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

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

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

3. SAMS will add a new entry in its list of databases. 3. descriptive name. Select a base directory.1 Creating a database Use the option Database -> New.2 Importing signatures Use the option Database -> Import signatures from -> Directory. 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. Assign a short. SAMS will ask you for some options to perform the operation. 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.

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

8 .SAMS includes a Selected menu containing these options: 3.4 Performing an operation – an example Average the current selected signatures: Selected -> Compute -> Average.

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 .

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

4.9 for options. ƒ ƒ ƒ Imported signatures Computed signatures My groups These groups are created automatically with every database and cannot be deleted.Only one focused element (surrounded by a square) can be selected at a time. Page-up. Home.2. are in the Computed signatures group.4 Automatic groupings SAMS can generate groups automatically. 4. 4.2. See section 6. as described in Section 5. To change the focused element.2 Computed signatures All signatures resulting from an operation. 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.1. 4. hold down the Ctrl key and use the navigational keys (Up and Down arrows.1 Imported signatures All imported signatures are in the Imported signatures group. Page-down. There are three main groups in a SAMS database. 4.3 My groups Define as many groups as you want by right-clicking on My groups and using the pop-up menu. End).2.2.3 Status info 12 .

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

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

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 6.10 6. you can define new attributes. sn ) → s' reference-based.1 6.3.1.7.. f ( s ) → s ' many-to-one.2.2.3 6. s2 .4 6. 4..4. Although each SAMS database has a default set of associated attributes.2.1.4 6.1. Choose Database -> Edit metadata structure. f ( s1 .5 6.2..6 6.1.1.5 6. too.5 Metadata Metadata associated with each signature is shown in the above table.3 6.2 6.2..7 5 Signature operations In SAMS a signature operation f can be: ƒ ƒ ƒ one-to-one. Attributes are specific to each database.2 6.6 Keyboard shortcuts Most frequent commands have keyboard shortcuts as follows. f r ( s ) → s ' 15 . See Section 6.2.1.

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

. and Golay.4 Derivative SAMS calculates s ' by taking the first discrete derivative of s : s ' ( wk ) = s ( wk +1 ) − s( wk ) .. SAMS will create s ' by applying the filter on s over the interval [a..2. c .. where a jump in s values occurs (a break-point).” Analytical Chemistry. 36. a and b . 1627-1639.  c × s( wk ) if multiplicative correction s '( wk ) =  if additive correction  s ( wk ) − c The correction. In the interval of modification.E. vol. is calculated as follows. SAMS automatically can apply a Savitzky-Golay smoothing filter to s.5 Jump correction Given a wavelength.. Second Edition.2. wk +1 − wk Before taking the derivative. wk > b (or wk < b ). 650655. b . Original reference is Savitzky A. 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. b] : s '( wk ) = j =+ nR ∑c j =− nL j × s ( wk + j ) for wavelengths. Press. c0 .. pp. where a ≤ wk ≤ b .. 1964. so s ' will not have a jump. M. Numerical Recipes in C. and two wavelength values.5. c . 5..H. Cambridge University Press. pp. W. 1992. 6 17 .. c+ nR ] (see Appendix B for available filters). “Smoothing and differentiation of data by simplified least squares procedure.3 Smooth Given a Savitzky-Golay filter6 c = [c− nL .J. s '( wk ) will differ from s ( wk ) by a correction value. et al.2. wk . SAMS will perform an algorithm to adjust the values for wavelengths. 5.

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

3 Many-to-one operations f ( s1 . In a constructed signature. Averages and standard deviations are examples. SAMS computes single values from corresponding input signature operations (e... SAMS treats them as such. c . NDWI in Section 5.6). SAMS outputs one signature from point-wise operations on selected signatures. sn ) → s' Two types of many-to-one operations exist: ƒ ƒ In aggregate operations. For example.6 Change wavelength unit Given a conversion factor.7 and absorption feature analysis in Section 5.3. if wavelength values are measured in nanometers. Although the resulting signatures are not necessarily “real” signatures..g.3. SAMS computes s' as a copy of s such that s '( k ) = s(k ) .001 will convert them to microns. s2 ..2. 19 . 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. then a conversion factor of 0. 5. but where wavelengths are multiplied by c : wk ' = c × wk .

j in [1. sn are expected to conform to each other by: ƒ ƒ having the same length. s2 . m ] ..1 Conform requirement For aggregate many-to-one operations. n ] and all k in [1.5 Maximum Gives point-wise maximum of selected signatures s '( wk ) = max si ( wk ) .4 Minimum Gives point-wise minimum of selected signatures s '( wk ) = min si ( wk ) . all selected signatures s1 .3. 5. SAMS alerts you if this requirement is not satisfied.2 Average Calculates point-wise average of selected signatures: s '( wk ) = 1 n ∑ si ( wk ) ..3.3.. 5. i 5.3.5. n i =1 5. i 20 .3. m being sampled at the same wavelengths: si ( wk ) = s j ( wk ) for all i.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. wk ..

