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SIMIS FeatureSearch Version 1.5.

User Manual

This is the User Manual for the SIMIS FeatureSearch 1.5. package. The
manual is based largely on the on-line help provided with the package.

Modifications in Version 1.5. include,

Feature Extraction using reflectance data and hull difference data.


Improved error trapping for unmixing using least squares.
Additional input data formats are now acceptable for PIMA.
Reflectance data feature depth extraction modifications.
User option selected wavelength position for a library search.
ASD formats supported.
Security features added.

Planned modifications include,

Spanish Language Version.


Import of spectrum descriptions from additional data formats for
PIMA.

For more information please contact Dr. Stephen Mackin,

Phone : +44 1727 845 467


E-Mail : stephen.mackin@merseymail.com

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Contents

1. Introduction 3

2. Commands 4

2.1. Plot Menu 4

2.2. Library Menu 9

2.3 Run Menu 25

2.4 Preferences Menu 37

2.5 History Menu 42

2.6. Printing Menu 49

2.7. Help Menu 53

2.8. Exit Command 54

Appendix 1 - Data Formats

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1. Introduction

The SIMIS FeatureSearch package is a tool to aid the identification of


end-members in unknown mineral spectra collected by a range of field
spectrometers (ASD, GER, PIMA, etc).

The primary uses are for the identification of rare mineral phases in
unknown spectra and as an aid to the novice spectral interpreter in
the identification of a wide range of commonly occurring mineral
phases.

The user can identify the end-members present in a mixture and save
the interpretation in an ASCII file or History Library file for later use
with more automatic unmixing methods.

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2. Commands
Below is a detailed listing of the commands available in the package.
These are also extensively covered in the on-line help file.

2.1. Plot Menu


The Plot menu functions allow plotting of unknown spectra to visually
inspect the data after downloading from the spectrometer in one of
three formats, PIMA format, ASD formats or the simple ASCII input
format default used by the package. Also to create a wavelength file
suitable for the input data for later library operations. NOTE : To
delete a plotted spectrum, just click on its name on the right of the
plot box, below the colored line.

There are three commands for this menu,

Spectrum Plots an unknown sample spectrum. (PIMA , ASCII two


column or ASD formats)
Preview Allows the user to preview spectra in the current input
and directory and select one for analysis or for overlay. Once
Analysis the plot preview is operating this command has the
Control function to hide or show the Preview window.
Add The user can add a new wavelength file for later library
Wavelength and spectrum handling routines.
File

2.1.1. Spectrum command (Plot menu)

The user selects the data file for plotting

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The data is then plotted in the main plot window and the features in
the spectra calculated and listed automatically. Up to eight plots can
be shown at any one time.

This option allows the user to plot an unknown spectrum collected


from any spectrometer after it has been downloaded from the
spectrometer as a PIMA file or in a simple ASCII two column format
(wavelength and reflectance), the first column is wavelength in
micrometres or nanometres, separated by spaces or tabs from the
second column which contains reflectance percent or values between
0 and 1.

To delete a plotted spectrum just click on its name to the right of the
plot box.

NOTE : A simpler alternative is to just drag a file from the Windows


Explorer and drop it into the plot window.

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2.1.2. Preview and Analysis Control command (Plot menu)

This command can also be called using the button on the toolbar.

The command calls the Plot Preview and Analysis Control dialog and
once active can be used to show or hide the dialog so as not to
obscure the main screen.

The list contains all the data files in the input directory (specified in
the path preferences). On selecting a file if it contains spectral data in
the default ASCII format or PIMA format, it is plotted to the right of the
list. If the data is from another source an error message is given.

This dialog can be considered the main control dialog for handling the
input data.

File List

This is a list of the current data files in the input directory. The
user can select a file (or scroll files) which are be plotted in a
small plot window to the right of the list. If the user selects a PIMA
(.dsp) file from the list, the description in the (.dsp) file header is
shown in the control below the list.

Analyse Button

Once a file is selected, this button is activated. On pressing the


button the selected file is placed in the first plot position of the
main plot window (black curve) replacing any previous curve and

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its features are extracted and listed in the Features in Spectrum


dialog box.
Overlay Button

Once a file is selected this button is activated. On pressing the


button, the selected file is placed in the first free plot position in
the main plot window (the main plot window can hold up to eight
plots). If there are no free spaces the operation is terminated with
an error message.

Description Control and Modify Description Button

As mentioned above, if a PIMA (.dsp) file is selected from the file


list, its description is placed in the edit control below the list and
the Modify Description button is activated. If the user presses the
Modify Description button, the Edit (.dsp) Text dialog is displayed.

The user can simply modify the description and Save the
changes. Additionally, the user can select a different directory in
which to save the edited data files. The Save button in this case
will copy the old data file with the new description to the directory
specified in this dialog. This different directory becomes the
default for all future saves. This allows the user to modify the
descriptions, but also keep the original data files intact.

Change Path Button

This changes the default INPUT path for data files. The user
preferences are modified and saved. Data files in the new
directory are displayed. The Save directory used to store modified
(.dsp) file descriptions is also reset to the new INPUT directory on
making the change.

2.1.3. Add Wavelength File command (Plot Menu)

The user may require a wavelength file for the Import Library and Import Spectrum
commands in the Library Menu.

To create a new wavelength file, simply select a data file that has the correct wavelength
characteristics,

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Then specify the name of the new wavelength file and its extension.

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2.2. Library Menu


There are numerous options to handle libraries and the corresponding
spectra in libraries.

The options can be selected from a menu or from toolbars. There are
two toolbars, the library toolbar and the spectrum toolbar, that can be
selected from the Library Menu (display pop-up menu) or by using the
toolbar shortcuts,

Toolbar : This button shows/hides the library operations toolbar

Create Creates an empty library shell


Open Opens a library for spectrum handling operations
Copy Copies a whole library and spectrum descriptions and
appends it to another library
Import Imports multiple spectra in ASCII, PIMA or ASD formats to
the currently opened library
Export Exports the currently loaded library spectra with several
different options for the export format.
Delete Deletes a spectral library and all associated descriptor
files, analysis libraries and dependent profiles and
processed files.
Edit Edits a selected library description. The user must SAVE
Description the modifications before exiting.

