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

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

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

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. descriptive name. SAMS will ask you for some options to perform the operation. Assign a short. 3. 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).2 Importing signatures Use the option Database -> Import signatures from -> Directory. The dialog box appears only once for a given machine/OS. 3. Select a base directory. 6 .1 Creating a database Use the option Database -> New.

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

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

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.

4 Overview 4.1 Graphical interface 10 .

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

Populate the group by copying and pasting. hold down the Ctrl key and use the navigational keys (Up and Down arrows. See section 6. To change the focused element. 4. Home. There are three main groups in a SAMS database. 4.2. 4.2.9 for options. as described in Section 5.3 Status info 12 .1 Imported signatures All imported signatures are in the Imported signatures group. The focused element is used as the reference signature for reference-based operations when the command Alt-Enter is used.4 Automatic groupings SAMS can generate groups automatically.2 Computed signatures All signatures resulting from an operation. End).2. 4. are in the Computed signatures group. ƒ ƒ ƒ Imported signatures Computed signatures My groups These groups are created automatically with every database and cannot be deleted. Page-down. Page-up. 4.Only one focused element (surrounded by a square) can be selected at a time.2.1.3 My groups Define as many groups as you want by right-clicking on My groups and using the pop-up menu.

If it is a signature. if only one signature is selected).3). Mouse interaction To zoom in. pressing Alt-Enter will make this element the reference.number of selected groups (or group’s name if only one group is selected). Also shows the mouse location in X-Y coordinates. Focused – name of current focused element (either a group or a signature).4 Plot area Includes buttons for common plot operations (see Section 6.ƒ ƒ ƒ ƒ Signature selection . Reference signature . 4.number of selected signatures (or its name. Group selection . 13 . 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).

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

2 6.1.5 6. f ( s ) → s ' many-to-one.2.1. Attributes are specific to each database. 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.. 4.1.2.2. you can define new attributes.7 5 Signature operations In SAMS a signature operation f can be: ƒ ƒ ƒ one-to-one.7..5 6.6 6.4 6. f ( s1 .3 6.4.10 6. sn ) → s' reference-based. s2 .3.2. Although each SAMS database has a default set of associated attributes. too.4 6.2 6.3 6. See Section 6.5 Metadata Metadata associated with each signature is shown in the above table. f r ( s ) → s ' 15 ..1.2. Choose Database -> Edit metadata structure.1.2.6 Keyboard shortcuts Most frequent commands have keyboard shortcuts as follows.1..1 6.

5. SAMS will make a copy s '( wk ) of s ( wk ) for wavelengths.… . 5.2.. Current reference signature. A point value of signature . such that a ≤ wk ≤ b . r2 ). sn are selected signatures. rk . wk . A defined signature... 5. 5. s2 . SAMS will compute s' from s by multiplying each ordinate point by a : s '( wk ) = a × s ( wk ) . A signature resulting from an operation. r1 ). 16 .. this value s( w) is computed by linear interpolation between nearest neighbors. wk . at wavelength .( w2 . SAMS will apply the operation n times to generate n resulting signatures.Signature operations are applied to the current selection where s1 . s2 . at an arbitrary wavelength. or.. k . w ..1 Notation Operations are described in this manual according to the following notations: s1 .( wm .. in [ w1 . a . wm ] . equivalently. s .1 Scale Given a scalar value. sn r s = [( w1 .2. If necessary. rm )] s ( wk ) = s( k ) = rk s ( w) s' Current selected signatures.2 One-to-one operations f ( s) → s ' A one-to-one operation takes one signature and produces one signature. A reflectance value.2 Crop Given two wavelength values.. at wavelength index. a and b .

M. 1964.5. et al. Cambridge University Press. 1992. is calculated as follows.J. 650655.. c . Press. Numerical Recipes in C. where a ≤ wk ≤ b . c+ nR ] (see Appendix B for available filters).3 Smooth Given a Savitzky-Golay filter6 c = [c− nL . W. Original reference is Savitzky A. SAMS automatically can apply a Savitzky-Golay smoothing filter to s.2. pp. wk > b (or wk < b ).  c × s( wk ) if multiplicative correction s '( wk ) =  if additive correction  s ( wk ) − c The correction. pp.H.” Analytical Chemistry... and Golay. wk +1 − wk Before taking the derivative. 36. b] : s '( wk ) = j =+ nR ∑c j =− nL j × s ( wk + j ) for wavelengths. c .5 Jump correction Given a wavelength. and two wavelength values. where a jump in s values occurs (a break-point). In the interval of modification.E. a and b .. 5. 1627-1639. 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. 6 17 . so s ' will not have a jump.. wk .. c0 .. “Smoothing and differentiation of data by simplified least squares procedure. SAMS will create s ' by applying the filter on s over the interval [a..4 Derivative SAMS calculates s ' by taking the first discrete derivative of s : s ' ( wk ) = s ( wk +1 ) − s( wk ) . SAMS will perform an algorithm to adjust the values for wavelengths.2. vol. 5..2. b . Second Edition. s '( wk ) will differ from s ( wk ) by a correction value.

