Simis Featuresearch 1.5. Tutorial

SIMIS FeatureSearch 1.5.
Tutorial
Welcome to SIMIS FeatureSearch.
The SIMIS FeatureSearch product is one of a range of products

produced in collaboration with Spectral International Inc. for the
identification of unknown mineral spectra for mineral exploration
and mining.
The algorithm can operate with data from any field spectrometer
(visible-Infrared and thermal Infrared) after conversion to the
standard ASCII input format or alternatively PIMA files can also be
used. ASD support has now been added.
This package enables the user to load an unknown spectrum (by

dropping the file into the plot window, or selecting it using the PLOT
SPECTRUM or PLOT PREVIEW commands), the user can find the
features in a spectrum (up to 20) 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 down the selection of possible
minerals for more automated procedures of determining mineral
proportions and in identifying unusual minerals or mineral
combinations. It is especially useful for novice users identifying
minerals present in mixtures based on feature position and shape
and for advanced users who wish to determine the less commonly
occurring mineral phases in spectral mixtures.
We welcome your comments.
For more information please contact Dr. Stephen Mackin,
Phone : +44 1727 845 467

E-Mail : stephen.mackin@merseymail.com
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SIMIS FeatureSearch 1.5. Tutorial
Contents
1. Installation 3
2. Tutorial 5
2.1. Setting up paths 6
2.2. Plotting an unknown spectrum 8
2.3. Library Routines 11
2.4. Setting up run options 13
2.5. Selecting a library for the search 15
2.6. Plotting an unknown spectrum and feature extraction

16
2.7. Searching the library 17
2.8. Attaching features and unmixing 21
2.9. History Libraries 27
2.10. Printing the results 30
2.11. Getting help 32
Appendix 1 - Data Formats
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1. Installation
The software is for 32 bit platforms only and operates on Windows
95, 98, 2000, XP and Windows NT. The software requires 5MB of
hard disk space and will occupy less than 4MB of main memory
when operating.
The installation is on a single WinZip zip file which contains the

data, executable and libraries.
Double click on the zip file to open WinZip and click on the WinZip
INSTALL button.
The installation program is run. You can modify the installation
location.
On completion, exit WinZip and run the installed software by
double clicking on the simfind.exe file. The opening paths
statement points to the top level directory specified 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
details. THESE MUST BE SENT as a counter-key is required to
operate the software. The counter-key will be sent by e-mail in a
file ckey.txt. Save it to the Desktop. Once it has arrived start up
FeatureSearch again and you can select the ckey.txt file from
the Desktop. Once selected the software will start normally. This
is only required once.
On completion you should have the following
Top level directory with...
mfc40d.dll
msvcr40d.dll
simfind.exe
simfind.hlp
prefs.dat
license.txt
feature-tutorial.doc
feature-tutorial_cover.doc
feature-user.doc
feature-user_cover.doc
/INPUT sub-directory
core1.dat to core7.dat
map1.dat to map22.dat
spectrum1.cse and spectrum2.cse
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/LIBRARY sub-directory
usgsr.slb
usgsr.dsc
usgsr.sld
usgs.wve
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2. Tutorial
This tutorial follows a step by step procedure in loading an unknown
spectrum, finding its features, searching a specified spectral library,
saving the end-members found and unmixing. Additionally we will
show the use of History Libraries to store output results and the
automatic searching capabilities for single and multiple unknown
spectra. In each case we show screen shots of each user interface
screen.
The extensive on-line help also covers many of these topics.
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2.1. Setting up paths

At the system start up you are presented with a copyright notice,
Followed by the PREFERENCES Menu PATHS command dialog. The

initial dialog points to the path specified during installation. You will
need to select the paths for the input data and the location of the
spectral libraries and their corresponding wavelength files.
In this case using the BROWSE button
select the pre-defined sub-directories (\library, \input ) and click

