Scientific
Code - is Code: Is there code? Is it submitted or existing? PY1/PY2 - If so add URL to parent wiki page!!!
Py1/Py2: Is it using PyClowder1 or , PyClowder 2 - expectation , or neither. Expectation for Beta is most will be in PY1 - Py1, moving forward with new ones we will use PY2
- Need to update templates to PY2
TC - Is it in the tools catalog?
Py2.
JSON-LD - is : Is proper JSON-LD generated in the MetaData and registration document - (make sure to use full URI
DPL -Deployed via Tools Catalog?
DL - Downloadable?
...
Test File - ).
DCKR: Dockerized?
Test File: Sample file available?
TC: Is the tool in the tools catalog?
DPL: Is the tool dockerized (if not Windows), managed by the elasticity service, and passing tests every other hour?
DL: Is the tool downloadable via Sandeep's modifications to move compute to the data?
Complete & Deployed |
Needs work |
Blocked |
Scientific
Description
Domain | Tool | Type | Description | Code | Py1/Py2 | JSON-LD | DCKR | Test File | TC | DPL | DL | Assignment | |
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Hydrology
| 1 | Advection Diffusion | Solve a general advection-dispersion equation. | No (Don't have a general tool. Seems like this was not done as per the description.) |
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Yes
Yes
Yes
Yes
Yes
Esther Lee (estherl2010@gmail.com)
Debsunder Dutta (debsunderdutta@gmail.com) leaving in July 2016
Sandeep Puthanveetil Satheesan Per Dr K this will be post beta | ||||||||||||
2 | Chemical Mean Age | Extractor | Determine the mean age of chemical constituents with inputs of chemical dynamics. | No (This is a simulation tool - don't have code.) |
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| Sandeep Puthanveetil Satheesan Per Dr K this will be post beta | ||
3 | Document Tables Extractor (ncsa.nlp.wordtables) | Extractor | Extract tables from documents. | Yes | No | No | No | No | No | No | No | |
4 | ESRI Shapefile Extractor by using GDAL (ncsa.geoshp.preview) | Extractor | Create a Geoserver layer for WMS service. It can be used in previewer | Yes | Py1 | Yes | Yes | Yes | No | Yes | No | |
5 | GeoTiff Extractor by using GDAL (ncsa.geotiff.preview) | Extractor | Create a Geoserver layer for WMS service. It can be used in previewer | Yes | Py1 | Yes | Yes | Yes | No | Yes | No | |
6 | GeoTiff Metadata Extractor by using GDAL (Another implementation) (ncsa.geotiff.metadata) | Extractor | Extract geospatial metadata from Geotiff. It should be combined with #5 Geotiff extractor. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | No | |
7 | Historical River Extractor (ncsa.cv.river) | Extractor | Extract the river networks from the ancient hand-drawing maps and compare them with current river networks | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | No | |
8 | Normalized Difference Vegetation Index (ncsa.arcgis.landsat7mosaic) | Extractor | Create a NDVI layer from Landsat data. Calculating vegetation indices such as NDVI and Surface Temperature from Landsat 7 and 8 satellite data. | Yes | Py1 | Yes | N/A (Windows, ArcGIS) | Yes | No | Yes (Windows VM) | No | |
9 | River Chi Index (ncsa.chi_analysis) | Extractor | Identify the river dynamics in a river basin and evaluate human activities' influences through Chi index in the streams. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | Yes | |
10 | GDAL Converter | Converter | Converts between TIFF and BIL (zip) and FLT (zip) | Yes | N/A | N/A | Yes | Yes | Yes | Yes | Yes | |
11 | River Sinuosity | Extractor | Study the maturity and equilibrium conditions of a stream through the sinuosity index. |
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| Sandeep Puthanveetil Satheesan Qina supposed to be delivering code - Dr K thinks it should make it in Beta | |||
12 | Soil Moisture Change | Extractor | Determine role of hydraulic redistribution in AZ (riparian site / upland site) by studying soil moisture change throughout different seasons. | No |
