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Welcome to SIMIS FeatureSe FeatureSearch. arch. The SIMIS FeatureSearch product is one of a range of products produ produced ced in collabo collaborat ration ion with with Spectr Spectral al Inter Internati national onal Inc. Inc. for the identication identication of unknown unknown mineral mineral spectra spectra for mineral exploration exploration and mining. The algorithm can operate with data from any eld spectrometer !is !isibl ible"I e"Inf nfra rarred and ther therma mall Infr Infrar ared# ed# afte afterr con! con!er ersio sion n to the the standard $S%II input format or alternati!ely &IM$ les can also be used. $S' support has now been added. This package enables the user to load an unknown spectrum by dropping the le into the plot window( or selecting it using the &)*T S&+%T,S&+%T,-M M or &)*T &)*T &,+I+ &,+I+W W command commands#( s#( the user user can nd the features in a spectrum up to /0# and search a spectral library of up to 1000 minerals to determine which minerals are likely candidate minerals for the unknown spectrum features. The output is a list of candidate minerals and a user description. The primary use is for narrowing narrowing down the selection of possible minera minerals ls for more more automa automated ted proce procedur dures es of deter determini mining ng minera minerall propor oporti tion ons s and and in iden identi tiffying ying unus unusua uall min miner eral als s or mine minerral combin combinatio ations. ns. It is especi especiall ally y useful useful for no!ice no!ice users users identif identifying ying minerals present in mixtures based on feature position and shape and for ad!anced users who wish to determine the less commonly occurring mineral phases in spectral mixtures. We welcome your comments. For more more information please contact 'r. Stephen Mackin( &hone +"Mail
2 344 15/5 647 485 stephen.mackin9merseymail.com
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%ontents 1. Installation
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/. Tutorial
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/.1. Setting up paths
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/./. &lotting an unknown spectrum
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/.:. )ibrary ,outines
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/.4. Setting up run options
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/.7. Selecting a library for the search
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/.8. &lotting an unknown spectrum and feature extraction 18 /.5. Searching the library
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/.6. $ttaching features and unmixing
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/.;.
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/.10. &rinting the results
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/.11. =etting help
:/
$ppendix 1 " 'ata Formats Formats
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%ontents 1. Installation
:
/. Tutorial
7
/.1. Setting up paths
8
/./. &lotting an unknown spectrum
6
/.:. )ibrary ,outines
11
/.4. Setting up run options
1:
/.7. Selecting a library for the search
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/.8. &lotting an unknown spectrum and feature extraction 18 /.5. Searching the library
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/.6. $ttaching features and unmixing
/1
/.;.
/5
/.10. &rinting the results
:0
/.11. =etting help
:/
$ppendix 1 " 'ata Formats Formats
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1. Installation The software software is for :/ bit platforms only and operates on Windows ;7( ;6( /000( >& and Windows ?T. The software re@uires 7MA of hard disk space and will occupy less than 4MA of main memory when operating. The installation is on a single WinBip Cip le which contains the data( executable and libraries. • • •
•
'ouble click on the Cip le to open WinBip and click on the WinBip I?ST$)) button. The installation program is run. Dou can modify the installation location. *n complet completion( ion( exit exit WinB WinBip ip and run the instal installed led softwa software re by double double clicki clicking ng on the Esimn Esimnd.e d.exe xe le. The opening opening paths paths statem statement ent points points to the top le!el le!el direct directory ory speci specied ed during during installation. Modify the paths to point to the correct input and library sub"directories created during installation#. The new security feature will then ask you to send registration detail details. s. T<+S+ T<+S+ M-ST M-ST A+ S+?T S+?T as a counte counterr"key "key is re@ui re@uirred to operate operate the software. software. The counter"ke counter"key y will be sent by e"mail in a le Eckey.txt. Sa!e it to the 'esktop. *nce it has arri!ed start up FeatureSearch again and you can select the Eckey.txt le from the 'esktop. *nce selected the software will start normally. This is only re@uired once.
