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Scientific

Domain ToolType
Description

Description                                     

RepositoriesContact
Deployed?
Hydrology




 

 
 








Advection Diffusion 
 https:
Solve a general advection-dispersion equation. 

 

 

Hydrology

Historical River Extractor (ncsa.cv.river)Extractor 
Chemical Mean AgeExtractorDetermine the mean age of chemical constituents with inputs of chemical dynamics. 
Document Tables Extractor (ncsa.nlp.wordtables)ExtractorExtract tables from documents.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
cv
nlp/browse/
river 
WordTablesExtractor 
 
GDAL (ncsa.geo.shpExtractor)
 Extractor
Extractor https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-geo/browse
  •   
GDAL (ncsa.geo.tiffExtractor)Extractor https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-geo/browse
  •   

GDAL (ncsa.image.geotiff)
 
Extractor https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-geotiff/browse
Rui, ArcGIS
  •   
Historical River Extractor (ncsa.
arcgis
cv.
landsat7mosaic 
river)
 
ExtractorExtract the river networks from the ancient hand-drawing maps and compare them with current river networkshttps://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
bd-cz
cv/browse/
ndviextractorArcGIS
river
Smruti
  •   
Normalized Difference Vegetation Index (ncsa.arcgis.
floodplain
landsat7mosaic)
 
Extractor https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-bd-cz/browse/
terex_floodplain/config.py

    

 

 

 

 

 

 

Biology

PEcAn (PEcAn#Ameriflux)  
ndviextractor
  •   
River Chi IndexExtractorIdentify the river dynamics in a river basin and evaluate human activities' influences through Chi index in the streams.https://opensource.ncsa.illinois.edu/bitbucket/projects/
POL
CATS/repos/
converters
extractors-bd-
pecan
cz/browse
  •   
PEcAn (PEcAn#DALEC)  https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-pecan/browse
  •   
PEcAn (PEcAn#ED2)  https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-pecan/browse
  •   
PEcAn (PEcAn#LINKAGES)  
/chi-analysis
River SinuosityExtractorStudy the maturity and equilibrium conditions of a stream through the sinuosity index.  
Soil Moisture ChangeExtractorDetermine role of hydraulic redistribution in AZ (riparian site / upland site) by studying soil moisture change throughout different seasons. 
Species ClassifierExtractorSAM based Species Classification from Hyperspectral data, Hyperspectral Indices, NDVI, SAVI, MSAVI, etc. 

Debsunder Dutta (debsunderdutta@gmail.com) leaving in July 2016

Sandeep Puthanveetil Satheesan

TerEx (ncsa.arcgis.floodplain)ExtractorIdentify the flat polygons and the heights inside a river valley.  https://opensource.ncsa.illinois.edu/bitbucket/projects/
POL
CATS/repos/
converters
extractors-bd-
pecan
cz/browse
  •   
PEcAn (PEcAn#Sipnet)  
/terex_floodplain
Topographic DepressionsExtractorIdentify topographic depressions (TDs) and their distribution on landscape (Number, location, area, volume of TDs).https://
opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-pecan/browse
  •   
PlantCV (terra.plantcv)  
github.com/HydroComplexity/TDI
Tree DelineationConverterTree-wise voxelization of waveform data for lidar metrics that describes canopy structure (max intensity, height, etc...).  Individual tree delineation, tree leaf area density to describe vertical leaf distribution. https://opensource.ncsa.illinois.edu/bitbucket/projects/
CATS
BD/repos/
extractors
ir-
plantcv 
lidar/browse
Yan Liu
  •   
netcdf (ncdump)  https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-ncdump/browse
  •   

 

 

 

Civil & Environmental Engineering

Stanford CoreNLP Sentiment (ncsa.nlp.SNLPSentiment) 
Valley Safety ZonesExtractorEstimate submerging areas and water depths under extreme floods and map the safety zones in a river valley.
 
Vegetation IndicesExtractorCalculating vegetation indices such as NDVI and Surface Temperature from Landsat 7 and 8 satellite data. 

Debsunder Dutta (debsunderdutta@gmail.com) leaving in July 2016

Sandeep Puthanveetil Satheesan

Ecology

 






netcdf (ncdump)ConverterConvert from binary netcdf to text.https://opensource.ncsa.illinois.edu/bitbucket/projects/
CATS
POL/repos/
extractors
converters-
nlp
ncdump/browse
/SNLP/SNLPSentimentExtractorLiana, Marcus(?)
  •   

Body of Water Detector (ncsa.image.ponddetect)

