ARSF Scripts and Binaries

Please keep this page updated. Also please keep it sorted in a sensible order or we're never going to be able to find anything...

LiDAR

Script Language Use Author
alspp.exe bash Runs wine version of ALSPP
arsf_winesetup.sh bash Configure wine environment for ARSF users
attune bash Runs wine version of Attune (boresight calibration)
batch_fw_class.sh bash Runs get_class_las on full directories, so it doesn't have to be done one by one. Does NOT check if las files are sorted dap
check_ascii_lidar.sh bash Checks the ASCII LiDAR files in the delivery for erroneous data
check_ascii_lidar Binary (C) Checks the ASCII LiDAR files in the delivery for erroneous data, prints the bounds of the ascii file
classify_las Binary (C) LiDAR classification
classify_las_files.sh bash Runs classify_las on a set of LAS files using a specified classification algorithm
create_latex_lidar_readme.py Python Creates a LaTeX file for generating a PDF read-me for delivery
demcompare.py Python Used to compare lidar patched aster dems and raw aster dems stgo
fugroviewer.exe bash Runs wine version of Fugroviewer
fwf_extract.py python Extracts waveform data for specified area
getDEMbufferpy Python Get the buffer size around LiDAR data for use when creating a DEM for use with apl
get_class_las c++ Copy the classification from one las file to another unknown - adbe?
get_first_return.sh bash Creates new ASCII lidar files with 1st returns only
import_ldr_txt_to_grass.sh bash Imports lidar ascii file into grass (run from within grass) mark1
lag Binary (C++) LiDAR file viewer harg + chrfi
las2txt.sh bash Convert a directory of LAS files or a single LAS file into ascii format
las_hdr_pop.py Python Populates LAS file headers with information that may have been lost: min and max of x,y,z and number of points by return knpa
las_merge.sh bash Merges sets of LAS files of the form *_000.LAS, *_001.LAS... etc. together. Can also split a LAS file into several.
las_sampler.py Python Samples a LAS file at a specified interval and creates an output LAS file of these points knpa
las_single_class.py Python Classifies all points as a user defined number (quite slow) knpa
LASsorter Python sorts Las files by time, x, y, z , ascending and descending
leica_photo_processing bash Runs wine version of Leica's photo processor
lidardem.sh Bash Create a DEM from LiDAR data either las of ascii format
lidar_aster_dem.sh Bash Create a DEM from LiDAR and aster data, wrapper from lidardem.sh and asterdem.sh
lidar_stats.py Python Extracts statistics from a set of LAS files emca
make_lidar_delivery.py bash Create a LiDAR delivery folder
lidar_intensity.sh? bash Create a lidar intensity image from ascii / las + output jpgs + use vectors
pt_cloud_filter Binary (C) Removes points of a specified classification from ascii lidar point cloud knpa
split_las.py Python Splits las files using lasmerge. tipo