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Sandeep Puthanveetil Satheesan Per Dr. K - will need discussed and can not be in Beta | ||||
13 | Species Classifier | Extractor | SAM based Species Classification from Hyperspectral data, Hyperspectral Indices, NDVI, SAVI, MSAVI, etc. |
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Yes
Dr K does not think this will make it in Beta | ||||||||||||
14 | Floodplain Extractor by using TerEx (ncsa.arcgis.floodplain) | Extractor | Identify the flat polygons and the heights inside a river valley. | Yes (but procedure?) | Py1 | Yes | No (windows) | Yes | No | Yes (Windows) | no | |
15 | Topographic Depressions | Extractor | Identify topographic depressions (TDs) and their distribution on landscape (Number, location, area, volume of TDs). | Yes - ready to review |
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Debsunder Dutta (debsunderdutta@gmail.com) leaving in July 2016
Yes
Yes
Yes
16 | (ncsa.arcgis.treedelin) | Extractor | Create a shape-file with polygons of tree canopy polygon from LiDAR data | Yes | Py1 | Yes | N/A (Windows, ArcGIS) | Yes | Yes | Yes (Windows VM)
| No | ||
17 | Tree-wise voxelization | 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. | Yes (But extractor has to be developed) | No | No | No | No | No | No | No | |||
18 | Valley Safety Zones | Extractor | Estimate submerging areas and water depths under extreme floods and map the safety zones in a river valley. | Yes |
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Ecology
| 1 | netcdf (ncdump) | Converter | Convert from binary netcdf to text. | N/A | N/A | N/A | Yes | Yes | Yes | Yes | Yes | |
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2 | PEcAn (PEcAn#Ameriflux) | Converter | Convert Ameriflux data to PEcAn's netcdf CF format. | Yes | N/A | N/A | Yes | Yes | Yes | Yes | Yes | ||
3 | PEcAn (PEcAn#DALEC) | Converter | Convert PEcAn's netcdf CF format to the format required by the DALEC model. | Yes | N/A | N/A | Yes | Yes | Yes | Yes | Yes | ||
4 | PEcAn (PEcAn#ED2 |
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
) | Converter | Convert PEcAn's netcdf CF format to the format required by the |
ED model. | Yes |
N/A | N/A |
Yes | Yes |
Yes | Yes | Yes | |
5 |
PEcAn ( |
PEcAn#LINKAGES) | Converter | Convert PEcAn's netcdf CF format to the format required by |
Yes
the LINKAGES model. | Yes |
Yes
Yes
N/A |
N/A |
Yes | Yes | Yes | Yes | Yes | ||
6 |
PEcAn ( |
PEcAn#Sipnet) | Converter |
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)
Yes
Yes
Yes
Yes
Yes
Body of Water Detector (ncsa.image.ponddetect)
Yes
Convert PEcAn's netcdf CF format to the format required by the Sipnet model. | Yes | N/A | N/A | Yes | Yes | Yes | Yes | Yes | |||||
7 | 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) | Yes | N/A | N/A | No | Yes | Yes | Yes | No | ||||
8 | PlantCV (terra.plantcv) | Extractor | Extract plant height, area, and color distribution from photographs. | Yes | Py1 | yes | yes | yes | yes | no (bamboo test available, not being deployed) | no | ||
9 | BIL (hyperspectral) | Converter | Convert bil.zip (contains raw & *.hdr) to *.terra.nc | Yes (The original code has been updated. Need to figure out if we want to update this) | N/A | N/A | yes | no, only test files available are very large and would take a long time | yes | no (bamboo test available, not being deployed) | no | ||
Civil & Environmental Engineering
| 1 | Body of Water Detector (ncsa.image.ponddetect) | Extractor | Land coverage, extract locations of bodies of water from satellite data. | Yes | No | No | No | Yes | No | No | No | ??who?? |
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2 | GI Identification | Extractor | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | No | |||