OK. These are now the default paths and will be used during this
session and as the default for later sessions.
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If you wish to set up paths for another user or another project, this
can be done at start up (as the paths dialog is always shown at
start up) or during a session by choosing the PATHS command from
the PREFERENCES menu. The flexibility allows different users to
have different libraries and input sub-directories or different set-ups
for different projects.
NOTE : the directories must exist, they can not be created within
the Paths dialog. Paths to different drives can be selected using the
BROWSE button. The system automatically determines the drives
available, the user can select any media (excluding read-only) for
the path.
NOTE : If the user modifies the INPUT path, this also modifies the
SAVE directory for PIMA (.dsp) text descriptions to the same INPUT
path.
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2.2. Plotting an unknown spectrum

There are three ways of plotting an unknown spectrum,
(a) use the PLOT menu, SPECTRUM command and select the file
from those shown in the INPUT sub-directory or other directory.
(b) or more simply, open the Windows Explorer and select a file and
drag it into the plot window and simply drop it.
(c) or use the PLOT menu, PREVIEW and ANALYSIS CONTROL
command to look at thumbnail plots of the spectra in the INPUT
sub-directory and select one from the available list to plot in the
main window. This control once activated provides a simple
means of selecting and analysing the data files in the selected
INPUT directory.
The data can be in one of three formats, simple two column ASCII
data with column 1 as wavelength (micrometres or nanometres)
and column 2 as the data value (percent reflectance or values
between 0 and 1), separated by a space or tab, PIMA format (.dsp
or .fos) and a range of ASD formats.
Plot the spectrum core7.dat provided in the input demonstration

data.
The spectrum is plotted with a 0 to 100 reflectance scale.
The data is shown with vertical 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 off
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this preference the user can select the PREFERENCES menu, SHOW
sub-menu, FEATURE POSITION BARS command.
We can click with the right mouse button in the plot area. We are
presented with the scaling toolbar,
It has two wavelength options and four reflectance options.
Choose the scale option under wavelength. The current spectral

range of the plots defines the minimum and maximum values
displayed,
Modify the minimum to have a value of 2.0 and click OK. The
spectral range is modified and the spectra redrawn.
Now select the PREVIEW command from the PLOT Menu and click on
the first spectrum in the list. The file is plotted to the right of the
list. Scroll down the list using the arrow keys.
Choose sample spectrum1.cse and click the OVERLAY button. The

spectrum is plotted in the main plot window within the user defined
wavelength range.
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Now we wish to adjust the reflectance. We choose the Reflectance

Scale option (right mouse button to raise toolbar) and are asked for
a minimum and maximum value. Select a minimum of 40 and a
maximum of 60. Note that the extremes of the plotted range are
clipped. A better alternative might be to use the FLOAT option, this
rescales the spectra to fit in the maximum and minimum limits of
all the plotted spectra. Rescale again using the FLOAT option.
However, the spectrally flat materials are difficult to study using
this scaling, so we have an alternative to IGNORE reflectance and
just scale the data to the minimum and maximum of each individual
spectrum. This allows us to study the spectral shape while ignoring
the absolute reflectance values. Rescale again using the IGNORE
option.
We may wish to find a position of a feature, click on the major

absorption shown (left mouse button) and note that the wavelength
position is shown in the top left hand corner of the plot box, with a
reflectance value of zero as reflectance is being ignored. OK, using
a right click raise the scaling dialog and choose reset for the
wavelength, the data are now rescaled to the minimum and
maximum wavelength values. Now we wish to remove a spectrum
from the plot box (we can plot up to eight simultaneously in
different colours), move the cursor over the name spectrum1.cse
beneath the coloured bar and click once with the left mouse button.
The spectrum is deleted. Note that the remaining spectral range is
smaller and the screen is automatically rescaled.
An alternative method of scaling the data can be selected. Choose