  
PEcAn (PEcAn#Ameriflux)ConverterConvert Ameriflux data to PEcAn's netcdf CF format.https://opensource.ncsa.illinois.edu/bitbucket/projects/
CATS
POL/repos/
extractors
converters-
maps
pecan/browse
/feature_detectionMarcus, Ankit
  •   
Human Preference Score (ncsa.image.humanpref)  https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-maps/browse/humanprefMarcus, Ankit
  •   

ncsa.xml.greenindexroute, ncsa.csv.greenindexroute

  
PEcAn (PEcAn#DALEC)ConverterConvert PEcAn's netcdf CF format to the format required by the DALEC model.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-pecan/browse
PEcAn (PEcAn#ED2)ConverterConvert PEcAn's netcdf CF format to the format required by the ED model.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-pecan/browse
PEcAn (PEcAn#LINKAGES)ConverterConvert PEcAn's netcdf CF format to the format required by the LINKAGES model.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-pecan/browse
PEcAn (PEcAn#Sipnet)ConverterConvert PEcAn's netcdf CF format to the format required by the Sipnet model.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-pecan/browse

PEcAn (PEcAn#AmerifluxBNL)

PEcAn (PEcAn#FLUXNET2015)

PEcAn (PEcAn#FACE)

PEcAn (PEcAn#PALEON)

PEcAn (PEcAn#NLDAS)

PEcAn (PEcAn#CURNCEP)

PEcAn (PEcAn#GLDAS)

PEcAn (PEcAn#GFDL)

PEcAn (PEcAn#BIOCRO)

PEcAn (PEcAn#CLM)

PEcAn (PEcAn#GDAY)

PEcAn (PEcAn#JULES)

PEcAn (PEcAn#LPJ-GUESS)

PEcAn (PEcAn#MAAT)

PEcAn (PEcAn#MAESPA)

PEcAn (PEcAn#PRELES)

   
PlantCV (terra.plantcv)ExtractorExtract plant height, area, and color distribution from photographs.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
maps
plantcv/browse
/greenroute 
Marcus
  •   
 census-section-segmentor Extractor
Yan Liu
Civil & Environmental Engineering



 

Body of Water Detector (ncsa.image.ponddetect)

ExtractorLand coverage, extract locations of bodies of water from satellite data.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
cv
maps/browse/
censusLiana, Inna
  •   
 ncsa.image.knn_numerals
feature_detection
GI IdentificationExtractor  
 
  •   
 ncsa.nlp.wordtables  
Human Preference Score (ncsa.image.humanpref)ExtractorAssign a model derived human preference score to a given image of an urban environment.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
nlp
maps/browse/
WordTablesExtractor 
humanpref
Liana
  •   
 LSVA 

Route Greenness (ncsa.xml.greenindexroute)

ExtractorDerive the green index of a city route.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
lsva/browseLiana, Constantinos
  •   
 LSVA integrated  
maps/browse/greenroute
Social Media GI PreferencesExtractor  
Stanford CoreNLP - Sentiment (ncsa.nlp.SNLPSentiment)ExtractorAssign a sentiment score to a piece of text.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
lsva-integrated/browse
  •   
 ncsa.movieslice  
nlp/browse/SNLP/SNLPSentimentExtractor
TUV TriaxusExtractor  
Social Science & Humanities













Bertillon Card Cell Extractor (ncsa.image.dmp)ExtractorExtract table cells from a Bertillon Card.https://opensource.ncsa.illinois.edu/bitbucket/projects/
CATS
DEBOD/repos/extractors-
movieslice/browse
debod
  •   
 mri2mesh  
Census Form Cell Extractor (census-section-segmentor) ExtractorExtract table cells from a 1930s Census form.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
mri
cv/browse/
mri2mesh msc-ChemCBCExtractor  
census
Marcus
  •   
Handwritten Decimals Extractor (ncsa.image.sphog.debod)ExtractorExtract handwritten decimal values from an image.https://opensource.ncsa.illinois.edu/bitbucket/projects/
CATS
DEBOD/repos/extractors-
msc/browse/ChemCBCExtractorYan
  •   
 msc-IsletExtractor  
handwrittendecimals
Killed Photos (ncsa.image.iarp_remove_circle)ExtractorIdentify depression era photos "killed" by Farm Security Administration director Roy Stryker, indicated by a hole punch in the image.https://opensource.ncsa.illinois.edu/bitbucket/projects/
CATS
IARP/repos/
extractors-msc
image_fetcher/browse/
IsletExtractorYan
  •   
 msc-MonitorExtractor  
extractors/remove_circleMarcus Slavenas
Mean Grey (ncsa.cv.meangrey)ExtractorMean grey values of black and white photos.https://opensource.ncsa.illinois.edu/bitbucket/projects/
CATS
IARP/repos/
extractors-msc
image_fetcher/browse/extractors/
MonitorExtractorYan
  •   
 ncsa.msc.dailymonitor 
mean_greyMarcus Slavenas
Movie Slice (ncsa.movieslice)Extractor https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
msc
movieslice/browse
/OldMonitorExtractor 
Ashwini
  •   
 msc-PhenotypeExtractor 
Person Detector (person-detector)ExtractorExtract locations of people in an image.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors
-msc/browse/PhenotypeExtractorYan
  •   
 person-detector  
-person-detector
Person Tracker (ncsa.person-tracker)ExtractorExtract locations and paths of people moving in videos.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-person-
detector/browse/python
tracking
  •   
 ncsa.person-tracker  
Video Analytics Toolbox (ncsa.cinemetrics_batch)ExtractorExtract shot descriptors from videos.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
person
lsva-
tracking
integrated/browse
/python
  •   
 lsva-cedd 
Biology, Genomics, MedicineFSL (mri2mesh)Extractor https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
cedd ncsa.cinemetrics  
mri/browse/mri2mesh
Constantinos
  •   
Marcus Slavenas
Glomeruli (ncsa.msc.diagnosis)ExtractorExtract glomeruli from Kidney biopsy images.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-
cinemetrics
msc/browse
Constantinos
  •   
/Kidney

