samsmanual | File Format | Menu (Computing)

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

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

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

5 Appendix A describes the currently recognized formats. 7 . Only-Reflectance. SAMS will attempt to automatically recognize each file. or for files with different formats. Select for unknown format. GER. 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.Search subdirectories? Check to scan all files in the directory and its subdirectories. Best guess. ASD binary format. ASD.3 Browsing spectra Use your mouse to select some signatures in the left window. File type. ASDb. ASD ASCII format. 3.

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

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

4 Automatic groupings SAMS can generate groups automatically.2. as described in Section 5. To change the focused element. are in the Computed signatures group. 4.3 My groups Define as many groups as you want by right-clicking on My groups and using the pop-up menu.9 for options.3 Status info 12 . There are three main groups in a SAMS database.Only one focused element (surrounded by a square) can be selected at a time.2.2 Computed signatures All signatures resulting from an operation. 4.2. hold down the Ctrl key and use the navigational keys (Up and Down arrows. See section 6. Page-down. ƒ ƒ ƒ Imported signatures Computed signatures My groups These groups are created automatically with every database and cannot be deleted. The focused element is used as the reference signature for reference-based operations when the command Alt-Enter is used. End). 4. Page-up.2.1. Populate the group by copying and pasting.1 Imported signatures All imported signatures are in the Imported signatures group. 4. Home. 4.

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

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

1.2. f ( s1 . f r ( s ) → s ' 15 . you can define new attributes.6 6.2 6. f ( s ) → s ' many-to-one.2.4.2. too.1.1 6. Choose Database -> Edit metadata structure. See Section 6.6 Keyboard shortcuts Most frequent commands have keyboard shortcuts as follows. s2 .. 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 6.1. Attributes are specific to each database.2.1.1.3 6. 4.2. sn ) → s' reference-based.2..7 5 Signature operations In SAMS a signature operation f can be: ƒ ƒ ƒ one-to-one.5 6.1.3..4 6. Although each SAMS database has a default set of associated attributes.3 6.7.2 6.5 Metadata Metadata associated with each signature is shown in the above table.5 6..10 6.

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

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

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

3.6).001 will convert them to microns.7 and absorption feature analysis in Section 5. 19 .6 Change wavelength unit Given a conversion factor. SAMS treats them as such. c . if wavelength values are measured in nanometers. 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. Averages and standard deviations are examples.g. 5. sn ) → s' Two types of many-to-one operations exist: ƒ ƒ In aggregate operations. For example. SAMS computes single values from corresponding input signature operations (e. 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.3.2.... NDWI in Section 5. Although the resulting signatures are not necessarily “real” signatures.3 Many-to-one operations f ( s1 .. then a conversion factor of 0. In a constructed signature. s2 .

wk .3. i 5.3. sn are expected to conform to each other by: ƒ ƒ having the same length.3. 5.. j in [1..3.1 Conform requirement For aggregate many-to-one operations. SAMS alerts you if this requirement is not satisfied. i 20 ... m being sampled at the same wavelengths: si ( wk ) = s j ( wk ) for all i.5 Maximum Gives point-wise maximum of selected signatures s '( wk ) = max si ( wk ) . n ] and all k in [1.3. 5. n i =1 5.2 Average Calculates point-wise average of selected signatures: s '( wk ) = 1 n ∑ si ( wk ) . s2 .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. m ] .4 Minimum Gives point-wise minimum of selected signatures s '( wk ) = min si ( wk ) .5. all selected signatures s1 .

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

. wq ] area under line segment connecting si ( w p ) and si ( wq ) .3.. pp.. where each value. Gao. ai . 1996: NDWI: A normalised difference water index for remote sensing of vegetation liquid water from space. b . 5.8 Simple extraction This construction extracts a single reflectance value at a given wavelength. 257-266. B. a1 ).(2. 58.( n.. a2 ). an )] where ai = si (b) .( n.. SAMS creates the signature s ' = [(1. Remote Sensing of Environment.3.. a2 ). from each of the signatures selected.(2.C. 7 22 ..SAMS computes ai as one minus the ratio between the area under the function in the interval [ w p . is the NDWI7 of signature..7 NDWI This construction uses wavelengths in nanometers. wq ] and the area under the straight line segment connecting the maxima: ai = 1 − area under curve in [ w p . a1 ). SAMS constructs s ' = [(1. an )] . si (860nm) + si (1240nm) 5. si : ai = si (860nm) − si (1240nm) .

4. r : s '( wk ) = s ( wk ) − r ( wk ) . 5. it can be written f r (s ) and be treated as a one-to-one operation (see above). and reference. The command to establish the reference signature is Alt-Enter.2 Subtraction Takes a point-wise difference between selected signature. whose second argument is taken as a reference. r :  s( wk )  s '( wk ) =  r ( wk )  0  r ( wk ) ≠ 0 . r ) . s .4. SAMS includes these reference-based operations: 5. and reference.3 Normalize Uses point-wise scaling according to reflectance ratio at a given wavelength. s '( wk ) = ∑ si ( wk ) .3. r ( wk ) = 0 5. b :  r (b) × s ( wk ) s(b) ≠ 0  s '( wk ) =  s (b) .1 Simple ratio Calculates a point-wise ratio between selected signature. f ( s.4.5.4 Reference-based operations f r ( s ) → s' A reference-based operation is a binary operation.  s( w ) s ( b) = 0 k  23 . s .9 Sum Calculates a point-wise sum of selected signatures. So. i 5.