the PREFERENCES menu, INTERFACE SET-UP sub-menu, ZOOM
USING CURSOR command. Move the cursor over the plot, note that
the wavelength and reflectance values in the top left red-coloured
areas are now updated as you move the mouse. In this mode, the
user can zoom a plot (scale it), by selecting the top left hand corner
of the plot with the left mouse button and while keeping the button
depressed, move the mouse to the bottom right. Try this. An outline
rectangle is drawn that represents the zoom area. On releasing the
mouse the area selected is scaled (this is the equivalent of carrying
out two operations, a manual SCALE of reflectance and a manual
SCALE of wavelength). Additionally in this mode the user can also
use the normal scaling toolbar.
Click with the right mouse button and the scaling toolbar is shown
as before. The user can now use the default scaling options to
change the reflectance scaling. Click with the right mouse button
and select FLOAT. Then click again with the right mouse button and
select WAVELENGTH RESET to get back to the original plot.
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2.3. Library Routines

There are many spectral library and individual spectrum handling
routines. A spectral library has been provided 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 individual
spectrum or complete library. Additionally three methods of
resampling are included to allow the user to convert the data
(modify wavelength ranges, number of spectral bands and their
positions) to use in both simulations of other instruments or to
convert one library to have characteristics of the field instrument
used in the analysis.
A library is included with this software. The library is the USGS

library (usgsr.slb), which covers a much larger wavelength range
than most currently available field spectrometers.
From the Library Menu choose OPEN,
You are presented with a list of spectral libraries. A single click on a

library name provides a library description. Select the usgsr.slb
library by either double clicking on its name or single clicking and
choosing OK. Its name is placed in the status bar at the bottom of
the screen. The spectrum operations are now available.
To make the data handling easier, raise the Library and Spectrum
Operations floating toolbars. These can be activated by pressing
the toolbar icons,
Library toolbar Spectrum Toolbar
Each toolbar can be dragged to a point where they do not obscure

the screen. The toolbars contain most of the major library and
spectrum operations,
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Library Spectrum
To remove the toolbars simply click again on the icon below the
main menu.
Now click on the PLOT 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 available).
Either double click on a name or single click and select OK to plot a

spectrum.
The library routines include those to Create new library shells, Open
libraries for plotting, copy, delete and export spectral libraries,
create new libraries by importing spectra in ASD, ASCII or PIMA
formats and edit library descriptions.
Also the user can resample libraries from one instrument

configuration to another.
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 provide a great deal of flexibility in creating spectral

libraries to use with the SIMIS FeatureSearch and other SIMIS
products and to export to other external software products.
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2.4. Setting up run options
The user can now set up the run to find features. Click on the setup
options toolbar icon, or choose the RUN menu, SETUP OPTIONS
command. A dialog is shown with the current setup,
The user can select several parameters. The Search Width is the
distance from an unknown spectral feature position that the
algorithm can search for library features. The default is 5nm.
The noise threshold is used in the extraction algorithm to

highlight only the important features. If the user lowers this value,
more features are found. If raised, less features are found. The
value is not the depth of the feature, but is the size of feature
required 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 specified noise
level.
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 specified feature. This operates on the basis
that in some cases the impure sample spectra will have features
which are smaller than the pure laboratory measured library
spectra. This reduces the number of hits significantly and speeds
up the interpretation process.
The user can also exclude up to three wavelength regions. This

is more useful for analysis of field spectra collected with ASD or
GER spectrometers where the water absorption features from field
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collected spectra are often extremely noisy. The values chosen are
the default for the session (but are reset on restarting). They maybe
modified 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
Differences for feature extraction (the default) or Use
Reflectance for feature extraction. Hull differences provide an
upper baseline for determining each feature shape, position and
depth. Features extracted using Hull Differences can be moved in
position by several nanometers relative to the reflectance
spectrum.
Hulls have the advantage of providing the upper baseline for

feature depth extraction and in extracting small shoulders in
doublet features such as Kaolinite that can not be extracted easily
with reflectance data. However, both methods produce very similar
results. Those users working with the SPECMIN spectral library may
wish to use reflectance rather than hulls as the SPECMIN features
are based on reflectance data analysis.
Both methods are provided. The reflectance method baseline for

determining depths of features is the highest reflectance value of
the spectrum.
Click OK to accept the current set of set-up values.
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2.5. Selecting a library for the search

