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

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

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

6 .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. 3. SAMS will add a new entry in its list of databases. SAMS will ask you for some options to perform the operation. 3.1 Creating a database Use the option Database -> New. The dialog box appears only once for a given machine/OS. 3 Getting started – a brief tour This brief tour assumes you have a number of spectra files in a recognized format (Appendix A).2 Importing signatures Use the option Database -> Import signatures from -> Directory. Select a base directory. Assign a short. descriptive name.

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

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

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 .

4 Overview 4.1 Graphical interface 10 .

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

There are three main groups in a SAMS database. Home. Page-up. are in the Computed signatures group.2. ƒ ƒ ƒ Imported signatures Computed signatures My groups These groups are created automatically with every database and cannot be deleted. 4. hold down the Ctrl key and use the navigational keys (Up and Down arrows. 4. Page-down. See section 6.9 for options. The focused element is used as the reference signature for reference-based operations when the command Alt-Enter is used.2.2.3 My groups Define as many groups as you want by right-clicking on My groups and using the pop-up menu.1 Imported signatures All imported signatures are in the Imported signatures group.3 Status info 12 .1.4 Automatic groupings SAMS can generate groups automatically.2 Computed signatures All signatures resulting from an operation. 4. To change the focused element.2. Populate the group by copying and pasting.Only one focused element (surrounded by a square) can be selected at a time. 4. 4. as described in Section 5. End).

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

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

4.7 5 Signature operations In SAMS a signature operation f can be: ƒ ƒ ƒ one-to-one.2. Although each SAMS database has a default set of associated attributes. f r ( s ) → s ' 15 . 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 6.1. Choose Database -> Edit metadata structure.7.5 Metadata Metadata associated with each signature is shown in the above table.2 6..4.1.2.6 Keyboard shortcuts Most frequent commands have keyboard shortcuts as follows.4 6.1.1 6. Attributes are specific to each database.3 6. too.2.6 6. See Section 6. s2 .2.1. f ( s ) → s ' many-to-one.5 6. sn ) → s' reference-based.3 6.1.5 6..1. you can define new attributes...2.2 6.2. f ( s1 .3.4 6.10 6.

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

where a ≤ wk ≤ b .. c ..  c × s( wk ) if multiplicative correction s '( wk ) =  if additive correction  s ( wk ) − c The correction. wk . b] : s '( wk ) = j =+ nR ∑c j =− nL j × s ( wk + j ) for wavelengths. 5. 650655.” Analytical Chemistry. Numerical Recipes in C. M. and two wavelength values.4 Derivative SAMS calculates s ' by taking the first discrete derivative of s : s ' ( wk ) = s ( wk +1 ) − s( wk ) . Second Edition.H. et al. is calculated as follows. pp.E. Press.. and Golay. wk > b (or wk < b ).5 Jump correction Given a wavelength. SAMS will perform an algorithm to adjust the values for wavelengths. vol. In the interval of modification. 1964.2. 5. Cambridge University Press.... c+ nR ] (see Appendix B for available filters). so s ' will not have a jump. SAMS will create s ' by applying the filter on s over the interval [a. wk +1 − wk Before taking the derivative. 6 17 ..5.2. c . b . where a jump in s values occurs (a break-point). Original reference is Savitzky A.. 36. SAMS automatically can apply a Savitzky-Golay smoothing filter to s. 1992. c0 .J. s '( wk ) will differ from s ( wk ) by a correction value. 1627-1639. pp.3 Smooth Given a Savitzky-Golay filter6 c = [c− nL . a and b . “Smoothing and differentiation of data by simplified least squares procedure.2. 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. W..

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

s2 . sn ) → s' Two types of many-to-one operations exist: ƒ ƒ In aggregate operations.3.g. In a constructed signature. SAMS computes single values from corresponding input signature operations (e. c . but where wavelengths are multiplied by c : wk ' = c × wk .. 5.6 Change wavelength unit Given a conversion factor. 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..2.. if wavelength values are measured in nanometers. Although the resulting signatures are not necessarily “real” signatures. Averages and standard deviations are examples. SAMS treats them as such. For example. then a conversion factor of 0. NDWI in Section 5. SAMS outputs one signature from point-wise operations on selected signatures.3.3 Many-to-one operations f ( s1 . SAMS computes s' as a copy of s such that s '( k ) = s(k ) .001 will convert them to microns.6).7 and absorption feature analysis in Section 5.. 19 .

3.5 Maximum Gives point-wise maximum of selected signatures s '( wk ) = max si ( wk ) . m being sampled at the same wavelengths: si ( wk ) = s j ( wk ) for all i. n ] and all k in [1. j in [1.1 Conform requirement For aggregate many-to-one operations.5.3. sn are expected to conform to each other by: ƒ ƒ having the same length. all selected signatures s1 . n i =1 5. s2 . wk .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.3. 5. SAMS alerts you if this requirement is not satisfied. i 20 .3... 5.. m ] .3..4 Minimum Gives point-wise minimum of selected signatures s '( wk ) = min si ( wk ) . i 5.2 Average Calculates point-wise average of selected signatures: s '( wk ) = 1 n ∑ si ( wk ) .

