) - y(i+2) ) Limit = 2 PC i for highest i where w(i) > Limit Precise Secondary PC selection: Test 2.2 : Q-Value maxima (limited) test PC i for Max ( QValue(i) ) I < NumPrimaryPCs NIRCal calculates the allowed residual using the primary principal components for reconstruction. Default parameter for residual Residual Blow Up = 2.
Chemometrics Radii Blow Up limit. The number of "Total not identified, Cluster OK (%)" can be reduced by reducing the number of primary PCs or by increasing the Residual Blow Up limit. Using SIMCA in application For the identification of an unknown substance the residual should be below the allowed limit and the unknown spectrum distance should be smaller as the allowed tolerance sphere to the nearest known calibration spectrum (inside the "inner space").
NIRCal 5.5 Software Manual 3.1.6 Principal Component Regression: PCR Principal Component Analysis (PCA) with subsequent MLR is called Principal Component Regression (PCR). As a first step, the principal components and scores are calculated with PCA. The second step is a multiple linear regression MLR using the scores and property values (concentrations).
Chemometrics If two parameters are not systematically correlated, the mathematical approximation of the spectra via PLS can never be performed for both parameters when each parameter is calibrated using its own PLS. For this reason, it is recommended to calculate properties which are not systematically correlated (e.g. ethanol and acetone contents in any given solvent mixture) in separate calibrations.
NIRCal 5.5 Software Manual Cross Validation Grouping Menu: Calibration \ Change Data Sets \ Edit CV Groups... Icon: In order to define the cross validation groups, the CV Group selector is opened. The various possibilities for selections are summarized in the following table. Methods One leave out Alternate Sequence Random Property Segments Property Equal Spectra Name Spectra Name (autom.) 56 Each spectrum represents a group.
Chemometrics Custom assign Group to Spectra This is the default method when the CV Group Selector is started . In this mode it is possible to display a plot (Group Plot) and/or a table (Group Table) with the CV Group Index Buttons / Selections Method Select a method from the drop-down list. Group Table Display table: CV Group Index. Enabled only for the method: Custom assign Group to Spectra Group Plot Display plot: CV Group Index.
NIRCal 5.5 Software Manual Alternate The spectra are grouped successively by increasing number (1st spectrum to the 1st group, 2nd spectrum to the 2nd group, etc.). The number of Groups or the number of Spectra per Groups can be changed by clicking on the + or symbols. The number of Groups and Spectra per Groups are depending on each other. 58 NIRCal 5.
Chemometrics Sequence The spectra are grouped with consecutive number (1st to 3rd spectra to the 1st group, 4th to 6th spectra to the 2nd group, etc.). The number of Groups or the number of Spectra per Groups can be changed clicking on the + or symbols. The number of Groups and Spectra per Groups are depending on each other. NIRCal 5.
NIRCal 5.5 Software Manual Random The spectra are grouped randomly. The number of Groups or the number of Spectra per Groups can be changed clicking on the + or symbols. The number of Groups and Spectra per Groups are depending on each other. The smallest number of Group is 2. 60 NIRCal 5.
Chemometrics Property Segments For the selected property the min.-max. value range will be divided into Number of Segments (default: 20). Each spectrum, which has the value belonging to a segment, builds a group. Segments without property value are empty (here e.g. concentration range from 5 till 10 %). The cross validation calculates the groups for the selected property. Only one property must be selected. NIRCal 5.
NIRCal 5.5 Software Manual Property Equal Spectra with the same property value (concentration) selected for a group. Each property is taken into account. 62 NIRCal 5.
Chemometrics Spectra Name Spectra with the same name are selected for a group. The comparison will start from the 1st character (default), but it can be changed by the user. The length of spectra name can be limited by: Number of Characters. Default: 500. NIRCal 5.
NIRCal 5.5 Software Manual Spectra Name (autom) Spectra with the same name are selected for a group. The comparison will start always from the 1st character. The length of spectra name will automatically be determined. 64 NIRCal 5.
Chemometrics Custom assign Group to Spectra For custom-defined grouping, open the Matrix CV Group Index with the button "Group Table". NIRCal 5.
NIRCal 5.5 Software Manual Group Index numbers define to which group a spectrum is assigned. There are 4 different types of selection possible: Group name In C-Set Unused Spectra CV-unused Group CV-permanent C-Set CV-mutable V-Set No No Yes Yes In CV-Group (CV Group Index > 0) No Yes No Yes Spectra with Group Index zero and not selected in the C-Set: unused spectra. Spectra with Group Index higher than 0, but the spectra are not selected in the C-Set build the CVunused Group.
Chemometrics CV Plots It is possible to show the result of each calibration step (e.g. CV Predicted Property) and also the result of the final calibration (e.g. Predicted Property). The Overview contains the following plots: [1] The 1st C-Set property is chosen automatically for the plots. Pretreated Spectra: it is suggested to start the first calibration without pretreatment, but try later some pretreatments and combinations. CV Property Residuum vs.
NIRCal 5.5 Software Manual case several minimum SECV exist. Use the Factor Selection Wizard. The selected number of secondary PCs will be red. Beside these plots there are several other plots to choose outlier spectra or to make a better view of the results. The plots under 68 has the following plots: Property Residuum: The property residuum of each spectra showed with the final calibration. Spectra Residuals vs.
Chemometrics 3.3 Selections 3.3.1 Calibration Method Selection Menu: Calibration / Method / ... Icon: for Principal Component Regression / Multiple Linear Regression for Cluster / for Partial Least Squares / for for SIMCA Example: For the calibration of Saccharose the method PCR is selected and for the calibration of Lactose PLS is chosen. NIRCal 5.
NIRCal 5.5 Software Manual 3.3.2 Validation Method Selection Menu: Calibration / Validation Method / ... Icon: for Validation Set for Cross Validation The default method is VS (Validation Set). For quantitative calibrations CV (Cross Validation) is available. 3.3.3 Data Sets Data sets are permanent selections that are stored and loaded with the project.
Chemometrics 3.3.4 Edit Data Sets Dialog Menu: Calibration / Change Data Set / Edit Data Sets... Icon: Under the drop-down list Name you can choose to edit the selections of the sets: Calibration Spectra Validation spectra and more NOTE Click Apply after a selection, click OK to close the Dialog. Invert: a simple tool to invert the selections previously made. It is very useful when dealing with large numbers of spectra.
NIRCal 5.5 Software Manual Parameter Range from ... to ... Block select ... leave ... Amount ... % The first and the last spectra index. Number of selected and left out spectra per block. Amount of selected spectra in %. 3.3.5 Spectra Data Set Samples of known characteristics, both chemical and physical are used to generate calibrations. Measurement conditions should remain constant for all samples using the full spectrum range.
Chemometrics Spectra Selection in the NIR-Explorer Open NIR-Explorer Steps sequence: 1. Open the folder “Calibrations” by clicking on the box + in front of the folder or double clicking the folder 2. Open the active calibration, indicated by the red dot. 3. Open the folder “Data Sets”. 4. Select "Spectra". 5. Select "Calibration Spectra" in the right part of the window. To open the Edit window press the right mouse button and click on Edit Set or double click on the selected line.
NIRCal 5.5 Software Manual Selection methods: Monte Carlo Random: this selection is suggested, when only one spectrum for each substance was measured, which is not recommended (measurement mistake is not clear). For 3 spectra / samples this method is not suggested, while the 3 spectra can be randomly in C- or V-Set. Sequence: e.g. 70 % of the spectra are selected automatically into the C-Set.
Chemometrics The table consists of the spectrum number, the name of spectrum with batch number and the property membership (1 indicates: it belongs to a property, 0 indicates: it does not belong to a property). NIRCal 5.
NIRCal 5.5 Software Manual Creating the selection: mark the first selected row with the mouse, press the left button only once. Press the “Shift-key” and double click on the last marked row. All selected spectra are highligthed in red colour. To remove spectra from the selection: mark the selected row with the mouse, press the left button only once. Press the “Ctrl-key” and double click on the row.
Chemometrics Spectra should not be designated to both, Calibration and Validation-Set. Should this happen the system forces the user to make a clear decision. Clicking "Yes" will remove the overlapping spectra from the Calibration Set and keep them in the Validation Set. Spectra Selection in Graphic A very practical way to make the spectra selection is in the calibration plot using the mouse. This is especially useful for the quantitative calibration because in the plot "Predicted Property vs.
NIRCal 5.5 Software Manual When the selection is created, the spectra can be copied to the calibration spectra, the validation spectra or the user spectra. 1. press the right mouse button in the graphic and Copy Selection to – Row - Calibration Spectra; 2. for setting the Validation Spectra select in the Popup-Menus the command Invert Selection. The rest of the spectra will be selected; 3. copy this selection in the Popup-Menus with the command Copy Selection to – Row Validation Spectra.
Chemometrics NOTE In general, the calibration wavelength / wavenumber range should be as wide as possible. Suggested wavenumber range for NIRFlex N-500 for measuring options with -1 Solids and Liquids: 4'000-10'000 cm ; -1 Fiber Optics: 4'500-10'000 cm . -1 Solids with Tablet Accessory: 6'000-11'520 cm .
NIRCal 5.5 Software Manual In the project, the selected wavenumber as data points and range are shown (here: 1376 data points -1 in the range of 4'500-10'000 cm ). Selecting Calibration Wavelengths using Graphics To review and select the suitable calibration wavelength range, several graphics can be used. An example is shown with the pretreated spectra, but it can also be done in the original spectra, loading or property wavelength regression graphic in the same way.
Chemometrics Now it is possible to select the wavelengths with the mouse. The cursor position as wavenumber can be read in the status bar. Keep the left button pressed for selection. The selected range is marked with red color. Copy the selected range into the calibration wavelengths with the right mouse button Popup-Menu: Copy Selection to / Calibration Wavelengths. NIRCal 5.
NIRCal 5.5 Software Manual 3.3.7 Properties Data Set In qualitative methods the calibration properties are the substances that are required to be identified in the application. In cluster calibration the mathematical algorithm of PCA will be applied for the selected properties. Normally all qualitative properties are used in the calibration. In quantitative methods the calibration property (single property calibration) is the selected parameter which should be predicted.
Chemometrics In the project the selection is shown Selecting the Calibration Properties using the Property Table NIRCal 5.