Hyperspectral

Script Language Use Author
adjustBPF.py Python Generate a bad pixel file in CSV for a delivery, uses the CSV bad pixel file from calibration
aplxml_delivery_wrapper Python Generate an aplxml command for a flight in delivery format
bil_binning.py Python Spectrally bins (x2) a hyperspectral raw file knpa
bounding_box.py Python Get the North/South/East/West extent of a number of raw hdr files in bng coords knpa
cal_radiometric.py Python Generates a calibration curve in each band given input data in BIL or BSQ format and a known lamp file benj
correlate.py Python Wrapper for phasecorrelator.py
check_apl_cmd bash Runs the apl commands in the config file for all level1 flightlines, output to tmp_cmd_check dir adbe
check_bil.py Python Checks quality of bil files in hyperspectral delivery adbe
check_fenix_spectra_py6s.py Python Plots the at-sensor radiance spectra recorded by hyperspectral sensor and compare it to the at-sensor Py6S model asm/dac
check_fsm.py Python Works out the corrected value for frame shift smear at a given band assuming a constant DN value through the spectrum benj
check_qpftiming.py Python Test specified Eagle/Hawk framerates against actual framerates calculated from qpfTiming benj
checkpeaks.py Python Matches measured spectral lines to fityk-detected peaks and eagle/hawk pixel numbers for use in spectral calibration benj
create_latex_hyperspectral_readme.py Python Create a LaTeX file for a PDF Readme for Hyperspectral azgcorr deliveries
create_latex_hyperspectral_apl_readme.py Python Create a LaTeX file for a PDF Readme for Hyperspectral APL deliveries
dimfixer.py Python Truncates BIL files so that the file size matches what the header file says it should benj
dummy_linecount.py Python Replaces a broken line counter on the first band of eagle and hawk (values 0 to number of lines) knpa
fastcheckoverflows.py Python Checks a BIL or BSQ file to see if it contains a specified overflow value benj
fastQC Binary (C) Program for viewing BIL files (raw data or level 1) harg
gen_bandsets.py Python Generates bandset (.prn, .bnd, .wls) files from a wavelength scale file benj
gen_synth_radcal.py Python Generates a synthetic Eagle or Hawk calibration file benj
gen_synth_raw.py? Python Generates a synthetic Eagle or Hawk dataset benj
gen_synth_sbet.py? Python Generates a synthetic SBET file benj
generate_prn.py Python Generates a .prn file from some subset of bands in a given .wls file benj
generate_apl_runscripts.py Python Generates config file for APL hyperspectral processing
get_ascii_fov_for_level1.py Python Generates an ascii file containing binned and trimmed sensor fov view vectors for level 1 files mark1
get_boresight_vals.py Python Extracts boresight values for given day from csv file
get_calib_vals.py Python Extracts calibration file names for given day from data file
gen_eg_cmds.py Python Generates example commands for APL for the read me file
get_sbet_bounds.py Python Gets North/South/East/West extent of (part of) an SBET file in lat/lon benj
getposition Python Gets position information at from an SBET file for a specified time (or file limits) benj
getsync.py Python Finds sync records on one or more AISA nav files
gettiles.sh bash Determines BNG grid squares for flight from Eagle/Hawk header files benj
hdr_fps_check.py Python Checks if a Specim file has a mismatch between recorded and actual frame rate (Hawk problem)
hyper_latex_table_tools.py Python Python tools for hyperspectral readme table creation
igm2map.sh
igm2map.pro
bash Script to use IGM files to generate a GLT file and map level 1 data
interleave_convert.py Python Convert interleave of a 3D file between BIL/BSQ
logwriter.py Python Outputs mean altitude, heading and speed from an SBET file for a number of Eagle or Hawk lines benj
make_mosaic.sh
make_mosaic.grass
bash Script to convert GeoTIFFs into JPGs and create a mosaic image (with vectors)
make_hyper_delivery.py Python Make a hyperspectral delivery fro APL data
match_dark_frames.py Python Checks which of a selection of Eagle/Hawk header files have compatible binning, framerate and integration time settings benj
mergeCFSync.py Python Merges a .cfg and a .sync (eagle/hawk line sct offsets)
nav2txt Binary (C) Output contents of an AISA nav file to an ASCII text file
NCom2SBET Binary (C) Convert NCom .nav files to sbet format dac
new_nav_file_fixer.py Python Script to remove once-per-second sync messages from a eagle/hawk nav file that were introduced with the firmware upgrade in October 2011 and sometimes break aplcorr knpa
phasecorrelator.py Python Perform phase correlation on a lidar intensity image and a hyperspectral image
plot_1b_spectra.py Python Plot spectral profile from BIL file for a given pixel and line dac
process_specim_apl_line.py Python Process the specim data using APL
qsub_correlate.py Python Submit a correlation job to the grid
process_specim_line.py Python Runs az suite on specified Eagle/Hawk flightline for processing benj
run_calibration.py Python Master script for running calibration scripts benj
sbet_datum_offset.py Python Change altitudes in sbet file from EGM96 datum to WGS-84 elipsoid dac
split_autodark.py Python Script to split Eagle or Hawk raw files containing autodark frames into a light file and a dark file. benj
splitline.py Python Script/Library for splitting Eagle/Hawk flightlines, using headers
slice_nav.py Python Cuts a chunk of an AISA nav file out into a smaller nav file
specim_gap_check.py Python Searches Eagle/Hawk raw files for dropped frames by looking at the band 1 frame counter
specim_qsub.py Python Submits an ARSF project for processing through the grid engine benj
split_bils.py Python Splits hyperspectral lines using apl processing tipo
update_delivery_mask_headers.py Python Re-writes the comment in the APL level 1 mask header files so that it refers to re-named level-1 file. Run after delivery has been created
wavelength_scale.py Python Generates a new wavelength scale from matching spectral peaks benj

