SAMS

Spectral Analysis and Management System
Ve r s i o n 2 . 0

U s e r ’s M a n u a l

C a r l o s A . Ru e d a a n d A n n e F. Wr o n a
C e n t e r f o r S p a t i a l Te ch n o l o g i e s a n d Re m o t e S e n s i n g
D e p a r t m e n t o f L a n d , A i r, a n d Wa t e r Re s o u r c e s
U n ive r s i t y o f C a l i f o r n i a , D av i s
April, 2003

Table of Contents
1 Introduction..................................................................................................................................4
2 Installation ....................................................................................................................................5
3 Getting started – a brief tour ......................................................................................................6
3.1 Creating a database.................................................................................................................6
3.2 Importing signatures................................................................................................................6
3.3 Browsing spectra .....................................................................................................................7
3.4 Performing an operation – an example ...................................................................................8
4 Overview .....................................................................................................................................10
4.1 Graphical interface................................................................................................................10
4.2 Selection area and group management..................................................................................11
4.2.1 Imported signatures .........................................................................................................12
4.2.2 Computed signatures .......................................................................................................12
4.2.3 My groups........................................................................................................................12
4.2.4 Automatic groupings .......................................................................................................12
4.3 Status info ..............................................................................................................................12
4.4 Plot area ................................................................................................................................13
4.5 Metadata ................................................................................................................................15
4.6 Keyboard shortcuts ................................................................................................................15
5 Signature operations ..................................................................................................................15
5.1 Notation .................................................................................................................................16
5.2 One-to-one operations ...........................................................................................................16
5.2.1 Scale ................................................................................................................................16
5.2.2 Crop .................................................................................................................................16
5.2.3 Smooth.............................................................................................................................17
5.2.4 Derivative ........................................................................................................................17
5.2.5 Jump correction ...............................................................................................................17
5.2.6 Change wavelength unit...................................................................................................19
5.3 Many-to-one operations.........................................................................................................19
5.3.1 Conform requirement.......................................................................................................20
5.3.2 Average............................................................................................................................20
5.3.3 Standard deviation ...........................................................................................................20
5.3.4 Minimum .........................................................................................................................20
5.3.5 Maximum.........................................................................................................................20
5.3.6 Absorption feature analysis .............................................................................................21
5.3.7 NDWI ..............................................................................................................................22
5.3.8 Simple extraction .............................................................................................................22
5.3.9 Sum..................................................................................................................................23

5.4 Reference-based operations...................................................................................................23
5.4.1 Simple ratio......................................................................................................................23
5.4.2 Subtraction.......................................................................................................................23
5.4.3 Normalize ........................................................................................................................23
5.5 Operations on groups ............................................................................................................24
6 Reference ....................................................................................................................................24
6.1 Database menu ......................................................................................................................24
6.1.1 New (Ctrl-N)....................................................................................................................24
6.1.2 Open (Ctrl-O) ..................................................................................................................24
6.1.3 Save (Ctrl-S) ....................................................................................................................25
6.1.4 Close (Ctrl-W) .................................................................................................................25
6.1.5 Delete...............................................................................................................................25
6.1.6 Properties .........................................................................................................................25
6.1.7 Edit metadata structure ....................................................................................................26
6.1.8 Import signatures from.....................................................................................................27
6.1.9 New grouping by… .........................................................................................................28
6.1.10 Quit (Ctrl-Q) ..................................................................................................................30
6.2 Selected menu ........................................................................................................................30
6.2.1 Compute...........................................................................................................................30
6.2.2 Plot (Enter) ......................................................................................................................30
6.2.3 Add to plot (Ctrl-Enter) ...................................................................................................30
6.2.4 Set as reference (Alt-Enter) .............................................................................................30
6.2.5 Copy (Ctrl-Insert) ............................................................................................................30
6.2.6 Cut (Shift-Delete) ............................................................................................................31
6.2.7 Delete (Delete).................................................................................................................31
6.2.8 Export options..................................................................................................................31
6.3 Plot menu ...............................................................................................................................32
6.3.1 Clear ................................................................................................................................33
6.3.2 Range ...............................................................................................................................33
6.3.3 Export ..............................................................................................................................33
6.3.4 Format..............................................................................................................................33
6.3.5 Print (Ctrl-P) ....................................................................................................................34
6.3.6 Legends window..............................................................................................................34
6.3.7 Anti-aliased......................................................................................................................35
6.4 Query menu............................................................................................................................35
6.5 Help menu ..............................................................................................................................35
6.5.1 About SAMS ...................................................................................................................35
6.5.2 The BeanShell window....................................................................................................35
6.6 Pop-up menus ........................................................................................................................35
6.6.1 Signature popup menu .....................................................................................................35
6.6.2 Group pop-up menu.........................................................................................................36
Appendix A