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

a1 ). a2 ).(2..7 NDWI This construction uses wavelengths in nanometers.C.( n.(2. B.. ai . si : ai = si (860nm) − si (1240nm) . SAMS constructs s ' = [(1. Remote Sensing of Environment.. 5. Gao. 7 22 . a2 ).3. from each of the signatures selected. wq ] area under line segment connecting si ( w p ) and si ( wq ) .. SAMS creates the signature s ' = [(1.3.8 Simple extraction This construction extracts a single reflectance value at a given wavelength. a1 ). 257-266.SAMS computes ai as one minus the ratio between the area under the function in the interval [ w p . pp. an )] . an )] where ai = si (b) . is the NDWI7 of signature... where each value.. 58. si (860nm) + si (1240nm) 5. 1996: NDWI: A normalised difference water index for remote sensing of vegetation liquid water from space. b .. wq ] and the area under the straight line segment connecting the maxima: ai = 1 − area under curve in [ w p .( n.

and reference. s .4. whose second argument is taken as a reference.1 Simple ratio Calculates a point-wise ratio between selected signature.4 Reference-based operations f r ( s ) → s' A reference-based operation is a binary operation. i 5. b :  r (b) × s ( wk ) s(b) ≠ 0  s '( wk ) =  s (b) . it can be written f r (s ) and be treated as a one-to-one operation (see above).9 Sum Calculates a point-wise sum of selected signatures. s . r ) .2 Subtraction Takes a point-wise difference between selected signature.4. f ( s.3 Normalize Uses point-wise scaling according to reflectance ratio at a given wavelength. The command to establish the reference signature is Alt-Enter. and reference. r ( wk ) = 0 5.3. r :  s( wk )  s '( wk ) =  r ( wk )  0  r ( wk ) ≠ 0 . 5. s '( wk ) = ∑ si ( wk ) . SAMS includes these reference-based operations: 5.4.5. So. r : s '( wk ) = s ( wk ) − r ( wk ) .  s( w ) s ( b) = 0 k  23 .

5. 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 . descriptive name. If any signatures are selected at the same time as groups.1. To apply an operation to selected signatures. SAMS ignores them since group selection takes precedence over signature selection.5 Operations on groups SAMS can apply a many-to-one operation on a selection of groups.2 Open (Ctrl-O) Opens a database and first saves and closes any other already-open database. make sure no groups are selected. 6 Reference This section gives descriptions of options available from the menu bar and pop-up menus. SAMS adds a new entry in its list of databases and lets you assign a short.1 Database menu 6. 6.1 New (Ctrl-N) Creates a new database.

it shows: ƒ ƒ database name directory under which data are stored.6. SAMS asks for confirmation.3 Save (Ctrl-S) Saves database. Specifically. SAMS confirms. 6.sams/dbs/. 6.1.4 Close (Ctrl-W) Saves and closes database.1.6 Properties Shows database properties.5 Delete Deletes database. It also saves automatically when you close a database or quit the program.1. Find the directory under <base directory>/. [SAMS created <base directory> as a user-defined setting the first time it was run. See Section 2.] 25 .1. 6.

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. To change an attribute.1. Click on the Add attribute button. Humm and not so good were added to the comment column in this table.6. SAMS will update your database as shown. 26 . Add species and comment attributes.7 Edit metadata structure Modifies metadata associated with database.

8.1.2 ENVI Standard file Reads an ENVI standard file in BIP format after you specify which location to read.1. 27 .6. 6.8 Import signatures from Opens a submenu. Use it to import signatures into a database from different sources. See Appendix A.1.8. 6.1 Directory Specifies a directory to have SAMS search for spectra files. 6.8.3 ASCII file Reads multiple signatures from an ASCII file.1.

1.4 System clipboard Pastes copied spectra files from the system clipboard.9. 6. In this example: 6.9.6. Ignore suffix.1 Attribute value Creates a group for each value of an attribute. 28 . SAMS uses characters like “.1.1.1.8. 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. ƒ ƒ Separators. 6.” to separate groups.9 New grouping by… Opens a submenu with options to make automatic groupings. Use this option as an alternative to dragand-drop.