The user has only to select a library (*.slb) file from the presented
selection using the RUN menu, SELECT LIBRARY command or the
corresponding toolbar icon . The library is automatically
converted into a temporary feature library (maximum 20 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 RUN menu,
SETUP OPTIONS command. The temporary library is modified if the
set-up options are modified during a run.
The library must consist of files that have the same number of
bands and wavelength range. If you have created a spectral library
with PIMA data, with ASD data and with USGS data you will need to
use the resampling options in the Library Menu to produce a
resampled spectral library to provide to the feature extraction step.
Note : That although all the spectra in the library have to

have the same number of bands and wavelength range,
these values can be different from the input data being
analysed.
In other words we can use a PIMA library in the analysis of

ASD spectra or an ASD library in the analysis of data from
the USGS instrument.
To prepare for our run, turn off the spectrum and library toolbars
and delete the plotted spectra from the plot screen (click on their
names). Now choose the RUN menu, SELECT LIBRARY option and
select the USGSR.SLB file. The preparation takes several seconds
and a temporary feature library will be created (.wlb) and its name
written above the plot window.
The user can select another library at any time, by clicking on the
feature library selection icon or choose the RUN menu, SELECT
LIBRARY command.
On selecting a library it is listed as the loaded feature library and

the Search Library routines are activated. If a spectrum is already
plotted the Search Library button at the bottom of the feature list
becomes active, if there is no library selected the button is
disabled.
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2.6. Plotting an unknown spectrum and feature

extraction
Plot spectrum core7.dat using the PLOT menu SPECTRUM command,
the ANALYSE button on the PLOT PREVIEW window or by drag and
drop from the Windows Explorer. The unknown spectrum needs to
be in the first plot position for drag and drop or PLOT SPECTRUM
(black spectral curve). If it is not, then delete the spectrum that is in
this position and Plot the unknown spectrum again.
The Find Features is activated automatically and a feature list

produced.
You are presented with a screen similar to this. The features are
listed in a dialog box. There are three lists, the first list is the
controlling list with the first item being the position in
micrometres, then depth in percent reflectance. The other lists are
subsidiary lists and only contain the feature positions. If you click
on a feature in the controlling list, its position is indicated in the
plot box.
You can now change the set-up options to alter the noise
threshold. The list is updated automatically on changing any set-up
option. Open the set-up options and change the noise threshold to
0.7 and click OK. Note that the number of features matched is
reduced. Change the value back again to 0.5 and click OK. The
original feature list is now re-created.
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The features list can be toggled on and off if it obstructs the screen
using the icon in the toolbar. Even if hidden it remains active.
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2.7. Searching the library

Now we can search the loaded feature library for features.
Select the feature 2.21 from the list (this is a feature of alunite) and
click the SEARCH LIBRARY button on the Features in Spectrum
dialog box. The library is searched and the minerals which have a
feature at the chosen position (within the search width) are listed
with the library mineral in first position that has more features that
coincide with the unknown. This is the default behaviour known as
Search by Hits.
This is the best matching scheme for determining major

mineralogy, the dominant minerals which have plenty of features in
the spectrum.
The alternative 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
first). This is better for minor mineralogy when you have a single
feature of an unknown mineral and wish to try and determine the
likely mineral identity.
To choose this option select the RUN menu, and choose the checked
SEARCH BY HITS command. The option is switched off and the
command unchecked.
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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 2.21 have bigger features at this location.
This lengthens the search process. So for major mineralogy switch
the Search by Hits back on by going to the command again and
clicking on it to activate it.
Now select the feature at 2.264 which is from jarosite and press the
Search Library button. Two of the top three minerals do contain
jarosite, which suggests that more than one feature in the spectrum
is from jarosite.
Now click on the RUN menu, SEARCH BY HITS command to switch it

