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

After a database has been created. The new version is a stand-alone Java application requiring a Java Runtime Environment (JRE). metadata management. adds new options to import. 3 ENVI. < xn holds.. y2 ). Analytical Spectral Devices. SAMS 2. Features include: import/export options in various formats. Files can be from: ƒ a given directory 1 ASD. SAMS usually assumes values are measured in nanometers. 4 . organize. SAMS 2. y1 ). and export spectral data.. import spectra files into an existing database. Environment for Visualizing Images.( xn . signature groupings.( x2 . When importing signatures. a signature. Use SAMS to create new database(s). Signature Defined as an ordered sequence of real points. a new version of SAMS originally written by Michael O’Neill in 1999.0. This operation is called importation of signatures.… . the user imports a number of spectra files in a recognized format. 2 GER. Linux. common operations on single or multiple signatures. and a richer set of plotting capabilities. open existing database(s). Main concepts Database Spectra files are organized in databases. and UNIX). Geophysical & Environmental Research Corporation. s = [( x1 . Databases are interchangeable among these platforms. manipulate. yn )] where xi is a wavelength value and yi is the reflectance value at wavelength.0 does not require Matlab and runs on multiple platforms (Windows. and delete database(s). Recognized formats are (Appendix A): ƒ ƒ ƒ ƒ ASD1 (binary and ASCII variants) GER2 ASCII ENVI3 Standard file. It will make any necessary rearrangement so that x1 < x2 < . SAMS can read multiple files at once which facilitates importing a lot of files. visualize.1 Introduction The Spectral Analysis and Management System (SAMS) is used to manage field spectra databases and analyses. drag-and-drop. Each database is managed by SAMS as an independent entity and can have its own spectra metadata definition. xi .

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

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. 6 . SAMS will add a new entry in its list of databases. 3 Getting started – a brief tour This brief tour assumes you have a number of spectra files in a recognized format (Appendix A). The dialog box appears only once for a given machine/OS.2 Importing signatures Use the option Database -> Import signatures from -> Directory. SAMS will ask you for some options to perform the operation. descriptive name. 3. Assign a short.1 Creating a database Use the option Database -> New. 3. Select a base directory.

ASD. 3.3 Browsing spectra Use your mouse to select some signatures in the left window. SAMS will attempt to automatically recognize each file. ASD ASCII format. 5 Appendix A describes the currently recognized formats. ASD binary format. 7 . Choose these options to import files of these formats:5 ƒ ƒ ƒ ƒ ƒ GER. File type. GER. ASDb.Search subdirectories? Check to scan all files in the directory and its subdirectories. Select for unknown format. Best guess. Only-Reflectance. ASCII files with at least one column (reflectance values). or for files with different formats.

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

9 .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.

1 Graphical interface 10 .4 Overview 4.

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

4 Automatic groupings SAMS can generate groups automatically. as described in Section 5. 4.1. To change the focused element. There are three main groups in a SAMS database. Page-down. hold down the Ctrl key and use the navigational keys (Up and Down arrows. 4. See section 6.2.2. The focused element is used as the reference signature for reference-based operations when the command Alt-Enter is used. ƒ ƒ ƒ Imported signatures Computed signatures My groups These groups are created automatically with every database and cannot be deleted.3 Status info 12 .1 Imported signatures All imported signatures are in the Imported signatures group. Populate the group by copying and pasting. 4.2. are in the Computed signatures group.2.9 for options. Home.2 Computed signatures All signatures resulting from an operation. 4. 4. End).3 My groups Define as many groups as you want by right-clicking on My groups and using the pop-up menu.Only one focused element (surrounded by a square) can be selected at a time. Page-up.

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

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

2.7.5 6.1 6. too. f r ( s ) → s ' 15 ..1.10 6.4. s2 .. Although each SAMS database has a default set of associated attributes. f ( s ) → s ' many-to-one.1.6 Keyboard shortcuts Most frequent commands have keyboard shortcuts as follows. Attributes are specific to each database.2 6. 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 6.2.2.1. f ( s1 . 4.3 6.2.1.3. Choose Database -> Edit metadata structure.2 6. See Section 6..4 6..5 Metadata Metadata associated with each signature is shown in the above table.2.6 6.4 6. sn ) → s' reference-based.5 6.7 5 Signature operations In SAMS a signature operation f can be: ƒ ƒ ƒ one-to-one.2. you can define new attributes.1.1.3 6.