*n completion you should ha!e the following Top Top le!el directory with... mfc40d.dll ms!cr40d.dll simnd.exe simnd.hlp prefs.dat license.txt feature"tutorial.doc feature"tutorialGco!er.doc feature"user.doc feature"userGco!er.doc HI?&-T sub"directory core1.dat to core5.dat map1.dat to map//.dat spectrum1.cse and spectrum/.cse 3
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H)IA,$,D sub"directory usgsr.slb usgsr.dsc usgsr.sld usgs.w!e
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/. Tutorial This tutorial follows a step by step procedure in loading an unknown spectrum( nding its features( searching a specied spectral library( sa!ing the end"members found and unmixing. $dditionally we will show the use of
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/.1. Setting up paths $t the system start up you are presented with a copyright notice(
Followed by the &,+F+,+?%+S Menu &$T
In this case using the A,*WS+ button
select the pre"dened sub"directories HJlibrary( HJinput # and click *K. These are now the default paths and will be used during this session and as the default for later sessions. 6
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If you wish to set up paths for another user or another proLect( this can be done at start up as the paths dialog is always shown at start up# or during a session by choosing the &$T
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/./. &lotting an unknown spectrum There are three ways of plotting an unknown spectrum( a# use the &)*T menu( S&+%T,-M command and select the le from those shown in the I?&-T sub"directory or other directory. b# or more simply( open the Windows +xplorer and select a le and drag it into the plot window and simply drop it. c# or use the &)*T menu( &,+I+W and $?$)DSIS %*?T,*) command to look at Ethumbnail plots of the spectra in the I?&-T sub"directory and select one from the a!ailable list to plot in the main window. This control once acti!ated pro!ides a simple means of selecting and analysing the data les in the selected I?&-T directory. The data can be in one of three formats( simple two column $S%II data with column 1 as wa!elength micrometres or nanometres# and column / as the data !alue percent reectance or !alues between 0 and 1#( separated by a space or tab( &IM$ format .dsp or .fos# and a range of $S' formats. &lot the spectrum core5.dat pro!ided in the input demonstration data.
The spectrum is plotted with a 0 to 100 reectance scale. The data is shown with !ertical bars which correspond to the positions of the extracted features these positions are also shown in the list which appears when a spectrum is plotted#. To switch oN 8
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this preference the user can select the &,+F+,+?%+S menu( S<*W sub"menu( F+$T-,+ &*SITI*? A$,S command. We can click with the right mouse button in the plot area. We are presented with the scaling toolbar(
It has two wa!elength options and four reectance options. %hoose the scale option under wa!elength. The current spectral range of the plots denes the minimum and maximum !alues displayed( Modify the minimum to ha!e a !alue of /.0 and click *K. The spectral range is modied and the spectra redrawn. ?ow select the &,+I+W command from the &)*T Menu and click on the rst spectrum in the list. The le is plotted to the right of the list. Scroll down the list using the arrow keys.
%hoose sample spectrum1.cse and click the *+,)$D button. The spectrum is plotted in the main plot window within the user dened wa!elength range. 9
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?ow we wish to adLust the reectance. We choose the ,eectance Scale option right mouse button to raise toolbar# and are asked for a minimum and maximum !alue. Select a minimum of 40 and a maximum of 80. ?ote that the extremes of the plotted range are clipped. $ better alternati!e might be to use the F)*$T option( this rescales the spectra to t in the maximum and minimum limits of all the plotted spectra. ,escale again using the F)*$T option.
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/.:. )ibrary ,outines There are many spectral library and indi!idual spectrum handling routines. $ spectral library has been pro!ided for test purposes. The library handling routines are to enable a user to create and manage large spectral libraries for both analysis and reference purposes. The user can import( copy( delete or document any indi!idual spectrum or complete library. $dditionally three methods of resampling are included to allow the user to con!ert the data modify wa!elength ranges( number of spectral bands and their positions# to use in both simulations of other instruments or to con!ert one library to ha!e characteristics of the eld instrument used in the analysis. $ library is included with this software. The library is the -S=S library usgsr.slb#( which co!ers a much larger wa!elength range than most currently a!ailable eld spectrometers. From the )ibrary Menu choose *&+?(
Dou are presented with a list of spectral libraries. $ single click on a library name pro!ides a library description. Select the usgsr.slb library by either double clicking on its name or single clicking and choosing *K. Its name is placed in the status bar at the bottom of the screen. The spectrum operations are now a!ailable. To make the data handling easier( raise the )ibrary and Spectrum *perations oating toolbars. These can be acti!ated by pressing the toolbar icons( )ibrary toolbar
Spectrum Toolbar
+ach toolbar can be dragged to a point where they do not obscure the screen. The toolbars contain most of the maLor library and spectrum operations( 11
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Spectrum
To remo!e the toolbars simply click again on the icon below the main menu. ?ow click on the &)*T option in the spectrum toolbar( the user is presented with a list of possible spectra in the library. If you click once on any name in the list you are presented with the spectrum description if a!ailable#.