off.
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The jarosite now occupies all three top positions. Minor mineralogy
can be more easily determined using this method as it tends to
have 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 first jarosite) the
spectrum is plotted in red against the unknown spectrum. If the
PREFERENCES menu, SHOW sub-menu, FEATURE POSITION BARS
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 equal 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 DESCRIPTION button.
The spectral range shown is too large. Use the right mouse button
in the main plot window to change the WAVELENGTH scaling
(SCALE) to the 1.3 to 2.5 range of the input data. Now click on the
DESCRIPTION button and scroll through the description. Click
continue.
NOTE : the results dialog can be toggled on and off using the
toolbar icon. The window is hidden but is still active.
A new feature of the current update is the ability to select multiple

features (up to 3). You need to select a feature from the
controlling list and if you wish one from each of the subsidiary
lists. Now click on the RUN menu, SEARCH BY HITS command to
switch it back on. From the controlling list select 2.166, from the
other two subsidiary lists select 1.432 and 1.48 and search the
library. Only a single alunite is selected. Plot the alunite by clicking
on it in the Search Results window. It can be seem to closely match
the alunite of the unknown. This method can reduce the search
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time enormously and also increase the accuracy of the final

selection.
Finally, note that as the user selects a wavelength in the
controlling list the value is also placed in the edit control at the
bottom of the dialog (User Defined Wavelength). The user can
override the selection and input a user defined wavelength position
in this edit control. The inputted value will be used for the search
when the Search Library button is selected. The user can see the
position of the user defined 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. Note that if the subsidiary lists are selected
they will still be used in the search along with the user defined
wavelength.
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2.8. Attaching features and unmixing

There is also an ATTACH 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.
Click attach and the mineral (in this case Alunite) is added to the
Attached Minerals list. Move the Attached Minerals box to an empty
area of the screen or switch it off (invisible but still active) using the
toolbar button. Now click on the RUN menu, SEARCH BY HITS
command to change the searching method. Go to the Features in
Spectrum dialog box and select the feature at 2.264 double click on
the 1.432 and 1.48 features in the subsidiary lists to switch them off
and click on the Search library button. The first jarosite in the
Search Results list is jarosite1.spc. Select and attach it.
The minerals are listed with offset 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 Green against the unknown spectrum in the
main plot window (click on each mineral listed to see the effect). If
the user presses the DELETE button on the keyboard after
highlighting a mineral in the list it is deleted. This allows the user to
remove incorrect selections towards the end of the analysis. There
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are three buttons in the dialog, Unmix, Save to File and Save to
History.
Unmix
There are two unmixing options available in the package, a simple
option based on feature depth analysis and a more complex option
based on unconstrained Generalised Linear Least Squares. The
default at start up is the Least Squares method. The user may
change the method of unmixing by selecting the PREFERENCES
menu, INTERFACE SET-UP sub-menu, UNMIX USING FEATURE
DEPTHS command. The effective use of unmixing requires some
explanation as discussed below.
Least Squares Unmixing.

If we had a complete set of spectra that defined the mixture space
of our unknowns the application of this method would be simple.
However, in reality we may use a spectral library which is a sub-set
of reality and thus does not quite capture the range of variation in
the unknown mineral, introducing a small error in the determination
of proportions.
Using the core7.dat sample as an example, if we select a single

alunite and a single jarosite (these are correct GENERAL end-
members) we will find that not only are the proportions inaccurate,
but the proportions estimation depends on the SPECIFIC alunite and
jarosite used, so if we select an alternative alunite we end up with
different and quite possibly incorrect proportions.
As can be seen in the example shown above, the end-members