Recognized file formats......................................................................................38

ASCII file .....................................................................................................................................38
GER file .......................................................................................................................................38
Binary ASD file ............................................................................................................................39

ASCII ASD file .............................................................................................................................39
ENVI Standard file.......................................................................................................................39
Only-Reflectance..........................................................................................................................39
Appendix B

Available Savitzky-Golay filters........................................................................40

organize. Geophysical & Environmental Research Corporation. adds new options to import. 2 GER. y2 ). SAMS usually assumes values are measured in nanometers.. < xn holds. Databases are interchangeable among these platforms. Each database is managed by SAMS as an independent entity and can have its own spectra metadata definition. a signature. Features include: import/export options in various formats. 4 . 3 ENVI. and export spectral data. Environment for Visualizing Images. Recognized formats are (Appendix A): ƒ ƒ ƒ ƒ ASD1 (binary and ASCII variants) GER2 ASCII ENVI3 Standard file. the user imports a number of spectra files in a recognized format. y1 ). and UNIX). Main concepts Database Spectra files are organized in databases. Signature Defined as an ordered sequence of real points. s = [( x1 .( xn .( x2 .0. open existing database(s).… . SAMS can read multiple files at once which facilitates importing a lot of files. The new version is a stand-alone Java application requiring a Java Runtime Environment (JRE). common operations on single or multiple signatures. signature groupings. It will make any necessary rearrangement so that x1 < x2 < .0 does not require Matlab and runs on multiple platforms (Windows. import spectra files into an existing database. metadata management. SAMS 2.. Files can be from: ƒ a given directory 1 ASD. When importing signatures. a new version of SAMS originally written by Michael O’Neill in 1999. Linux. xi . After a database has been created. and delete database(s). Use SAMS to create new database(s). This operation is called importation of signatures. visualize. manipulate. drag-and-drop. Analytical Spectral Devices.1 Introduction The Spectral Analysis and Management System (SAMS) is used to manage field spectra databases and analyses. SAMS 2. yn )] where xi is a wavelength value and yi is the reflectance value at wavelength. and a richer set of plotting capabilities.

ƒ ƒ the system clipboard drag-and-drop operations. Follow the instructions for installation.edu/software/sams/.sun.html.4 but you can use a directory of your choosing. Grouping Groups of signatures can be created manually with user-defined criteria or. Typically “c:\Documents and Settings\username” on Windows systems. The first time it is run. and “/home/username” on UNIX or Linux systems. This dialog box appears: Typically you use your home directory according to your operating system.4/download.4 or newer) properly installed on your machine is the only requirement for SAMS. ƒ ƒ Go to: http://www. JRE can be downloaded from: http://java. automatically by SAMS. 2 Installation A Java Runtime Environment (JRE version 1. SAMS will ask you to set the base directory where settings and databases will be stored. 4 5 .ucdavis.cstars.com/j2se/1. sometimes.

1 Creating a database Use the option Database -> New. Select a base directory. 3 Getting started – a brief tour This brief tour assumes you have a number of spectra files in a recognized format (Appendix A). 3. descriptive name.This path setting is very useful if you are running SAMS from different machines and want to access the same data through a networked drive or directory. Assign a short. SAMS will ask you for some options to perform the operation. The dialog box appears only once for a given machine/OS. 6 . 3.2 Importing signatures Use the option Database -> Import signatures from -> Directory. SAMS will add a new entry in its list of databases.

