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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.
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Contents
1. Introduction 3
2. Commands 4
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1. Introduction
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.
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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.
To delete a plotted spectrum just click on its name to the right of the
plot box.
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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
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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.
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.
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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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,
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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.
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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.
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.
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.
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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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.
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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.
This dialog allows the user several options in the way the data is
resampled. The two main options are,
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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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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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,
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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.
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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File Name
Contains the name of the selected file.
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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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.
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 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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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.
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.
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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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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.
All the menu operations under the Library Menu are available.
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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.
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.
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.
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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.
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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.
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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.
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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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.
The results of the analysis are placed in the Search Results dialog.
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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
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.
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.
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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Paths Displays the paths to the input, output, library and profiles
sub-directories. The values can be modified by the user.
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.
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.
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.
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.
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This command switches the vertical lines that mark the feature
positions on or off. The default at start up is on.
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,
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.
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.
Feature Depths.
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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.
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View Views the analysis information for the selected file from the
Item History library.
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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.
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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.
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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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.
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Match Library
The working library name (*.wlb) of the original spectral library
(*.slb) used in the analysis process.
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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.
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.
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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.
Shortcuts
Toolbar:
Keys: CTRL+P
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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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Help Topics Offers you an index to topics on which you can get
help.
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.
Use this command to display the copyright notice, version number and
license details of your copy of SIMIS FeatureSearch.
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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).
1.3 83.4
1.32 84.7
1.34 83.9
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,
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.
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HISTORY LIBRARIES
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