+ither double click on a name or single click and select *K to plot a spectrum. The library routines include those to %reate new library shells( *pen libraries for plotting( copy( delete and export spectral libraries( create new libraries by importing spectra in $S'( $S%II or &IM$ formats and edit library descriptions. $lso the user can resample conguration to another.
libraries
from
one
instrument
There are also a large set of single spectrum operations for any library including plotting( copying( deleting( import and export as well as adding spectrum descriptions. The routines pro!ide a great deal of exibility in creating spectral libraries to use with the SIMIS FeatureSearch and other SIMIS products and to export to other external software products. 12
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/.4. Setting up run options The user can now set up the run to nd features. %lick on the setup options toolbar icon( or choose the ,-? menu( S+T-& *&TI*?S command. $ dialog is shown with the current setup(
The user can select se!eral parameters. The Search Width is the distance from an unknown spectral feature position that the algorithm can search for library features. The default is 7nm. The noise threshold is used in the extraction algorithm to highlight only the important features. If the user lowers this !alue( more features are found. If raised( less features are found. The !alue is not the depth of the feature( but is the siCe of feature re@uired to be recognised as a change of slope in the feature extraction algorithm. Modifying this option will cause a recalculation of the currently loaded feature library based on the specied noise le!el. The user also has an option default is on# to exclude library “hits” where the library feature depth is less than the unknown feature depth for a specied feature. This operates on the basis that in some cases the impure sample spectra will ha!e features which are smaller than the pure laboratory measured library spectra. This reduces the number of Ehits signicantly and speeds up the interpretation process. The user can also exclude up to three wavelength regions . This is more useful for analysis of eld spectra collected with $S' or =+, spectrometers where the water absorption features from eld 13
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collected spectra are often extremely noisy. The !alues chosen are the default for the session but are reset on restarting#. They maybe modied at any point during a session. Finally the user can also select the method of feature extraction for the analysis and interpretation step. This can either be Use Hull Diferences or eature extraction the default# or Use Reectance or eature extraction .
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/.7. Selecting a library for the search The user has only to select a library P.slb# le from the presented selection using the ,-? menu( S+)+%T )IA,$,D command or the corresponding toolbar icon . The library is automatically con!erted into a temporary feature library maximum /0 features per spectrum# based on the current set"up options for the feature extraction. The current set"up options can be found by using the ,-? menu( S+T-& *&TI*?S command. The temporary library is modied if the set"up options are modied during a run. The library must consist of les that ha!e the same number of bands and wa!elength range. If you ha!e created a spectral library with &IM$ data( with $S' data and with -S=S data you will need to use the resampling options in the )ibrary Menu to produce a resampled spectral library to pro!ide to the feature extraction step. !ote " #hat although all the spectra in the library have to have the sa$e nu$ber o bands and wavelength range% these values can be diferent ro$ the input data being analysed& 'n other words we can use a (')* library in the analysis o *SD spectra or an *SD library in the analysis o data ro$ the US+S instru$ent&
To prepare for our run( turn oN the spectrum and library toolbars and delete the plotted spectra from the plot screen click on their names#. ?ow choose the ,-? menu( S+)+%T )IA,$,D option and select the -S=S,.S)A le. The preparation takes se!eral seconds and a temporary feature library will be created .wlb# and its name written abo!e the plot window. The user can select another library at any time( by clicking on the feature library selection icon or choose the ,-? menu( S+)+%T )IA,$,D command. *n selecting a library it is listed as the loaded feature library and the Search )ibrary routines are acti!ated. If a spectrum is already plotted the Search )ibrary button at the bottom of the feature list becomes acti!e( if there is no library selected the button is disabled.