6.5 Operations on groups SAMS can apply a many-to-one operation on a selection of groups. descriptive name.1. 24 . make sure no groups are selected. SAMS ignores them since group selection takes precedence over signature selection. If any signatures are selected at the same time as groups.1 New (Ctrl-N) Creates a new database. 6 Reference This section gives descriptions of options available from the menu bar and pop-up menus. 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. To apply an operation to selected signatures.1. SAMS adds a new entry in its list of databases and lets you assign a short.2 Open (Ctrl-O) Opens a database and first saves and closes any other already-open database.5. 6.1 Database menu 6.

6 Properties Shows database properties.1.1.3 Save (Ctrl-S) Saves database. 6.1.4 Close (Ctrl-W) Saves and closes database.6. 6.1. it shows: ƒ ƒ database name directory under which data are stored. See Section 2. [SAMS created <base directory> as a user-defined setting the first time it was run. It also saves automatically when you close a database or quit the program.] 25 . Find the directory under <base directory>/. Specifically.5 Delete Deletes database. SAMS asks for confirmation. SAMS confirms.sams/dbs/. 6.

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

8.1. Use it to import signatures into a database from different sources. 6.8. 6.1.1 Directory Specifies a directory to have SAMS search for spectra files.2 ENVI Standard file Reads an ENVI standard file in BIP format after you specify which location to read.3 ASCII file Reads multiple signatures from an ASCII file.1.8 Import signatures from Opens a submenu. 27 .1.8. See Appendix A. 6.6.

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

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

3 Add to plot (Ctrl-Enter) Plots selected signatures in addition to those already displayed.6.4 Set as reference (Alt-Enter) Sets focused signature as the reference signature for reference-based operations.6.5 Copy (Ctrl-Insert) Copies selected signatures to an internal clipboard. See Section 5. See Section 5.2.2. 6.2. 6. To paste references to selected signatures into a group.2. See Section 5.2. 6.4. use Paste (Section 6. See Section 5. 30 .4.1). SAMS asks for confirmation.3. 6. Reference-based operations.2.10 Quit (Ctrl-Q) Quits program.2 Selected menu 6. One-to-one operations.1.2. allows reassignment of legends.1 Compute Choose one of these operations to perform on a selection: ƒ ƒ ƒ Many-to-one operations.2 Plot (Enter) Displays selected signatures in the plot area. 6.

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

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

2 Visible [400:700] Sets X range to ~400-700 nm. only EPS is supported.3. 6.3. 6.2.3. 6. 6. Any range can be specified–see format option below.3.3 NDVI [500:900] Sets X range to ~500-900 nm.2.3.6 Zoom current Y-range Rescales plot horizontally to fit data in Y range. Currently.1 Full range Rescales plot to fit data.3 Export Opens submenu with options to export the plot in different formats.2 Range Opens submenu with options to adjust X and Y ranges.3.2.6.3. 6.1 Encapsulated Postscript (EPS) format Opens dialog box in which to specify a name for the plot file compatible with word processors.1 Clear Clears contents of plot area.3. 6.4 Chlorophyll [550:680] Sets X range to ~550-680 nm.3.4 Format Opens a dialog box to modify plot parameters such as: 33 .5 Zoom current X-range Rescales plot vertically to fit data in X range. 6. 6.3. 6.2. 6.2.3.2.3.

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

5.6.3.6 Pop-up menus Appear by right-clicking over elements of the selection area like signatures and groups.2 The BeanShell window Do not use. 6.1 Signature popup menu Contains same options as Selected in the menu bar. 6.4 Query menu Do not use yet. and copyright agreement for SAMS. This menu is in an early stage of development.6. 6. Opens a tool for developers to use to test SAMS. 6. contact information.5.1 About SAMS Shows current version. 6.7 Anti-aliased Improves plot appearance.5 Help menu 6. 35 .

when only one signature is selected. 6.6.1.3 Rename Renames selected signature and associated groups.2.1 New subgroup Applies to My groups. wavelength and reflectance).2 Group pop-up menu Includes the following options when a group is selected: 6.Includes the following options. 6. Use option View data for binary sources. 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).1.6.6. 36 .1. 6.1 View data Shows contents of selected signature in SAMS’ memory (two columns.

6). 6.5 and 6. Imported signatures. 6.6. Computed signatures.2.3 Delete group Deletes selected group.6. Use Copy and Cut to put signatures on clipboard (Sections 6.4 Export options Applies to members of selected group as explained in Section 6.2. 37 . and My groups cannot be deleted.8.2 Paste reference Adds references to signatures to selected group from clipboard.6.2.2.2.6.2.

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

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

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

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