Additional options include spectral resampling of libraries, with three


options in a drop down menu,

Interpolatio Resamples broad band data to narrow band output using


n interpolation
Gaussian Resamples narrow band data to equivalent width or
larger bands with user control on output Full Width Half
Maximum (FWHM) using a Gaussian bandpass.
Square Resamples narrow band data to equivalent width or
wave larger bands with user control on output Full Width Half
Maximum (FWHM) using a top hat bandpass

Once a library is opened, the spectrum operations are activated, there


are several options in the spectrum operations drop-down menu, also
available in the spectrum operations toolbar,

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Toolbar : This button shows/hides the spectrum operations


toolbar

Plot Plots a spectrum from the currently loaded library.

Copy Copies a spectrum from the currently loaded library to a


specified target library
Import Imports a spectrum using the ASCII, PIMA (.dsp) or ASD
format into the currently loaded library
Export Exports a spectrum from the currently loaded library in
ASCII format.
Delete Deletes a spectrum and its corresponding description
from the currently loaded library
Edit Edits a spectrum description in the currently selected
Description library.

2.2.1. Create command (Library menu)

Use this command to create a spectral library. This command only


creates the shell, the user must modify the library description and add
spectra using the import commands before the library can be used.

2.2.2. Open command (Library menu)

Use this command to open an existing spectral library. The user is


presented with a list of libraries and the corresponding descriptions.

On selection of a library the spectrum operations are enabled for that


library.

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2.2.3. Copy command (Library menu)

The copy command copies a whole spectral library and spectrum


descriptions and appends them to a target library. The user first
selects the library to copy from a list of available libraries and then
the target library (which may or may not exist, if it does not exist it is
created).

2.2.4. Export command (Library menu)

This command allows the user to select a spectral library from a list
and export it using a variety of different output formats. After
selecting the library the user is then presented with the Export Library
Details dialog box,

Output Location : The user selects the path to the directory in which
the exported files are to be placed.

Output Format : The user may choose the output data size (float,
integer, double) and the data format (ASCII or binary) and whether to
produce a single library output file or one file per spectrum.

Include in header : The user has an option to add a header to the


output, either to the single library file or each spectrum file, with
options to include the name, wavelength file name, original library
name and number of bands.

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Wavelength information : The user can place the wavelength values


before each data point or write the wavelength information in a
separate file. The first case could be used when the data in the library
consists of spectra with different wavelength characteristics, the latter
when the library consists of spectra using the same wavelength file.

To export in the standard ASCII two column format, you would select,
float, ASCII. Multiple files, no header information (so leave everything
unchecked) and add wavelength information before data point.

2.2.5. Import command (Library menu)

The import command allows the user to select data files (with the
same wavelength file information) and import them directly into a
spectral library using the PIMA or simple ASCII two column format of
Wavelength in the first column (nanometres or micrometres) and
reflectance in the second column (either percent or values scales
between zero and one). The columns can be separated by tabs and
spaces.

Several hundred files can be selected for import (the actual number
depends on the file name lengths). For PIMA (.dsp) files the description
information in the files is also imported into the library descriptor file.

Limit : The input buffer size is 32768 bytes. Assuming a file name
length of 20 characters and a path length of 50 characters, the upper
limit on number of files for a single operation would be 1635 files.

2.2.6. Delete command (Library menu)

The user selects a library from the available list. On clicking OK, the
library and all associated descriptor files for the library and spectra are
also deleted. Additionally, all libraries created during the preparation
stage for the methods which use the deleted library, are also deleted.

Finally the user is informed of the profiles created by the user (using
the SIMIS Field 2.9. package) which are dependent on the presence of
this library,

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If the user presses continue all the profiles named will also be deleted,
along with all the output analyses produced with these profiles. This
management of the data files prevents the user from selecting profiles
which no longer have the necessary spectral libraries to complete the
analysis operation.

2.2.7. Edit Description command (Library menu)

The user can add or modify a library description at any time. The user
selects the library from a presented list and modifies the text in the
description.

The user must click on the Save button to save the changes, the user
can then edit more descriptions if necessary and then click OK to end
the editing session. The Save button is only enabled for this command.

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2.2.8. Interpolation command (Library Resampling menu)

This method of resampling is used when the input library has


significantly broader bands than the output library.

If we use the Gaussian or Square Wave options we just reproduce


values from a single point and produce a blocky output. The
interpolation provides a smooth output curve, by creating new output
values using the slope between data points.

It can not create a more detailed spectral curve but does have a use
where the input bands are larger but the curve shape is accurate
enough for the identification methods. An example of a USGS curve of
alunite resampled using Square Wave and interpolation options is
shown below.

Square Wave

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Interpolation

As can be seen the two curves are the same in overall shape, but the
square wave output is blocky making identification more difficult.

Comparisons of original curves with the interpolated curves shows no


major resampling induced changes in spectral curve shape.

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2.2.9. Gaussian command (Library Resampling menu)

The Gaussian resampling allows the user to resample from narrow


bands to equivalent or larger size bands.

The user needs to specify the Full Width Half Maximum value for each
output Gaussian. If no value is specified the half-way distance between
band centres is used. The user first selects the library to resample and
is then presented with a range of options for the resampling, in the
Select available data for Resampling dialog box

Note : This method is the equivalent of the Square Wave but slightly
more accurate.

2.2.9.1. Select Available Data for Resampling Dialog Box

This dialog allows the user several options in the way the data is
resampled. The two main options are,

Centre Wavelengths Only : The user supplies a wavelength


file for the resampling process. If this is chosen the user is then
given options for the Full Width Half Maximum (FWHM)
Estimation.

Automatic : In which a distance half-way between band


centres is chosen for the FWHM.
User Specified : A single value (in nanometres) applied to
all the bands.