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/.8. &lotting an unknown spectrum and feature extraction &lot spectrum core5.dat using the &)*T menu S&+%T,-M command( the $?$)DS+ button on the &)*T &,+I+W window or by drag and drop from the Windows +xplorer. The unknown spectrum needs to be in the rst plot position for drag and drop or &)*T S&+%T,-M black spectral cur!e#. If it is not( then delete the spectrum that is in this position and &lot the unknown spectrum again. The Find Features is acti!ated automatically and a feature list produced.
Dou are presented with a screen similar to this. The features are listed in a dialog box. There are three lists( the rst list is the Econtrolling list with the rst item being the position in micrometres( then depth in percent reectance. The other lists are Esubsidiary lists and only contain the feature positions. If you click on a feature in the Econtrolling list( its position is indicated in the plot box. Dou can now change the set"up options to alter the noise threshold. The list is updated automatically on changing any set"up option. *pen the set"up options and change the noise threshold to 0.5 and click *K. ?ote that the number of features matched is reduced. %hange the !alue back again to 0.7 and click *K. The original feature list is now re"created. 16
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The features list can be toggled on and oN if it obstructs the screen using the icon in the toolbar. +!en if hidden it remains acti!e.
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/.5. Searching the library ?ow we can search the loaded feature library for features. Select the feature /./1 from the list this is a feature of alunite# and click the S+$,%< )IA,$,D button on the Features in Spectrum dialog box. The library is searched and the minerals which ha!e a feature at the chosen position within the search width# are listed with the library mineral in rst position that has more features that coincide with the unknown. This is the default beha!iour known as ESearch by
This is the best matching scheme for determining maLor mineralogy( the dominant minerals which ha!e plenty of features in the spectrum. The alternati!e is a single feature search in which the features within the search width are listed in position order minerals with features closest to the unknown# followed by depth order deepest rst#. This is better for minor mineralogy when you ha!e a single feature of an unknown mineral and wish to try and determine the likely mineral identity. To choose this option select the ,-? menu( and choose the checked S+$,%< AD
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In this case the alunite is still present in the list but not at the top as all the clay minerals with /./1 ha!e bigger features at this location. This lengthens the search process. So for maLor mineralogy switch the ESearch by
?ow click on the ,-? menu( S+$,%< AD
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The Larosite now occupies all three top positions. Minor mineralogy can be more easily determined using this method as it tends to ha!e few or only a single feature to use in the analysis process. If the user clicks on an item in the list click on the rst Larosite# the spectrum is plotted in red against the unknown spectrum. If the &,+F+,+?%+S menu( S<*W sub"menu( F+$T-,+ &*SITI*? A$,S command is checked default# the feature positions of the library mineral selected from the list are also shown in red at the top of the plot. The width of the bars marking the position is e@ual to the search width used in the feature analysis. The user can also extract the library description of the mineral selected( by clicking on the '+S%,I&TI*? button. The spectral range shown is too large. -se the right mouse button in the main plot window to change the W$+)+?=T< scaling S%$)+# to the 1.: to /.7 range of the input data. ?ow click on the '+S%,I&TI*? button and scroll through the description. %lick continue. ?*T+ 2 the results dialog can be toggled on and oN using the toolbar icon. The window is hidden but is still acti!e. $ new feature of the current update is the ability to select multiple features up to :#. Dou need to select a feature from the Econtrolling list and if you wish one from each of the Esubsidiary lists. ?ow click on the ,-? menu( S+$,%< AD
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time enormously and also increase the accuracy of the nal selection. Finally( note that as the user selects a wa!elength in the Econtrolling list the !alue is also placed in the edit control at the bottom of the dialog -ser 'ened Wa!elength#. The user can o!erride the selection and input a user dened wa!elength position in this edit control. The inputted !alue will be used for the search when the ESearch )ibrary button is selected. The user can see the position of the user dened feature by pressing the draw position button to the right of the edit control. This is useful when the user has detected the presence of a small feature but it has not been picked up by the automatic feature detection method. The user can then search for this feature in the spectral libraries. ?ote that if the Esubsidiary lists are selected they will still be used in the search along with the user dened wa!elength.
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/.6. $ttaching features and unmixing There is also an $TT$%< button on the results dialog which is used when the user considers that the mineral selected in the results list is at least one of the components of the unknown mineral spectrum.