NIRCal 5.5 Software Manual Open the property table. Select the desired column. Copy the selection into calibration properties. 84 NIRCal 5.
Chemometrics 3.3.8 PC Data Set Principal Components or Loadings (old name Factors) are artificial difference spectra. All PCs: Number of selected primary PCs. User PCs: use this set as a selection buffer (e.g. for visibility). Calibration PCs: these secondary PCs are used to create the calibration model. Calibration PCs or secondary PCs form a subset of the primary PCs of the calibration. NIRCal 5.
NIRCal 5.5 Software Manual 3.4 Calibration Wizard 3.4.1 Calibration Wizard Menu: Wizard / Calibration Wizard Icon: The quality (robustness, sensitivity, selectivity, portability...) of a calibration for quantification and/or identification mainly depends on the data selections: choice of calibration and validation spectra, wavelength range, data pretreatments and PCs used.
Chemometrics Advanced Settings: remove detected Based upon outlier detection module with c=2.5, removed spectra are listed in Outlier from Cthe calibration protocol. Set and V-Set Not in all cases it is advantageous to use this option. Fast mode Every 5. wavelength value will be used to reduce the calculation time. reduces data Not suggested for the end calculation! Use "Turbo Mode" (M) in plots e.g. points up to 1/5 Loading plot.
NIRCal 5.5 Software Manual The Q-Value is a measure of the quality of the calibrations. It ranges from 0 to 1. The higher the QValue, the better the calibration. Q-Value 1 is theoretical, in practice not achievable, if the value is higher as 0.75 (green), the calibration is acceptable, between 0.5-0.75 (blue) the calibration is useable, but not very accurate. Calibrations with Q-Value below 0.5 (red) should be inspected very carefully before routine use.
Chemometrics It is possible to save or print this list by clicking on the appropriate buttons. The ten best calibrations are kept in the project. The calibration with the highest Q-Value is set active. For this calibration the results are summarized using the Overview. It is possible to inspect the active calibration manually. NOTE It is the responsibility of the user to judge the calibrations and to release them for routine use.
NIRCal 5.5 Software Manual The pretreatments can be selected in the toolbar via Icons as well; or select Pretreatments in the NIR Explorer and use the right mouse button; or select Pretreatments in the NIR Explorer, or in the Pretreated Spectra Plot and use the right mouse button. Removing Pretreatment with Undo Last it is possible to cancel the last pretreatment; with Undo Sequence the whole sequence of pretreatments will be canceled. 90 NIRCal 5.
Chemometrics 3.5.
NIRCal 5.5 Software Manual ** MSC and Mean Centering are also depending on the C-Set spectra selection. NIRCal handles this dependency automatically. The necessary data is stored in the pretreatments itself so they can also operate automatically in the predictor of the application. Legend of formula on the following pages: Capital Letters: Vectors Small Letters: Scalars T: Transmittance or Reflectance A: Absorbance S: Spectrum h: delta X, distance of base point on the x-axis 3.5.
Chemometrics Normalization by Sdev* Normalization to Unit Length* Normalization between 0 to 1* MSC Amplification* MSC Full* Divide by spectrum Standard Normal Variate* Variance Scaling NIRCal 5.
NIRCal 5.5 Software Manual * These pretreatments are wavelength dependent. Normalization by Closure Formula: Martens, Naes 1989, p. 337 Use Reduction of baseline variations. Type The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength. Normalization by Maxima Use Reduction of baseline variations. 94 NIRCal 5.
Chemometrics Type: The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength. Normalization by Sdev Division of each spectrum through the Standard Deviation of its Intensity Value within the Wavelength selection. Use Reduction of baseline variations.
NIRCal 5.5 Software Manual Type The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength. Normalization between 0 to 1 Use Reduction of baseline variations. Type The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength.
Chemometrics Use Can increase baseline effect, can be good for particle size separation. Type This pretreatment is not depending on the calibration wavelengths. MSC Full MSC Multiplicative Scatter Correction (full) Use Eliminates scattering effects. Reduction of baseline variations. Type The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength.
NIRCal 5.5 Software Manual In this way it is possible to enhance the differences in the data set. NOTE Having applied Divide by Spectrum the selected spectrum (spectrum No. 10 in this example) must not be put into the C-Set; its ordinate values will contain 1.0 only. The selected spectrum is copied into the pretreatment once. The selected spectra contains all previous pretreatments. Type This pretreatment is not depending on the calibration wavelengths.
Chemometrics Y_SNV = (y – mean(y)) / Sdev (Y) Use Reduction of baseline variations. Type The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength. Variance Scaling The spectra are divided by the standard deviation vector of the C-Set spectra. It is dependent on the C-Set selection.
NIRCal 5.5 Software Manual 3.5.4 Offset Offset The aim of Offset is to make baseline correction which caused by scattering. Overview of all Offset pretreatments: Original Spectra 100 Subtract DC* Shift negative to zero* MSC Offset* Add Constant NIRCal 5.
Chemometrics Mean Centering Subtract spectrum * These pretreatments are wavelength dependent. Subtract DC The integral of the spectrum is subtracted as a scalar from the spectrum. Formula: Use Baseline correction of spectra. Type: The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength.
NIRCal 5.5 Software Manual Formula: Use For each spectrum the minimum -if it is smaller than zero- is substracted from the spectrum. Type: The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength. MSC Offset 102 NIRCal 5.
Chemometrics Formula: Use Can increase the baseline shift, can be used for particle size separation. Type: The Calibration wavelengths are used when the pretreatment is added; the wavelength range can be changed afterwards in the pretreatment that can be different from the calibration wavelength. Add constant When selecting this pretreatment the constant to be added has to be entered first. e.g. Constant = 0.3 This pretreatment can be used for the correction of systematic errors.
NIRCal 5.5 Software Manual Mean Centering The mean spectrum of the C-Set spectra will be subtracted from each spectra, only the deviation is remaining. NOTE Do not use Mean Centering as the last step in the pretreatment sequence when the Mean Centering has already been activated in the Calculation Parameters dialog box. The Mean Centering defined in the Calculation Parameters box is calculated directly after the pretreatment sequence. Type This pretreatment is not depending on the calibration wavelengths.
Chemometrics Type This pretreatment is not depending on the calibration wavelengths. 3.5.5 Smoothing Smoothing Smoothing is used to reduce the noise level in spectra. However when using smoothing the spectral resolution will be affected. The smoothing function should be chosen according to the original data. NOTE Please choose the smoothing function carefully. No loss of spectral information should appear. Overview of all Smoothing pretreatments: Original Spectra Average 3 points NIRCal 5.
NIRCal 5.5 Software Manual Average Savitzky-Golay 9 points Average 3 points Formula: Type This pretreatment is not depending on the calibration wavelengths. Average 9 points 106 NIRCal 5.
Chemometrics Formula: Type This pretreatment is not depending on the calibration wavelengths. NOTE The information loss can be very high. Average Savitzky-Golay 9 points Savitzky-Golay Smoothing (=zero-order derivative), 9 points, cubic Type This pretreatment is not depending on the calibration wavelengths. 3.5.6 Derivatives Derivatives A derivative is used to reduce baseline effects and to increase smaller absorption peaks (shoulder effect).
NIRCal 5.5 Software Manual Overview of all Derivative pretreatments: Original Spectra 108 1st BCAP 1st Taylor 3 points 1st Savitzky-Golay 9 points 2nd BCAP 2nd Taylor 3 points 2nd Savitzky-Golay 9 points NIRCal 5.
Chemometrics 2nd Taylor 3 Points Segment5 Gap5 3rd Taylor 5 points 1st BCAP Formula: Type This pretreatment is not depending on the calibration wavelengths. 1st Taylor 3 points NIRCal 5.
NIRCal 5.5 Software Manual Formula: Type This pretreatment is not depending on the calibration wavelengths. NOTE More sensitive to noise than Savitzky-Golay 1st derivative, can be combined with smoothing (before or after). 1st Savitzky-Golay 9 points More useful for spectra with very sharp absorption bands with high noise spectra, for detecting very small wavelength shifts.
Chemometrics 2nd BCAP Formula: Type This pretreatment is not depending on the calibration wavelengths. NOTE The result is mainly noisy spectra. 2nd Taylor 3 points Formula: Type This pretreatment is not depending on the calibration wavelengths. NOTE The result is mainly noisy spectra. NIRCal 5.
NIRCal 5.5 Software Manual 2nd Savitzky-Golay 9 points Formula: Type This pretreatment is not depending on the calibration wavelengths. Literature: Savitzky, Golay Analytical Chemistry Vol. 36, No. 8, July 1964, p.1627-1639, "Smoothing and Differentiation of Data by Simplified Least Squares Procedures" NOTE This cited paper contains some errors in some coefficients. 2nd Taylor 3 Points Segment5 Gap5 Formula: See Linear Filter Type This pretreatment is not depending on the calibration wavelengths.
Chemometrics 3rd Taylor 5 points Formula: Type This pretreatment is not depending on the calibration wavelengths. NOTE The result is mainly very noisy spectra. 3.5.7 Transformation Transformation Transformation can be applied to modify the absorption peaks. Tip: for liquids, in case the absorption peaks are not too high (thickness is too high). Not suggested for solids (scattering). Overview of all Transformation pretreatments: Original Spectra NIRCal 5.
NIRCal 5.5 Software Manual 114 Absorbance Absorbance invers Second Derivative / Logarithm Kubelka Munk Square Reciprocal NIRCal 5.
Chemometrics Absorbance It is useful in case the Lambert-Beer law is valid (not too high absorption). Formula: Type This pretreatment is not depending on the calibration wavelengths. NOTE NIRCal 5 calculates maximum 10 absorption units (means: R = 0.0000000001). NIRCal 5.
NIRCal 5.5 Software Manual Absorbance inverse This is simply the inverse function of the ordinate transformation into absorbance; i.e. an absorbance spectrum will be transformed into transmission/reflectance. Formula: -x ilg = 10 Type This pretreatment is not depending on the calibration wavelengths. Second Derivative / Logarithm Formula: Type This pretreatment is not depending on the calibration wavelengths. 116 NIRCal 5.
Chemometrics Kubelka Munk Formula: Type This pretreatment is not depending on the calibration wavelengths. Square Square is a tool for contrast amplification in spectra. Formula: Use Contrast enhancement. Type This pretreatment is not depending on the calibration wavelengths. NIRCal 5.