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

vol. where a ≤ wk ≤ b .3 Smooth Given a Savitzky-Golay filter6 c = [c− nL .E. where a jump in s values occurs (a break-point). 650655.5 Jump correction Given a wavelength.H. c .. b . 5. so s ' will not have a jump. c0 . Second Edition. pp.” Analytical Chemistry.. Press.... and two wavelength values. 6 17 . 5. c .  c × s( wk ) if multiplicative correction s '( wk ) =  if additive correction  s ( wk ) − c The correction. b] : s '( wk ) = j =+ nR ∑c j =− nL j × s ( wk + j ) for wavelengths. “Smoothing and differentiation of data by simplified least squares procedure. SAMS automatically can apply a Savitzky-Golay smoothing filter to s.5. In the interval of modification. 1992. c+ nR ] (see Appendix B for available filters). M. is calculated as follows. pp. s '( wk ) will differ from s ( wk ) by a correction value.J. et al. wk +1 − wk Before taking the derivative.. SAMS will create s ' by applying the filter on s over the interval [a. wk > b (or wk < b ). W. 1964.. 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. Original reference is Savitzky A. a and b .2.4 Derivative SAMS calculates s ' by taking the first discrete derivative of s : s ' ( wk ) = s ( wk +1 ) − s( wk ) .2.2. 1627-1639. Cambridge University Press. wk .. and Golay. Numerical Recipes in C. SAMS will perform an algorithm to adjust the values for wavelengths. 36..

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

NDWI in Section 5. c .2.. For example. 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: 5.001 will convert them to microns. 19 . sn ) → s' Two types of many-to-one operations exist: ƒ ƒ In aggregate operations. SAMS outputs one signature from point-wise operations on selected signatures. SAMS computes single values from corresponding input signature operations (e. SAMS treats them as such.7 and absorption feature analysis in Section 5. 5. In a constructed signature.g.. Although the resulting signatures are not necessarily “real” signatures..3. SAMS computes s' as a copy of s such that s '( k ) = s(k ) .6 Change wavelength unit Given a conversion factor.3 Many-to-one operations f ( s1 . but where wavelengths are multiplied by c : wk ' = c × wk .3.. then a conversion factor of 0.6). s2 . if wavelength values are measured in nanometers. Averages and standard deviations are examples.

4 Minimum Gives point-wise minimum of selected signatures s '( wk ) = min si ( wk ) .5..3.3. n ] and all k in [1.3. m ] . 5. wk . all selected signatures s1 . sn are expected to conform to each other by: ƒ ƒ having the same length.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. s2 .5 Maximum Gives point-wise maximum of selected signatures s '( wk ) = max si ( wk ) . 5. m being sampled at the same wavelengths: si ( wk ) = s j ( wk ) for all i..3.. i 5. SAMS alerts you if this requirement is not satisfied.. i 20 .3. j in [1.2 Average Calculates point-wise average of selected signatures: s '( wk ) = 1 n ∑ si ( wk ) . n i =1 5.1 Conform requirement For aggregate many-to-one operations.

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

Gao. SAMS creates the signature s ' = [(1. pp. a1 ). wq ] area under line segment connecting si ( w p ) and si ( wq ) . 257-266..3. 5. b . 7 22 . a1 ). wq ] and the area under the straight line segment connecting the maxima: ai = 1 − area under curve in [ w p . si : ai = si (860nm) − si (1240nm) . from each of the signatures selected. a2 ). is the NDWI7 of signature. a2 ). 1996: NDWI: A normalised difference water index for remote sensing of vegetation liquid water from space. an )] where ai = si (b) ....C. SAMS constructs s ' = [(1.3..( n. Remote Sensing of Environment.7 NDWI This construction uses wavelengths in nanometers..(2.8 Simple extraction This construction extracts a single reflectance value at a given wavelength. B.(2. ai . 58.( n. an )] ..SAMS computes ai as one minus the ratio between the area under the function in the interval [ w p .. where each value. si (860nm) + si (1240nm) 5.

4.3 Normalize Uses point-wise scaling according to reflectance ratio at a given wavelength. and reference.  s( w ) s ( b) = 0 k  23 . r ( wk ) = 0 5. The command to establish the reference signature is Alt-Enter.9 Sum Calculates a point-wise sum of selected signatures. and reference. b :  r (b) × s ( wk ) s(b) ≠ 0  s '( wk ) =  s (b) .4.1 Simple ratio Calculates a point-wise ratio between selected signature. f ( s. s .4.5. s .4 Reference-based operations f r ( s ) → s' A reference-based operation is a binary operation. SAMS includes these reference-based operations: 5. 5.3. So. r : s '( wk ) = s ( wk ) − r ( wk ) . whose second argument is taken as a reference.2 Subtraction Takes a point-wise difference between selected signature. i 5. it can be written f r (s ) and be treated as a one-to-one operation (see above). r ) . s '( wk ) = ∑ si ( wk ) . r :  s( wk )  s '( wk ) =  r ( wk )  0  r ( wk ) ≠ 0 .

