HYPEX Toolkit Summary of Executables

HYPEX Toolkit Command Line Executables

In this section, each file present in the $HYPEX/bin directory is listed, with links to the appropriate documentation, where available. The list of executables has been organized to reflect the grouping of capabilities as defined in the "icon catalog", and "X-interface" renderings of the HYPEX Toolkit. In this manner, programs having similar processing functions are generally listed with other similar or related programs. As some programs have multiple uses, the same program may be listed in multiple groups.

Top Level Programs

These programs are the primary interface between the HYPEX Toolkit and the user. These elements include the programs that launch the the main HYPEX Toolkit "X-interface", and the browser that provides access to the Hypertext Documentation.

HYPEX_Toolkit launches the X-interface version of the HYPEX_Toolkit using the program arch.

arch is the reconfigurable architecture GUI used for installation and X-based operation of the HYPEX Toolkit.

HYPEX_Help launches Mosaic with the HYPEX Toolkit User Help Guide as it's input.

Mosaic -- is a hypertext viewer interface to on-line documentation. Once installed, the user can replace the delivered version of Mosaic with a link to their browser of choice, such as Netscape.

Spectral Radiance Simulation Models

SRSA is the Spectral Radiance Simulation and Analysis model for prediction, visualization, and analysis of spectral radiance from user-specified terrain materials and clouds.

mosart1.41 is the most current version of the MOSART code which performs radiative transfer calculations to characterize the atmospheric state for user-specified conditions.

spcalc9.7 convolves the spectral diffuse, directional and/or bidirectional reflectance distribution function (BRDF) databases with spectral atmospheric radiative environment data to produce tables of bidirectional radiance.

SR_mixture performs a spectral mixing of total radiance for up to 10 terrain materials.

Spectral Radiance Processing Tools

The following Spectral Radiance Tools (SR_Tools) operate on spectral radiance files associated with a particular terrain material or cloud type. These spectral radiance files can also be used to analyze measured data extracted from a Spectral Image cube by the visualization and analysis program Spectral Image Display (SID).

SRSA is the Spectral Radiance Simulation and Analysis model for prediction, visualization, and analysis of spectral radiance from user-specified terrain materials and clouds.

SRPlot.exe plots radiance as a function of wavelength for an input spectral radiance data file. In addition, the program will compute and plot spectral difference, spectral ratios, and mixtures.

SR_contrast performs spectral contrast operations (difference, ratio, and sensitivity) on input spectral radiance files.

SR_export converts the PRA internal ASCII spectral radiance files to formats amenable to import into spreadsheet or UNIX script programs.

SR_filter performs a moving window convolution over an input spectral radiance file using a user-supplied shaped filter.

SR_mixture performs a spectral mixing of total radiance for up to 10 terrain materials.

SR_quant converts radiance values to digital counts.

SR_sample extracts data from an input spectral radiance data file at some user-specified interval.

SR_sensor convolves the spectral response of an instrument with a radiative environment and the reflectance/emittance characteristics of a particular terrain material or cloud type.

SR_split splits a spectral radiance file into separate files; one file for each observer angle in the original file.

SR_uniform resamples the input spectral radiance data file from equal wavenumber intervals to equal wavelength intervals.

Make_spec_cal can be used to simulate a sensor response file for use with SR_sensor.

Spectral Image Importing Programs

These tools allow the user to ingest their own multispectral imagery for display (with SID and the Image File Viewers) and analysis. Three instruments are currently supported through the Spectral_Image_Import interface: ARES, AVIRIS and HYDICE. More general data ingestion routines have been written to support the importation of other types of data into the HYPEX format.

SI_Import combines several data import programs for multiple hyperspectral image types in a single program. The program reads the data and generates image data and calibration formats required by the PRA spectral radiance, display, modeling, and simulation tools.

SI_ingest imports hyperspectral data and generates a PRA band-interleaved-by-pixel image data file.

ARES_ingest reads data structures specific to the ARES instrument and converts them to the HYPEX Toolkit Spectral Image (SI), and Spectral Radiance (SR) file formats.

AVIRIS_ingest reads data structures specific to the AVIRIS instrument and converts them to the HYPEX Toolkit Spectral Image (SI), and Spectral Radiance (SR) file formats.

AVIRIS_spec_cal_read reads an AVIRIS calibration (spec_cal) file and generates a PRA spectral calibration format file.

HYDICE_ingest reads data structures specific to the HYDICE instrument and converts them to the HYPEX Toolkit Spectral Image (SI), and Spectral Radiance (SR) file formats.

HYDICE_spec_cal_read reads an HYDICE calibration (.wav) file and generates a PRA spectral calibration format file.

Spectral Image Display Tools

Tools documented in this section allow the user to view Spectral Image data, visualizing both the spatial and spectral domains of the data set. Programs required to develop the "movie" data sets are also included.