NIRCal 5.5 Software Manual Reciprocal Formula: Type This pretreatment is not depending on the calibration wavelengths. 3.5.8 Filter Linear Filter Linear filters allow the application of user defined pretreatments. For instance it is possible to apply average smoothing, derivative, low and high band pass filtering. The default linear filter in NIRCal contains a neutral setting of 1, 1. It is best to show examples for the explanation of linear filters.
Chemometrics Linear filters are very useful when spectra recorded with a different resolution have to be treated similarly to original spectra with e.g. only one third of data points (step from NIRFlex N-400 to NIRFlex N-500). For similar prediction results of calibrations smoothing and deriving functions should be adapted. In the following tables the linear filters for the basic smoothing- and derivative functions are summarized.
NIRCal 5.
Chemometrics In this example, 3 primary PCs are necessary, each loading contains spectral information. PCs 4 to 10 are very small and have only noise with no useful information. Check the number of primary PCs with the help of the graphic X-PRESS (in the Overview, or open the graphic in the Menubar : Graphics / X-PRESS) and Loading. Additional tool: The Eigenvalue of the PCs may provide information of the information content of the PCs.
NIRCal 5.5 Software Manual If too many primary PCs are selected, a calibration is overfitted. In this case only the calibration spectra will be identified correctly but not necessarily the validation samples in the project. Example of overfitting: The residuals of the C-Set are much lower, as for the V-Set. 122 If too few primary PCs are selected, the spectra are underfitted, the calibration might not be selective enough for the products. Example of underfitting: NIRCal 5.
Chemometrics There are spectral characteristics, which are still not fitted, the residuum spectra are bigger, as the noise of the instrument. NOTE Avoid underfitting and overfitting! The PCs / Factor Selection Wizard can help with an estimate. 3.7 Adjusting Primary PCs (Calculation Parameters) Menu: Calibration \ Parameter \ Calculation Icon: The primary PCs are edited in the Dialog called Calculation Parameters.
NIRCal 5.5 Software Manual Calculation Data Description [%] Num Primary PCs Advanced Mean centering after Pretreatments Max. Iterations To determine the number of primary PCs with a certain Data description (in %). Available for Cluster and PCR Method only. Change the value at Num Primary PCs to the number defined by the graphic “X-PRESS”. The limit of maximum number PCs is number of CSet spectra. Sets the Mean Centering after finishing Pretreatments ON or OFF.
Chemometrics View Scores Graphic Enlarge the Scores / Scores window in the Overview (3th column, 1st window). There is a clear separation of the 4 different properties spectra according to the PC 1 and 2. There is no separation with the scores of PC 4. PC 1, 2 and 3 are secondary PCs, the PC 4 is not chosen for a secondary PC. Scores against Spectra: Enlarge the Scores window in the Cluster Method Overview (1st column, 2nd window).
NIRCal 5.5 Software Manual Property Box Radii: Enlarge the Property Box Radii window in the Overview (1st column, 3rd window). Property Box Radii represents the scattering of the scores small values (normally below 0.1) mean repeatable scores, big values mean bad repeatability. The scores of PC 4 are not repeatable, PC 4 can not be used as calibration PC. Additional tool: 126 NIRCal 5.
Chemometrics The Property Score Disorder values show how effective a particular PC separates different properties (substances) from each other. By scanning the score values in one direction of a PC and counting the changes between the membership of A or B, the disorder value is achieved. If a PC completely separates all calibration properties, the smallest disorder value is: [the total number of calibration properties-1]. PCs with small disorder values are possible calibration PCs.
NIRCal 5.
Chemometrics 3.9 Secondary PC Selection The number of secondary PCs is limited by the number of primary PCs. From this number of PC any number can be selected using the NIR-Explorer or the Edit dta Set dialog. NOTE In PLS a secondary PC selection like in the PCR or CLU is not possible, NIRCal uses all PCs from PC 1 to the last selected PC as secondary PCs. 3.9.1 Secondary PC Selection using NIR-Explorer By double clicking on Calibration PCs, the selection dialog appears Steps sequence: 1.
NIRCal 5.5 Software Manual In the calibration the selection is shown. 3.9.2 Secondary PC Selection using Edit Data Sets Dialog Click on the icon: or open the Edit Data Sets dialog under the Menubar: Calibration / Change data Sets / Edit Data Sets. Select Calibration PCs from the drop down menu. Select Custom, edit the selection and press Apply. NOTE After setting the secondary principal components, the calibration should be recalculated. 130 NIRCal 5.
Chemometrics 3.10 PCs (Factor Selection Wizard) Menu: Calibration / Change Data Sets / PC Icon: Under actual the current settings for primary and secondary PCs (Factors) are displayed. Under estimated the wizard suggest an optimized selection. The selections are changed manually. See: Adjusting Primary PCs and Adjusting Secondary PCs NOTE The estimated selections can only be smaller then the actual selections in the current project.
NIRCal 5.5 Software Manual Limits Residual Scores The maximum residual, allowed for the application is determined by two (2) times the maximum residual of the calibration set. The default value is 2 and can be edited by the user. The calibration spectra "maximum and minimum Scores x Blow Up limit" are used for possible score outlier detection in the prediction protocol. Possible outliers are searched with the secondary PCs. The default value is 1.05 and can be edited by the user. 3.11.
Chemometrics Formula 2; Blow Up limit = 1 Formula 2; Blow Up limit = 2 Reducing the radii results more selective calibration but increases the danger to get separated cluster for the same substances (Cluster / Property> 1). 3.12 Outlier Detection Menu: Calibration / Outlier Detection / Advanced Icon: Outliers are spectra, that differentiate strongly from spectra of the same class. They can be detected visually, check the spectra in the menu Graphics, in the calibration curve or in e.g.
NIRCal 5.5 Software Manual This calculations can be made for the C-Set and/or V-Set as selected by the user. The confidence interval e.g. for 99 % level (mean value +/- c * stdev) can be determined according the number of C-set spectra: Calculate c. Press Recalculate beside the 4 different types of outliers to start the calculations. The found outlier type spectra are marked red after pressing Recalculate." By pressing Plot, the graphic is opened with scatter plot for easier spectra selection.
Chemometrics Spectrum No. 16 in the calibration set has the max. residual value (0.00449) and defines the limit for the calibration and application: Max. allowed residual = Max. C-Set residual * 2 2: default Residual Blow up, can be adjusted by the user. In this example, these spectra are not real residual outliers for NIRCal. In case these spectra would be real outliers, they can be selected as C-set spectra to entlarge the limits or eliminated from the calibration (U-Set = unused set).
NIRCal 5.5 Software Manual 3.13 Q-Value Menu: Calibration / Q-Value Protocol Icon: In NIRCal calibrations can be rated via the Q-Value. The Q-Value sums up all important criteria. The Q-Value is part of the calibration protocol, there is no separate calculation necessary After several calibration optimization and running the automatic calibration module (Step 2: Calibrate), there are several calibrations in the project. Sort the calibrations with a click on the Name or Q-Value.
Chemometrics 3.15.1 Procedure of Spectra Import NIRCal 5 can work as File- and as Database - oriented software. In case the File - oriented mode is used, the projects can be opened and stored as ".nir" Files (as NIRCal V 4.21), all function of editing and deleting of names, properties and values is allowed, also the use of "Find and Replace" module (like in NIRCal 4.21). NOTE Calibrations stored in file format cannot be used together with NIRFlex N-500.
NIRCal 5.5 Software Manual After conversion the spectra are available. NOTE E.g. each spectrum will have 1501 data points between 10.000 and 4.000 cm-1. In case some data are missing in the original spectra, the last measured value will be repeated, eg. by spectra measured between 10.000 and 4.500 cm-1, the value at 4.500 cm-1 will be repeated till 4.000 cm-1. To keep the spectrum as a constant graph (better for derivatives).
Chemometrics NOTE Calibration wavelength: deselect wavelength range, which were not measured with the original spectra. By several instrument spectra in the same project use the smallest measured range. NIRLab spectra have not integer wavenumber; the wave selection is after conversion rounded to integer. In case the calibration was calculated with a special wave selection, it is suggested to make several trials to find the best wavelength selection.
NIRCal 5.5 Software Manual but a spline function. 3.16 Calibration Handling In a NIRCal project several calibrations can be handled. Their status can be different according the project is stored as file or into the database. The calibrations, stored in file format are always editable. The calibrations which are stored in the database, underlying the Lifecycle and can have "Created" with "editing" or "Approved" status with "read-only" mode.
Chemometrics 3.16.1 Calibrations without Lifecycle Each new project in NIRCal 5 has an "unnamed" or master calibration, which is created automatically by importing spectra into the empty project. This calibration and every calibration created with the menu "Calibration / New" has an "all" selection for the C-Set spectra, wavelength and property selection automatically and has "editable" status.
NIRCal 5.5 Software Manual Lifecycle: Edit A calibration stored in the DB has the "created" status and " read-only" mode. The active calibration can be edited with the Lifecycle / Edit. There is no possibility to edit an approved calibration. NOTE If the first calibration in the project is approved, this calibration can never be extended with new spectra. Work around: use the spectra GUIDs to create the same project, the calibration protocol can be a valuable help.
Chemometrics Lifecycle: Copy A copy of the active calibration can be created with this LC function. There is a request for calculation in case after a modification the calculation is not yet made. The copy is automatically saved in the DB and set to active with the status: Created. The copy has the same GUID, as the original calibration, but a higher version number. For the copy of a calculated calibration the Prediction Protocols are available. Each calibration can be copied.
NIRCal 5.5 Software Manual NOTE It is not possible to delete the first master calibration. Calibrations, which are embedded in an application, can never be deleted. NOTE Calibrations, which are already used for sample measurement in the application, can be never deleted. Optimize the Calibration In order to optimize a calibration manually, the first calibration can be edited or copied: Lifecycle / Edit or Copy.
Chemometrics Extend the Calibration In case during the external validation there are unacceptable differences -property value or residual-, the calibration should be extended with the spectra of the external validation samples. These spectra are stored in the DB. The necessary steps are: editing the property values in the Manager Console / Sample Manager (see NIRWare manual); import the spectra into the original NIR-project; extend the calibration.