3 Browsing spectra Use your mouse to select some signatures in the left window. 7 . Choose these options to import files of these formats:5 ƒ ƒ ƒ ƒ ƒ GER. 5 Appendix A describes the currently recognized formats. Only-Reflectance. or for files with different formats. ASD ASCII format. ASD binary format. File type. SAMS will attempt to automatically recognize each file. GER. ASDb. Select for unknown format. 3. Best guess.Search subdirectories? Check to scan all files in the directory and its subdirectories. ASCII files with at least one column (reflectance values). ASD.

4 Performing an operation – an example Average the current selected signatures: Selected -> Compute -> Average.SAMS includes a Selected menu containing these options: 3. 8 .

SAMS will ask you to enter a name and a missing value indicator: AVERAGE automatically becomes a member of the Computed signatures special group: Clicking on this signature while holding down the Ctrl key adds it to the plot. 9 .

1 Graphical interface 10 .4 Overview 4.

None. Most SAMS commands act on the current selection.2 Selection area and group management Use your mouse and/or keyboard to operate in this area. 11 . one.4. or more signatures can be selected at a time. Above. four highlighted signatures were selected by clicking while holding down the Ctrl key. Each entry corresponds to a signature.

2. 4. There are three main groups in a SAMS database.2. Page-down. hold down the Ctrl key and use the navigational keys (Up and Down arrows.1. See section 6.1 Imported signatures All imported signatures are in the Imported signatures group. Page-up.2. 4. The focused element is used as the reference signature for reference-based operations when the command Alt-Enter is used. Populate the group by copying and pasting.2 Computed signatures All signatures resulting from an operation. To change the focused element. ƒ ƒ ƒ Imported signatures Computed signatures My groups These groups are created automatically with every database and cannot be deleted.3 My groups Define as many groups as you want by right-clicking on My groups and using the pop-up menu. End). are in the Computed signatures group. 4. Home.Only one focused element (surrounded by a square) can be selected at a time.3 Status info 12 . 4.9 for options.2. as described in Section 5. 4.4 Automatic groupings SAMS can generate groups automatically.

If it is a signature. Also shows the mouse location in X-Y coordinates. Reference signature . 13 . if only one signature is selected). drag the left mouse button down and to the right to draw a box around an area that you want to see in detail.number of selected signatures (or its name. 4.ƒ ƒ ƒ ƒ Signature selection . pressing Alt-Enter will make this element the reference.3). Focused – name of current focused element (either a group or a signature). Group selection .number of selected groups (or group’s name if only one group is selected).4 Plot area Includes buttons for common plot operations (see Section 6. Mouse interaction To zoom in.name of current signature (used as reference for reference-based operations).

use the fill command Plot -> Range -> Full scale. To just fill the drawing area with the available data. drag the left mouse button up and to the right. 14 .SAMS enlarges the area in the box. To zoom out.

Attributes are specific to each database. See Section 6.1.2.4.7. Key stroke Action See Ctrl-N Ctrl-O Ctrl-S Ctrl-W Ctrl-Q Alt-Enter Enter Ctrl-Enter Ctrl-P Ctrl-Insert Shift-Delete Delete Create new database Open existing database Save current database Close current database Quit SAMS Sets the “reference” signature Plot only selected signatures Plot selected signatures while keeping the already plotted ones Print plot Copy selected signatures to internal clipboard Cut selected signatures to internal clipboard Delete selected signatures 6. f r ( s ) → s ' 15 .3 6.2.1 6.1.3. you can define new attributes.10 6.2.. 4..2.1.1.5 Metadata Metadata associated with each signature is shown in the above table.4 6.6 Keyboard shortcuts Most frequent commands have keyboard shortcuts as follows. sn ) → s' reference-based.4 6.2. too.3 6.5 6. s2 .6 6.5 6.2 6. Although each SAMS database has a default set of associated attributes..2.. Choose Database -> Edit metadata structure. f ( s1 .2 6. f ( s ) → s ' many-to-one.7 5 Signature operations In SAMS a signature operation f can be: ƒ ƒ ƒ one-to-one.1.1.