based on a feature search are GENERALLY correct for the mineral
mixture. However, the two minerals selected from the library are
different from those in the original mixture, producing incorrect
proportions as can be seen in the comparison of the mixture against
the unknown shown on the following page. To test this click UNMIX
on the Attached Minerals dialog.
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Clearly we need to improve the result. How do we improve the

result ?. Previous studies of soil-vegetation unmixing in a European
Space Agency study showed that by using multiple end-members
of similar materials we can reduce the inaccuracy of the proportions
estimation. In this case, it means using several alunites and several
jarosites to try to cover the range of variation of the unknown
compared to the library. In the case shown below after the end-
members were determined (alunite and jarosite in this case),
several examples of each mineral were included and the total for
jarosite and the total for alunite calculated manually.
The corresponding comparison of mixture and unknown is on the

following page.
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A single alunite and jarosite account for most of the variation, the
result gives a better approximation of the alunite and jarosite
proportions (within 2.5%). This method can operate when you have
a large library with several examples of each end-member. But
what happens in the case were you are using a small library, or the
matrix will not invert using Least Squares (which is possible). The
alternative is a simpler method based on feature depths (discussed
below).
NOTE : If the input data has a wider wavelength range than

the library data, this method can not be used, as part of the
analysis step is to resample the library data to create an
unmixing matrix and if the wavelength range of the input
data is not covered, this is not possible. If this case occurs
the program automatically chooses the unmixing based on
feature depths as dicussed below.
Unmixing based on Feature Depths

There is a simple unmixing option available 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 jarosite
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and only one alunite, otherwise the results will be incorrect. Use
those plotted.
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 incorrect.
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.
In this case make sure that the jarosite feature is that at 2.264m
and that of the alunite is 2.166m. Now select the PREFERENCES
menu, INTERFACE SET-UP sub-menu, UNMIX USING FEATURE
DEPTHS command. Now, Click on the Unmix button and the
proportions are given in the window to the right of the button.
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. If you
do have more than one jarosite and one alunite, you can select for
example three jarosites for the 2.264m feature and three alunites
for the 2.166m feature (it must be the same number for each end-
member in this case three and three) and sum the jarosites and
alunites to get average values that may be more accurate.
Save to File
This button is used to save the results of the analysis to a simple
ASCII text file. Click on the button and choose an output file name.
Open the file with NOTEPAD later to look at the contents which will
be similar to those shown below.
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core7.dat Tuesday, February 23, 1999

LIBRARY USED : c:\simis\librar~1\usgsr.wlb
1 23.72 2.264 jarosit7.spc
1 25.09 2.264 jarosit1.spc
1 26.88 2.264 jarosit5.spc
1 28.65 2.166 alunite1.spc
USER COMMENTS
This is an alunite-jarosite mixture.
Three jarosites were selected based on a small 2.264 feature.
Alunite dominates the mixture.
Save to History
A more recent alternative is to save the spectrum and analysis
results in a History Library (discussed in detail in the next section)
as a History Item.
Each item in the library (spectra listed in the top right) can be
highlighted and the details of the analysis recovered. This provides
a simpler, faster and more effective way of storing the output
results.
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2.9. History Libraries.

History libraries have two purposes, firstly they provide a means to
store the analysed data and access it at the push of a button in a
far more useful fashion than the data stored as ASCII files.
Secondly, they can be used to speed up the processing of data files

taken from a single site.
History libraries have a similar command set as those for standard

spectral libraries. The user needs to create a history library using
the HISTORY menu, CREATE LIBRARY command. This creates a
library with a (.his) extension.
Create a library called myhist.his. Edit the library description using