NIRCal 5.
Chemometrics Row 32 34 36 37 38 40 41 42 44 45 48 49 51 52 53 Name Spectra unused (USet) Validation Method C-Set Spectra Instrument type / serial y-Unit / Measurements / Scans V-Set Spectra Instrument type / serial y-Unit / Measurements / Scans Spectra Resolution Spectra y-Unit Wavelengths Project Set Wavelengths Calibration Set Number of Data Pretreatments Data Pretreatment Sequence (short) Data Pretreatment Sequence (detailed) NIRCal 5.
NIRCal 5.5 Software Manual Row 56 57 58 59 60 62 63 64 65 66 68 69 72 73 75 76 77 78 79 80 81 148 Name Method Max Iterations Mean Centering Number of Primary PCs Secondary/Calibration PCs Blow Up Parameter Residual Blow Up Score Blow Up Radii Blow Up Radii Formula Max C-Set Spectra Residual Max Allowed Residual for Calibration Description Selected calculation method / algorithm Calculation steps before default stop (max.
Chemometrics Row 84 85 Name Property Overview Total Sum Description Number of clusters and selected spectra Num Cluster = Total number of clusters, should be equal to the number of calibration properties Num Cluster = should be 1, the spreading of C-and V-Set 86 1st Property spectra about 2/3-1/3 Num Cluster = should be 1, the spreading of C-and V-Set 87 2nd Property spectra about 2/3-1/3 Num Cluster = should be 1, the spreading of C-and V-Set 88 3rd Property spectra about 2/3-1/3 90 Property Separation
NIRCal 5.5 Software Manual Row 104 105 106 Name 1st Property 2nd Property 3rd Property Description Normally all are zero Normally all are zero Normally all are zero NOTE Number of cluster of each property must always be 1. Number of any outliers in the C-and V-Set must always be 0. 109124 Explanation of the legend Short form Some statistics: 128133 136141 150 C-Set Spectra Residual C-Set Spectra Radii Statistic of residual: min.-max.
Chemometrics Information of the C-Set and V-Set spectra: Row Name 145166 Validation for C-Set Spectra 167 Total No.of Spectra with X 171181 Validation for V-Set Spectra 182 Total No.of Spectra with X Description List of C-Set spectra with predicted and original property, radii, residual. Number of possible outliers should be 0. .The last column shows the GUID of each spectra. It should be all type zero. List of V-Set spectra with predicted and original property, radii (0), residual.
NIRCal 5.5 Software Manual The spectrum 2B is not a real outlier, but spectrum 1A is dangerous: it is better to select into the CSet. 3.17.2 Calibration Protocol Quantitative Menu: Calibration / Calibration Protocol Calculate or Show Icon: Short Key: F8 The calibration protocol is an important validation report giving all information about the data selection and result of the chemometrics calculation. The calibration protocols are stored in the DB (or .nir project file).
Chemometrics Result of the calculation Row 59 60 61 63 64 Name Blow Up Parameter Residual Blow Up Score Blow Up Max C-Set Spectra Residual Max Allowed Residual for Calibration 67 Q-Value V5 68 Validation Method 70 C-Set Residual too big* 71 V-Set Residual too big* 73 Num Properties 74 Rel.
NIRCal 5.5 Software Manual Property statistics Row 84 85 Name C-Set BIAS V-Set BIAS 86 C-Set SEE (SEC) 87 V-Set SEE (SEP) 88 Consistency 90 C-Set Regression Coefficient 91 V-Set Regression Coefficient 92 C-Set Regression Intercept V-Set Regression Intercept C-Set Regression Slope 93 94 154 Description Always zero by definition. Average deviation between the predicted = NIR and original = lab method values. Should be as close to zero as possible (no systematic deviation).
Chemometrics Row 95 Name V-Set Regression Slope 97 98 99 100 101 102 103 104 106113 C-Set Orig. min. V-Set Orig. min. C-Set Orig. max. V-Set Orig. max. C-Set Orig. mean. V-Set Orig. mean. C-Set Orig. sdev V-Set Orig. sdev 115 C-Set RSS 116 V-Set RSS 118 C-Set Durbin-Watson 119 C-Set Durbin-Watson in range 1.5 to 2.5 V-Set Durbin-Watson 120 121 123 124 125 126 128 129 131 132 V-Set Durbin-Watson in range 1.5 to 2.5 C-Set Resid. min V-Set Resid. min C-Set Resid. max V-Set Resid.
NIRCal 5.5 Software Manual Explanation of V-Set t-test: Original property and the Predicted property are compared via a paired t-test to show if the results are statistically equivalent. where: e is the mean residual (original – predicted property); s d is the standard deviation of the residuals. Example: The two-sided critical value of students’"t" e.g. at 5% significance level for n-1 degrees of freedom is protocoled as V-Set t (5%,n-1) and the calculated t as V-Set t-value.
Chemometrics 3.17.3 Calibration Protocol Quantitative CV Menu: Calibration / Calibration Protocol Calculate or Show Icon: Short Key: F8 The calibration protocol is an important validation report giving all information about the data selection and result of the chemometrics calculation. The calibration protocols are stored in the DB (or .nir project file). Explanation of the content of the calibration protocols.
NIRCal 5.
Chemometrics Row 47 50 51 55 56 57 60 61 62 63 64 66 67 68 70 71 Name Spectra y-Unit Wavelengths Project Set Wavelengths Calibration Set Number of Data Pretreatments Data Pretreatment Sequence (short) Data Pretreatment Sequence (detailed) Method Max Iterations Mean Centering Number of Primary PCs Secondary/Calibration PCs Blow Up Parameter Residual Blow Up Score Blow Up Max C-Set Spectra Residual Max Allowed Residual for Calibration Description Measuring principle Measured wavelength range Selected wavel
NIRCal 5.5 Software Manual Row 82 Name Validity* 83 Comparability* 84 Precision* 85 Weighted Accuracy* Description The V-Set regression coefficient should be near to 1: 1-VsetRegr. Validity should be close to 0 C- and V-Set should have similar high regression coefficient of prediction: Abs(CsetRegr-VsetRegr).
Chemometrics Row 98 99 100 101 103106 108 110 111 113 114 117 Name Description Statistics of the original property values (labor method, X-axis) C-Set Orig. min. The smallest property value in the C-Set C-Set Orig. max. The highest property value in the C-Set C-Set Orig. mean. The mean property value of the C-Set C-Set Orig. sdev The standard deviation of the property values in the C-Set C-Set Pred. Statistics of the predicted property values (NIR, Y-axis).
NIRCal 5.5 Software Manual Result of the CV-steps Row Name Description 194Validation for CV-Group Name, number of spectrum, original, predicted property and the 253 Spectra difference (Orig-Pred); an X for "extrapolation", in case the value is outside the calibration range; residual value and an X for "redidual too big",in case the value is outside the allowed range; spectrum GUID 3.17.
Chemometrics Important: The statistics only gives relevant estimates of calibration performance if the prediction protocol is made using an independent test set. The statistics reported here can deviate from what is reported in the Original vs Predicted Property plots of two reasons: 1) outliers are not included, and 2) the linear regression to find slope and offset is made using the predicted values as the independent variable.
NIRCal 5.5 Software Manual RMSEP (Root Mean Square Error of Prediction): The RMSEP is an estimate of the random and systematic errors in the predictions. SEP (Standard Error of Prediction): The SEP is an estimate of the random error. Slope and offset: The slope and offset of the regression line are both indicated in the figure above.
Chemometrics Prediction Protocol of qualitative Calibration The prediction protocol (SIMCA and Cluster) can be configurated: LINK: Cluster Prediction Protocol.
NIRCal 5.5 Software Manual On the top of the protocol about some general information about the calibration, the calibrated properties are listed and the filter setting are visible. The calibration max. allowed residual is important to note. Each spectra name is listed with the number. Behind the number there is the symbol, which identification case it is. The actual residual will be compared with the allowed max.
Chemometrics In case the predicted and original properties are different, it is a wrong identification: spectra 73-77 and 83. These spectra are in a false cluster, but will not be identified, while the residuals are much higher (0.0042) as the allowed residual (0.0002). Correct identifications -case 3- and not identified unknown -case 7- are less important, deactivating e.g. case 3 and 7 will give a shorter protocol. Especially cases 1 and 5 are critical.
NIRCal 5.5 Software Manual NOTE The warning: incompatible spectra means, that the number of data point or the wavelength range of the calibration and predicted spectra are not matching because of different resolution or different instrument type. 3.18 Matrices 3.18.1 How to display matrices Each matrix can be displayed in different plots. Available views are: 1D Scatter 2D Line 2D Scatter 2D Combined Scatter 3D Scatter 3D Surface Table Export: Export the matrix to a *.dat File.
Chemometrics 1. Select Matrices in the NIR-Explorer tree 2. then select the two matrices in the NIR-Explorer 3. click the right mouse and then 2D-Scatter NOTE To save such a created plot a workspace can be saved and reused within other projects. 3.18.2 Calibration Residual Limits Description Use Method Matrices ID Tip Details Related Topic The min. and max. residual is depending on the number of primary PCs. The maximum allowed residual of the calibration is valid for the application.
NIRCal 5.5 Software Manual 3.18.4 Calibration Score Limits Description Use Method Matrices ID Tip Details Related Topic Allowed minimum and maximum score values of the calibration. Score outlier detection in the validation set, especially in Cluster calibration. PCR / PLS / Cluster (CLU) / SIMCA 45 Only scores outliers according the secondary PCs are important. Scores The allowed score limits for the validation: 1.05 x min. and max. scores of the C-set spectra. The default blow up limit of 1.
Chemometrics It is possible, that different numbers of PCs are ideal for a certain parameter. In this situation the different secondary PCs should be selected, the calibrations recalculated and compared. Very low consistency indicates an overfitting (too many secondary PCs used). 3.18.7 Correlation Spectra Description Use Method Matrices ID Tip Details Related Topic Called also as synchronous 2D correlation spectra. Shows the correlating spectra.
NIRCal 5.5 Software Manual 3.18.10 Description Use Method Matrices ID Tip Details Related Topic 3.18.11 Description Use Method Matrices ID Tip Details Related Topic 3.18.12 Description Use Method Matrices ID Tip Details Related Topic 3.18.13 Description Use Method Matrices ID Tip Details Related Topic 172 CV C-Set PRESS CV C-Set PRESS is the Predicted Residual Error Sum Square for the samples in case they are in the C-Set of the calibration. To estimate the number of PCs.
