Scientific
Use Case
Description
Software
Historical River
cv
river
OpenCV (python), convert (from imagemagick), and Gdal
cv
river
Liana
Extractor
gdal
gdal
GDAL, Cython, numpy,
pygeoprocessing
Rui, Mostafa Elag ncsa.arcgis.landsat7mosaic ArcGIS
.arcgis.floodplain ArcGIS
/config.pySmruti Biology terra.plantcv pika
requests
wheel
CATS
extractors
plantcv
Yan Green Infrastructure Stanford CoreNLP Sentiment (ncsa.nlp.SNLPSentiment
Stanford CoreNLP tool, java, maven
nlp
/SNLP/SNLPSentimentExtractorLiana, Marcus(?)
Matlab
, Ankit
Matlab
, Ankit
, ncsa.csv.greenindexroute
OpenCV
census-section-segmentor Extractor
cv
censusLiana, Inna
ncsa.image.knn_numerals
OpenCV Marcus
ncsa.nlp.wordtables requests, pika, win32com
nlp
WordTablesExtractor
Liana
| Domain | Tool | Type |
|---|
Description |
|---|
| Repositories | Contact |
|---|---|
| Hydrology |
| Advection Diffusion | Solve a general advection-dispersion equation. | |||
|---|---|---|---|---|---|
| Chemical Mean Age | Extractor | Determine the mean age of chemical constituents with inputs of chemical dynamics. | |||
| Document Tables Extractor (ncsa. |
| nlp. |
| wordtables) | Extractor |
| Extract tables from documents. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| nlp/browse/ |
| WordTablesExtractor |
| GDAL (ncsa.geo.shpExtractor) |
| 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 |
pygeoprocessing
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-geotiff/browse |
| Historical River Extractor (ncsa.cv.river) | Extractor | Extract the river networks from the ancient hand-drawing maps and compare them with current river networks | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/river | |
| Normalized Difference Vegetation Index (ncsa.arcgis.landsat7mosaic) | Extractor | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-bd-cz/browse/ndviextractor | ||
| River Chi Index | Extractor | Identify 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/CATS/repos/extractors-bd-cz/browse/chi-analysis | ||||
| River Sinuosity | Extractor | Study the maturity and equilibrium conditions of a stream through the sinuosity index. | ||
| Soil Moisture Change | Extractor | Determine role of hydraulic redistribution in AZ (riparian site / upland site) by studying soil moisture change throughout different seasons. | Esther Lee (estherl2010@gmail.com) | |
| Species Classifier | Extractor | SAM based Species Classification from Hyperspectral data, Hyperspectral Indices, NDVI, SAVI, MSAVI, etc. | Debsunder Dutta (debsunderdutta@gmail.com) leaving in July 2016 | |
| TerEx (ncsa.arcgis.floodplain) | Extractor | Identify the flat polygons and the heights inside a river valley. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-bd-cz/browse/terex_floodplain |
requests
wheel
| Topographic Depressions | Extractor | Identify topographic depressions (TDs) and their distribution on landscape (Number, location, area, volume of TDs). | https://github.com/HydroComplexity/TDI | ||
| Tree Delineation | Converter | Tree-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/BD/repos/ir-lidar/browse | ||
| Valley Safety Zones | Extractor | Estimate submerging areas and water depths under extreme floods and map the safety zones in a river valley. | |||
| Vegetation Indices | Extractor | Calculating vegetation indices such as NDVI and Surface Temperature from Landsat 7 and 8 satellite data. | Debsunder Dutta (debsunderdutta@gmail.com) leaving in July 2016 | ||
| Ecology
| netcdf (ncdump) | Converter | Convert from binary netcdf to text. | https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-ncdump/browse | |
|---|---|---|---|---|---|
| PEcAn (PEcAn#Ameriflux) | Converter | Convert Ameriflux data to PEcAn's netcdf CF format. | https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-pecan/browse | ||
| PEcAn (PEcAn#DALEC) | Converter | Convert 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) | Converter | Convert 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) | Converter | Convert 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) | Converter | Convert 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) | Extractor | Extract plant height, area, and color distribution from photographs. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| plantcv/browse |
| Yan Liu | |
| Civil & Environmental Engineering
| Body of Water Detector (ncsa.image.ponddetect) |
|---|
| Extractor | Land coverage, extract locations of bodies of water from satellite data. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-maps/browse/feature_detection |
| GI Identification | Extractor | |||
| Human Preference Score (ncsa.image.humanpref) |
| Extractor | Assign a model derived human preference score to a given image of an urban environment. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-maps/browse/humanpref |
Route Greenness (ncsa.xml.greenindexroute |
) | Extractor | Derive the green index of a city route. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-maps/browse/greenroute | |||
| Social Media GI Preferences | Extractor |
| Stanford CoreNLP - Sentiment (ncsa.nlp.SNLPSentiment) | Extractor | Assign a sentiment score to a piece of text. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| nlp/browse/ |
| SNLP/SNLPSentimentExtractor | |
| TUV Triaxus | Extractor |
| Social Science & Humanities | Bertillon Card Cell Extractor (ncsa.image.dmp) | Extractor | Extract table cells from a Bertillon Card. | https://opensource.ncsa.illinois.edu/bitbucket/projects/DEBOD/repos/extractors-debod | |
|---|---|---|---|---|---|
| Census Form Cell Extractor (census-section-segmentor) | Extractor | Extract table cells from a 1930s Census form. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| cv/browse/ |
| census |
General