Centre Wavelengths and FWHM : In this case the user


supplies two files, a wavelength file and an ASCII FWHM file in
which there is one floating point entry for each spectral band.
The FWHM file has a (.fwh) file extension.
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2.2.10. Square Wave command (Library Resampling menu)

The Square Wave resampling allows the user to resample from narrow
bands to equivalent or larger size bands.

The user needs to specify the Full Width Half Maximum value for each
output. If no value is specified the half-way distance between band
centres is used. The user first selects the library to resample and is
then presented with a range of options for the resampling, in the
Select available data for Resampling dialog box

Note : This method is the equivalent of the Gaussian but faster and
slightly less accurate.

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2.2.11. Plot command (Library Spectrum Operations menu)

The plot command (as with all spectrum operations) is enabled once a
library is opened. The user simply selects a spectrum from the plot list
(as the user picks a spectrum name a full description is given, if
available) and clicks OK (or double clicks on the name if the
description is not required)

The spectrum is then plotted in the main plot window. To delete is just
click on the name of the plot to the right of the plot window.

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Up to eight plots may be selected at any one time, each is displayed in


a different system colour. To delete a plot simply click on its name to
the right of the plot box in the area underneath the colour bar
indicating the plot.

Once displayed the user can alter the reflectance and wavelength
scaling. By clicking with the right mouse button in the plot area, the
user is presented with a scaling toolbar.

Scaling Toolbar

The user may select the wavelength range and choose a variety of
methods to rescale the reflectance range,

Reset : Resets the reflectance range from 0-100.


Scale : Allows the user to set the minimum and maximum values
manually.
Float : The maximum and minimum value of all the displayed plots is
used to scale the data.
Ignore : Each spectrum is scaled independently to maximise it in the
plot box.

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2.2.12. Copy command (Library Spectrum Operations menu)

Enabled when a spectral library is loaded. The copy command copies a


selected spectrum from the currently loaded library to a specified
target library, including the descriptor file if present.

The copied file is appended to the library. The copied spectrum does
not have to have the same spectral characteristics as the other
spectra in the target library, it can be from a different spectrometer
with different wavelength ranges and sampling intervals.

Note : there is no name checking of the spectra present in the target


library, so it is possible to have two copies of the same spectrum in a
spectral library by using this command.

2.2.13. Import command (Library Spectrum Operations menu)

The user may import a spectrum directly into the currently loaded
spectral library. The spectrum is selected and then the user provides
the appropriate information when prompted in the Import Spectrum
Details dialog box.

There are three import formats, the ASD, PIMA (.dsp) and the ASCII two
column are available presently. However, the dialog options allow for
the inclusion of more complex input formats at a later date. If PIMA
(.dsp) is chosen the PIMA data file description is also imported into the
library descriptor file.

The user needs to provide details of the method of import in this case
ASD, ASCII or PIMA and a wavelength file (.wve extension) for the data
if there is no suitable wavelength file in the library sub-directory. The
data is then appended to the spectral library.

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2.2.13.1. Import Spectrum Details dialog box

The dialog box is shown in the figure below

File Name
Contains the name of the selected file.

First Line of File


Contains an ASCII representation of the first line of the file,if
ASCII format there are two values separated by a tab or spaces.
The first is wavelength (micrometres or nanometres) and
reflectance (% or in the range 0 to 1).

Standard Formats
There are currently three standard import formats, ASD, PIMA
(.dsp) and an ASCII two column format called ASCII. This option
allows future expansion and the inclusion of alternative formats.

Wavelength File
If this is left blank the user is asked to select a wavelength file
from a list of previously created wavelength files. If the user
types in a name with a (.wve) extension this new wavelength file
is created using the wavelength information in the first column
of the data. This is one method of adding a new wavelength file
to the system.

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2.2.14. Export command (Library Spectrum Operations menu)

The user may export a spectrum from the currently loaded spectral
library in a simple two column ASCII format (wavelength, reflectance).

The user selects a spectrum from the file list and then confirms the
details in the Export Spectrum Details dialog box. Currently there is
only one export format, but the capabilities to add more complex
export formats are present for future releases.

2.2.14.1. Export Spectrum Details dialog box

The export spectrum details dialog box gives the name of the
spectrum to export and the wavelength file for the spectrum as
illustrated below,

The user must then select a method of export, currently there is


only one method, using a simple two column ASCII format. The
option to choose an export method is for future modifications in
later releases of the software.

2.2.15. Delete command (Library Spectrum Operations menu)

The delete command deletes a spectrum and corresponding


description from the currently loaded spectral library.

The user selects the spectrum to delete from a list and is prompted to
confirm the deletion. The command is intended for use in the
preparation stage of creating new spectral libraries.

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2.2.16. Edit Description command (Library Spectrum


Operations menu)

The user selects a spectrum from the available list. The description
box is enabled for editing.

The user can edit a spectrum description then press the SAVE button
to save the changes. The user may then select another spectrum,
modify the description and again save the changes using the SAVE
button. On completion of al changes click OK.

2.2.17. Spectrum Toolbar (Library Menu, display sub-menu)

The spectrum toolbar can be activated from the Library Menu (display
sub-menu) or by using a toolbar shortcut. Each button runs a
command listed in the spectrum operations sub-menu of the Library
menu.

Toolbar : This button shows/hides the spectrum operations


toolbar

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All the menu operations under the Library Menu spectrum operations
sub-menu are available. The operations are not enabled until a library
is opened.

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2.2.18. Library Toolbar (Library Menu, display sub-menu)

The library toolbar can be activated from the Library Menu (display
sub-menu) or by using a toolbar shortcut. Each button runs a
command in the library menu.

Toolbar : This button shows/hides the library operations toolbar

All the menu operations under the Library Menu are available.

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2.3. Run Menu


The Run menu has three commands.

Setup Allows the user to set up the run parameters to extract


Options the features in the unknown spectrum.
Select Library The user can select a library to be used in the search
process. Up to 20 features are calculated for each
library spectrum and a temporary feature library
created.