r2 ). s . rk .( wm . A point value of signature .2 One-to-one operations f ( s) → s ' A one-to-one operation takes one signature and produces one signature.. in [ w1 . at an arbitrary wavelength.2 Crop Given two wavelength values.( w2 . a . this value s( w) is computed by linear interpolation between nearest neighbors. 5. sn r s = [( w1 .2. A signature resulting from an operation. SAMS will compute s' from s by multiplying each ordinate point by a : s '( wk ) = a × s ( wk ) . SAMS will make a copy s '( wk ) of s ( wk ) for wavelengths. 16 ... such that a ≤ wk ≤ b . equivalently. 5. 5. wk . A reflectance value..1 Scale Given a scalar value. s2 . r1 ).2. sn are selected signatures. or.. Current reference signature.. wm ] .Signature operations are applied to the current selection where s1 . w . k . s2 . a and b ... 5. SAMS will apply the operation n times to generate n resulting signatures.… . at wavelength . A defined signature.1 Notation Operations are described in this manual according to the following notations: s1 . at wavelength index. wk . rm )] s ( wk ) = s( k ) = rk s ( w) s' Current selected signatures. If necessary.

c+ nR ] (see Appendix B for available filters).E.3 Smooth Given a Savitzky-Golay filter6 c = [c− nL . c0 . c .J. Cambridge University Press..2. wk .” Analytical Chemistry. Numerical Recipes in C. and two wavelength values. pp.. 1992. 650655. M. Original reference is Savitzky A.2. 5. c .. that can be applied either multiplicatively or additively: This operation can be used to correct spectra recorded by an instrument which was calibrated incorrectly in a limited section of its spectral range. where a jump in s values occurs (a break-point). and Golay. SAMS will create s ' by applying the filter on s over the interval [a. b ... 1627-1639.. “Smoothing and differentiation of data by simplified least squares procedure. SAMS automatically can apply a Savitzky-Golay smoothing filter to s. a and b . Press. et al... W. where a ≤ wk ≤ b . s '( wk ) will differ from s ( wk ) by a correction value. vol. In the interval of modification. wk +1 − wk Before taking the derivative. wk > b (or wk < b ).2.4 Derivative SAMS calculates s ' by taking the first discrete derivative of s : s ' ( wk ) = s ( wk +1 ) − s( wk ) .5 Jump correction Given a wavelength.  c × s( wk ) if multiplicative correction s '( wk ) =  if additive correction  s ( wk ) − c The correction. 1964. 36. pp..5. so s ' will not have a jump. SAMS will perform an algorithm to adjust the values for wavelengths. Second Edition. 5. 6 17 .H. is calculated as follows. b] : s '( wk ) = j =+ nR ∑c j =− nL j × s ( wk + j ) for wavelengths.

Let o . and r be indices of four consecutive points of interest. SAMS will calculate the first tangent. will be used to estimate the value at point. from points o and p and the second tangent. t = (t1 + t2 ) / 2 . t2 . the estimated value. So the correction will be 18 . The average tangent. we have: s '( q) = (t1 + t2 )( wq − w p ) 2 + s( p) . p . lying between w p and wq . q . with a break-point. wq − w p Solving for s '( wq ) . according to the following equation: t= s '( q) − s ( p ) . q . from points q and r . t1 . b .