Camera

Script Language Use Author
create_latex_camera_readme.py Python Creates a LaTeX file for generating a PDF read_me for delivery
image_events_file_fixer.py Python Corrects image event files, mainly by using a sol/sbet file to correct position accuracy
make_camera_delivery.py Python Create a camera delivery
photo2thumb.sh bash Converts RCD TIF files to JPG thumbnails
rcdimages_in_pdf.py Python Converts RCD TIF files into JPG thumbnails using lidar log files to filter out of bounds images
rename_photos_update_events_file.py Python generates new file names for tiffs and their entries in the image events file
tag_tiffs.py Python Adds tags to tiff files (using image event files) which define position, attitude and other metadata
pitch_roll_correction.py Python Swap pitch and roll in tiff if different from that in csv file

General

Script Language Use Author(s)
add_to_dem.sh bash/grass Adds an ascii or binary grid to a DEM - useful when doing geoid-spheroid seperation knpa
archiving_tarballer.sh bash Tarballs projects for NEODC mggr/knpa
asterdem.sh Bash Creates a ASTER DEM for use with aplcorr knpa/adbe
atcor bash Runs ATCOR-4
auto_grass_vector_tiff_conversion_driver.sh auto_grass_vector_tiff_conversion_control_script.grass Python uses grass to produce tiff images of vectors
binary_converter.py Python Converts binary files from one data type to another (eg. Float32 -> Int16)
bil2tiff Bash Convert bil files to geotiffs using gdal
bnglookup.py Python Converts BNG numeric grid references to OS grid square co-ordinates
build_structure.py Python Allows easy building of project directory structure from the command line.
checkoverflows.py Python Checks binary data files for presence of a specified overflow value
convert_delivery.sh Bash Will convert a delivery to a new project code and PI name. Can also be used on single deliveries to correct PI/proj-code inconsistencies
convert_nonuk_dem.sh Bash / Grass Convert a non-UK DEM into APL format (may have to be in WGS84 heights?)
convert_uk_dem.sh Bash / Grass Convert a UK DEM into APL format
createimage.py Python Convert file formats and create images
data_arithmetic.py Python Performs an arithmetic operation on all of the values from two data files and writes the results to an output data file
demgen.py Python Reads eagle or hawk header files and SBET file to generate a list of the DEM tiles that the SBET covers
demhdr_az2grass.sh bash Converts dems from az format header to grass header
demheaderconvert.sh bash Converts dems from grass format header to az header
doc2pdf.py Python Converts .doc or .odt files to PDF format
embargocheck.py Python Tests if a project folder is still in embargo (1 year from last delivered data) stgo
DocumentConverter.py Python Converts between various document formats using Open Office
findbaseline.py Python Script to find the baseline value of a list of numbers containing value spikes. Intended for part of Specim cal procedure.
fix_naughty_chars.py Python Finds linux-unfriendly characters in filenames
fix_undessirable_chars.py Python Finds linux-unfriendly characters in filenames, solves some problems found on fix_naughty_chars.py and do not need to be run as part of a pipe asm
fixnames_sct.py Python Auto-renames (line numbers and removes sct section) level 1, level 3, screenshots or rcd images/thumbnails/raws for a delivery.
freelook bash Runs ENVI Freelook
gen_fityk_script.py Python Generates a fityk script file that can be used to fit peaks to particular datasets
generate_readme_config.py Python Creates a config file for hyperspectral and camera read_me generators
generateKMLforPI.py Python Generate a KML file containing Eagle, Hawk or RCD information
GML2Shape.sh bash Convert GML Vector files to Shapefiles
gpstime Python Converts GPS time-of-week to human-readable format and vice-versa
hdf_output.py Python Lists contents of an HDF file to the terminal
hdf_to_bil.py Python Extracts navigation data from hdf files to a bil file chrfi/knpa
julian CShell Converts between julian day+year and day/month/year
kmloverview_all_projects_this_year.py Python Generate KML Overview for all projects in repository for a given year
ll2bng.sh bash Converts specified lat/lon into BNG co-ordinates (wrapper around appropriate proj command)
lsolder bash Like ls, but can filter list to get files/directories older than a certain time
mask_bad_pixels.py Python Sets defined bad pixels in a BIL or BSQ file to be a mask value
make_delivery_letter_email.py Python Automatically produce delivery letters and emails for a PI
make_kmloverview.py Python Make the KML file and overview support files - part of unpacking procedure
nextmapdem.sh bash Generates a DEM from NextMap data benj/mggr/knpa
projdir bash Automatically CDs to a project directory anch
proj_tidy.sh bash Checks that a specified project conforms to the current defined structure and file name formats knpa
raw_eagle_hawk_bil2jpg.sh
raw_eagle_hawk_bil2jpg.grass
Create JPGs of raw eagle/hawk data for KML overview
spatial_average.py Python Averages a BIL or BSQ file in the spatial direction
symlink_src_dir.sh bash Symlinks all files in a source directory into a target directory
teqc Binary (third-party) Program for slicing/splicing/fiddling with RINEX or other GPS base station data (like raw data)
times4grafnav.py Python Searches E/H headers and gets start/stop times for importing into Grafnav to show on trajectory
trmdatefinder.py Python Extracts date from Trimble GPS format file names
unpack_project.py Python Moves/copies files and folders from given structure to our structure using a config file approach (unpacking_template.cfg) asm