General

Domain

Tool

Type
Description
Description                                     RepositoriesContact
Deployed?

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

General

Calibre (ebook-converter)ConverterConvert e-books to a number of document formats.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-ebook-convert/browse
 
 

CMU Sphinx (ncsa.audio.speech2text)

ExtractorAudio recognition to extract text for speech within audio.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-core/browse/audio/speech2text
  •  
Daffodil (daffodil)ConverterConvert formats with a provided DFDL schema to XML.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-daffodil/browseKenton McHenry
  •  
FFMPEG
DBPedia (ncsa.dbpedia)ExtractorFind and define named entities within the given text.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-dbpedia/browse
  •  
FFmpeg(ffmpeg)ConverterConvert between a large number of video formats.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-ffmpeg/browse
  •  
FLAC (flac)ConverterConvert to and from the FLAC format from other audio formats.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-flac/browse
 
  •  
  •  
Ghostscript (ghostscript)ConverterConvert between document formats.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-ghostscript/browse
htmldoc (htmldoc)ConverterConvert HTML to a number of document formats.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-htmldoc/browseKenton McHenry
  •  
ImageMagick (ImageMagick)ConverterConvert between a large number of image formats.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-imagemagick/browseKenton McHenry
  •  
ImageMagick (ncsa.image.metadata)ExtractorPull available EXIF image metadata from a given image.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-core/browse/image/metadata
  •  

Kabeja (kabeja)ConverterConvert between a handful of 3D and image formats.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-kabeja/browse
 
 

OpenCV - Faces (ncsa.cv.faces)

ExtractorFind faces in an image and return their locations.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/extractors-opencv/extractors-opencv-facesKenton McHenry
  •  

OpenCV - Eyes (ncsa.cv.eyes)

ExtractorFind eyes in an image and return their locations.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/extractors-opencv/extractors-opencv-eyesKenton McHenry
  •  

OpenCV - Closeups (ncsa.cv.closeups)

ExtractorDetermine whether an image is a closeup of a person or not.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/extractors-opencv/extractors-opencv-closeupsKenton McHenry
  •  

OpenCV - Profiles (ncsa.cv.profiles)

ExtractorFind human face profiles in an image and return their locations.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/extractors-opencv/extractors-opencv-profilesKenton McHenry
  •  
  •  
Langid (ncsa.nlp.simplelanguage)ExtractorIdentify the language of the given text.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-nlp/browse/SimpleLanguage
 
  •  
LibreOffice (unoconv)ConverterConvert to and from a variety of document formats.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-unoconv/browse
 
Bing Zhang
NLTK - Summary (ncsa.nlp.simplesummary)ExtractorSummarize a body of text.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-nlp/browse/SimpleSummary
 
  •  
Siegfried (
sigfried
siegfried)ExtractorExtract information about a given file relevant to identifying its type and validating its format.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-siegfried/browse
  •  

Stanford CoreNLP (ncsa.nlp.SNLP)ExtractorNatural Language Process extractions such as parts of speech, named entities, langauge, etc.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-nlp/browse/SNLP/SNLPExtractor 
  •  
Tesseract (ncsa.image.ocr)ExtractorObject Character Recognition (OCR) to extract text from images containing text.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/extractors-tesseractKenton McHenry
  •  
Tika (ncsa.nlp.tika)ExtractorDocument extractions such as language identification, ...https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-nlp/browse/tika
  •  

txt2html (txt2html)ConverterConvert text documents to HTML.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-txt2html/browseKenton McHenry
  •  
Versus - Color Distribution (ncsa.versus.image)ExtractorGenerate a distribution of color values within an image to be used for comparing how similar two images are.https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-versus/browse
  •  

VLFeat (ncsa.image.caltech101)

ExtractorClassify images as to whether they contain objects from the Caltech101 dataset (e.g. people, airplanes, motorcycles, cougars, ...).https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/extractors-vlfeatKenton McHenry
  •  
Zip (zip)ConverterUnzip zip archives.https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-zip/browse
  •  

https://opensource.ncsa.illinois.edu/confluence/display/BD/ExtractorsTransformations (Under development, Being Refactored)