.3 Many-to-one operations f ( s1 .7 and absorption feature analysis in Section 5. SAMS outputs one signature from point-wise operations on selected signatures. Averages and standard deviations are examples.6 Change wavelength unit Given a conversion factor. but where wavelengths are multiplied by c : wk ' = c × wk . 5.. then a conversion factor of 0. SAMS computes s' as a copy of s such that s '( k ) = s(k ) . SAMS treats them as such.6).g. s '( q) / s ( q) for multiplicative correction c= for additive correction  s ( q) − s '( q) A multiplicative correction was applied to the right of the break point in this graph: 5. if wavelength values are measured in nanometers.2. 19 . In a constructed signature. s2 .3.001 will convert them to microns.. SAMS computes single values from corresponding input signature operations (e. sn ) → s' Two types of many-to-one operations exist: ƒ ƒ In aggregate operations.3. Although the resulting signatures are not necessarily “real” signatures. c . For example. NDWI in Section 5..

. m being sampled at the same wavelengths: si ( wk ) = s j ( wk ) for all i. i 5. m ] . j in [1..3. SAMS alerts you if this requirement is not satisfied.3.3. n i =1 5.. 5. 5. i 20 .3 Standard deviation Takes point-wise square root of sample variance of selected signatures 1/ 2  1  s '( wk ) =  [ si ( wk ) − si ( wk )]2  ∑  n −1 i  where s ( wk ) is the average at wavelength. sn are expected to conform to each other by: ƒ ƒ having the same length..2 Average Calculates point-wise average of selected signatures: s '( wk ) = 1 n ∑ si ( wk ) .3.5 Maximum Gives point-wise maximum of selected signatures s '( wk ) = max si ( wk ) .3. wk .5.1 Conform requirement For aggregate many-to-one operations. s2 . all selected signatures s1 . n ] and all k in [1.4 Minimum Gives point-wise minimum of selected signatures s '( wk ) = min si ( wk ) .

a2 )..5.( n. [b. wq . in [d .. from signature. 21 . si . For this example. a1 ). wavelength. w p . c ] and [d ..6 Absorption feature analysis This construction quantifies the magnitude of an absorption feature over selected signatures. e] . SAMS constructs s ' = [(1. as follows. First SAMS identifies the local maxima within each interval.. c ] and wavelength. Given two wavelength intervals. ai . e] are the maxima. in [b.3.(2. an )] by computing each value.

pp. 5. SAMS creates the signature s ' = [(1. an )] . a1 )..( n. where each value. b . 7 22 ..C. a2 ). a1 ). B.( n. 257-266. ai . si : ai = si (860nm) − si (1240nm) .(2. is the NDWI7 of signature. si (860nm) + si (1240nm) 5.. Gao.. an )] where ai = si (b) . wq ] area under line segment connecting si ( w p ) and si ( wq ) .SAMS computes ai as one minus the ratio between the area under the function in the interval [ w p ..7 NDWI This construction uses wavelengths in nanometers. Remote Sensing of Environment.(2.. 58. SAMS constructs s ' = [(1.3.3. from each of the signatures selected... 1996: NDWI: A normalised difference water index for remote sensing of vegetation liquid water from space.8 Simple extraction This construction extracts a single reflectance value at a given wavelength. wq ] and the area under the straight line segment connecting the maxima: ai = 1 − area under curve in [ w p . a2 ).

b :  r (b) × s ( wk ) s(b) ≠ 0  s '( wk ) =  s (b) . The command to establish the reference signature is Alt-Enter.9 Sum Calculates a point-wise sum of selected signatures.4 Reference-based operations f r ( s ) → s' A reference-based operation is a binary operation. 5. i 5. SAMS includes these reference-based operations: 5.  s( w ) s ( b) = 0 k  23 . r : s '( wk ) = s ( wk ) − r ( wk ) . and reference.4.1 Simple ratio Calculates a point-wise ratio between selected signature. whose second argument is taken as a reference. and reference. So.4.5.4. s .2 Subtraction Takes a point-wise difference between selected signature. r ( wk ) = 0 5. f ( s.3 Normalize Uses point-wise scaling according to reflectance ratio at a given wavelength. it can be written f r (s ) and be treated as a one-to-one operation (see above). s '( wk ) = ∑ si ( wk ) . r :  s( wk )  s '( wk ) =  r ( wk )  0  r ( wk ) ≠ 0 . r ) . s .3.