%lick attach and the mineral in this case $lunite# is added to the $ttached Minerals list. Mo!e the $ttached Minerals box to an empty area of the screen or switch it oN in!isible but still acti!e# using the toolbar button. ?ow click on the ,-? menu( S+$,%< AD
The minerals are listed with oNset and depth information( the feature selected and the mineral name from the library. The user can add comments about the analysis. If the user clicks on an item in the list it is plotted in =reen against the unknown spectrum in the main plot window click on each mineral listed to see the eNect#. If the user presses the '+)+T+ button on the keyboard after highlighting a mineral in the list it is deleted. This allows the user to remo!e incorrect selections towards the end of the analysis. There 22
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are three buttons in the dialog( -nmix( Sa!e to File and Sa!e to
-SI?= F+$T-,+ '+&T
-sing the core5.dat sample as an example( if we select a single alunite and a single Larosite these are correct =+?+,$) end" members# we will nd that not only are the proportions inaccurate( but the proportions estimation depends on the S&+%IFI% alunite and Larosite used( so if we select an alternati!e alunite we end up with diNerent and @uite possibly incorrect proportions.
$s can be seen in the example shown abo!e( the end"members based on a feature search are =+?+,$))D correct for the mineral mixture. on the $ttached Minerals dialog.
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%learly we need to impro!e the result.
The corresponding comparison of mixture and unknown is on the following page. 24
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$ single alunite and Larosite account for most of the !ariation( the result gi!es a better approximation of the alunite and Larosite proportions within /.7R#. This method can operate when you ha!e a large library with se!eral examples of each end"member. Aut what happens in the case were you are using a small library( or the matrix will not in!ert using )east S@uares which is possible#. The alternati!e is a simpler method based on feature depths discussed below#. !.#/ " ' the input data has a wider wavelength range than the library data% this $ethod can not be used% as part o the analysis step is to resa$ple the library data to create an un$ixing $atrix and i the wavelength range o the input data is not covered% this is not possible& ' this case occurs the progra$ auto$atically chooses the un$ixing based on eature depths as dicussed below& Un$ixing based on 0eature Depths There is a simple unmixing option a!ailable in this package. The method is based on a comparison of the unknown feature depths to the library mineral feature depths of those library materials listed. To operate correctly( make sure that there is only one example of each mineral group present in the list. In our case only one Larosite 25
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and only one alunite( otherwise the results will be incorrect. -se those plotted. It operates on the principle that the depth of the unknown features ha!e a linear relationship to the depths of the library end"members chosen. This at best will be approximate. If your library mineral of Larosite has feature depths !ery diNerent from the unknown then the proportions estimate will be incorrect. $lso make sure that each feature selected for a particular end" member is not strongly inuenced by the presence of features from other end"members present( otherwise the results will be less accurate. In this case make sure that the Larosite feature is that at /./84 µm and that of the alunite is /.188 µm. ?ow select the &,+F+,+?%+S menu( I?T+,F$%+ S+T"-& sub"menu( -?MI> -SI?= F+$T-,+ '+&T
The method pro!ides an approximate guide to the proportions present and is less sensiti!e to odd continuum shapes than a standard least s@uares unmixing method. ?ote that if you change your Larosite or your alunite then of course the relati!e feature depths will change and the nal result will also be aNected. If you do ha!e more than one Larosite and one alunite( you can select for example three Larosites for the /./84 µ m feature and three alunites for the /.188 µm feature it must be the same number for each end" member in this case three and three# and sum the Larosites and alunites to get a!erage !alues that may be more accurate. Save to 0ile This button is used to sa!e the results of the analysis to a simple $S%II text le. %lick on the button and choose an output le name. *pen the le with ?*T+&$' later to look at the contents which will be similar to those shown below. 26
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core5.dat Tuesday( February /:( 1;;; )IA,$,D -S+' 2 c2JsimisJlibrar1Jusgsr.wlb 1 /:.5/ /./84 Larosit5.spc 1 /7.0; /./84 Larosit1.spc 1 /8.66 /./84 Larosit7.spc 1 /6.87 /.188 alunite1.spc -S+, %*MM+?TS This is an alunite"Larosite mixture. Three Larosites were selected based on a small /./84 feature. $lunite dominates the mixture. Save to History $ more recent alternati!e is to sa!e the spectrum and analysis results in a
+ach item in the library spectra listed in the top right# can be highlighted and the details of the analysis reco!ered. This pro!ides a simpler( faster and more eNecti!e way of storing the output results.