descriptive name.5 Operations on groups SAMS can apply a many-to-one operation on a selection of groups. SAMS ignores them since group selection takes precedence over signature selection. 6. 6 Reference This section gives descriptions of options available from the menu bar and pop-up menus. 6. If any signatures are selected at the same time as groups.1.5.1 Database menu 6. 24 . To apply an operation to selected signatures.2 Open (Ctrl-O) Opens a database and first saves and closes any other already-open database. 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. SAMS adds a new entry in its list of databases and lets you assign a short.1. make sure no groups are selected.1 New (Ctrl-N) Creates a new database.

1.3 Save (Ctrl-S) Saves database. [SAMS created <base directory> as a user-defined setting the first time it was run. See Section 2.1. Specifically.6 Properties Shows database properties.1. Find the directory under <base directory>/. 6. It also saves automatically when you close a database or quit the program.4 Close (Ctrl-W) Saves and closes database.5 Delete Deletes database. 6.6.] 25 .sams/dbs/.1. it shows: ƒ ƒ database name directory under which data are stored. 6. SAMS confirms. SAMS asks for confirmation.

Humm and not so good were added to the comment column in this table.7 Edit metadata structure Modifies metadata associated with database. SAMS will update your database as shown. 26 . To change an attribute. Click on the Add attribute button.6.1. click on the cell in the spectra table and make changes. SAMS opens a window of default attributes. Add as many attributes as you need. Add species and comment attributes.

6.1. Use it to import signatures into a database from different sources. 6.1.8.1.8 Import signatures from Opens a submenu.3 ASCII file Reads multiple signatures from an ASCII file.8.1.1 Directory Specifies a directory to have SAMS search for spectra files. See Appendix A.8. 27 . 6.2 ENVI Standard file Reads an ENVI standard file in BIP format after you specify which location to read. 6.

ƒ ƒ Separators. SAMS uses characters like “.9.1. 28 .1. 6. In this example: 6.1. SAMS ignores this suffix in separator processing.8. 6.” to separate groups.2 Filename Creates a group for each prefix (set-off by separators assigned by the user) in signature filenames. Ignore suffix.9 New grouping by… Opens a submenu with options to make automatic groupings.1 Attribute value Creates a group for each value of an attribute. Use this option as an alternative to dragand-drop.4 System clipboard Pastes copied spectra files from the system clipboard.6.9.1.

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

5 Copy (Ctrl-Insert) Copies selected signatures to an internal clipboard. See Section 5.2.4 Set as reference (Alt-Enter) Sets focused signature as the reference signature for reference-based operations.4. Reference-based operations.2.2.6.2 Selected menu 6. 6.2 Plot (Enter) Displays selected signatures in the plot area. 30 . use Paste (Section 6. 6.4.1). 6. 6.10 Quit (Ctrl-Q) Quits program.2.3 Add to plot (Ctrl-Enter) Plots selected signatures in addition to those already displayed.6.2. SAMS asks for confirmation.3.1 Compute Choose one of these operations to perform on a selection: ƒ ƒ ƒ Many-to-one operations.2. allows reassignment of legends.1.2. One-to-one operations. See Section 5. To paste references to selected signatures into a group. 6. See Section 5. See Section 5.

…. and  x  is the smallest integer that is not less than x . The identification name for signature si is id( si ) in the following discussion. s1 ( w2 ) . s2 . s2 .6. s1 .2 Export to ENVI format SAMS exports n selected signatures... sn ( wm ) 6. id( s1 ) .8. s2 ( wm ) . s1 .1 Export to ASCII format SAMS exports selected signatures. If N > n .8 Export options For all export options.1. selected signatures.6 Cut (Shift-Delete) Removes selected signatures from a selection and copies them to an internal clipboard.1).8...... sn . sn . 8 31 . must conform to each other as explained in Section 5. 6. sn . use Paste (Section 6. lines = 4 and samples = 5 .2.2. sn ( w1 ) sn ( w2 ) wm . if n = 18 . w2 . SAMS asks for confirmation.. id( sn ) w1 . 6. To paste references to removed signatures into a group.3. s1 ( wm ) .2.. id( s2 ) ..2. 6.6. Each signature is located in the image as shown: Where  x  is the greatest integer that is not greater than x .. ….. ….2. s1 . Wavelength. then the remaining N − n elements will be zero-filled.7 Delete (Delete) Deletes selected signatures from the group. s2 . 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. s2 ( w2 ) . s2 ( w1 ) . to a CSV (comma-separated-values) file. So. s1 ( w1 ) .2.