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

(2. ai . a1 ).(2.C. from each of the signatures selected..3. a2 ). where each value... SAMS constructs s ' = [(1. a2 ). SAMS creates the signature s ' = [(1. si (860nm) + si (1240nm) 5. an )] . 58.. a1 ). an )] where ai = si (b) . B. 7 22 .. b . 1996: NDWI: A normalised difference water index for remote sensing of vegetation liquid water from space. is the NDWI7 of signature.( n. Remote Sensing of Environment. wq ] and the area under the straight line segment connecting the maxima: ai = 1 − area under curve in [ w p .. 257-266. pp. wq ] area under line segment connecting si ( w p ) and si ( wq ) . 5. si : ai = si (860nm) − si (1240nm) .( n. Gao.7 NDWI This construction uses wavelengths in nanometers.8 Simple extraction This construction extracts a single reflectance value at a given wavelength..SAMS computes ai as one minus the ratio between the area under the function in the interval [ w p .3..

The command to establish the reference signature is Alt-Enter. b :  r (b) × s ( wk ) s(b) ≠ 0  s '( wk ) =  s (b) . r : s '( wk ) = s ( wk ) − r ( wk ) .3 Normalize Uses point-wise scaling according to reflectance ratio at a given wavelength. 5.5.4. r ( wk ) = 0 5.  s( w ) s ( b) = 0 k  23 .4 Reference-based operations f r ( s ) → s' A reference-based operation is a binary operation. and reference. s . and reference.9 Sum Calculates a point-wise sum of selected signatures. SAMS includes these reference-based operations: 5.4. f ( s. it can be written f r (s ) and be treated as a one-to-one operation (see above). r :  s( wk )  s '( wk ) =  r ( wk )  0  r ( wk ) ≠ 0 . r ) .1 Simple ratio Calculates a point-wise ratio between selected signature.3. i 5.2 Subtraction Takes a point-wise difference between selected signature. s '( wk ) = ∑ si ( wk ) . whose second argument is taken as a reference. So. s .4.

make sure no groups are selected.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. SAMS ignores them since group selection takes precedence over signature selection. 24 .2 Open (Ctrl-O) Opens a database and first saves and closes any other already-open database.1 Database menu 6. 6.5 Operations on groups SAMS can apply a many-to-one operation on a selection of groups.1. 6 Reference This section gives descriptions of options available from the menu bar and pop-up menus.1 New (Ctrl-N) Creates a new database. SAMS adds a new entry in its list of databases and lets you assign a short. To apply an operation to selected signatures.5. If any signatures are selected at the same time as groups. 6. descriptive name.

1.3 Save (Ctrl-S) Saves database. [SAMS created <base directory> as a user-defined setting the first time it was run. it shows: ƒ ƒ database name directory under which data are stored. 6.6 Properties Shows database properties.6.sams/dbs/. Specifically. 6. 6. SAMS confirms.1. Find the directory under <base directory>/. See Section 2.4 Close (Ctrl-W) Saves and closes database.1.1. SAMS asks for confirmation. It also saves automatically when you close a database or quit the program.] 25 .5 Delete Deletes database.

Humm and not so good were added to the comment column in this table.1.7 Edit metadata structure Modifies metadata associated with database. Click on the Add attribute button. SAMS opens a window of default attributes. SAMS will update your database as shown.6. To change an attribute. Add as many attributes as you need. Add species and comment attributes. click on the cell in the spectra table and make changes. 26 .

6.8 Import signatures from Opens a submenu.1.1 Directory Specifies a directory to have SAMS search for spectra files. 27 . 6.1. 6.2 ENVI Standard file Reads an ENVI standard file in BIP format after you specify which location to read.8.8. See Appendix A.3 ASCII file Reads multiple signatures from an ASCII file.8.1. 6. Use it to import signatures into a database from different sources.1.

4 System clipboard Pastes copied spectra files from the system clipboard. SAMS ignores this suffix in separator processing. Ignore suffix.2 Filename Creates a group for each prefix (set-off by separators assigned by the user) in signature filenames.1. 6. 28 .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.6. SAMS uses characters like “.9.9.1. Use this option as an alternative to dragand-drop.” to separate groups.1.1.8. 6. In this example: 6. ƒ ƒ Separators.