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

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

3.3.3.3..5. m being sampled at the same wavelengths: si ( wk ) = s j ( wk ) for all i. all selected signatures s1 . n ] and all k in [1.5 Maximum Gives point-wise maximum of selected signatures s '( wk ) = max si ( wk ) . sn are expected to conform to each other by: ƒ ƒ having the same length. j in [1..4 Minimum Gives point-wise minimum of selected signatures s '( wk ) = min si ( wk ) . wk . SAMS alerts you if this requirement is not satisfied.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.. i 5.1 Conform requirement For aggregate many-to-one operations. i 20 . n i =1 5..3. s2 . 5. 5. m ] .2 Average Calculates point-wise average of selected signatures: s '( wk ) = 1 n ∑ si ( wk ) .

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

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

and 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.3.4. it can be written f r (s ) and be treated as a one-to-one operation (see above). So.3 Normalize Uses point-wise scaling according to reflectance ratio at a given wavelength. 5. b :  r (b) × s ( wk ) s(b) ≠ 0  s '( wk ) =  s (b) . f ( s.4. s . r ) .  s( w ) s ( b) = 0 k  23 .4. i 5. SAMS includes these reference-based operations: 5. s . whose second argument is taken as a reference. and reference.5. s '( wk ) = ∑ si ( wk ) . r ( wk ) = 0 5.2 Subtraction Takes a point-wise difference between selected signature. r :  s( wk )  s '( wk ) =  r ( wk )  0  r ( wk ) ≠ 0 .9 Sum Calculates a point-wise sum of selected signatures. The command to establish the reference signature is Alt-Enter. r : s '( wk ) = s ( wk ) − r ( wk ) .

SAMS ignores them since group selection takes precedence over signature selection. SAMS adds a new entry in its list of databases and lets you assign a short. 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 New (Ctrl-N) Creates a new database.1.2 Open (Ctrl-O) Opens a database and first saves and closes any other already-open database. 6. To apply an operation to selected signatures. 6.1.5. make sure no groups are selected. If any signatures are selected at the same time as groups.5 Operations on groups SAMS can apply a many-to-one operation on a selection of groups.1 Database menu 6. 24 . descriptive name. 6 Reference This section gives descriptions of options available from the menu bar and pop-up menus.

6 Properties Shows database properties.5 Delete Deletes database.4 Close (Ctrl-W) Saves and closes database. [SAMS created <base directory> as a user-defined setting the first time it was run. See Section 2. It also saves automatically when you close a database or quit the program. SAMS asks for confirmation.6.1.sams/dbs/. SAMS confirms.3 Save (Ctrl-S) Saves database.1.1. 6. Specifically. it shows: ƒ ƒ database name directory under which data are stored. 6. Find the directory under <base directory>/.1. 6.] 25 .

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

27 .8.6. 6.8 Import signatures from Opens a submenu. 6.8.2 ENVI Standard file Reads an ENVI standard file in BIP format after you specify which location to read. 6.1 Directory Specifies a directory to have SAMS search for spectra files.1.3 ASCII file Reads multiple signatures from an ASCII file.8.1.1. See Appendix A.1. Use it to import signatures into a database from different sources.

1. Ignore suffix.8.1 Attribute value Creates a group for each value of an attribute.1. In this example: 6.6. SAMS uses characters like “.” to separate groups.9.9.9 New grouping by… Opens a submenu with options to make automatic groupings.1. 28 . SAMS ignores this suffix in separator processing.2 Filename Creates a group for each prefix (set-off by separators assigned by the user) in signature filenames. 6. Use this option as an alternative to dragand-drop.1. ƒ ƒ Separators.4 System clipboard Pastes copied spectra files from the system clipboard. 6.

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

5 Copy (Ctrl-Insert) Copies selected signatures to an internal clipboard.1). 6. SAMS asks for confirmation. Reference-based operations.3.4.2 Selected menu 6. use Paste (Section 6. 6.2.2. To paste references to selected signatures into a group.10 Quit (Ctrl-Q) Quits program. 6. See Section 5. See Section 5.2.4. 6.1.6.2.3 Add to plot (Ctrl-Enter) Plots selected signatures in addition to those already displayed. One-to-one operations.6.2. 30 .1 Compute Choose one of these operations to perform on a selection: ƒ ƒ ƒ Many-to-one operations. See Section 5. See Section 5. allows reassignment of legends. 6.2.2 Plot (Enter) Displays selected signatures in the plot area.2.4 Set as reference (Alt-Enter) Sets focused signature as the reference signature for reference-based operations.