If any signatures are selected at the same time as groups.5 Operations on groups SAMS can apply a many-to-one operation on a selection of groups. SAMS adds a new entry in its list of databases and lets you assign a short.1. SAMS performs an operation on a group’s signature members and assigns the resulting name signature from the name of the group and the suffix given in the dialog box.1. 6. 24 .1 New (Ctrl-N) Creates a new database. descriptive name. SAMS ignores them since group selection takes precedence over signature selection. 6 Reference This section gives descriptions of options available from the menu bar and pop-up menus.5.2 Open (Ctrl-O) Opens a database and first saves and closes any other already-open database. make sure no groups are selected. To apply an operation to selected signatures.1 Database menu 6. 6.

1. 6.1. Specifically.1. SAMS asks for confirmation. [SAMS created <base directory> as a user-defined setting the first time it was run.] 25 .6 Properties Shows database properties. See Section 2.sams/dbs/.1. 6.3 Save (Ctrl-S) Saves database. Find the directory under <base directory>/.4 Close (Ctrl-W) Saves and closes database. SAMS confirms. it shows: ƒ ƒ database name directory under which data are stored.5 Delete Deletes database.6. 6. It also saves automatically when you close a database or quit the program.

26 .6. Add as many attributes as you need.7 Edit metadata structure Modifies metadata associated with database.1. click on the cell in the spectra table and make changes. Humm and not so good were added to the comment column in this table. SAMS will update your database as shown. Click on the Add attribute button. To change an attribute. SAMS opens a window of default attributes. Add species and comment attributes.

1. 27 .8. 6.1.8.6. See Appendix A. 6. 6. Use it to import signatures into a database from different sources.1.1 Directory Specifies a directory to have SAMS search for spectra files.8 Import signatures from Opens a submenu.3 ASCII file Reads multiple signatures from an ASCII file.1.8.2 ENVI Standard file Reads an ENVI standard file in BIP format after you specify which location to read.

1.4 System clipboard Pastes copied spectra files from the system clipboard.” to separate groups. 28 . SAMS uses characters like “.9.9. 6.6.1 Attribute value Creates a group for each value of an attribute.1. ƒ ƒ Separators. SAMS ignores this suffix in separator processing.2 Filename Creates a group for each prefix (set-off by separators assigned by the user) in signature filenames. 6.1.8. Ignore suffix.1.9 New grouping by… Opens a submenu with options to make automatic groupings. Use this option as an alternative to dragand-drop. In this example: 6.

Several signatures are in this example database: Using ‘.’ as the only separator and leaving the suffix blank: SAMS creates this group structure: 29 .

2 Selected menu 6. SAMS asks for confirmation. See Section 5.1). 6.2.6. 30 . See Section 5.5 Copy (Ctrl-Insert) Copies selected signatures to an internal clipboard. 6.2. 6.2.3.4.4.2.2.2 Plot (Enter) Displays selected signatures in the plot area. Reference-based operations.2.1. See Section 5. 6.4 Set as reference (Alt-Enter) Sets focused signature as the reference signature for reference-based operations.3 Add to plot (Ctrl-Enter) Plots selected signatures in addition to those already displayed. To paste references to selected signatures into a group. See Section 5. allows reassignment of legends. 6.2. use Paste (Section 6.10 Quit (Ctrl-Q) Quits program. One-to-one operations.1 Compute Choose one of these operations to perform on a selection: ƒ ƒ ƒ Many-to-one operations.6.