Libraries

Script Language Use Author
alphaconv.py Python Functions to convert numbers to letters and back (A=1, B=2 etc)
arsf_database.py Python Functions to access key/value ARSF database (please use arsf_db_reader.py)
arsf_db_reader.py Python Provides classes and functions to read from the ARSF database
band_reader.py Python Reads AISA band (.prn) files
configSorter.py Python Sorts config files into sensible order (can also be executed directly)
convert_interpolate.py Python Interpolates an array and/or many arrays wrt. one array. Finds peaks/Derivates/Integrates for 1D arrays.
common_readme_functions.py Python Functions for latex readme generator scripts
correlator_reader.py Python Read data in that is required for the correlator
csv_handler.py Python Reads CSV columns as lists and writes lists to a CSV file
data_handler.py Python Reads/writes BIL and BSQ files
egm96 Python / Fortran Calculate offset between EGM96 and WGS-84. Python wrapper for Fortran functions dac
flightlineclass.py Python Class to hold info on Eagle/Hawk flight lines (used in generateKMLforPI.py)
folder_structure.py Python Holds the current arsf folder structure
geographic.py Python For converting between different geographic coordinate systems knpa
GRASS_library.py Python For working with Envi DEM files in grass stgo
hyperconfigutils.py Python Set of functions for reading and checking hyperspectral config files
kml_writer.py Python Creates and writes KML files.
las1_3_handler.py Python Reads LAS 1.3 files
libgpstime.py Python Converts GPS time-of-week to human-readable format and vice-versa
liblogwriter.py Python Gets mean altitude, heading and speed from an SBET file for a number of Eagle or Hawk lines
navparser.py Python Basic Specim nav file parser for ASCII nav files
project_info.py Python Returns basic project info (project code, jday etc) from an available source
rcdclasses.py Python Class for holding RCD image information (used in generateKMLforPI.py)
sbet_handler.py Python Functions to manipulate SBET files, also limited AISA nav file support
sol_handler.py Python Sol handling library chrfi and adth

Obsolete

These are not in everyday use but are still useful on occasion

Script Language Use Author
arsf_processing_monitor.py Python Part of old processing job submission system
az_log_parser.py Python Parse output from az* programs to remove cruft - not kept up to date with newer versions and possibly too ambitious
create_lidar_readme.py Python Creates a .txt ReadMe for lidar deliveries
fastcopy_arsf_proj_dir.sh bash Script to make a workspace copy of a project directory (ie. avoid copying raw files, etc)
generate_mask.py & generate_mask.sh Python Script for generating mask file for use in GRASS for old Optech LiDAR
generate_runscripts.py Python Generates AZ runscripts or config files for hyperspectral data processing mark1/benj
gtiff2jpg.py Python Convert GeoTIFFs to JPEGs
kqsub bash Handy for quick submission of individual flightlines and sct values. Designed for use with old rune/runh scripts
kmlise_project.py Python
lidar2dem.sh bash Generates an azgcorr-format ASCII DEM from old Optech lidar point cloud files
lidar_histogram.py & lidar_histogram.sh Python Reads old Optech LiDAR files and outputs a numeric histogram for use in filtering
make_delivery_folder.sh bash Old script for making deliveries
ppv_to_envi_igm.py Python Converts azgcorr's ppv (per-pixel view vector) output to an ENVI IGM chrfi
trim_lidar.sh bash Cuts UTM zone number off old Optech LiDAR point cloud files
unpack_file_check.py Python Unpacking check files script
unpack_folder_structure.py Python Unpacking check the folder structure
make_lidardem_or_intensity.sh make_lidardem_or_intensity.grass? bash Create a lidar dem or intensity image from ascii lidar files

Explanation of symlinks in ~arsf/usr/bin

Link name Link target Use
configSorter /users/rsg/arsf/usr/lib/python/site-packages/configSorter.py Link to configSorter library (see Libraries section) - library is also executable

Unknown

Note: See also Python resources/libraries on main RSG wiki at http://rsg.pml.ac.uk/intranet/trac/wiki/Python

Last modified 3 years ago Last modified on Mar 1, 2016 12:27:31 PM