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

SAMS asks for confirmation.2. 6.4 Set as reference (Alt-Enter) Sets focused signature as the reference signature for reference-based operations.1.2 Selected menu 6.3 Add to plot (Ctrl-Enter) Plots selected signatures in addition to those already displayed.3. Reference-based operations.2. 6.10 Quit (Ctrl-Q) Quits program. See Section 5. See Section 5.2 Plot (Enter) Displays selected signatures in the plot area.2.2.2.1). 30 .1 Compute Choose one of these operations to perform on a selection: ƒ ƒ ƒ Many-to-one operations.4.6. One-to-one operations.2. use Paste (Section 6. 6. 6. 6.6. allows reassignment of legends. See Section 5.4.2. See Section 5. To paste references to selected signatures into a group.5 Copy (Ctrl-Insert) Copies selected signatures to an internal clipboard.

s2 .1 Export to ASCII format SAMS exports selected signatures.. lines = 4 and samples = 5 . id( sn ) w1 .6.2.8. id( s2 ) .6 Cut (Shift-Delete) Removes selected signatures from a selection and copies them to an internal clipboard.. s1 ( w1 ) . sn . and  x  is the smallest integer that is not less than x . s1 . s1 . The identification name for signature si is id( si ) in the following discussion... s1 ( w2 ) . 8 31 .2 Export to ENVI format SAMS exports n selected signatures. 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. …. sn ( wm ) 6.. s2 ( wm ) . must conform to each other as explained in Section 5. to a CSV (comma-separated-values) file.1.. s2 ( w2 ) . …..1). sn . if n = 18 . s1 . use Paste (Section 6... selected signatures. s2 . ….2. sn . then the remaining N − n elements will be zero-filled. s2 ( w1 ) .2. Each signature is located in the image as shown: Where  x  is the greatest integer that is not greater than x . 6. If N > n .3.. id( s1 ) . sn ( w1 ) sn ( w2 ) wm . 6. SAMS asks for confirmation.8.. To paste references to removed signatures into a group.2. 6..2.6. w2 .8 Export options For all export options. s1 ( wm ) . s2 .7 Delete (Delete) Deletes selected signatures from the group.2. So. Wavelength.

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

6. Any range can be specified–see format option below.3.1 Clear Clears contents of plot area.2. 6.2. 6. 6. 6. only EPS is supported.2 Range Opens submenu with options to adjust X and Y ranges. 6.5 Zoom current X-range Rescales plot vertically to fit data in X range.2.6.2. 6. Currently.3.2.4 Chlorophyll [550:680] Sets X range to ~550-680 nm.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 Export Opens submenu with options to export the plot in different formats. 6.6 Zoom current Y-range Rescales plot horizontally to fit data in Y range.3. 6.2 Visible [400:700] Sets X range to ~400-700 nm.3.3.3.3.3.1 Full range Rescales plot to fit data.3.2.3.4 Format Opens a dialog box to modify plot parameters such as: 33 .3.3 NDVI [500:900] Sets X range to ~500-900 nm.

3. 6. orientation. Add marks specified to distinguish spectra. margins.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. Specifies how axes are labeled. SAMS automatically computes them. enter into the X Ticks or Y Ticks entry boxes a string of the following form: label position.. X range and Y range. 6. Use color. . X ticks and Y ticks. Marks. 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. Connect. 34 . A position is a number assigning the location of the tick mark along the axis. label position. Check to connect point values with lines. Stems.5 Print (Ctrl-P) Prints plot.3. To change tick marks. Check to plot stems. Labels X and Y axes.ƒ ƒ ƒ ƒ ƒ ƒ ƒ ƒ ƒ Title. X label and Y label. Assigns title to plot. Check to show background grid. Grid. Check to plot spectra with different colors. printer.

contact information.6 Pop-up menus Appear by right-clicking over elements of the selection area like signatures and groups. 6.4 Query menu Do not use yet.6. 6.7 Anti-aliased Improves plot appearance. 6.6. 35 .2 The BeanShell window Do not use. This menu is in an early stage of development. and copyright agreement for SAMS.1 About SAMS Shows current version.3.5.5. 6. 6.5 Help menu 6. Opens a tool for developers to use to test SAMS.1 Signature popup menu Contains same options as Selected in the menu bar.

6.2 View source Shows contents of source file where selected signature is stored (ASCII sources only). 36 .2 Group pop-up menu Includes the following options when a group is selected: 6.1.1. SAMS prompts you for a name and a description. Use option View data for binary sources.2. 6. when only one signature is selected.Includes the following options. 6.1 View data Shows contents of selected signature in SAMS’ memory (two columns.6.6. 6.6.1 New subgroup Applies to My groups.3 Rename Renames selected signature and associated groups. wavelength and reflectance).1.6.6.

4 Export options Applies to members of selected group as explained in Section 6.6. Computed signatures.6. Use Copy and Cut to put signatures on clipboard (Sections 6.3 Delete group Deletes selected group.5 and 6.2 Paste reference Adds references to signatures to selected group from clipboard.2. 6. Imported signatures. and My groups cannot be deleted.6).2.2.2.2.2.6.6. 37 . 6.8.

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

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

Appendix B Available Savitzky-Golay filters Savitzky-Golay filters in SAMS are named by the convention. 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 . 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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