3.2..1).1 Export to ASCII format SAMS exports selected signatures. id( s2 ) . then the remaining N − n elements will be zero-filled. s2 . s1 ( wm ) . s1 . sn ( wm ) 6....2. sn ( w1 ) sn ( w2 ) wm .. to a CSV (comma-separated-values) file. s2 ( w1 ) .6. So. s2 ( w2 ) . use Paste (Section 6. 8 31 . if n = 18 . s1 .2.2 Export to ENVI format SAMS exports n selected signatures. s2 ( wm ) .. sn .2.2.8.8. w2 . s1 ( w1 ) . s2 . id( s1 ) . sn . The identification name for signature si is id( si ) in the following discussion. must conform to each other as explained in Section 5. 6.. lines = 4 and samples = 5 .6. selected signatures. id( sn ) w1 . …. Each signature is located in the image as shown: Where  x  is the greatest integer that is not greater than x .6 Cut (Shift-Delete) Removes selected signatures from a selection and copies them to an internal clipboard.. and  x  is the smallest integer that is not less than x . s2 . …. sn . 6.2.8 Export options For all export options. If N > n . Wavelength.1. To paste references to removed signatures into a group... to a multi-band image in ENVI standard format with dimensions:8 lines =  n   n  samples =   lines  bands = m It follows that the image can store N = lines × samples ≥ n signatures. SAMS asks for confirmation. s1 .7 Delete (Delete) Deletes selected signatures from the group.. 6. s1 ( w2 ) . …..

version 5. *. SAMS prompts you for a file name to export the selected signatures and writes a corresponding header file.8.edu/java/ptplot/ 9 32 .berkeley.hdr.3 Plot menu9 Plot capabilities based on Ptolemy 2D data plotter package. The header displays signature identifications. SAMS prompts you for a file name and writes a corresponding header file.3 Export to ENVI Spectral Library An ENVI spectral library file is an ENVI binary image with the number of samples equal to the number of bands and the number of lines equal to the number of signatures in the selection: lines = n samples = m bands = 1 Signatures are ordered as shown: s1 ( w1 ) .2.s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 ∅ ∅ Where ∅ denotes a signature with m zero values. s1 ( w2 ) . s1 ( wm ) s2 ( w1 ) .1p2: http://ptolemy. s2 ( w2 ) .hdr. …. and spectral library for the ENVI file type. ….eecs. 6. s2 ( wm ) … sn ( wm ) … …. … sn ( w2 ) . wavelengths. … sn ( w1 ) . 6. *.

6. only EPS is supported.3.1 Clear Clears contents of plot area. 6.4 Chlorophyll [550:680] Sets X range to ~550-680 nm.3. 6.6 Zoom current Y-range Rescales plot horizontally to fit data in Y range.3.2.3.3.3 Export Opens submenu with options to export the plot in different formats.6.1 Full range Rescales plot to fit data. 6.4 Format Opens a dialog box to modify plot parameters such as: 33 .3.2.3. 6.2. 6.2.2.2 Visible [400:700] Sets X range to ~400-700 nm.3.3.3.2 Range Opens submenu with options to adjust X and Y ranges. Any range can be specified–see format option below.3. 6.3 NDVI [500:900] Sets X range to ~500-900 nm.2. 6.1 Encapsulated Postscript (EPS) format Opens dialog box in which to specify a name for the plot file compatible with word processors.5 Zoom current X-range Rescales plot vertically to fit data in X range. Currently. 6.3. 6.

3. enter into the X Ticks or Y Ticks entry boxes a string of the following form: label position. X ticks and Y ticks. Use color. label position. SAMS automatically computes them.5 Print (Ctrl-P) Prints plot. Grid. Check to connect point values with lines. Stems..3. Assigns title to plot. Check to show background grid. To change tick marks. Specifies how axes are labeled. Add marks specified to distinguish spectra. Labels X and Y axes.ƒ ƒ ƒ ƒ ƒ ƒ ƒ ƒ ƒ Title. printer. 6. Check to plot stems. A label must be surrounded by quotation marks if it contains any spaces.. Stipulates plotted ranges by separating low values from high with a comma. 34 . . Marks. X label and Y label. margins. A position is a number assigning the location of the tick mark along the axis. Check to plot spectra with different colors. orientation. 6. Connect. X range and Y range.6 Legends window Opens a floating window containing plot legends – a useful tool when many signatures are displayed and there is not enough room for the legends to fit in their normal location. opens print dialog box with options to choose paper.

