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).
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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
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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Yes
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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| Sandeep Puthanveetil Satheesan 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
| 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
Yes (Windows VM) |
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| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
- Yes
- Yes
- Yes
- Yes
- 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 |
| DALEC model. |
- Yes
- Yes
- Yes
Yes | N/A | N/A | Yes | Yes | Yes | Yes | Yes | |
| 4 | PEcAn (PEcAn#ED2) | Converter | Convert PEcAn's netcdf CF format to the format required by the ED model. |
Yes | N/A |
N/A |
| Yes |
| Yes |
PEcAn (PEcAn#AmerifluxBNL)
PEcAn (PEcAn#FLUXNET2015)
Yes | Yes | Yes | |
| 5 |
| PEcAn ( |
| PEcAn#LINKAGES) |
- Yes
- Yes
- Yes
- Yes
- Yes
| Converter |
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)
| Convert PEcAn's netcdf CF format to the format required by the LINKAGES model. | Yes | N/A | N/A | Yes | Yes | Yes | Yes | Yes | ||||
| 6 | PEcAn (PEcAn#Sipnet) | Converter | 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
Yes | No | No | No | Yes | No | No | No | ??who?? |
| 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
| . | 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 | 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 |
|---|
| 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 | Extract glomeruli from Kidney biopsy images. |
Yes |
| Py1 |
Yes |
| Yes |
Yes |
Yes |
no | no |
General
| Domain | Tool | Type | Description |
|---|
| Code | Py1/Py2 |
|---|
| JSON-LD |
|---|
| DCKR | Test File | TC |
|---|
| DPL | DL |
|---|
| Assignment |
|---|
|
General | 1 | Calibre (ebook-converter) | Converter | Convert e-books to a number of document formats. |
|---|
| Yes | N/A |
| N/A |
| 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) | Extractor | Find |
| and define named entities within the given text. | Yes | Py1 | Yes | Yes | Yes | Yes | Yes |
| |||
| 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 their locations |
| . | Yes | Py1 | Yes | Yes | Yes | Yes | Yes | Yes |
| 13 | OpenCV - Eyes (ncsa.cv.eyes) | Extractor |
| 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 | 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 | No | Yes |
| Bing Zhang | |||
| 18 | NLTK - Summary (ncsa.nlp.simplesummary) | Extractor | Summarize a body of text. |
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 |
| 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 |
| Tesseract (ncsa.image.ocr) | Extractor | Object Character Recognition (OCR) to extract |
| text 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 | 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