Search by Hits When checked (default) the results are ordered by


total number of features that coincide that are present
in both the unknown and library mineral.

To carry out the search itself use the Search Library button at
the bottom of the Features in Spectrum dialog box. This is
highlighted as soon as a library has been selected for analysis.

2.3.1. Setup Options command (Run menu)

This option allows the user to change the conditions for the feature
extraction. Increasing or decreasing the level of reflectance change to
qualify as a feature and allowing the user to exclude wavelength
ranges from the analysis. The command calls the Run Setup Options
dialog box.

Toolbar : Calls a dialog to allow control over the feature extraction


process.

2.3.1.1. Run Setup Options dialog box

The Run Setup Options dialog can be called from the menu or
from the toolbar. The dialog allows the user to set up the
parameters for extraction of features positions and depths from
an unknown spectrum.

The options chosen affect the features extracted when selecting


a library for analysis. The chosen noise level affects the feature
extraction process. If the user changes the noise level after
selecting a library, the library features will be recalculated based
on the new noise level.

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Search Width :
This is the value in nanometres to use in the search process.
Features that are more than the search width away from the
unknown spectrum selected feature are not included in the
analysis. The minimum value is 5nm. If this value is changed any
current search of a library is updated.

Noise Threshold :
This value can be set by the user and is used in the feature
search algorithm to ignore changes in the spectrum shape less
than the value specified in percent reflectance.(Default 0.5%
reflectance). The feature list is automatically updated on
changing this value as is the feature library.

Library Feature Depths :


This option was added to reduce the number of spectra matched
in the library. It is based on the assumption that data of pure
minerals measured in the laboratory normally have larger
feature depths than spectra collected during normal field
sampling. This is the default operation. To override this simply
uncheck the check box.

Exclude Wavelength Regions :


The user can set this flag and then give the start and end of
three wavelength regions that should be ignored (in
micrometres). These regions are excluded from the feature

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extraction analysis. (Default is not to exclude). The feature list is


automatically updated when changing these values.

Use Reflectance for feature extraction.


Use Hull Differences for feature extraction :
The user can choose the method employed to extract and
analyse the features. The default at start up is hull differences. A
Hull difference is a baseline stretched across the top of the
spectrum. The feature depths are measured from this baseline.
The creation of the hull also affects the position of the deepest
point of some features and so causes small wavelength shifts in
features.

The current reflectance option determines the depth from a


highest reflectance value in the spectrum and does not change
the position of the features. The two methods produce similar
results. The Hull spectra sometimes extract small important
shoulders (such as the 2.164 feature in Kaolinite), but of course
miss some features picked out using the reflectance method.

For users working with the SPECMIN spectral library the best
choice may be reflectance as the feature positions in the library
are based on reflectance spectra not hull differenced spectra.

Hull differences have one distinct advantage. Most spectra are


high in reflectance towards 1.3 micrometres and the continuum
decreases towards longer wavelengths. As the Hull fits the
continuum, features of equal depth from the Hull are selected
equally. With reflectance data the features at longer wavelengths
are preferentially chosen as they tend to be deeper due to the
drop off in the continuum towards longer wavelengths and so
apparently larger feature depths in this region.

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2.3.2. Select Library (Run Menu)

The user can select a library to use in the analysis. The library is in
the standard SIMIS format (*.slb file). On selection the library is
converted into a temporary feature library. Each spectrum in the
library is converted into a hull difference spectrum and the deepest 20
features extracted from the spectrum. The extraction operation is
dependent on the current Setup Options (RUN menu).

If the user modifies the setup options (such as the noise threshold) the
library features are recalculated.

Toolbar : This button selects a library for analysis.

2.3.3. Search by Hits (Run Menu)

There are two alternative methods of analysis. The default method is


Search by Hits. In this case the Search by Hits command is checked in
the menu.

When checked, if the user selects a feature and searches the library,
all minerals which have a feature at the selected position (or within
the search width specified in the setup options) are chosen. For each
library mineral the number of features in the spectrum which
correspond with the unknown are calculated and the output placed in
the search results dialog, with the mineral with most hits listed first.
This is ideal for determining the major mineralogy, where a dominant
component has many features expressed in a mixture.

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The alternative is to switch off this default processing (uncheck the


command) by clicking on it in the RUN menu.

Now the search process involves searching for all minerals that have
features at the chosen location (as before), but this time the data is
ordered in nearness to the unknown in terms of difference in position
between the unknown feature and the library mineral feature, followed
by depth order. This is effective if the mineral phase has only a single
or perhaps a few features expressed in a mixture, in other words
suitable for the minor mineralogy.

2.3.4. Search Library command (Features in Spectrum dialog)

The Features in Spectrum dialog is shown on loading an unknown


spectrum in the first plot position.

Based on the setup options up to 20 spectra are listed in depth order


in the dialog box. If the user selects a feature in the first controlling
list a line is drawn through the feature in the plot box to indicate its
position. On selecting a library the button at the bottom of the dialog
is highlighted. From this point on, if the user selects a feature from the
list and clicks on the search library button the analysis will take place.
The user may also input a user defined wavelength range which will
be used in place of the feature selected in the controlling list when
carrying out a search.

The results of the analysis are placed in the Search Results dialog.
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2.3.4.1. Features in Spectrum dialog box

This dialog is created when a user places an unknown spectrum


in the first plot position (black curve).

There are three lists, the first list is the controlling list, you
must select a feature from this list. The first item in the list is the
feature position in micrometres, while the second item contains
the feature depth in percent reflectance. If the user selects a
feature from the list it is indicated in the main plot screen as a
black line. The feature position is also listed in the edit control at
the bottom of the dialog (User Defined Wavelength).

