PDS Spectroscopy Subnode

Brown University

Spectrafinder Manual

Version 3.0

Manual Text Table of Contents

Manual Figures


Spectroscopic data provide a principal interpretive base for remote compositional studies. The PDS Subnode organizes spectroscopic and ancillary data and makes them available to the scientific community for research. Spectrafinder is a mouse controlled search and retrieval system that is maintained on-line for the user community. The Spectrafinder system allows users to identify and locate spectroscopic information that has been obtained and published previously as well as to become familiar with more recent data associated with on-going research. The purpose is to promote broad communication and exchange of spectroscopic data among investigators, enabling or enhancing scientific return.

Principal data include visible, near-infrared and mid-infrared spectra, acquired both in the laboratory and with remote sensors (including telescopic instruments). Associated data provided with the spectra include information about the sample or object, sample composition (as available), instrument used, Principal Investigator (and address), references to published data, etc.

Spectroscopic data are classified either as PUBLIC (public domain) or BROWSE (ongoing research). Although both types of data can be accessed through Spectrafinder for viewing, only PUBLIC data can be transferred to the user for further analysis. If a user is interested in acquiring data in the BROWSE category, he/she must contact the PI for permission to use. Most spectroscopic categories maintained by PDS are dynamic (continually growing and expanding) and necessarily consist of both Public and Browse data.

The Spectrafinder structure has been developed and tested; and data are presently ingesting into the spectral database. The database is expected to grow considerably over the next several years. It should be noted that since spectra are derived from diverse sources, not all data within PDS may contain detailed information about the sample or the object for which spectra were acquired. Much valuable spectroscopic data for planetary materials and planetary bodies have been produced through NASA's Research and Analysis program and these form the principal PDS data collection. Only a few data acquisition programs, however, were designed to produce "library quality" data, e.g., data with complete documentation of physical and compositional properties. Ancillary data for spectra within PDS will continually be upgraded as data become available, and "library quality" data sets will be identified as they are incorporated into the Spectrafinder structure.

Contact George He with any suggestions or requests for Spectrafinder capabilities. Please report any errors, major or minor, that occur in PDS Spectrafinder data bases. Address comments to the Internet address: he@pds.geo.brown.edu.


Spectrafinder has been developed on a Sun SPARC 10 station and uses basic X-Window calls. Login through a X-Window compatible machine (X Window, MacX, etc.). A 1024 by 800 pixel screen would be the best choice for display. Moving windows around may be required for a screen that has 800 by 600 pixels in resolution. The following is a list of necessary fonts for this release:

	a) "-adobe-courier-bold-r-normal--10-100-75-75-m-60-iso8859-1"
	b) "-adobe-courier-bold-r-normal--18-180-75-75-m-110-iso8859-1"
	c) "-adobe-courier-bold-r-normal--14-140-75-75-m-90-iso8859-1"
	d) "-adobe-courier-bold-r-normal--12-120-75-75-m-70-iso8859-1"
	e) "-adobe-helvetica-bold-r-normal--12-120-75-75-p-70-iso8859-1"
	f) "-adobe-helvetica-bold-r-normal--10-100-75-75-p-60-iso8859-1"

Operational functions and data available are indicated with buttons and are shown with CAPITAL letters. Labels are not capitalized. Inactive functions are shown without buttons. [Capabilities expected in the near future are also shown without buttons, but longer term structure is not shown.]

Login Procedure [typed commands]

Any NASA funded researcher may gain acces to Spectrafinder. Contact George He for user ID and password. NASA grant/contract number or RTOP number may be requested. Phone: 401-863-1062. Internet: he@pds.geo.brown.edu.

   a)  Log into an X-Window compatible machine at your own site.
   b)  Open an X-window compatible terminal or window.
   c)  Open host machine at Brown
	On SUN:
	On a DEC machine, grant the privilege to pds.geo.brown.edu
   d)  Login to Host machine at Brown:
	[telnet pds.geo.brown.edu ]
	username:   [yourname]
	password:   [yourpass]
   e)  Set environment on Sun if necessary 
	e.g.  [setenv DISPLAY  yourmachineIP:0.0]
             where yourmachine is the IP address for your machine.
   f)  Run spectrafinder

Operation Summary

A Control Panel and an Introduction message with short instructions [Figure 1] will appear after login. Almost all operations other than data selection are performed from the Control Panel. Clicking on a button anywhere in Spectrafinder activates that function or selects that information (clicking a second time deactivates or deselects).

If telecommunications is unacceptably slow, a streamlined display is available that eliminates many of the nice visuals (click FULL/SHORT). Brief on-line help is available. When HELP is clicked from the control panel, a short explanatory message will be shown at the bottom of the control panel. When the mouse is clicked at a new location, a message appears describing the function of that area or button. Note: help must be off to perform Spectrafinder functions.

There are three general types of windows in the current Spectrafinder structure, one for searching or locating data, one for data viewing and presentation, and one for information and/or data transfer. These are summarized here with detailed descriptions of functions in the following sections.

To begin a session, click NEW under Spectrafinder Start Functions. The first level data structure will be displayed [see Figure 2]. Click on whatever type of data are to be examined. Some data categories will display a second level structure (e.g. Figure 3). After selecting the data category(ies) desired, click SEARCH. The data base will be searched to find how many samples and spectra exist in the category selected. The number of spectra and the number of samples available in the designated category are shown in the message area at the bottom of the Control Panel. To narrow the field (for example, limit the data to that for a more narrow range or properties or that acquired by a particular PI), simply click additional properties and search again.