3 | Human Preference Score (ncsa.image.humanpref) | Extractor | Assign a model derived human preference score to a given image of an urban environment. | Yes | no | no | no | yes | no | yes | no | ??who?? | |
4 | Route Greenness (ncsa.greenindex) | Extractor | Derive the green index of a city route. | Yes | Py1 | Yes | yes | yes | Yes | Yes | No | ||
5 | Social Media GI Preferences | Extractor | Determine if text contains references to visual or functional green infrastructure. | Yes | Py1 | Yes | Yes | Yes | No | no | No | ||
6 | Stanford CoreNLP - Sentiment (ncsa.nlp.SNLPSentiment) | Extractor | Assign a sentiment score to a piece of text. | Yes | Py2 Java equiv. | Yes | Yes | Yes
| Yes
| No
| No
| ||
7 | TUV Triaxus | Extractor | Towed Undulating Vehicle Data Analyzing Tools | Yes | Py1 | yes | yes | yes | yes | yes | No | ||
Social Science & Humanities | 1 | Bertillon Card Cell Extractor (ncsa.image.dmp) | Extractor | Extract table cells from a Bertillon Card. | Yes | Py1 | Yes | No | No | No | No | No | |
2 | Census Form Cell Extractor (census-section-segmentor) | Extractor | Extract table cells from a 1930s Census form. | Yes | No | No | No | Yes | No | No | No | ||
3 | Handwritten Decimals Extractor (ncsa.image.sphog.debod) | Extractor | Extract handwritten decimal values from an image. | Yes | Py1 | Yes | No | No | No | No | No | ||
4 | (ncsa.image.killedphoto) | Extractor | Identify depression era photos "killed" by Farm Security Administration director Roy Stryker, indicated by a hole punch in the image. | Yes | Py2 | Yes | Yes | Yes | Yes | no | no | ||
5 | Mean Grey (ncsa.cv.meangrey) | Extractor | Mean grey values of black and white photos. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | no | ||
6 | Movie Slice (ncsa.movieslice) | Extractor | Generates movie slice visualization from video files | Yes | Py1/Py2 not used | No | No | No | No | No | No | ||
7 | Person Detector (ncsa.video.person_detector) | Extractor | Extract locations of people in an image. | Yes | Py2 | Yes | Yes (MATLAB external) | Yes | Yes | Yes | No | ||
8 | Person Tracker (ncsa.video.person_tracking) | Extractor | Extract locations and paths of people moving in videos. | Yes | Py2 | Yes | Yes (MATLAB external) | Yes | Yes | Yes | No | ||
9 |
Yes
Yes
Yes
Yes
Route Greenness (ncsa.xml.greenindexroute)
Yes
Video Analytics Toolbox (ncsa.cinemetrics_batch) | Extractor |
Extract shot descriptors from videos. | Yes | Py1/Py2 not used | No | No | No | No | No | No |
Biology, Genomics, Medicine | 1 | FSL (mri2mesh) | Extractor |
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Creates a finite element mesh from a set of mr images | Yes | Py2 | no | yes | yes | no | no | no | |
2 |
Glomeruli (ncsa.msc.diagnosis) | Extractor |
Yes
Extract glomeruli from Kidney biopsy images. | Yes | Py1 |
Yes | Yes |
Yes | Yes |
no |
no |
General
Domain | Tool | Type | Description |
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Code | Py1/Py2 |
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JSON-LD |
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DCKR | Test File |
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TC |
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DPL |
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DL |
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Assignment |
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General
Yes
Yes
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CMU Sphinx (ncsa.audio.speech2text)
General | 1 | Calibre (ebook-converter) | Converter | Convert e-books to a number of document formats. | Yes | N/A | N/A |
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Yes |
Yes |
Yes |
No |
Yes |
2 |
CMU Sphinx (ncsa.audio.speech2text) |
Extractor | Audio recognition to extract text for speech within audio. | Yes | N/A |
Yes |
Yes |
Yes | Yes |
No |
No | ??who?? | |||
3 | Daffodil (daffodil) | Converter | Convert formats with a provided DFDL schema to XML. | Yes |
Yes | Yes |
Yes |
4 |
DBPedia ( |
ncsa.dbpedia) |