Chemometrics 3.18.14 Description Use Method Matrices ID Tip Details Related Topic 3.18.15 Description Use Method Matrices ID Tip Details Related Topic 3.18.16 Description Use Method Matrices ID Tip Details Related Topic 3.18.17 Description Use Method Matrices ID Tip Details Related Topic CV Property Residuum CV Property Residuum is the difference between the original and CV predicted property value. It gives information of outlier sample. PCR / PLS 67 It should be as close to zero as possible.
NIRCal 5.5 Software Manual 3.18.18 Description Use Method Matrices ID Tip Details Related Topic CV Regression Coefficients[1] t-test Uncertainty testing in regression model. Used for selecting most relevant and stable wavelength. PCR / PLS 92 Explanation: t = Abs( xm ) / sx * sqrt(g) where t = CV Regression Coefficients[1] t-Test; xm = Regression Coefficients[1] (of the final calibration); sx = CV Regression Coefficients[1] Sdev; g = number of CV groups.
Chemometrics 3.18.20 Description Use Method Matrices ID Tip Details Formula Related Topic 3.18.21 Description Use Method Matrices ID Tip Details Related Topic 3.18.22 Description Use Method Matrices ID Tip Details Related Topic 3.18.23 Description Use Method Matrices ID Tip Details Related Topic CV SECV CV SECV: Standard Error Cross Validated The CV selects the number of secondary PCs, where CV SECV has a minimum. PCR / PLS 72 The secondary PCs selection is indicated with red color.
NIRCal 5.5 Software Manual 3.18.24 Description Use Method Matrices ID Tip Details C-Set BIAS Bias provides information on the average deviation of the predicted values from the true values. BIAS of the calibration set spectra. To compare with the V-Set Bias. PCR / PLS 17 The C-Set Bias is zero by definition. Available in the calibration protocol. Formula Related Topic 3.18.25 Description Use Method Matrices ID Tip Details Related Topic 3.18.
Chemometrics The optimum number of PC is always given by the smallest number of PC where the PRESS function for the calibration and for the validation set is approximately equal and minimal. If the error of the prediction diminishes only very slightly by the addition of another PC, it is not worth while to add that PC. This is because higher PCs with little influence will often result in a poorer reproducibility or stability of the calibration. 3.18.
NIRCal 5.5 Software Manual The regression curve can be described better with the slope (a) and intercept (b): 3.18.30 Description Use Method Matrices ID Tip Details Related Topic 3.18.31 Description Use Method Matrices ID Tip Details Related Topic 3.18.32 Description Use Method Matrices ID Tip Details f(x)= ax + b C-Set Regression Intercept Intercept of the regression line equation of the calibration set.
Chemometrics The SEC and SEP provide the magnitude of the standard deviation for the calibration set and the independent validation set. The two values should be as small as possible, but they are likely to be comparable with the standard deviation of the conventional laboratory method. With an acceptable calibration, the two values are also roughly equal (Consistency: around 100).
NIRCal 5.5 Software Manual 3.18.35 Description Use Method Matrices ID Tip Details Related Topic 3.18.36 Description Use Method Matrices ID Tip Details Related Topic 3.18.37 Description Use Method Matrices ID Tip Details Related Topic 3.18.38 Description Use Method Matrices ID Tip Details Related Topic 3.18.
Chemometrics 3.18.40 Description Use Method Matrices ID Tip Details Related Topic Durbin-Watson Factor Statistics Statistical test for the determination of the linearity. Addition information for statistics like regression slope and intercept. PCR / PLS / Cluster (CLU) / SIMCA 62 The C-Set and V-Set selection has a big influence on the Durbin-Watson value.
NIRCal 5.5 Software Manual The spectra are internal for the Durbin-Watson calculation ascending sorted according the original property values of each properties. By the same property values the original sequence will be kept. C-Set / V-Set : the dw will be calculated separately. If the V-Set is empty dw = 2 protocoled. Durbin-Watson test is available in NIRCal: the calibration protocol of quantitative calibration has the dw value for C-Set and V-Set; the dw values are in the matrices. 3.18.
Chemometrics 3.18.42 Instrument Description Use Method Matrices ID Tip Details Related Topic Contains the used instrument index. For 1D-scatter and dependency plots. Can be used for Outlier selection. PCR / PLS / Cluster (CLU) / SIMCA / MLR 104 Description Use Method Matrices ID Tip Details Related Topic Contains the used instrument index. For 1D-scatter and dependency plots. Can be used for Outlier selection. PCR / PLS / Cluster (CLU) / SIMCA / MLR 105 3.18.
NIRCal 5.5 Software Manual The formula of spectra reconstruction: where: I n (k) : : v in : U i (k) : Rn: spectrum ( n: number of spectra, k: wavenumber); mean spectrum; scores (i: number of PC); PCs / loadings; residuum spectrum. A more detailed formula for the matrix is: Eigenvalue. Minimum number of loading is one, the maximum number of PCs is never higher than the number of C-Set spectra or C-Set Wavelengths. See the PCs under the menubar: Graphics / Loadings. 3.18.
Chemometrics 3.18.46 Description Use Method Matrices ID Related Topic Original Spectra Original Spectra in the project (Independent variable) Overview of all spectra in the project. all 0 Pretreated Spectra Original spectra are plotted as the intensity values (reflectance, transmittance, transflectance) were measured according the wavelengths. Available in the Menubar: Graphics / Spectra / Original. The values are also available in table form. 3.18.
NIRCal 5.5 Software Manual 3.18.48 Description Use Method Matrices ID Tip Details Related Topic PCR B-Matrix Shows the influence of the PCs to the property value. Useful for secondary PC selection. PCR 7 Select the PCs with high absolute correlation value to optimize the prediction. Also known as correlation coefficient or B-matrix. Depends only from the number of primary factors. The selected secondary PCs take no effect on the PCR B-matrix.
Chemometrics 3.18.50 Description Method Matrices ID Tip Details Related Topic 3.18.51 Description Use Method Matrices ID Tip Details Related Topic Pretreated Property A copy of Original Property all 3 Editing is not allowed. In a later version there will be special property pretreatments. Original Property Pretreated Spectra Original spectra with the selected data pretreatments applied. Looks at the effects of the various data pretreatments.
NIRCal 5.5 Software Manual 3.18.52 Property Description Use Method Matrices ID Tip Details Related Topic Contains the property index. For 1D-scatter plots. PCR / PLS / Cluster (CLU) / SIMCA / MLR 84 Description Use Method Matrices ID Tip Details Related Topic Contains the property index. For 1D-scatter plots.
Chemometrics 3.18.54 Description Use Method Matrices ID Tip Details Related Topic 3.18.55 Description Use Method Matrices ID Tip Details Related Topic 3.18.56 Description Use Method Matrices ID Tip Details Related Topic 3.18.57 Description Use Method Matrices ID Tip Details Related Topic Property Box Center The center position (expressed as score) of the smallest possible box in the score space that contains each C-Set spectra of a property.
NIRCal 5.5 Software Manual 3.18.58 Description Use Method Matrices ID Tip Details Related Topic 3.18.59 Description Use Method Matrices ID Tip Details Related Topic 3.18.60 Description Use Method Matrices ID Tip Details Related Topic Property F-Test forward Significance of additional PCs. For secondary principal component selection.
Chemometrics 3.18.62 Description Use Method Matrices ID Tip Details Related Topic Property Residuum The difference between the original property and the predicted property. See where (property, spectra) the major differences are. PCR / PLS / Cluster (CLU) / SIMCA 11 Original Property,Predicted Property Qualitative calibrations The predicted property value depends on the cluster, in which the spectrum is located. For the property residuum, only a value of 0 is acceptable.
NIRCal 5.5 Software Manual 3.18.64 Description Use Method Matrices ID Tip Details Related Topic Property Score Disorder Property Score Disorder: number of different property spectra according the scores of different PC. Useful for secondary PCs selection in higher dimensional space (> 3). Cluster (CLU) 57 The smallest number of property score disorder = (number of selected property -1). This value indicates a clear separation of the different properties.
Chemometrics 3.18.68 Q-Values Description Value between 0 and 1. 0 means a bad 1 would be a good calibration. But 1 cannot be reached. Q-Values depending on the number of PCs. There is a warning limit for the stored calibration: 0.8 for qualitative 0.6 for quantitative Select the number of secondary PC according the highest Q-Value. PCR / PLS / Cluster (CLU) / SIMCA 64 In generell: the highest the Q-Value the better the calibration.
NIRCal 5.5 Software Manual Q-Value V5: Q = 1 / ( 1 + sum (weights * value)) NOTE The weights are changed between the NIRCal 4.21 Q-Value calculation weights, so the NIRCal 5 QValues are differing against NIRCal 4.21. The Q-Value calculation is not changed for the Cluster calibration between NIRCal 4.21 and NIRCal 5.
Chemometrics 3.18.70 Description Use Method Matrices ID Tip Details Related Topic Reconstructed Spectra Reconstructed pretreated spectra with the number of primary PCs. See how good the reconstruction works. PCR / PLS / Cluster (CLU) / SIMCA 8 It should be as similar to the pretreated spectra as possible. Reconstructed spectra are plotted as the intensity values after the used pretreatments according the wavelengths after the reconstruction of the PCA using the primary PCs.
NIRCal 5.5 Software Manual Y = (X-X mean) * P + Y mean Where: Y X X mean Y mean P predicted property value pretreated spectrum Mean of C-Set spectra ("C-Set Mean Spectrum") Mean Property value of the C-Set spectra ("C-Set Mean Property") Regression Coefficients The Regression Coefficients can be opened as Excel table in the Regression Coefficients plot pressing "G". The value of "Y mean" can be found in the Matrices: "C-Set Mean Property". 3.18.
Chemometrics There is a clear separation of the 4 different properties spectra according to the PC 1 and 2. There is no separation with the scores of PC 4, this PC is necessary for the acetone spectra. Here PC 1, 2 and 3 are secondary PCs, the PC 4 is not a secondary PC. The separation with 3 selected calibration PCs is visible in a 3 D graphics. NIRCal 5.