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. allows reassignment of legends.3. 6.2.2.2 Plot (Enter) Displays selected signatures in the plot area. Reference-based operations.1).1.2. One-to-one operations. See Section 5.4. use Paste (Section 6. To paste references to selected signatures into a group.6. 6. See Section 5. 6. 6. See Section 5.3 Add to plot (Ctrl-Enter) Plots selected signatures in addition to those already displayed.4.4 Set as reference (Alt-Enter) Sets focused signature as the reference signature for reference-based operations. See Section 5.5 Copy (Ctrl-Insert) Copies selected signatures to an internal clipboard.1 Compute Choose one of these operations to perform on a selection: ƒ ƒ ƒ Many-to-one operations.6.2. 30 .2. 6.2.2 Selected menu 6.10 Quit (Ctrl-Q) Quits program.

8. s1 .1.. must conform to each other as explained in Section 5.6 Cut (Shift-Delete) Removes selected signatures from a selection and copies them to an internal clipboard. sn ( w1 ) sn ( w2 ) wm . s2 . w2 . 6. selected signatures.2. To paste references to removed signatures into a group. 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 ( w1 ) .8 Export options For all export options. sn . Each signature is located in the image as shown: Where  x  is the greatest integer that is not greater than x . id( s1 ) . lines = 4 and samples = 5 . id( sn ) w1 .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.6. SAMS asks for confirmation. 6.. s2 ( wm ) . So. …. s2 ( w1 ) .1).. then the remaining N − n elements will be zero-filled.2.. If N > n ...2. s1 ( w2 ) .2. sn . Wavelength. sn . 8 31 . to a CSV (comma-separated-values) file. s1 ( wm ) .. sn ( wm ) 6. s1 . s1 . s2 ( w2 ) .2...1 Export to ASCII format SAMS exports selected signatures.6. 6.7 Delete (Delete) Deletes selected signatures from the group..8.2.3.. use Paste (Section 6. s2 . if n = 18 . id( s2 ) . s2 .

version 5.edu/java/ptplot/ 9 32 . *. The header displays signature identifications. wavelengths. … sn ( w2 ) .berkeley. …. SAMS prompts you for a file name to export the selected signatures and writes a corresponding header file. s2 ( w2 ) . s1 ( wm ) s2 ( w1 ) . SAMS prompts you for a file name and writes a corresponding header file. …. s1 ( w2 ) .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 ) .eecs.8.hdr.3 Plot menu9 Plot capabilities based on Ptolemy 2D data plotter package.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.hdr. s2 ( wm ) … sn ( wm ) … …. … sn ( w1 ) .2. *. 6. and spectral library for the ENVI file type. 6.1p2: http://ptolemy.

2 Visible [400:700] Sets X range to ~400-700 nm.2. 6. 6.3.4 Chlorophyll [550:680] Sets X range to ~550-680 nm.3. 6. 6. 6.3.2. Any range can be specified–see format option below.4 Format Opens a dialog box to modify plot parameters such as: 33 .6 Zoom current Y-range Rescales plot horizontally to fit data in Y range. 6. Currently.3 Export Opens submenu with options to export the plot in different formats. only EPS is supported.2 Range Opens submenu with options to adjust X and Y ranges.1 Full range Rescales plot to fit data.2.2.3.2.5 Zoom current X-range Rescales plot vertically to fit data in X range.3. 6. 6.3.3. 6.1 Encapsulated Postscript (EPS) format Opens dialog box in which to specify a name for the plot file compatible with word processors.2.6.3.3.3 NDVI [500:900] Sets X range to ~500-900 nm.3. 6.3.1 Clear Clears contents of plot area.3.

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

6. 6. and copyright agreement for SAMS.7 Anti-aliased Improves plot appearance.5.2 The BeanShell window Do not use.6. contact information.3. This menu is in an early stage of development.1 About SAMS Shows current version. Opens a tool for developers to use to test SAMS.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.5 Help menu 6. 6. 6.1 Signature popup menu Contains same options as Selected in the menu bar.5. 6. 35 .

6. Use option View data for binary sources. wavelength and reflectance).1 New subgroup Applies to My groups. 6. when only one signature is selected. SAMS prompts you for a name and a description.6.2 Group pop-up menu Includes the following options when a group is selected: 6. 36 . 6.6.1.3 Rename Renames selected signature and associated groups.2.Includes the following options.2 View source Shows contents of source file where selected signature is stored (ASCII sources only).6.1. 6.1 View data Shows contents of selected signature in SAMS’ memory (two columns.6.1.6.

Use Copy and Cut to put signatures on clipboard (Sections 6.2.5 and 6.2.2. Computed signatures. 37 . and My groups cannot be deleted.6.6.6).6.8.4 Export options Applies to members of selected group as explained in Section 6.2 Paste reference Adds references to signatures to selected group from clipboard. Imported signatures.2. 6.3 Delete group Deletes selected group.2. 6.2.6.

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

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

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

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