SID is the spectral image display, an interactive tools that displays in a linked and interactive environment image bands from a hyperspectral image data cube with corresponding spectral plots.

SI_extract extracts individual image bands from a hyperspectral cube. The cube must be in an acceptable PRA image format.

SI_2_movie creates a spectral movie file of a hyperspectral data cube that allows each image band to be sequentially viewed by the program.

Spectral_Movie Displays spectral image data as a movie. This spectral image file is NOT the same as that used by the program SID (Spectral Image Display). The input cube must be in an acceptable PRA image format.

Spectral Image Analysis Tools

The tools documented below allow the user to process and analyze Spectral Image data.

SI_extract extracts individual image bands from a hyperspectral cube. The cube must be in an acceptable PRA image format.

SI_filter passes a one-dimensional spectral convolution filter over the image data.

SI_ingest imports hyperspectral data and generates a PRA band-interleaved-by-pixel image data file.

SI_resync sorts a hyperspectral image data cube and its spectral calibration file so that all data are in ascending wavelength order. The input cube must be in an acceptable PRA image format.

SI_2_movie creates a spectral movie file of a hyperspectral data cube that allows each image band to be sequentially viewed by the program Spectral_Movie.

Spectral_Movie displays hyperspectral data as a movie. The input spectral movie file must be created by the program SI_2_movie. This spectral image file is NOT the same as that used by the program SID (Spectral Image Display).

nrmdif calculates a normalized difference image frm two input images. The normalized difference is (band A - band B)/(band A + band B). The user can scale the ratio by entering values for gain and tare.

Image Display Tools

xv calls the Image Magick viewer for graphical and image displays in Mosaic. It can also be used as a standalone viewer for the common condensed image formats, e.g., gif, tif, and jpeg.

PRA_browse provides a visual menu of icons for all images within a directory.

PRA_scope displays images in SGI RGB or PRA binary format. PRA_scope is efficient for viewing of large images.

SAOimage.exe was originally developed by the Smithsonian Astrophysical Observatory and amended by PRA for display of PRA-format single band binary image files. The utility includes limited interactive image enhancements.

newsao was originally developed by the Smithsonian Astrophysical Observatory and amended by PRA for display of single band binary image files. The utility includes limited interactive image enhancements.

Image Format Conversion Tools

RGB_2_GIF converts a SGI RGB image format to GIF format using imconv.

imconv is an image converter developed by the San Diego Super Computer Center. It converts between several condensed image types, (e.g., GIF to TIFF, RGB to TIFF, and JPEG to RGB).

SI_ingest imports hyperspectral data into the HYPEX Spectral Image format. It also serves as a general file reformatting routine, converting among spectral image file types (BSQ, BIL, and BIP).

ARES_ingest reads and translates ARES image (.hdc) and calibration (.hdr) data files to formats required by PRA's image display, spectral radiance, simulation, and modeling tools.

AVIRIS_ingest reads and translates AVIRIS image (.bil_image) and calibration (spec_cal) data files to formats required by PRA's image display, spectral radiance, simulation, and modeling tools.

HYDICE_ingest reads and translates HYDICE image (.cub) image and calibration (.wav) data files to formats required by PRA's image display, spectral radiance, simulation, and modeling tools.

Utility Shells

These simple shell programs allow the user easy access to the Unix shell (command line) from either the HYPEX the X-interface or "icon catalog" environments.

Run_Big_Shell opens a new window (shell) directly in the directory from which the "run" command is executed.

Run_Mosaic launches Mosaic in the $HYPEX/doc directory.

Run_TOP executes the unix command "top" that monitors systems usage.

Run_VI starts the "vi" editor directly in the directory from which the "run" command is executed.

X - Interfaces

Executables beginning with "x" launch "X" applications for interactive user-input of required and optional parameters for a given program. After the user enters the parameters, the program is then executed. Links to the User Manuals for each of these codes is provided. Short explanations about the individual programs are included in other sections of this document.

xSID
xSI_Import
xSRPLOT
xSRSA
xmosart
xspcalc

Run Files

Executables beginning with the expression "Run" are shell programs that were developed to support direct execution of programs from the SGI "icon catalog". Double clicking any of these icons in the "icon catalog" will launch the shell program, while entering the appropriate string at the command line will also launch the processes. Where available, links between each of these codes and the appropriate documentation are made. Explanations for the programs being executed are provided in other sections of this document.

Spectral Radiance Modeling Tools

Run_MOSART
Run_SPCALC
Run_SRSA

Spectral Radiance Analysis Tools

Run_SR_Contrast
Run_SR_Mixture
Run_SR_Plot
Run_SR_Tools

Spectral Image Analysis Tools

SI_Import
Run_SID
Run_SI_Tools

Spectral Movie Tools

Run_SI_2_Movie
Run_Spec_Movie

Image Viewing Tools

Run_SAOimage
Run_newsao
Run_Browse
Run_Scope