There are two narrower subsidiary lists that just contain the
feature positions of the unknown features. The user may select
an additional feature from each list, which will constrain the
search. If three different features are selected (one from each
list) then all three need to be present (within the specified
search width) for the mineral to be placed in the results list. For
the narrower lists, the user can de-select the chosen feature by
double-clicking the mouse with the cursor in the list window. To
search, the user presses the Search Library button and the
results are displayed in the Search Results dialog box

Alternatively the user can type in a value in the edit control


(User Defined Wavelength). This replaces the value of the
controlling list for the search. When the user presses the
Search Library button this time, the search is controlled by the
user defined value and any selected values in the subsidiary
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lists. The user can plot the User Defined Wavelength by pressing
the Draw Position button.

The user searches the currently loaded library based on the options
set up in the Run Setup Options dialog box. This command is activated
on loading a feature library and will operate only after a user has
selected a spectrum from the Features in Spectrum dialog box.

On completion the library minerals matching the unknown are listed in


the Search Results dialog box. If the user changes the setup options
for the search width the library search results are automatically
updated.

2.3.4.2. Search Results dialog box

The search results dialog contains details of the feature library,


the offset of the library minerals from the unknown (in
nanometres), the depth of the feature (% reflectance) and the
mineral name.

If the user selects the mineral name the mineral is plotted in the
main plot window (in red).

Library Name :
This is the name of the currently loaded feature library.

Feature Offset :
This is the difference in nanometres between the unknown
feature and the library feature.

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Feature Depth :
This is the depth of the library feature in percent reflectance.

Unknown Feature :
The position of the feature in the unknown that is being
analysed.

Mineral :
This is the library spectrum name as specified in the original
spectral library.

Attach Button :
This transfers the currently selected mineral from the library to a
list. The attached minerals are those considered minerals that
MAY be present in the unknown. On attaching a file this activates
the Attached Minerals dialog box (if it is not already active).

Description Button :
This retrieves the description (if any) of the currently selected
mineral. The details are displayed in the Spectrum Description
dialog box.

The Spectrum Description dialog box contains details of the


library mineral currently selected in the Search Results dialog
box

The description is to determine the identity and variation in


composition of minerals in the large (over 400 mineral) libraries
used in the search process.

Toolbar : This button shows/hides the Search Results dialog


box
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2.3.4.3. Attached Files dialog box

The Attached files dialog box contains a list of the minerals


considered as possible components in the unknown mineral. The
names, offsets and feature depths are given. The user can
choose any name in the list and it is plotted in green so the user
can confirm the likely presence of the attached mineral. To
delete a mineral from the list, click on it to highlight it and
press the delete button on the keyboard.

Offset :
This contains the offset in nanometres between the unknown
and library mineral for the selected feature.

Depth :
This contains the depth in percent reflectance of the library
mineral feature.

Feature :
This contains the feature position used in the analysis to select
this mineral.

Minerals :
This contains the list of the names of the minerals attached.

User Comments :
The user can add comments (up to 5000 characters) to describe
the output of the analysis and save it to a file.
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Unmix Button and Proportions Window


The user can unmix the unknown based on the library minerals
listed, the proportions are shown in the window next to the
Unmix button along with the mineral names.

There are two unmixing options, the default (more complex


method) based on Unconstrained Generalised Linear Least
Squares and a simpler method based on analyis of feature
depths. To change methods use the Unmix using Feature Depths
command (if feature depth unmixing is operating already, this
command reads Unmix using Least Squares).

Least Squares Unmixing


The unconstrained method is essentially a shape matching
algorithm, trying to determine the contribution of each selected
(attached) mineral to a mixture. Since we are using a library to
match unknown mixtures, there is a possibility that the end-
member assignment may be incorrect, that is although we have
the right GENERAL end-members, we need SPECIFIC examples of
these end members that are closer in shape to the original
mixture components, otherwise the proportions will be very
different from those expected (this can be seen in the mixture
curve (blue) compared to the unknown). Experiments have
shown that if the user selects several examples of each end-
member (if several are present in the library), then the results
can be much improved.

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However, if we only have single examples of some end-members


or we have problems with the matrix inversion of the Least
Squares method (which is possible) we may have to use an
alternative method of unmixing.

Feature Based Unmixing.


This method operates as follows. The user selects features which
are present (if possible) in only a single end-member of the
possible mixture. This takes place when attaching a feature. For
example in a mixture of kaolinite and gypsum, the 2.162 mm of
kaolinite and the 1.446mm feature of gypsum would be good
examples.

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These features occur in regions where there are little or no


effects of the other end-member. The unmixing is based on the
depth of the unknown features relative to the end-members
selected. It is an approximate method providing information on
the proportions of each selected component. The results are
displayed in the box to the right of the button.

Save To File Button :


Saves the results (feature offset, depths, minerals and
description) to a file in an ASCII format with analysis date
information.

Save To History Button :


Saves the spectrum and analysis results (feature offset, depths,
minerals and description) and user comments to the currently
opened History Library for later review. This button is activated
on opening a History library using the Open Library command
from the History menu.

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2.4. Preferences Menu


These commands are to set up the environment in a suitable manner
for the user. Most of the commands also have toolbar shortcuts to
make selection even simpler. There is a Show drop down menu with
four options and an Interface set-up drop down menu with two
options.

Paths Displays the paths to the input, output, library and profiles
sub-directories. The values can be modified by the user.

Features in Shows/Hides the feature list dialog box containing


Spectrum features extracted from the plotted unknown
spectrum.
Search Results Shows/Hides the Search Results dialog box
containing a list of minerals from the library with
offsets and depths produced by searching for the
selected feature in the unknown spectrum.
Attached Features Shows/Hides the Attached Features dialog box
containing lists of minerals selected from the
search results as possible candidate minerals for
the chosen features.
Feature Position Shows/Hides the vertical lines that mark the
Bars position of the spectral features found in the
unknown spectrum. Default is checked.

Zoom using Cursor This option modifies the way the user can scale
the spectra.

Unmix using Feature This option modifies the way the user unmixes
Depths end-member spectra in the attached minerals
dialog.