To display information about a sample (ancillary data) and plots of spectra click DISPLAY. A new window environment will appear with graphics display for the spectra and ancillary data in text (Figure 4). There are several options to step through the data selected. Depending on whether SAMPLE or SPECTRUM is depressed, FORWARD goes to the next sample or spectrum and BACK goes back to the previous sample or spectrum. [Subsequent versions of Spectrafinder will allow the ancillary information to be searched without plotting the data.] Individual spectra can be stored in a temporary file and retrieved for comparison (KEEP - RECALL).

There are currently three ways to identify and prepare data to be transferred to the user: 1) BUFFER contains all the public data identified in the search operation. 2) DATASET identifies specific prepared data sets (e.g., Gaffey's 1976 meteorite collection of spectra). 3) SELECT contains the spectra selected and stored temporarily (through keep).

Control Panel

There are several sub-panels on the Spectrafinder Control Panel. These currently include groups of General, Primary Operations, and Data Display commands and a small sub-panel at the bottom that displays text information from several commands.


INTRO. The introduction that appears at the beginning of a session can be recalled at any time with this command. This text panel contains general background information (see Figure 1).

HELP. When help is activated, place the cursor on the item for which more information is desired and click the mouse. Brief information will be displayed in the small sub panel located at the bottom of the Control Panel. Be sure to disengage this mode (click help again) when returning to the principal search and plotting functions of Spectrafinder.

EXIT. This command exits Spectrafinder and returns to the host computer.

SOFTW. If network connections are too slow to be practical, the Spectrafinder software can be transferred to a local computer (although the spectra data bases remain on the PDS computer). This command displays a text screen that provides instructions on how to transfer Spectrafinder software and ancillary data (see Figure 5). Since both the PDS data and Spectrafinder itself continually expand in capabilities and scope, it is recommended that newer versions of the software and ancillary data be downloaded regularly.

FULL/SHORT. This button is a toggle switch between a full and a streamlined display style. Full/Short display mode can be changed at any time. When the network is slow, a streamlined display can increase the speed of a session quite a lot.

Primary Operations:

Start. These buttons initiate a search or expand a previous search.

Transfer. Selection of any of these buttons will allow a data file to be prepared in order to transfer spectra to the user through a FTP command. All data is prepared in ASCII using PDS format and standard labels. [Currently all PDS labels are prepared for transfer. Subsequent versions of Spectrafinder will allow the user to select which labels and ancillary data to be transferred with the data.] Only Public data will be included in the data file. No Browse data will be transferred without permission of the PI. INSTRUCTIONS are available for each selection (see Figure 6).

Data Display:

Display of plots and ancillary data is currently initiated from the Data Structure windows (click DISPLAY, see below). This section of the Control Panel controls how the data are displayed.

Text Information Subpanel

During help, a brief description of the function selected is provided.

During Data Display, the number of samples (or bodies) in the search buffer is shown as well as which spectrum is being displayed for that sample. (The total number of spectra in the buffer is shown in the Plot Window title as well as the plotindex of the spectum displayed.)

Data Structure Windows

These windows allow specific data or information to be identified. Once characterizing parameters have been selected, the PDS data base will be searched and a data buffer created that contains all spectra (both Public and Browse) that fulfill the selected parameters. Both the Top and Second Levels of the data structure contain several buttons along the top of the window that perform or initiate operations. These can be selected from any Data Structure window.

Top Level Data Structure Window. This window displays the primary organization of PDS spectroscopic data, which includes both laboratory spectra of planetary materials and remotely acquired spectra of planetary bodies (see Figure 2). Any button can be selected to identify or characterize the desired spectra. When the PDS data base is searched (search operation), spectra must fulfill all the selected properties to be included in the buffer. Most categories are very broad and require further definition of properties. When these categories are selected a Second Level Data Structure will appear with subcategories for selection (see below).

Once a category is selected, the button will appear depressed. To deselect a category simply click the depressed button and it will return to the un-selected mode (a normal button). Categories for which data currently exist in the PDS structure are indicated with buttons. Categories for which data should be available soon are listed without buttons. Empty spaces are placeholders for future input.

Second Level Data Structure Window. These windows provide more detailed information about the category selected in the Top Level Data Structure. Each window (see Figure 3) may also have subcategories within a column category (indicated with >). Individual subcategories may be selected or whole categories may be selected. Once selected, the button will appear depressed. To deselect a category simply click the depressed button and it will return to the un-selected mode (a normal button). reset from this window will clear only the depressed buttons in the Second Level Data Structure window.

Ancillary Data Windows

There are several types of Ancillary Data windows, depending on the type of data selected. These divide into three general types: Sample, Planetary Body, and Spectrum. Information about the sample measured in the laboratory. Unless otherwise specified, information about the data selected are displayed in order of their identification (ID) number.

Parameters common to many Ancillary Data windows:

Additional parameters frequently used for Sample windows:

Additional parameters frequently used for Spectrum windows:

For remote measurements:

For laboratory measurements:

Plot Windows

This window displays spectra as a function of wavelength (see Figure 4). Operations are controlled from the Control Panel (see Data Display section of the Control Panel). The plotindex of the spectrum will be shown in the window label along with the total number of spectra selected during the search. Unless otherwise specified, the data selected are plotted in order of their sample ID (see Ancillary Data).

Manual Figures