6. contact information.6.5 Help menu 6.5. 6.4 Query menu Do not use yet. 6.2 The BeanShell window Do not use. 6.6 Pop-up menus Appear by right-clicking over elements of the selection area like signatures and groups.1 Signature popup menu Contains same options as Selected in the menu bar. This menu is in an early stage of development.3.5. 35 . Opens a tool for developers to use to test SAMS. and copyright agreement for SAMS. 6.7 Anti-aliased Improves plot appearance.6.1 About SAMS Shows current version.

6.2 Group pop-up menu Includes the following options when a group is selected: 6.3 Rename Renames selected signature and associated groups.1.6.Includes the following options.2 View source Shows contents of source file where selected signature is stored (ASCII sources only).6.2.1. SAMS prompts you for a name and a description.1 View data Shows contents of selected signature in SAMS’ memory (two columns.1. Use option View data for binary sources. 6. 6.6. 36 . 6. wavelength and reflectance). when only one signature is selected.6.6.1 New subgroup Applies to My groups.

2. Use Copy and Cut to put signatures on clipboard (Sections 6.6. and My groups cannot be deleted.2.3 Delete group Deletes selected group.4 Export options Applies to members of selected group as explained in Section 6.8. 6. Imported signatures.6).5 and 6.2.2.2 Paste reference Adds references to signatures to selected group from clipboard.2.6.2.6.6. 6. 37 . Computed signatures.

consecutive floating point values found in a line are denoted by v0 . commas. is interpreted as the abscissa value for all imported signatures. Lines that cannot be parsed to at least three values are ignored. is parsed successfully. then w / 100 is taken as the reflectance value. 38 . Each line is scanned as a sequence of tokens.. A line is recognized if it starts with at least two floating point values. The first value is always taken as a wavelength. ASCII file SAMS imports this simplest file type using these rules. Each token is a floating point value.Appendix A Recognized file formats File formats that SAMS currently recognizes in importing signatures into a database. If a fourth value. ƒ ƒ ƒ ƒ ƒ ƒ ƒ ƒ ƒ The file is scanned one line at a time. Otherwise. and/or tabs. The first column in the file. v1 . v0 will be its abscissa and vi its ordinate. the point ( v0 . Recognized lines in the same file can contain different numbers of tokens (columns).. The scanned.. vi ) is assigned to signature i -th. that is. vn . although the usual case is to have exactly the same number of columns. the line is ignored. For 1 ≤ i ≤ n . A GER file is an ASCII file that SAMS reads following these rules. GER file GER files are identified as GER. say w . v0 . ƒ The first line is expected to be one of the following: ///GER SIGNATUR FILE/// ///GER ASCII FILE/// ƒ ƒ ƒ ƒ Subsequent lines are parsed for three or four numerical values. Separators for tokens are simple spaces..

where y and z are the second and third values in the line. Only-Reflectance This ASCII file is scanned for at least one column assumed to contain reflectance values. SAMS imports ASCII ASD files using the same rules it uses for ASCII files except for the assumption that only one signature comes in the file. the reflectance value will be y / z . 10 BIP. These values are associated with fixed wavelengths: 350. …. Reflectance data files generated by an ASD instrument can be read directly by SAMS as long as they are float and little-endian formatted.ƒ Otherwise. ENVI Standard file SAMS can read directly ENVI Standard files in BIP10 format. Band Interleaved by Pixel: Reflectance values for each signature are stored together. Binary ASD file Binary ASD files are identified as ASDb. ASCII ASD file ASCII ASD files are identified as ASD. 351. In this way the first two tokens (columns) are taken into account. 352. 39 .

nL is the number of left data points used. where M is the order of the fitting polynomial. M − nL − nR .Appendix B Available Savitzky-Golay filters Savitzky-Golay filters in SAMS are named by the convention. M − nL − nR 3-40-40 3-20-20 3-12-12 2-2-2 2-3-1 2-4-0 2-5-5 4-4-4 4-5-5 40 . and nR is the number of right data points used.

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