2.4.1. Path Preferences

At the start up the user has the option to specify the paths for input
and output files, profiles (used in the SIMIS Field product) and libraries.
The user can also modify the paths during the session by choosing the
Preferences menu and selecting the Paths command. In each case the
user is presented with the information below,

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The user may browse the directories to find the correct paths for input,
output, libraries and profiles and save any modifications. These saved
changes will be the default start up paths for the next session. The
user accepts the changes by pressing OK, or restores the original
paths by pressing cancel. The changes become operable immediately.
The SAVE directory for text modifications of PIMA (.dsp) files is also
reset if the INPUT path is changed.

Note : To change drives, press the Browse button and select


the correct drive. Only write-enabled drives are acceptable.

2.4.2. Features in Spectrum (Preferences Menu, show sub-


menu)

This command hides the feature list if it is obscuring the screen and
shows it to select from the list. The list is still active although hidden.

Toolbar : This button shows/hides the feature list.

2.4.3. Search Results (Preferences Menu, show sub-menu)

This command hides the Search Results list if it is obscuring the screen
and shows it to select from the list. The list is still active although
hidden.

Toolbar : This button shows/hides the search results list.

2.4.4. Attached Features (Preferences Menu, show sub-menu)

This command hides the Attached Features list if it is obscuring the


screen and shows it to select from the list. The list is still active
although hidden.

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Toolbar : This button shows/hides the attached features list.

2.4.5. Feature Position Bars (Preferences Menu, show sub-


menu)

This command switches the vertical lines that mark the feature
positions on or off. The default at start up is on.

2.4.6. Zoom using Cusor (Preferences Menu, Interface set-up


sub-menu)

There are two scaling options the default Zoom using scaling toolbar
which is available at start up. By clicking with the right mouse button
in the plot area, the user is presented with a scaling toolbar.

The user may select the wavelength range and choose a variety of
methods to rescale the reflectance range,

Reset : Resets the reflectance range from 0-100.


Scale : Allows the user to set the minimum and maximum values
manually.
Float : The maximum and minimum value of all the displayed plots is
used to scale the data.
Ignore : Each spectrum is scaled independently to maximise it in the
plot box.

The alternative is provided with the Zoom using Cursor command.


When selected, as the user moves the cursor over a plot the
wavelength and reflectance are shown continuously to the top left of
the plot window. If the user depresses the left mouse button and
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moves the cursor (with the button depressed) to the bottom right, an
outline rectangle is drawn that defines the area to scale.

To return back to the original scaling click with the right mouse button
and the normal scaling toolbar is shown, select RESET in wavelength
and reflectance to return to the original plot.

2.4.7. Unmix using Feature Depths (Preferences Menu,


Interface set-up sub-
menu)

There are two possible ways of unmixing end members selected in the
Attached Minerals dialog box, the default start-up method based on
generalized linear least squares unmixing, and a simpler method
based on the analysis of feature depths. This menu command allows
you to toggle between the two methods.

Least Squares
This is the default method the user can select a single mineral from
the spectral library used for each end-member. On clicking on the
Unmix button in the Attached Minerals dialog box, the proportions are
estimated and the mixture drawn in blue on the main plot screen.
However, the method is essentially a shape matching method and
thus the closer the selected end-members are to the true materials in
the mixture, the more accurate the proportions estimation. Choosing
single end-members that satisfy this constraint is difficult and often
the proportions are not correct and this can be seen when comparing
the estimated mixture to the unknown.

An alternative is to select several examples of each mineral as end-


members instead of a single example. If we have a mixture of alunite
and jarosite, we can select three or four alunites and a similar number
of jarosites. When unmixed the sum of the alunites and jarosites tends
to give a more accurate representation of the true proportions in the
mixture. However, when using small libraries with single examples or
when the least squares method fails due to matrix inversion problems
(which can happen) then there is an alternative more approximate
method.

Note : If the wavelength range of the library used is smaller


than the input data, the least squares method can not operate.
In this case the program will inform the user and the feature
depths method of unmixing will be applied instead.

Feature Depths.
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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 jarosite and only
one alunite, otherwise the results will be incorrect.

It operates on the principle that the depth of the unknown features


have a linear relationship to the depths of the library end-members
chosen. This at best will be approximate. If your library mineral of
jarosite has feature depths very different from the unknown then the
proportions estimate will be inaccurate.

Also make sure that each feature selected for a particular end-member
is not strongly influenced by the presence of features from other end-
members present, otherwise the results will be less accurate.

The method provides an approximate guide to the proportions present


and is less sensitive to odd continuum shapes than a standard least
squares unmixing method. Note that if you change your jarosite or
your alunite then of course the relative feature depths will change and
the final result will also be affected.

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2.5. History Menu


History libraries contain the saved analyses from previous analysis and
interpretation sessions. Each spectrum in the library contains details
of the interpreted composition, notes on the analysis and the original
spectrum.

There are numerous options to handle history libraries

Create Library Creates an empty history library shell

Open Library Opens a history library for spectrum handling


operations

Copy Library Copies a whole history library, spectra and analysis


descriptions and appends it to another history
library

Delete Library Deletes a history library and all associated


descriptor files.

Edit Description Edits a selected history library description. The user


Library must SAVE the modifications before exiting.

Once a history library is opened, the spectrum operations are


activated, currently there is a single command,

View Views the analysis information for the selected file from the
Item History library.

2.5.1. Create Library (History Menu)

Use this command to create a history library. This command only


creates the shell, the user must modify the library description and add
analysis results by using the Save to History button of the
Attached Minerals dialog box

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2.5.2. Open Library (History Menu)

Use this command to open an existing history library. The user is


presented with a list of libraries (*.his files) and the corresponding
descriptions.

On selection of a library the spectrum operations are enabled for that


library.

2.5.3. Copy Library (History Menu)

The copy command copies a whole history library (spectra and


analysis descriptions) and appends it to a target library. The user first
selects the library to copy from a list of available libraries and then
the target library (which may or may not exist, if it does not exist it is
created).