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Extractor | Find and define named entities within the given text. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes |
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5 | FFmpeg (ffmpeg) | Converter | Convert between a large number of video formats. | Yes | N/A | N/A | Yes | Yes | Yes | No | Yes | |
6 | FLAC (flac) | Converter | Convert to and from the FLAC format from other audio formats. | Yes | N/A | N/A | Yes | Yes | Yes | No | Yes | Bing Zhang |
7 | Ghostscript (ghostscript) | Converter | Convert between document formats. | Yes | N/A | N/A | Yes | Yes | Yes | No | Yes | Bing Zhang |
8 | htmldoc (htmldoc) | Converter | Convert HTML to a number of document formats. | Yes | N/A | N/A | Yes | Yes | Yes | No | Yes | |
9 | ImageMagick (ImageMagick) | Converter | Convert between a large number of image formats. | Yes | N/A | N/A | Yes | Yes | Yes | No | Yes | |
10 | ImageMagick (ncsa.image.metadata) | Extractor | Pull available EXIF image metadata from a given image. | Yes | Py2 | Yes | Yes | Yes | Yes | Yes | Yes | |
11 |
Kabeja (kabeja) | Converter | Convert between a handful of 3D and |
image formats. | Yes | N/A | N/A | Yes |
Yes | Yes |
Yes |
Yes | |
12 |
OpenCV - Faces (ncsa.cv.faces) | Extractor | Find faces in an image and return |
Yes
Yes
Yes
their locations. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | Yes | |
13 | OpenCV - Eyes (ncsa.cv.eyes) | Extractor |
Yes
Yes
Yes
OpenCV - Profiles (ncsa.cv.profiles)
Yes
Yes
Yes
Find eyes in an image and return their locations. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | Yes | |
14 | OpenCV - Closeups (ncsa.cv.closeups) | Extractor | Determine whether an image is a closeup of a person or not. |
Yes
Yes
Yes
Yes | Py1 | Yes | Yes | Yes | Yes | Yes | Yes | |||||
15 | OpenCV - Profiles (ncsa.cv.profiles) | Extractor | Find human face profiles in an image and return their locations. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | Yes | |
16 |
Langid (ncsa.nlp.simplelanguage) | Extractor | Identify |
the language of the given text. | Yes | Py2 | Yes | Yes | Yes | Yes | No | No | |
17 |
LibreOffice (unoconv) | Converter | Convert to and from a variety of document formats. |
Yes | N/A | N/A |
Yes |
Yes
Yes | Yes |
No | Yes |
Bing Zhang | |||
18 | NLTK - Summary (ncsa.nlp.simplesummary) | Extractor | Summarize a body of text. |
Yes
Yes | Py2 | Yes | Yes | Yes | Yes | No | No | |
19 |
Siegfried (siegfried) | Extractor | Extract information about a given file relevant to identifying its type and |
validating its format. | Yes | Py2 | Yes | Yes | Yes | Yes | No | No |
Yes
20 | Stanford CoreNLP (ncsa.nlp.SNLP) | Extractor | Natural Language Process extractions such as parts of speech, |
named entities, langauge, etc. | Py2 Java equiv. | Yes | Yes | Yes | Yes | No | No | ||
21 |
Yes
Yes
Tesseract (ncsa.image.ocr) | Extractor | Object Character Recognition (OCR) to extract text |
Yes
Yes
Yes
from images containing text. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | Yes | ||||
22 | Tika (ncsa.nlp.tika) | Extractor | Document extractions such as language identification, ... | older Py1 | Yes | Yes | Yes | Yes
| No
| Yes
| ||
23 | txt2html (txt2html) | Converter | Convert text documents to HTML. | Yes | N/A | N/A | Yes | Yes | Yes | Yes | Yes | |
24 |
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. | Yes |
Py1 |
Yes |
Yes |
Yes |
Yes |
Yes | Yes |
25 | VLFeat (ncsa.image.caltech101) | Extractor | Classify images as to whether they contain objects from the Caltech101 dataset (e.g. people, airplanes, motorcycles, cougars, ...). |
Yes
Yes
Yes | Py2 | yes | yes | yes | Yes | yes | no | ||
26 |
Zip (zip) | Converter | Unzip zip archives. | Yes |
N/A | N/A | Yes |
Yes | Yes |
No | Yes |
Bing Zhang |
https://opensource.ncsa.illinois.edu/confluence/display/BD/Transformations (Under development, Being Refactored)
GeoTiff Extractor by using