| Handwritten Decimals Extractor (ncsa.image.sphog.debod) | Extractor | Extract handwritten decimal values from an image. | https://opensource.ncsa.illinois.edu/bitbucket/projects/DEBOD/repos/extractors-handwrittendecimals | |
| Killed Photos (ncsa.image.iarp_remove_circle) | Extractor | Identify 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/IARP/repos/image_fetcher/browse/extractors/remove_circle | Marcus Slavenas |
| Mean Grey (ncsa.cv.meangrey) | Extractor | Mean grey values of black and white photos. |
Tool
| https://opensource.ncsa.illinois.edu/bitbucket/projects/ |
| IARP/repos/ |
| image_fetcher/browse/extractors/mean_grey | Marcus Slavenas | ||
| Movie Slice (ncsa.movieslice) | Extractor | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| movieslice/browse |
| Person Detector (person-detector |
| ) | Extractor |
| Extract locations of people in an image. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| person-detector | |
| Person Tracker (ncsa.person-tracker) | Extractor |
| Extract locations and paths of people moving in videos. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| person-tracking | |
| Video Analytics Toolbox (ncsa.cinemetrics_batch) | Extractor |
| Extract shot descriptors from videos. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| lsva-integrated/browse |
| Biology, Genomics, Medicine | FSL (mri2mesh) | Extractor |
|---|
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| mri/browse/ |
| mri2mesh |
| Marcus Slavenas |
| Glomeruli (ncsa. |
| msc. |
| diagnosis) | Extractor |
| Extract glomeruli from Kidney biopsy images. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| msc/browse/ |
VLFeat (ncsa.image.caltech101)
| Kidney |
General
| Domain | Tool | Type | Description | Repositories | Contact |
|---|---|---|---|---|---|
|
General | Calibre (ebook-converter) | Converter | Convert 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) |
| Extractor | Audio recognition to extract text for speech within audio. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-core/browse/audio/speech2text |
| Daffodil (daffodil) | Converter | Convert formats with a provided DFDL schema to XML. | https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-daffodil/browse | Kenton McHenry |
| DBPedia (ncsa.dbpedia) | Extractor | Find and define named entities within the given text. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| dbpedia/browse |
Natural Language Toolkit (NLTK) for Python, NLTK Data or at least:
| FFmpeg (ffmpeg) | Converter | Convert between a large number of video formats. | https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-ffmpeg/browse | |
| FLAC (flac) | Converter | Convert to and from the FLAC format from other audio formats. | https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-flac/browse | |
| Ghostscript (ghostscript) | Converter | Convert between document formats. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/ |
| POL/repos/ |
| converters- |
| ghostscript/browse |
| htmldoc (htmldoc) | Converter | Convert HTML to a number of document formats. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/ |
| POL/repos/ |
| converters- |
| htmldoc/browse | Kenton |
| McHenry | ||||
| ImageMagick (ImageMagick) | Converter | Convert between a large number of image formats. | https://opensource.ncsa.illinois.edu/bitbucket/projects/POL/repos/converters-imagemagick/browse | Kenton McHenry |
| ImageMagick (ncsa.image.metadata) | Extractor | Pull available EXIF image metadata from a given image. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| core/browse |
| /image/metadata | ||
| Kabeja (kabeja) | Converter | Convert 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) | Extractor | Find faces in an image and return their locations. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| cv/browse |
| /extractors-opencv/extractors-opencv-faces | Kenton McHenry | ||
OpenCV - Eyes (ncsa.cv.eyes) | Extractor | Find eyes in an image and return their locations. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| cv/browse/ |
| extractors-opencv/extractors-opencv-eyes | Kenton McHenry | ||
OpenCV - Closeups (ncsa.cv.closeups) | Extractor | Determine 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-closeups | Kenton McHenry | |
OpenCV - Profiles (ncsa.cv.profiles) | Extractor | Find 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-profiles | Kenton McHenry | |
| Langid (ncsa.nlp.simplelanguage) | Extractor | Identify the language of the given text. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| nlp/browse/ |
| SimpleLanguage | ||||
| LibreOffice (unoconv) | Converter | Convert 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) | Extractor | Summarize a body of text. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| nlp/browse/ |
| SimpleSummary |
| Siegfried (siegfried) | Extractor | Extract 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) |
| Extractor | Natural 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) |
| Extractor | Object Character Recognition (OCR) to extract text from images containing text. | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| cv/browse/ |
| extractors-tesseract | Kenton McHenry | |
| Tika (ncsa.nlp.tika) | Extractor | Document extractions such as language identification, ... |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors- |
| nlp/browse/ |
| tika |
| txt2html (txt2html) | Converter | Convert text documents to HTML. |
| https://opensource.ncsa.illinois.edu/bitbucket/projects/ |
| POL/repos/ |
| converters- |
| txt2html/browse |
| Kenton McHenry |
| Versus - Color Distribution (ncsa.versus.image) | Extractor | Generate 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) | Extractor | Classify 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-vlfeat | Kenton McHenry | |
| Zip (zip) | Converter | Unzip 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)