2.5.4. Delete Library (History Menu)

The user selects a history library from the available list. On clicking
OK, the library and all associated descriptor files for the library and
spectra are also deleted.

The currently loaded history library can be deleted.

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2.5.5. Edit Description Library (History Menu)

The user can add or modify a history library description at any time.
The user selects the history library from a presented list and modifies
the text in the description.

The user must click on the Save button to save the changes, the user
can then edit more descriptions if necessary and then click OK to end
the editing session. The Save button is only enabled for this command.

2.5.6. View Item (History Menu)

This command is only activated when a History library is opened. On


selecting this item the user is presented with a list of spectra and
corresponding analysis information in the History Spectra dialog box.

The user can now view past analysis results, modify the user
comments associated with a history file and in later versions use the
history data to analyze spectra in a more automatic manner.

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2.5.6.1. History Spectra dialog box

The History Spectra dialog shows all the details of the previous
analysis results stored in a History Library. The library has its
own menu which is activated by pressing the right mouse button
in the dialog box.

Spectrum Plot
The spectrum of the item selected in the Spectra list is plotted.

Spectra
List of the spectra stored in the history library. The list is sorted
in alphabetical order.

User Comments
Comments added by the user to describe the spectrum or the
results of the analyses. The user may modify these comments at
any time.

Best Comparison Fits (Single)


This list is activated when a single unknown spectrum is
compared to the History Library. A perfect fit score is 200
(identical in feature positions and relative feature depths). The
list shows the name of the mineral in the library and the
comparison score. The unknown is also drawn in green in the
plot window and the nearest fitting material is selected from the
History Library and plotted in black.

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Match Library
The working library name (*.wlb) of the original spectral library
(*.slb) used in the analysis process.

Offset, Depth, Feature, Minerals


These are the values present in the Attached Minerals dialog
box, saved and stored in the History library. The ( ) to the right of
the mineral name contain the proportions based on the
unmixing based on feature depth. If zero no unmixing was
carried out.

Additionally there are seven menu commands in a drop


down menu,

Delete Spectrum Deletes the highlighted spectrum from


the list of Spectra in the History library.

Edit User Comments Allows the user to modify the user


comments

Library Mineral Information List details of the library mineral selected


in the list of matched minerals (if
information is available).

Save LIBRARY as EXCEL Details of the sample name, library


input minerals matched and proportions are
saved in a tab-delimited text file for input
directly into EXCEL.

Process SINGLE UNKNOWN Uses the currently opened History Library


spectrum to process an unknown spectrum and
determine its closeness of fit to the
previously processed spectra in the
library. (Not available in this release).
Process MULTIPLE Uses the currently opened History Library
UNKNOWN spectra to process a batch of unknown spectra
and determine their closeness of fit to the
previously processed spectra in the
library. (Not available in this release).
Print Item Prints the currently displayed item
(spectra and analysis details). Not
complete in this release.

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These commands are used for item manipulations in the History


Library and to process unknown spectra in an automatic manner
based on previous analyses present in the History Library.

Delete Spectrum command (History Spectra dialog,


Popup Menu)
The delete command removes the highlighted spectrum and the
corresponding analysis results from the History Library.

Edit User Comments command (History Spectra dialog,


Popup Menu)
The user can modify the comments in the User Comments text
window. Therefore any later information can be added to the
History Library without re-running the analysis.

Library Mineral Information (History Spectra dialog,


Popup Menu)
The user selects a mineral from the list at the bottom of the
dialog. Once selected the user can access information on the
library mineral using this menu command.

Save LIBRARY as EXCEL input (History Spectra dialog,


Popup Menu)
The user can extract the sample names, library minerals
matched and library mineral proportions into a tab-delimited
text file for input into EXCEL. The data file execel_in.tmp is
stored with the FeatureSearch executable in the top level
directory. If the user specifies a path to the EXCEL executable,
EXCEL is opened automatically and the data loaded.

Process SINGLE UNKNOWN spectrum (History Spectra


dialog, Popup Menu)
This option allows the user to compare a SINGLE UNKNOWN
spectrum to all the spectra in the History Library.

The principle is that for each site of interest there are a limited
number of spectra that define the overall composition. By
identifying the composition of a selected sub-set of the original
data and saving the results to a History Library, the user can
then automatically and more speedily identify the composition of
further unknowns by comparing them to those already
processed.

Any spectra which are very different from those in the History
Library will not match the History data closely and this is
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indicated to the user. The user can then identify these spectra
manually and then add them to the History Library to provide a
more complete set for the automatic analysis of the remaining
data.

Process MULTIPLE UNKNOWN spectra (History Spectra


dialog, Popup Menu)
This option allows the user to compare MULTIPLE UNKNOWN
spectra to all the spectra in the History Library.

The principle is that for each site of interest there are a limited
number of spectra that define the overall composition. By
identifying the composition of a selected sub-set of the original
data and saving the results to a History Library, the user can
then automatically and more speedily identify the composition of
further unknowns by comparing them to those already
processed.

Any spectra which are very different from those in the History
Library will not match the History data closely and this is
indicated to the user. The user can then identify these spectra
manually and then add them to the History Library to provide a
more complete set for the automatic analysis of the remaining
data.

The output from the multiple analysis can be displayed in a Map


or Core form in later versions.

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2.6. Printing Menu


There are four printing options,

Print Use this command to print a document.

Print Preview Use this command to display the active document as it


would appear when printed.
Print Setup Use this command to select a printer and a printer
connection.
Add Title and The user can add a Title and Description (up to 1000
Description characters) that can be added to any printed output.

The preview screen looks like this,

The print command scales the SIMIS FeatureSearch screen to fit on the
printed page, it is device independent. Note that if you resize the
SIMIS FeatureSearch screen, only the portion visible is scaled and
printed.

Additionally the user may save a window to the clipboard using the
ALT+PRINT SCREEN buttons and then paste it into a document for
printing. If the user wishes to save all the windows of the screen, use
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the PRINT SCREEN button alone and the whole of the screen will be
saved to the clipboard and can be later pasted in a document and
printed.