. use Paste (Section 6. So.. s2 . then the remaining N − n elements will be zero-filled.2. Each signature is located in the image as shown: Where  x  is the greatest integer that is not greater than x . s1 ( wm ) . sn ( w1 ) sn ( w2 ) wm . s1 . sn . w2 . ….6.1). id( s2 ) .2. Wavelength.2. to a multi-band image in ENVI standard format with dimensions:8 lines =  n   n  samples =   lines  bands = m It follows that the image can store N = lines × samples ≥ n signatures. SAMS asks for confirmation.. …. s2 ( w1 ) .. s2 ( w2 ) . s2 .. s1 ( w2 ) ... If N > n . s1 . id( s1 ) . To paste references to removed signatures into a group. 8 31 . s1 ( w1 ) . s1 . lines = 4 and samples = 5 .6. sn ( wm ) 6. ….3.6 Cut (Shift-Delete) Removes selected signatures from a selection and copies them to an internal clipboard.2.. 6. must conform to each other as explained in Section 5.8 Export options For all export options. to a CSV (comma-separated-values) file.. s2 .1. sn .2 Export to ENVI format SAMS exports n selected signatures.. id( sn ) w1 . s2 ( wm ) .7 Delete (Delete) Deletes selected signatures from the group. selected signatures. and  x  is the smallest integer that is not less than x .1 Export to ASCII format SAMS exports selected signatures..2. 6. sn . The identification name for signature si is id( si ) in the following discussion. 6.8. if n = 18 ..2.8.

and spectral library for the ENVI file type.berkeley. … sn ( w2 ) . SAMS prompts you for a file name to export the selected signatures and writes a corresponding header file.eecs. ….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.2. wavelengths.hdr.edu/java/ptplot/ 9 32 . version 5.3 Plot menu9 Plot capabilities based on Ptolemy 2D data plotter package. s1 ( wm ) s2 ( w1 ) . s2 ( wm ) … sn ( wm ) … …. *. … sn ( w1 ) .8.1p2: http://ptolemy. …. 6. SAMS prompts you for a file name and writes a corresponding header file. The header displays signature identifications. s2 ( w2 ) . 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 ) . 6.

3. 6.2 Range Opens submenu with options to adjust X and Y ranges.2. 6. 6.2.3. 6.4 Format Opens a dialog box to modify plot parameters such as: 33 . 6. 6.3. 6.2.3.2.3.1 Encapsulated Postscript (EPS) format Opens dialog box in which to specify a name for the plot file compatible with word processors.3 NDVI [500:900] Sets X range to ~500-900 nm. Any range can be specified–see format option below.2.3 Export Opens submenu with options to export the plot in different formats. 6.2 Visible [400:700] Sets X range to ~400-700 nm.3.5 Zoom current X-range Rescales plot vertically to fit data in X range. 6.2.3.6 Zoom current Y-range Rescales plot horizontally to fit data in Y range.6. 6. only EPS is supported.3.1 Full range Rescales plot to fit data.3.1 Clear Clears contents of plot area.4 Chlorophyll [550:680] Sets X range to ~550-680 nm.3. Currently.3.3.

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

5.2 The BeanShell window Do not use. 35 . 6.1 Signature popup menu Contains same options as Selected in the menu bar.1 About SAMS Shows current version.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.7 Anti-aliased Improves plot appearance. 6. 6. This menu is in an early stage of development.5.5 Help menu 6. and copyright agreement for SAMS.6. contact information.3.6. 6.4 Query menu Do not use yet.

Includes the following options.6. Use option View data for binary sources.3 Rename Renames selected signature and associated groups. 6.6. 6. SAMS prompts you for a name and a description.2 View source Shows contents of source file where selected signature is stored (ASCII sources only). 36 . when only one signature is selected. 6.6.6.2 Group pop-up menu Includes the following options when a group is selected: 6. 6.2.1.1.1 View data Shows contents of selected signature in SAMS’ memory (two columns. wavelength and reflectance).1 New subgroup Applies to My groups.6.1.

6. Use Copy and Cut to put signatures on clipboard (Sections 6.6).2.6. Computed signatures. and My groups cannot be deleted.2 Paste reference Adds references to signatures to selected group from clipboard.6. Imported signatures.2.4 Export options Applies to members of selected group as explained in Section 6.2. 6. 37 .6.2.3 Delete group Deletes selected group.5 and 6.8.6.2.2.

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

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

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 . M − nL − nR .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. where M is the order of the fitting polynomial. nL is the number of left data points used.

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