the HISTORY menu, EDIT DESCRIPTION LIBRARY command, with the
text My first history library and then click on the SAVE button.
Click OK. Now open the library using the HISTORY menu, OPEN
LIBRARY command.
The library name is placed in the status bar at the bottom of the
screen and the HISTORY menu, VIEW ITEM command now becomes
operational. Click on this command. You are informed that the
library has no items. Go to the Attached Mineral dialog and click the
Save as History button. The analysis data has now been
transferred to the currently opened History Library.
Click on the HISTORY menu, VIEW ITEM command again. This time
you are presented with the History Item dialog,
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 05/04/2017
add numerous spectra from a site. On selecting a spectrum name in

the list, the spectrum is plotted, the User Comments 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 above 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 User Comments. Use the right mouse
button and click once in the area of the History item dialog box. You
are presented with a pop-up menu with seven items,
Delete Spectrum
This is used to delete the currently highlighted spectrum in the
Spectra list.
Edit User Comments.

Click on this command and you are presented with the current text
(if any) in a small edit control. Modify the text and click OK. The
comments are updated. Up to 5000 characters can be placed in the
comments box.
Library Mineral Information

Click 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 retrieved.
Save LIBRARY as EXCEL input

This command takes the sample name information, minerals
matched and the corresponding proportions and creates an ASCII
text file excel_in.tmp in the top level directory (with the
FeatureSearch executable). The user may then select the path to
the EXCEL executable and the data is loaded as a tab delimited file
directly into EXCEL.
Process SINGLE UNKNOWN spectrum

29 05/04/2017
This command allows you to compare a single unknown spectrum

to those in the History Library. If a very close fit is found the same
analysis results are provided for the unknown. The principle of
operation is that if the History Library covers the spectral variation
found at a site and a new sample needs to be analysed, the fastest
way to do it is to compare it to other samples from the same site. If
it is VERY similar then it is given the results of a previous analysis
run. The unknown is plotted in GREEN against its nearest fitting
History Library sample. A perfect comparison (unknown and library
mineral identical in both feature positions and relative depths) has
a score of 200. The results are shown in the Best Comparison Fits
(Single) window.
Process MULTIPLE UNKNOWN spectra

This is an extension of the SINGLE analysis and allows the user to
compare a batch of spectra (over 1000 at a time) to the History
Library. If selected spectra from a site have been used to manually
characterise the variation, the other spectra can be analysed at
high speed using this method. The accuracy of the results is used to
indicate spectra that are different from those present in the History
library and need further manual detailed analysis. This allows the
user to create spectral libraries that are suitable for AUTOMATIC
unmixing of data from a specific area and can be used in the SIMIS
QSearch package (due for release in September 1999).
The results are currently saved in a text file in the INPUT path
(batchres.dat). However, in future releases the data will be
automatically viewed using the SIMIS CoreViewer module. The
output consists of the unknown name, best matching library
material name and comparison score (200 is a perfect fit).
Print Item
The user can print the currently displayed spectrum and analysis
details using this command. Operational, but not complete in
this release.
Select the Edit User Comments command from the list. A new
dialog is shown, add the text My comments in the dialog shown
and click OK.
NOTE : The dialog must be closed before processing can

continue using the OK button.
Now use the HISTORY menu, COPY LIBRARY command and copy the
history library to another named backup.his. Now use the HISTORY
menu, DELETE LIBRARY command and select myhist.his. The library
is deleted and the status bar entry is changed to No History.
30 05/04/2017
2.10. Printing the results

There are device independent print options. The user can preview
the printing and modify the print attributes. Note that the print only
covers the region of the SIMIS FeatureSearch screen, so if you resize
the screen to be smaller, the printed region also becomes smaller
by clipping of the screen contents.
The user can add a Title and Description (up to 1000 characters in
this release). Simple select the ADD TITLE and DESCRIPTION
command from the PRINTING menu. You 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 just below the main plot window.
NOTE : when using a 640 x 480 screen resolution, there is
only space for a single description line when using
Landscape prints.
An example of a print preview with title and description is shown on

the following page. The Title and Description remain active until
deleted or modified.
31 05/04/2017
Try the print options and modify the screen size to see some of
these effects.
Additionally, not that the History Items can be printed using the
Print Item command in the drop down menu for the History
Dialog.
Finally, the normal range of standard print screen options are

available. If the user wishes to incorporate the results shown
directly into a document, then highlight the window you wish to
copy and press the ALT+PRINT SCREEN buttons at the same time to
save it to the clipboard and then using a program such as WORD,
paste the clipboard contents into your document.
If you want all the dialogs and main screen, just press the PRINT
SCREEN button and the entire screen contents are copied to the
clipboard and can later be pasted in a document.
32 05/04/2017
2.11. Getting Help