NIRCal 5.5 Software Manual 3.18.76 Description Use Method Matrices ID Tip Details Related Topic 3.18.77 Description Use Method Matrices ID Tip Details Related Topic Score Adjacency Distance in score space between each spectra against all others. The neighborhood relationships between the spectra for all PCs at once. For special interest with the Cluster method. PCR / PLS / Cluster (CLU) / SIMCA 40 Look at it in a 2D-Plot in top view to see hidden effects. Secondary PCs take an effect.
Chemometrics 3.18.79 Spectra Property Index Description Each spectra is assigned to exactly that property index with the 1 (one) in the Original Property matrix. The property index value is in the range from 0 to the number of properties minus 1. Use it to select all spectra with the same property (see Tip). Cluster (CLU) / SIMCA / PCR / PLS / MLR 48 Open it as 2D-plot, PopUp Menu -> Options -> Show All Values, Set in PopUp Menu -> Transpose Data.
NIRCal 5.5 Software Manual 3.18.81 Spectra Residuals Description Use Method Matrices ID Tip Details Formula The RMSD (Root Mean Squared Deviation) of the spectra residuum. To look at residual outlier. PCR / PLS / Cluster (CLU) / SIMCA 41 Special tip to optimize the calibration The secondary PCs take no effect. Related Topic X-PRESS, Spectra Residuum Indicates the difference of the pretreated spectra and the reconstructed spectra with the number of primary PCs.
Chemometrics principal components has been selected. These difference spectra should have only noisy signal, but no unfitted peaks. 3.18.84 Description Use Method Matrices ID Tip Details Related Topic Description Use Method Matrices ID Tip Details Related Topic Spectrum Nearest Neighbor Spectrum Nearest Neighbor is the smallest distance in the score plots between two spectra. Check, which spectra have big deviation. Similar small distances indicate good repeatability and reproducibility.
NIRCal 5.5 Software Manual 3.18.85 Description Use Method Matrices ID Tip Details Related Topic Description Use Method Matrices ID Tip Details Related Topic 3.18.86 Spectrum Nearest Neighbor Index Spectrum Nearest Neighbor Index contains the spectrum index of the nearest spectrum in the calibration. Best shown as 1D-Scatter-Plot for selected spectra. This matrix is related to "Spectrum Nearest Neighbor" which contains the Mahalanobis Distance between nearest spectra pairs.
Chemometrics 3.18.88 Description Use Method Matrices ID Tip Details V-Set BIAS BIAS of the validation set spectra. Judge the V-Set results. PCR / PLS 26 Should be as close to zero as possible. This is a value for accuracy. Available in the calibration protocol. Formula Related Topic C-Set BIAS The V-Set Bias provides information on the average deviation of the predicted values from the true values.
NIRCal 5.5 Software Manual 3.18.90 Description Use Method Matrices ID Tip Details V-Set Regression Coefficient Validation Set Regression Coefficient of Original Property and Predicted Property (also known as correlation coefficient or Pearson's correlation coefficient) To compare with the C-Set regression Coefficient PCR / PLS 27 Should be as close to 1 as possible. Visible on the calibration curve and in the calibration protocol.
Chemometrics 3.18.91 Description Use Method Matrices ID Tip Details Related Topic 3.18.92 Description Use Method Matrices ID Tip Details Related Topic 3.18.93 Description Use Method Matrices ID Tip Details V-Set Regression Intercept Validation Set Regression Intercept of Original Property and Predicted Property To compare with the C-Set Regression Intercept PCR / PLS 28 A value around zero is expected for a good calibration. A better description of the V-Set regression coefficient.
NIRCal 5.5 Software Manual 3.18.94 Description Use Method Matrices ID Tip Details Related Topic 3.18.95 Description Use Method Matrices ID Tip Details Related Topic 3.18.96 Description Use Method Matrices ID Tip Details Related Topic 206 V-Set Spectra Residuum Max Shows the maximum residuum of the V-Set spectra using different number of PCs in the selected wavelength range. To find the optimum number of primary PCs.
Chemometrics 3.18.97 Description Use Method Matrices ID Tip Details Related Topic 3.18.98 Description Use Method Matrices ID Tip Details Related Topic 3.18.99 V-Set Std Pred Property Standard deviation of the predicted property values of the validation set spectra (standard deviation of the whole predicted validation range, Y-axis). To compare with the V-Set Std Orig Property PCR / PLS 24 Gives information about the size of the predicted validation range.
NIRCal 5.5 Software Manual Interpretation: difference between pretreated spectrum and reconstructed spectrum will be summed up and squared. It is with the: 1. PC: X-PRESS 1= [pretreated spectrum-(mean spectrum + score 1 x PC 1)]2 2. PC: X-PRESS 2= [pretreated spectrum-(m.s. + score 1 x PC 1+ score 2 x PC 2)]2 3. PC: X-PRESS 3= [pretreated spectrum-(m.s. + score 1 x PC 1+ score 2 x PC 2 + score 3 x PC 3)]2 etc.
Chemometrics Related Topic Loadings, Y-Scores Matrices of the final PLS calculation: Spectra are decomposed to Scores and Loadings. Properties are decomposed to Y-Scores and Y-Loadings. Y-Scores are predicted from the Scores and Properties are predicted from the Y-Scores. 3.19 NIRCal Configuration Options 3.19.1 Configuration Dialog Menu: Edit / Options Icon: Different NIRCal functions can be configured here individually for each NIRCal Windows user account.
NIRCal 5.5 Software Manual Settings Short Popup Menus Sound Events Backup Files before Safe plot wave axis in descending order flip Original vs Predicted in Property plot Database Terminology Displays short pop-up menus (right mouse button). It is recommended to deactivate so that the long, extended pop-up menu is available. Activates acoustic messages/sounds about the actual status of NIRCal (e.g. loading spectra, calculating PLS, ....) Create a backup copy before a file is saved.
Chemometrics The selected topics will be documented in the project journal. It is an important feature for the audit trail, therefore the selection should be done carefully. NOTE The small buttons on the top right of a frame resets all values of the frame to the default setting. NOTE This feature was used in the file-mode. In database mode there is as System Logger in the Administrative Tools of the NIRWare Management Console.
NIRCal 5.5 Software Manual 3.19.4 Calibration Defaults Edits the default parameters for calibrations. Settings Method Spectra Selection Method Percent Spectra in Calibration Set CLU or MLR, PCR, PLS. Default: PCR Monte Carlo or Sequence. Default: Sequence between 0% and 100%. Default: 66.66% (2/3) Calculation Calculate all Outliers Create Spectra V-Set if empty show Cross Validation reminder dialogs. Directs to calculate all outliers.
Chemometrics 3.19.5 Tables Sets/changes the parameters for the Table window. NOTE The small buttons on the top right of a frame resets all values of the frame to the default setting. General Initial Zoom default Column Width Show Gridlines Audit Column Heading default 80% default 3250 Enable / Disable, default OFF Enable / Disable, default ON Fixes the column heading, default OFF Font Name Size default Arial default 10 3.19.6 2D-Plots Sets/changes the parameters for a 2D graphic window. NIRCal 5.
NIRCal 5.5 Software Manual NOTE The small buttons on the top right of a frame resets the all values of the frame to default setting. General Snap X Snap Y Anti-Aliasing Turbo Points Linewidth Default Linecolors None Default Linecolors Sets Default Linecolors Cycle Default Linecolors Property Snaps the zooming so that there is always a value at the beginning and at the end of the x-axis, default OFF.
Chemometrics Line Colors: 02 Line Color = 1st color; 03 Line Color = 2nd color. Font Sizes Font Drop Down List Title Subtitle Description Label Axis Defines the Font used in any 2D-Plot, default Arial Defines the size of the font used for titles, default 0,6. Defines the size of the font used for subtitles, default 0,3. Defines the size of the font used for descriptions, default 0,15. Defines the size of the font used for labels, default 0,15.
NIRCal 5.5 Software Manual Display Precision Data Point Radius Data Point Slices Data Point Stacks Defines the radius in generalized units for displaying data points in the 3DPlot, default 2. Defines the number of slices in generalized units for displaying data points in the 3D-Plot, default 11 Defines the number of stacks in generalized units for displaying data points in the 3D-Plot, default 7 Data Point Display Semisolid (0-1) Grid Pins Displays the "spheres" semisolid (transparent), default: off.
Chemometrics 3D without boxes 3.19.8 System Modules Sets the path for the system modules. NOTE The path should be changed only for your own created or modified modules: it is not recommended to use it. 3.19.9 Calibration Protocols The content of the full calibration protocol can not be defined, this field has no function anymore. NIRCal 5.
NIRCal 5.5 Software Manual 3.19.10 Directories The default paths for various files can be set individually. NOTE It is NOT suggested to change the path for Modules and Data Exchange Filters! 218 NIRCal 5.
Chemometrics 3.19.11 Cluster Prediction Protocol Sets/changes the filter for the Prediction Protocol of Cluster and SIMCA calibrations. Filter Settings not in a cluster (!) false identified (?) identified (*) not identified CLU OK (%) not identified CLU BAD (&) not identified known (-) not identified unknown (=) residual is within limits, but the distance is higher than allowed (spectrum is not in a cluster), default: on.
NIRCal 5.5 Software Manual Case 1 2 3 4 5 6 7 Group not in a cluster false identified identified not identified CLU OK not identified CLU BAD not identified known not identified unknown Symbol ! ? * % & = Residual OK OK OK not OK not OK not OK not OK Distance not OK OK OK OK OK not OK not OK Name/Property not OK not OK OK OK not OK OK not OK Especially cases 1 and 5 are critical. By case 5 the residual relationship (actual against allowed) should be controlled. Case 2 is inacceptable.
Chemometrics Close Project Closes the project. The following message appears: It is recommended to press „Yes”. Database Open Project Menu: File / Database / Open Project... Icon: Opens a NIRCal Project from the NIRWare Database. NIRCal 5.
NIRCal 5.5 Software Manual Save Project Menu: File \ Database \ Save Project As... Icon: Saves the active project to the NIRWare Database. This function is needed to save a NIRCal-Project (opened from file *.nir) to the NIRWare Database. Saving the spectra with the setting : [x] save Spectra (incl. properties and concentrations) will force a duplicate spectra check.