2.6.1. Print command (File menu)

Use this command to print a document. This command presents a


Print dialog box, where you may specify the range of pages to be
printed, the number of copies, the destination printer, and other
printer setup options.

Shortcuts
Toolbar:
Keys: CTRL+P

2.6.1.1. Print dialog box

The following options allow you to specify how the document


should be printed:
Printer
This is the active printer and printer connection. Choose the
Setup option to change the printer and printer connection.
Setup
Displays a Print Setup dialog box, so you can select a printer
and printer connection.
Print Range
Specify the pages you want to print:

All Prints the entire document.


Selectio Prints the currently selected text.
n
Pages Prints the range of pages you specify in the From
and To boxes.
Copies
Specify the number of copies you want to print for the above
page range.
Collate Copies
Prints copies in page number order, instead of separated
multiple copies of each page.
Print Quality
Select the quality of the printing. Generally, lower quality
printing takes less time to produce.

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2.6.1.2. Print Progress Dialog

The Printing dialog box is shown during the time that


<<YourApp>> is sending output to the printer. The page
number indicates the progress of the printing.

To abort printing, choose Cancel.

2.6.2. Print Preview command (File menu)

Use this command to display the active document as it would appear


when printed. When you choose this command, the main window will
be replaced with a print preview window in which one or two pages will
be displayed in their printed format. The print preview toolbar offers
you options to view either one or two pages at a time; move back and
forth through the document; zoom in and out of pages; and initiate a
print job.

2.6.2.1. Print Preview toolbar

The print preview toolbar offers you the following options:


Print
Bring up the print dialog box, to start a print job.
Next Page
Preview the next printed page.
Prev Page
Preview the previous printed page.
One Page / Two Page
Preview one or two printed pages at a time.
Zoom In
Take a closer look at the printed page.
Zoom Out
Take a larger look at the printed page.
Close
Return from print preview to the editing window.

2.6.3. Print Setup command (File menu)

Use this command to select a printer and a printer connection. This


command presents a Print Setup dialog box, where you specify the
printer and its connection.

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2.6.3.1. Print Setup dialog box

The following options allow you to select the destination printer


and its connection.
Printer
Select the printer you want to use. Choose the Default
Printer; or choose the Specific Printer option and select one of
the current installed printers shown in the box. You install
printers and configure ports using the Windows Control Panel.
Orientation
Choose Portrait or Landscape.
Paper Size
Select the size of paper that the document is to be printed
on.
Paper Source
Some printers offer multiple trays for different paper sources.
Specify the tray here.
Options
Displays a dialog box where you can make additional choices
about printing, specific to the type of printer you have
selected.
Network...
Choose this button to connect to a network location,
assigning it a new drive letter.

2.6.4. Add Title and Description command (Printing menu)

The user may add a large title (20pt Arial), placed above the plot and a 1000 character
description (placed immediately below the plot) using this command.

The user adds the information in the Add Title and Description dialog box.

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2.7. Help Menu


The Help menu offers the following commands, which provide you
assistance with this application:

Help Topics Offers you an index to topics on which you can get
help.

About Displays the version number of this application.

2.7.1. Index command (Help menu)

Use this command to display the opening screen of Help. From the
opening screen, you can jump to step-by-step instructions for using
SIMIS FeatureSearch and various types of reference information.

Once you open Help, you can click the Contents button whenever you
want to return to the opening screen.

2.7.2. Using Help command (Help menu)

Use this command for instructions about using Help.

2.7.3. About command (Help menu)

Use this command to display the copyright notice, version number and
license details of your copy of SIMIS FeatureSearch.

2.7.4. Context Help command

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Use the Context Help command to obtain help on some portion of


SIMIS FeatureSearch. When you choose the Toolbar's Context Help
button, the mouse pointer will change to an arrow and question mark.
Then click somewhere in the SIMIS FeatureSearch window, such as
another Toolbar button. The Help topic will be shown for the item you
clicked.

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2.8. Exit Command


Use this command to end your SIMIS FeatureSearch session.

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Appendix 1 : Data formats


IMPORT and EXPORT

The standard import and export format is a simple two column ASCII
format without headers. Most commonly used field spectrometers
provide this output as an alternative (PIMA, GER, ASD).

An example is shown below,

1.3 83.4
1.32 84.7
1.34 83.9

A PIMA format is also acceptable.


ASD formats are also acceptable.

WAVELENGTH FILES and SPECTRAL LIBRARIES

The wavelength files for the spectral libraries are binary files (float).
Temporary wavelength files are created for plotting unknown spectra.
There is one value for each band.

Spectral libraries (.slb) files have a fixed format with each spectrum
having the following information,

Mineral Name (50 bytes)


Library Name (50 bytes)
Wavelength file name (50 bytes)
Number of bands (Integer, 4 bytes)
LOOP Number of Bands
Spectral Data (Float, 4 bytes)

The descriptions for each spectrum are saved in one file which has the
library name with a (.dsc) extension. Each entry starts with the
number of bytes in the file, followed by the description. Up to 5000
bytes of information can be stored for each spectrum.

Each library can also have a description of up to 5000 characters. This


is stored with the same file name and a (.sld) extension.

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HISTORY LIBRARIES

These libraries hold the analysis results of previous FeatureSearch


runs. Each History library (*.his) file contains the following information,

Mineral Name (50 bytes)


Library Name (256 bytes)
Number of bands (Integer, 4 bytes)
LOOP Number of Bands
Spectral Data (Float, 4 bytes)
Wavelength data (Float, 4 bytes)
ENDLOOP
Number of matched library minerals from analysis.
LOOP Number of minerals
Analysis Data (50 bytes)
Unmixing proportion (Float, 4 bytes)
ENDLOOP
Number of bytes of information in the user comments.
User Comments (bytes = Number of bytes, Maximum 5000)

Each library can also have a description of up to 5000 characters. This


is stored with the same file name and a (.hid) extension.

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