There is extensive online help covering all the commands and
providing more details on methods and formats. Choose the Help
Menu HELP TOPICS.
The user may also use the Context Help option ( toolbar
button). When active the user can select any menu command,
toolbar button or non-modal dialog box and jump to the
corresponding help information.
For additional help on the methods of analysis or any other query

regarding the use of the software, contact Dr. Stephen Mackin
(stephen.mackin@uam.es).
33 05/04/2017
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.

The ASD format is also available in this release.
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.
34 05/04/2017
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.
35 05/04/2017

Simis Featuresearch 1.5. Tutorial

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Simis Featuresearch 1.5. Tutorial

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SIMIS FeatureSearch 1.5.

Welcome to SIMIS FeatureSearch.

The SIMIS FeatureSearch product is one of a range of products

This package enables the user to load an unknown spectrum (by

The output is a list of candidate minerals and a user description.

We welcome your comments.

For more information please contact Dr. Stephen Mackin,

Phone : +44 1727 845 467

2.1. Setting up paths 6

2.2. Plotting an unknown spectrum 8

2.3. Library Routines 11

2.4. Setting up run options 13

2.5. Selecting a library for the search 15

2.6. Plotting an unknown spectrum and feature extraction

2.7. Searching the library 17

2.8. Attaching features and unmixing 21

2.9. History Libraries 27

2.10. Printing the results 30

2.11. Getting help 32

Appendix 1 - Data Formats

The installation is on a single WinZip zip file which contains the

On completion you should have the following

Top level directory with...

The extensive on-line help also covers many of these topics.

2.1. Setting up paths

Followed by the PREFERENCES Menu PATHS command dialog. The

In this case using the BROWSE button

select the pre-defined sub-directories (\library, \input ) and click

2.2. Plotting an unknown spectrum

Plot the spectrum core7.dat provided in the input demonstration

The spectrum is plotted with a 0 to 100 reflectance scale.

The data is shown with vertical bars which correspond to the

It has two wavelength options and four reflectance options.

Choose the scale option under wavelength. The current spectral

Choose sample spectrum1.cse and click the OVERLAY button. The

Now we wish to adjust the reflectance. We choose the Reflectance

We may wish to find a position of a feature, click on the major

An alternative method of scaling the data can be selected. Choose

2.3. Library Routines

A library is included with this software. The library is the USGS

From the Library Menu choose OPEN,

You are presented with a list of spectral libraries. A single click on a

Library toolbar Spectrum Toolbar

Each toolbar can be dragged to a point where they do not obscure

Either double click on a name or single click and select OK to plot a

Also the user can resample libraries from one instrument

The routines provide a great deal of flexibility in creating spectral

2.4. Setting up run options

The noise threshold is used in the extraction algorithm to

The user also has an option (default is on) to exclude library

The user can also exclude up to three wavelength regions. This

Hulls have the advantage of providing the upper baseline for

Both methods are provided. The reflectance method baseline for

Click OK to accept the current set of set-up values.

2.5. Selecting a library for the search

Note : That although all the spectra in the library have to

In other words we can use a PIMA library in the analysis of

On selecting a library it is listed as the loaded feature library and

2.6. Plotting an unknown spectrum and feature

The Find Features is activated automatically and a feature list

2.7. Searching the library

This is the best matching scheme for determining major

The alternative is a single feature search in which the features