Chemometrics Save Project As... Saves the active project to the NIRWare Database with a new Name This function is needed: To save a project if the spectra are loaded from the database; To create a copy of a NIRCal-Project (opened from database) with another name. Not recommended to use. Note: the calibrations are not copied; they are linked to the project. To copy the calibration use Lifecycle/Copy. NOTE Use a unique project name with Latin letters (a-z) only.
NIRCal 5.5 Software Manual This Dialog also appears when a NIRCal Project is saved to DB. Search and Import Spectra... Opens the dialog to search and import spectra from the NIRWare Database to NIRCal. The list displays per default only spectra from last 30 days [Time = e.g. from 05.01.2005 to 4.02.2005] and with an assigned reference value [Reference Values >0].
Chemometrics change the filter settings and click ok. Clicking Cancel disables the time filter completely. Same effect when clicking the grey cell below [Time] with the right mouse. click in the cell below [Reference Values] , delete >0 and press ENTER Filtering options: Time Filter, see above Drop Down list for [Instrument], [Measurement Cell], [Measurement Cell Option], [Spectrum Type], [Characteristic] Text for [Sample], [Application]; e.g.
NIRCal 5.5 Software Manual Import Import Project Imports NIRCal Project Files (*.nir) NOTE BCAP Series can be loaded adjusting "Files of type" to "all files" (*.*) and selecting the spectra file "...Sxx" 226 NIRCal 5.
Chemometrics Import Spectra Imports Spectra from a File. Several data formats can be imported. Export Export Project Save a NIRCal Project as *nir File. The question: “Store the project into the database before?” appears. It is better to export without storing (the calibration will be closed and will not be editable). NIRCal 5.
NIRCal 5.5 Software Manual Export Spectra Print Prints the current view. Print Preview Print Preview of the current view. 228 NIRCal 5.
Chemometrics Print Setup Opens dialog to setup the default printer. Exit Closes NIRCal incl. all opened NIRCal-Projects. 3.20.2 Edit menu Undo Undos text editing Cut Ctrl+X Copy Copies the active object to the clipboard View Type Clipboard Object 2D-Plots Metafile 3D-Plots Bitmap Tables ASCII-Text cells separated by TAB Paste Pastes text from the clipboard into the actual document. Options Opens the Dialog Box to change NIRCal Configuration Settings. NIRCal 5.
NIRCal 5.5 Software Manual 3.20.3 View menu Overview Recalculates the calibration and opens several graphics for an overview of the calibration. Depending on the selected calibration method the most useful graphics are opened. Example: Overview of a Cluster calibration For detailed information see the description of the corresponding matrices: X-PRESS, Scores, Property Box Radii, Property Residuum, Spectra Residuals too big, Cluster per Property, Pretreated Spectra 230 NIRCal 5.
Chemometrics Example: Overview of a Quantitative calibration For detailed information see the description of the corresponding matrices: Pretreated Spectra, Regression Coefficients / Property Spectra (CLU), Consistency, V-Set PRESS, CSet Regression Coefficient NIRCal 5.
NIRCal 5.5 Software Manual Spectra Selection Opens a few windows for spectra selection: You can select spectra in the plot by double clicking on the displayed spectra or changing the selection mode to "Mouse Window Select" using the popup menu of the window. Example of a Spectra Selection Plot 232 NIRCal 5.
Chemometrics Wavelength Selection Opens a few windows for wavelength selection: You can select wavelengths in the plots by changing the selection mode to x axis selection and then marking a region in the plot keeping the left mouse button pressed. Example of a Wavelength Selection Plot NIRCal 5.
NIRCal 5.5 Software Manual Property Selection Opens a few windows for property selection: You can select property in the plot by double clicking on the displayed property or changing the selection mode to "Mouse Window Select" using the popup menu of the window. Example of a Property Selection Plot 234 NIRCal 5.
Chemometrics Primary PCs (Factor) Selection Example of a Primary PCs Selection Plot NIRCal 5.
NIRCal 5.5 Software Manual Secondary PCs (Factor) Selection Example of a Secondary PCs Selection Plot 236 NIRCal 5.
Chemometrics Outlier Detection Example of an Outlier Selection Plot NIRCal 5.
NIRCal 5.5 Software Manual Time Dependency Example of a Time Dependency Plot Creator Dependency Instrument Dependency 238 NIRCal 5.
Chemometrics Property Dependency Example of a Property Dependency Plot Custom For customizing workspaces with the plugin System Module "WIZARD PLOTS". If no plugin is installed the menu item is gray. NIRCal 5.
NIRCal 5.5 Software Manual Toolbars Toggles the display of each toolbar. Same can be done using the right mouse in the toolbar region. Show all Toolbars Displays all toolbars. Hide all Toolbars Hides all toolbars. Status Bar Displays/hides the status bar at the bottom of the NIRCal window. Depending on the active window or the called function the status bar contains different information. Toolbars save positions Saves the actual set of displayed toolbars and their position. 240 NIRCal 5.
Chemometrics Toolbars load positions Displays and repositions all toolbars saved as user toolbar positions. See Toolbars save positions 3.20.4 Workspace Workspace It is possible to create ones own workspace. Open a set of graphics and/or protocols and arrange them as wished. Then Save the workspace. It is also possible to save and load workspaces (1-3) with Icons in the Toolbar "Wizard Window" Save Workspace New Creates a new workspace based on the actual opened windows.
NIRCal 5.5 Software Manual 3.20.5 Project Edit Selections Opens the Dialog Box to edit selections. Load Selection from Spectra C-Set Load selection from the Spectra C-Set. Spectra V-Set Load selection from the Spectra V-Set. Wavelengths C-Set Load selection from the Wavelength C-Set. Properties C-Set Load selection from the Properties C-Set. PCs C-Set Load selection from the PCs C-Set. 242 NIRCal 5.
Chemometrics Change X-Unit to Wavenumbers cm-1 Wavelength nm Spectra Add empty spectra Only possible in NIRCal file-mode. Delete selected spectra Deletes the red selected spectra from the project. To remove spectra from the calibration, they can be deleted in the calibration data set selection C-Set and V-Set. Property Add property Only possible in NIRCal file-mode. Delete selected property Only possible in NIRCal file-mode. Journal Show Displays the project journal.
NIRCal 5.5 Software Manual Custom defined size It is possible to use NIRCal as a tool for multivariate analysis of any type of data. For this purpose the dimensions of the data matrices have to be defined and prepared for input. Open a new project (Menu File / New) and select “Custom defined Size” in the Menu Project: Define the size of your data in the appearing window: NOTE Since NIRCal normally is used for the analysis of spectra, the terminology might be unusual for the statistician.
Chemometrics The easiest way to enter data is via copy and paste (e.g. from EXCEL files). Custom defined size: NIRCal works in file-mode which allows to resize the spectra and property afterwards as well. The given waves or variables are constant after Custom defined size. NOTE X-variables have to be entered in transposed format if the number of variables is smaller than the number of samples. Under Modules / Settings Advanced...
NIRCal 5.5 Software Manual Default Parameter Opens the dialog to edit the calibration default settings.
Chemometrics Lifecycle Edit Switches the lifecycle state of the calibration to Editing. The Calibration-Icon changes . so that the calibration settings can be changed. See Calibration Handling for details regarding the use of the lifecycle model on calibrations. More detailed general information regarding the NIRWare Lifecycle can be found in the NIRWare Software Manual. Save Switches the lifecycle state of the calibration to Saved.
NIRCal 5.5 Software Manual 3.20.8 Modules Edit Module Opens the macro-editor for entering BASIC macro code. Click F1 for the Help File. Run Module Opens the dialog to select NIRCal Module (*.bas) to be executed. Organize Menu Add Opens a dialog to select a module which will be added to the modules list. The modules are saved in the following folder: C:\Program Files\Buchi\NIRSolutions\Modules 248 NIRCal 5.
Chemometrics Edit Select a module from the module list to be opened with the Module Editor. Remove Select a module that shall be removed from the module list. Modules List Default list of modules. The list can be adapted by Organize Menu. Chemical Bonding Translates the wavelengths to chemical bondings. See mouse cursor position in the status bar. Settings Advanced Opens the dialog to change advanced NIRCal settings.
NIRCal 5.5 Software Manual 3. keep x% of the spectra: an iterative similar search is used to find as much spectra to thin out the amount of spectra. When you click Advanced, the following dialog opens: The following fields, areas and buttons are available: Search type: defines the search logic. Search: defines the search criteria and method. Distance Search: The Mahalanobis Distance -MD- Limit depends on the data and the calibration settings.
Chemometrics Invert: Inverts the selection. Spectra (Delete, Graphics) Delete: Deletes selected spectra from the project. Typically the smart selection can be deleted to shrink the amount of calibration spectra. Graphics: Opens a pretreated spectra plot to visualize the selection. Project (Update, Data Sets...) Update: Updates the calibration calculation. Used when data sets are edited or spectra are deleted. Data Sets: Opens the Edit Data Sets dialog to change the calibration selections.
NIRCal 5.5 Software Manual Spectra Nearest Neighbor Select The Matrix "Spectrum Nearest Neighbor Index": (NIRExplorer / Matrices / "Spectrum Nearest Neighbor Index") contains the spectrum index of the nearest spectrum to each spectrum in the project. The best is to show it as 1D-Scatter-Plot for selected spectra. This matrix is related to "Spectrum Nearest Neighbor" which contains the Mahalanobis Distance between nearest spectra pairs. As referred in the ASTM E1655-05 "16.4.8 Nearest Neighbor Distance".
Chemometrics Check Module Signature Choose the folder: C:\Program Files\Buchi\NIRSolutions\Modules Can be used to check the software for original content. Checks the Digital Signature in NIRCal Macro Modules. A detailed log lists all Modules that are not correctly signed or modified. The modification date/time is also listed. Spectra Name find and replace NOTE This module is installed but not added to the Modules menu.
NIRCal 5.5 Software Manual Close All Closes all opened windows except the NIR-Explorer. Fit All Windows Fits the content of every window to default. E.g. the zooming factor. Related to View Fit which fits only the content of the active window. Toggle Plot Size Toggles the plot size of every window. Related to Large Plots which changes the plot size of only the active window. Arrange Icons Windows List List of all opened window. The active window is marked with a checkmark. 3.20.