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/.;.
The history library name is in the title bar. The added spectrum is listed in the Spectra box in the top right hand corner. The user can 28
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add numerous spectra from a site. *n selecting a spectrum name in the list( the spectrum is plotted( the -ser %omments shown and the details of the analysis are presented in a window at the bottom of the dialog( with the original library used in the matching process listed abo!e the analysis details. If the user clicks on a mineral name in the window at the bottom of the dialog it is plotted in red if the library still exists and the spectrum has not been deleted#. The user can modify the -ser %omments. -se the right mouse button and click once in the area of the
Delete Spectru$ This is used to delete the currently highlighted spectrum in the Spectra list. /dit User 1o$$ents& %lick on this command and you are presented with the current text if any# in a small edit control. Modify the text and click *K. The comments are updated. -p to 7000 characters can be placed in the comments box. ,ibrary )ineral 'nor$ation %lick on this command and the currently highlighted mineral in the list at the bottom of the dialog is selected from the library used in the analysis and its description retrie!ed. Save ,'2R*R3 as /41/, input This command takes the sample name information( minerals matched and the corresponding proportions and creates an $S%II text le EexcelGin.tmp in the top le!el directory with the FeatureSearch executable#. The user may then select the path to the +>%+) executable and the data is loaded as a tab delimited le directly into +>%+). (rocess S'!+,/ U!5!.W! spectru$ 29
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This command allows you to compare a single unknown spectrum to those in the
The results are currently sa!ed in a text le in the I?&-T path batchres.dat#.
Select the +dit -ser %omments command from the list. $ new dialog is shown( add the text EMy comments in the dialog shown and click *K. !.#/ " #he dialog $ust be closed beore processing can continue using the .5 button&
?ow use the
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/.10. &rinting the results There are de!ice independent print options. The user can pre!iew the printing and modify the print attributes. ?ote that the print only co!ers the region of the SIMIS FeatureSearch screen( so if you resiCe the screen to be smaller( the printed region also becomes smaller by clipping of the screen contents. The user can add a Title and 'escription up to 1000 characters in this release#. Simple select the $'' TIT)+ and '+S%,I&TI*? command from the &,I?TI?= menu. Dou are presented with a dialog(
The title is placed in a large Font at the top of the printed page( while the description is placed Lust below the main plot window. !.#/ " when using a 678 x 798 screen resolution% there is only space or a single description line when using ,andscape prints& $n example of a print pre!iew with title and description is shown on the following page. The Title and 'escription remain acti!e until deleted or modied.
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Try the print options and modify the screen siCe to see some of these eNects. $dditionally( not that the
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/.11. =etting
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$ppendix 1 2 'ata formats IM&*,T and +>&*,T The standard import and export format is a simple two column $S%II format without headers. Most commonly used eld spectrometers pro!ide this output as an alternati!e &IM$( =+,( $S'#. $n example is shown below( 1.: 1.:/ 1.:4 HH
6:.4 64.5 6:.; HH
$ &IM$ format is also acceptable. The $S' format is also a!ailable in this release. W$+)+?=T< FI)+S and S&+%T,$) )IA,$,I+S The wa!elength les for the spectral libraries are binary les oat#. Temporary wa!elength les are created for plotting unknown spectra. There is one !alue for each band. Spectral libraries .slb# les ha!e a xed format with each spectrum ha!ing the following information( Mineral ?ame 70 bytes# )ibrary ?ame 70 bytes# Wa!elength le name 70 bytes# ?umber of bands Integer( 4 bytes# )**& ?umber of Aands Spectral 'ata Float( 4 bytes# The descriptions for each spectrum are sa!ed in one le which has the library name with a .dsc# extension. +ach entry starts with the number of bytes in the le( followed by the description. -p to 7000 bytes of information can be stored for each spectrum. +ach library can also ha!e a description of up to 7000 characters. This is stored with the same le name and a .sld# extension.
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