and spectral library for the ENVI file type. version 5. …. …. *.eecs.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 ) . SAMS prompts you for a file name to export the selected signatures and writes a corresponding header file. s1 ( w2 ) . 6.hdr.1p2: http://ptolemy.2. s2 ( wm ) … sn ( wm ) … ….3 Plot menu9 Plot capabilities based on Ptolemy 2D data plotter package. *. s1 ( wm ) s2 ( w1 ) . … sn ( w1 ) .berkeley.8. wavelengths.hdr. The header displays signature identifications.edu/java/ptplot/ 9 32 . SAMS prompts you for a file name and writes a corresponding header file.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. … sn ( w2 ) . 6. s2 ( w2 ) .

3 NDVI [500:900] Sets X range to ~500-900 nm.4 Chlorophyll [550:680] Sets X range to ~550-680 nm.3.3.3. only EPS is supported. 6.6 Zoom current Y-range Rescales plot horizontally to fit data in Y range. Any range can be specified–see format option below.2.1 Clear Clears contents of plot area. 6. 6.1 Full range Rescales plot to fit data.2.3.3. 6.3.2.2 Visible [400:700] Sets X range to ~400-700 nm.3.2.5 Zoom current X-range Rescales plot vertically to fit data in X range. 6.2 Range Opens submenu with options to adjust X and Y ranges.3. 6.2.3. Currently. 6. 6.2.3.3 Export Opens submenu with options to export the plot in different formats. 6.1 Encapsulated Postscript (EPS) format Opens dialog box in which to specify a name for the plot file compatible with word processors.3.6.3. 6.4 Format Opens a dialog box to modify plot parameters such as: 33 .

X range and Y range.. Check to plot spectra with different colors. X label and Y label. Check to show background grid. Check to connect point values with lines. 6. Use color.5 Print (Ctrl-P) Prints plot. SAMS automatically computes them. label position. Specifies how axes are labeled. Add marks specified to distinguish spectra. opens print dialog box with options to choose paper. orientation. enter into the X Ticks or Y Ticks entry boxes a string of the following form: label position. Check to plot stems.3. Labels X and Y axes. Connect. Marks.. 34 . Assigns title to plot.ƒ ƒ ƒ ƒ ƒ ƒ ƒ ƒ ƒ Title. printer. X ticks and Y ticks.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. A label must be surrounded by quotation marks if it contains any spaces. 6. To change tick marks.3. Grid. Stipulates plotted ranges by separating low values from high with a comma. A position is a number assigning the location of the tick mark along the axis. margins. . Stems.

3.5 Help menu 6.5. 6.6 Pop-up menus Appear by right-clicking over elements of the selection area like signatures and groups. 6. Opens a tool for developers to use to test SAMS. 6.2 The BeanShell window Do not use. contact information. 35 .6. and copyright agreement for SAMS.1 About SAMS Shows current version.1 Signature popup menu Contains same options as Selected in the menu bar.6. 6. 6.4 Query menu Do not use yet.5. This menu is in an early stage of development.7 Anti-aliased Improves plot appearance.

2.1 View data Shows contents of selected signature in SAMS’ memory (two columns.3 Rename Renames selected signature and associated groups.2 Group pop-up menu Includes the following options when a group is selected: 6.1 New subgroup Applies to My groups.2 View source Shows contents of source file where selected signature is stored (ASCII sources only). SAMS prompts you for a name and a description. 36 . when only one signature is selected.6.1.1. wavelength and reflectance). 6.6. 6.6. 6.6.6.1. Use option View data for binary sources.Includes the following options. 6.

4 Export options Applies to members of selected group as explained in Section 6.6).2.3 Delete group Deletes selected group.2.2 Paste reference Adds references to signatures to selected group from clipboard.2.6.6. Computed signatures. and My groups cannot be deleted.2. Use Copy and Cut to put signatures on clipboard (Sections 6. Imported signatures. 6. 6.2.6.6.2.5 and 6.8. 37 .

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

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

M − nL − nR . 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 .Appendix B Available Savitzky-Golay filters Savitzky-Golay filters in SAMS are named by the convention. and nR is the number of right data points used. nL is the number of left data points used. where M is the order of the fitting polynomial.

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