Chemometrics Import License Import the licence file: “BuchiLic-550021-…” for NIRCal and “BuchiLic-550041-…” for NIRCal toolbox. About NIRCal BASIC About NIRCal 3.21 Context menu (right mouse) 3.21.1 Add Selection to Set Add the objects currently selected in the plot to the chosen set. CAUTION: This action will change the contents of your validation or calibration set if you add data to these sets. 3.21.
NIRCal 5.5 Software Manual 3.21.5 Choose [x][y] Independent Applies to 2D scatter plots only. This means that the value of each cell in one column or row of matrix 1 is plotted against the value of the same cell in any column or row of matrix 2. If you open the "Original Property" plot and transpose it you will be able to plot one property against another and check for dependencies. Related Topic: Choose [xy] Independent 3.21.6 Choose [xy] Independent Applies to 2D scatter plots only.
Chemometrics 3.21.11 Edit Selection Opens the Edit Selection Dialog. Note: Changes to the current selection do not effect your calibration or validation set. 3.21.12 Export Table Export the table as Excel sheet. 3.21.13 Fix Table Titles Fixes the row and table titles for better scrolling. 3.21.14 Flip X-Axis Flips the plot x-axis. Draws the x-axis from lower to upper or vice versa. 3.21.15 Flip Y-Axis Flips the y-axis. Draws the y-axis from lower to upper or vice versa. 3.21.
NIRCal 5.5 Software Manual 3.21.21 Mouse X-Axis Select Menu: Options > Mouse X-Axis Select Keyboard : Q Edit the selection displayed in the small window above the x-Axis. The selection displayed in this window applies to the other side of the matrix (see Transpose). In a spectra plot the wavelength selection will be displayed in that window by default. Select one corner of the region that corresponds to your x value and open a rubber banded rectangle keeping the left mouse button pressed.
Chemometrics 3.21.25 Plot Defaults The Nircal Configuration dialog will be opened. The default parameters for all views can be edited in that dialog. See also 2D-Plots. 3.21.26 Plot Settings The titles and zoom of a plot can be edited before printing. 3.21.27 Regression Draw Line A regression line will be drawn for each set that you activate here. The corresponding regression formula will be displayed as a legend. 3.21.
NIRCal 5.5 Software Manual 3.21.32 Show Plane Menu: Options > Show Plane Available in Plot : 3D-Scatter Planes for all 3 dimension can be displayed: Blue and Yellow Axis, X-Plane Red and Blue Axis, Y-Plane Red and Yellow Axis, Z-Plane 3.21.33 Show Labels Show numbers at all points of the plot. 3.21.34 Show Line Show Scatter as Line. 3.21.35 Show Selection Colors Line Coloring by Set. 3.21.36 Show Cycle Colors The color table is used to color each object.
Chemometrics 3.21.42 View Fit The current plot is resized in such a way, that all objects are inside the visible region. If you have applied a visibility (e.g. calibration set) to the view, it is possible that certain objects not contained in that set (e.g. validation spectra) will not be visible. 3.21.43 Visibility Restrict the visibility of the objects displayed in the plot to the chosen set. REMARK: no data will be changed or deleted by this action. NOTE Use the shortkeys Ctrl+0,Ctrl+1,...
NIRCal 5.5 Software Manual Calculates the active calibration and shows the Full Calibration Protocol Predict Project Application Predict Project Multipredict Project Predict external Application predict external Multi Predict external Predict external GUID file Multi Predict external GUID file Application Predict external GUID file 3.22.
Chemometrics 3.22.4 Lifecycle See Calibration Handling for details regarding the use of the lifecycle model on calibrations. More detailed general information regarding the NIRWare Lifecycle can be found in the NIRWare Software Manual. Edit calibration Save calibration Copy calibration Next state Delete calibration 3.22.5 Modules Edit module Run module 3.22.6 Options Toolbar Opens Dialog to change NIRCal Configuration 3.22.
NIRCal 5.5 Software Manual Normalization Multiplicative Scatter Correction Full Normalization Multiplicative Scatter Correction Amplification Offset Multiplicative Scatter Correction Normalization Standard Normal Variate Normalization Variance Scaling Offset Mean Centering Transformation Kubelka Munk Second Derivative / Logarithm Transformation Absorbance Transformation Absorbance inverse Undo Last Undo Sequence 3.22.
Chemometrics Offset Mean Centering Transformation Absorbance Linear Filter Undo Last Undo Sequence Fits the hole plot to the window Opens Pretreated Spectra Graphic in new window Opens Original Spectra Graphic in a new window Opens Original Property Table in a new window 3.22.
NIRCal 5.5 Software Manual Load selection from C-Set spectra Load selection from V-Set spectra Load selection from C-Set wavelengths Load selection from C-Set properties Load selection from C-Set factors 3.22.12 Search Import Export Toolbar Import spectra file to project. Export spectra from project to file. Search spectra in file and import to project. 3.22.
Chemometrics Shows instrument dependency plots Shows property dependency plots Loads all plots saved as workspace 1 Loads all plots saved as workspace 2 Loads all plots saved as workspace 3 Saves all opened plots as workspace 1 Saves all opened plots as workspace 2 Saves all opened plots as workspace 3 3.22.
NIRCal 5.5 Software Manual Edit selection (E) Line coloring by set (1) Line coloring by cycle (2) Line coloring by property (3) Copy selection to User set Visibility to all sets (Ctrl+0) Visibility to user set (Ctrl+1) Visibility to calibration set (Ctrl+2) Visibility to validation set (Ctrl+3) Visibility to residual outlier set (Ctrl+4) Visibility to loading outlier set (Ctrl+5) Visibility to property outlier set (Ctrl+6) Visibility to leverage outlier set (Ctrl+7) 268 NIRCal 5.
4 Appendix 4.
NIRCal 5.5 Software Manual Button Ctrl+r Ctrl+S Ctrl+T Ctrl+V Ctrl+X Ctrl+Z Ctrl+Shift+M Ctrl+Shift+S Ctrl+Alt+R F5 F8 Ctrl+F5 Shift+F5 Status Show full labels Save Project Fix Table titles during scrolling Paste selection Cut selection Undo Import latest Application spectra from DB Save Project Run module Update Show Calibration Protocol Overview Plot Calculate all 4.2 Tips and Tricks 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.
Appendix To have faster access to your workspaces, there are 3 custom workspace icons on the toolbar "Wizard Workspace". L1,L2,L3 for loading it and S1,S2,S3 for saving it before.
NIRCal 5.5 Software Manual Merge : combines sets Intersect : keeps only the overlapping of the sets Exclusive : keeps only the non overlapping of the sets "Copy to Selection" means that the result of the set calculation is copied or added by "Add to Selection" or removed by "Remove from Selection" to the selection. The "Selection" is the temporarily visualised red selection in the plots and tables.
Appendix Customize derivatives and smoothing pretreatments The pretreatment "Savitzky Golay 2nd derivative (15 pt.
NIRCal 5.5 Software Manual 4.3.1 Temporary Settings Open the folder Matrices in the NIR-Explorer. Right clicking the mouse on the appropriate matrix name opens a pop-up menu. Clicking on Rename enables the user to change the name of the matrix. 4.3.2 Permanent Settings In order to change the names permanently it is necessary to perform the changes in the registry settings. HKEY_CURRENT_USER\Software\Buchi\NIRCAL\Terminology When performing the changes (including All Factors, etc.
Appendix Wavelength [nm] 1360 1395 1410 1415 1417 1420 1430 1440 1446 1450 1460 1471 1480 Wavenumber -1 [cm ] 7353 7168 7092 7067 7057 7042 6993 6944 6916 6897 6849 6798 6757 1483 6743 1490 6711 1492 1500 1510 6702 6667 6623 1520 6579 1528 6545 1530 1533 1540 6536 6523 6494 1570 1580 6369 6329 1620 1645 1660 1685 1695 1705 1725 1740 1765 1780 1820 6173 6079 6024 5935 5900 5865 5797 5747 5666 5618 5495 1900 5263 1908 1920 1940 1950 1960 5241 5208 5155 5128 5102 NIRCal 5.
NIRCal 5.5 Software Manual Wavelength [nm] 1980 276 Wavenumber -1 [cm ] 5051 2000 5000 2030 4926 2050 4878 2080 2100 2110 2132 2140 2150 2160 2180 2190 2200 2242 2252 2276 2280 2294 2310 2323 2336 2347 2352 2380 2461 4808 4762 4739 4690 4673 4651 4630 4587 4566 4545 4460 4440 4394 4383 4359 4329 4305 4281 4261 4252 4202 4063 Chemical bonds 2x O-H def.+ C-O def. N-H sym.str.+amide II C=O str.second overtone N-H sym.str.+ amide II N-H asym.str.+ amide II O-H str.+ O-H def. 2x O-H def.
5 Software installation 5.1 Software installation 5.1.1 Important Notes The latest NIRWare and NIRCal cannot be installed together with previous versions. Should there be an existing installation of NIRWare and NIRCal it will be removed during installation. An existing NIRWare Database from a prior installation will be upgraded.
NIRCal 5.5 Software Manual 278 NIRCal 5.
Software installation The InstallShield Wizard is opened. Click OK Accept the license agreement to continue the installation and click Next to continue. NIRCal 5.
NIRCal 5.5 Software Manual 280 We recommend to select the Complete installation. Then click Next to continue. Click Install to Install to start the installation process. NIRCal 5.
Software installation Click Finish to exit the Wizard. The applications are stored by default under C:\Program Files\Buchi\NIRSolutions\ and can be opened with Start > Programs > Buchi > NIRSolutions. The following modules are available: Management Console Operator Buchi Service Manager NIRCal 5.2 Software update Software update over internet is discontinued since NIRWare 1.4. 5.3 Software licenses After Installation of NIRWare or NIRCal the software can be used in DEMO mode for 60 days.
NIRCal 5.5 Software Manual The Software Registration dialog opens. 282 NIRCal 5.
Software installation Fill it out and send it to your Buchi sales representative. 5.3.2 Activating the License The license are generated based on the information provided in the registration form. To activate the license in NIRCal select Help > Import License. NOTE The user needs administrator rights on the OS to import the license file. NIRCal5, NIRWare Operator and also licenses for pre-calibrated applications are node locked.
