This page is for the refactoring of the existing extractors. The original wiki page Hosted VMs is still used for the deployments.
As we figure out who's working on what, please start with the following steps for the extractor(s) you chose:
- be able to run the extractor
- add a README, specifically a readme.md (i.e. in markdown), with information on how to install dependencies and run the extractor (in its current shape)
- start looking at dbpedia extractor for template on how to dockerize it
- ... more to come
Steps to take for every extractor in this list:
- Docker containers
- JSONLD
- Extractor info registration
- Use pyclowder (for python extractors)
- Add status messages to all extractors and fix level granularity
- Make status constants (DONE, ERROR)
- Arcgis multiprocessing extractor
- Register on on demand execution queues
- Add on demand key binding to configuration file: messageType = "*.file.text.plain", "extractors."+extractorName
- Standardize around python logging
- Figure out what to log and what format to follow
Add logstash to docker compose- Add sample input/ouput to git repository
- Add icon for tools catalog to git repository
- Add entry to Tools catalog, with icon
ID (Extractor Name from config file, same as queue name) | Programming Language | Software | OS | Can be Dockerized? | Assigned To | Link to repo | Who wrote or worked on the code |
|---|
| DEPLOYED | | | | | | | |
|---|
| ncsa.image.ocr | Python | Tesseract | Linux | | Rui | ocr | |
|---|
ncsa.cv.faces | Python | OpenCV | Linux | | Inna (may be?) | opencvcveyesOpenCVLinuxInnaopencvcvcloseupsOpenCVLinuxInnaopencvcvprofilesOpenCVLinuxInnaopencvfluorescentcometpymedici 
fly cellprofilerhuman| Matlab, mnist-sphog | Linux |
Windows cellprofilerLianacellprofiler.silvercometPythonWindowshttps://opensource.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/cellprofilerLiana | ncsa.cellprofiler.speckle| bisque.histogram (notes: disabled) | Python | | Linux | | | | |
|---|
| ncsa.bisque.metadata (notes: disabled) | Python | |
|---|
Windowshttps://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/cellprofiler | Liana | | | |
| census-section-segmentor | Java | | Linux | | |
|---|
ncsa.cellprofiler.trackobject | Python | | Windows | | cellprofilercellprofilertumorPython | | | Python | OpenCV (python), convert (from imagemagick), and Gdal | Linux |
Windows cellprofilercellprofileryeast Windows cv/cellprofilerLianaimagesphog Matlab, mnist-sphog Gregory Jansencv/handwritten/HandwrittenNumbers | | | | | | Gregory Jansen | | |
|---|
ncsa.bisque.histogram (notes: disabled) | Python | | Linux | | | | bisque.metadata (notes: disabled) GDAL, Cython, numpy,
pygeoprocessing | Linux | |
| | | census-section-segmentor | Java | cvcensusLiana Innacvriver Python | OpenCV (python), convert (from imagemagick), and GdalSmruti PadhycvriverLiana | | Marcus, Ankit |
ncsa.xml.greenindexroute, ncsa. |
|---|
geoshpExtractorgdalJong LeegeoJong LeegeotiffExtractor | OpenCV | Linux | | | | Marcus |
ncsa.audio.speech2text | Java | CMU Sphinx, ffmpeg, sox |
|---|
gdalJong LeegeoJong Leeimage.geotiffPython | GDAL, Cython, numpy,
pygeoprocessing | LinuxRuigeotiffRui, Mostafa ElagimageponddetectMatlabLinuxMarcusmapsfeature_detectionMarcus, Ankit | | SimpleLanguage | Liana |
| ncsa.nlp.simplesummary | Python | Natural Language Toolkit (NLTK) for Python, NLTK Data or at least: nltk.corpus,nltk.stem.porter and nltk.tokenize.punkt. | | | |
|---|
ncsa.image.humanpref | Python | Matlab | Linux | | MarcusmapshumanprefMarcus, Ankitxml.greenindexroute, ncsa.csv.greenindexroutePython | OpenCV | Linuxmapsbrowsegreenrouteimageknn_numeralsOpenCVLinux | | Marcus | | Marcus | ncsa.audio.speech2text | Java | CMU Sphinx, ffmpeg, sox | LinuxMarcuscoreaudio/speech2textMarcus | ncsa.audio.previewcore/audio/preview nlpsimplelanguagePythonnumpy nlp/SimpleLanguageLiananlp.simplesummaryPython | Natural Language Toolkit (NLTK) for Python, NLTK Data or at least:
| image.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | |
|---|
nltk.corpus,nltk.stem.porter and nltk.tokenize.punkt.Gregory JansennlpSimpleSummaryLiana.nlp.SNLPSentimentJava | Stanford CoreNLP tool, java, mavennlpSNLPSNLPSentimentExtractorLiana, Marcus(?)nlp.wordtablesPython | requests, pika, win32com | | | | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-nlp/browse/WordTablesExtractor | Liana | siegfriedsiegfriedGregory JansenversusimageJavaVersusLinuxSmruti Padhyversus/browseKenton, Smruti | ncsa.image.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | coreimage/previewRob, Sandeep | | poppler | |
| ncsa.cv.caltech101 | Python | Matlab and VLFeat | 64-bit Mac OS |
|---|
ncsa.pdf.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | | corepdf/previewRob | ncsa.video.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | core/video/previewRob | | | | | | | | | | | | |
|---|
| | | | | | | | |
|---|
NOT DEPLOYED | | | image.digitpyPython | opencvcv/handwritten/SimpleDigitPython | Liana, Constantinos |
| LSVA integrated | |
|---|
ncsa.cv.pdfimages | pdfimages, from poppler-utils | cv/poppler cv.caltech101Matlab and VLFeat64-bit Mac OS cv/vlfeat | dbpedia | Python | Natural Language Toolkit (NLTK) and rdflib. | Sandeep |
| mri2mesh | Python | pymedici, subprocess, logging, os, numpy, shutil, zipfile | | | |
|---|
Luigi MarinidbpediaLuigi Marini | | Marcus |
| msc-ChemCBCExtractor |
|---|
digest | Python | requests, pika, openpyxl, xlrd, pymongo |
|---|
digest | | Yan |
| msc-IsletExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux |
|---|
ncsa.hpc | Python | hpc | LSVA | Java | | /IsletExtractor | Yan |
| msc-MonitorExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux |
|---|
lsva | LSVA integrated | | | Yan |
| ncsa.msc.dailymonitor | Python | requests, pika, openpyxl, xlrd, pymongo |
|---|
lsva-integrated | | Ashwini |
| msc-PhenotypeExtractor |
|---|
ncsa.movieslice requests, pika, openpyxl, xlrd, pymongo | Linux | | |
moviesliceSandeep | mri2mesh | Python | pymedici, subprocess, logging, os, numpy, shutil, zipfilemrimri2meshMarcus | msc-ChemCBCExtractorrequests,pika openpyxl, xlrd, pymongoLinuxYanmscChemCBCExtractorYanmscIsletExtractor| detector | Python | MATLAB, FFMPEG, requests |
|---|
, pika, openpyxl, xlrd, pymongoLinuxYanmscIsletExtractorYanmscMonitorExtractorrequests, pika, openpyxl, xlrd, pymongo | | python, MATLAB, FFMPEG requests and pika | |
LinuxYanmscMonitorExtractorYanncsamsc.dailymonitor| plantcv | Python | pika
requests |
|---|
, pika, openpyxl, xlrd, pymongonot usedmsc/OldMonitorExtractorAshwini | msc-PhenotypeExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | | Yan |
| medici_PTM_thumbnails | Java | | |
|---|
LinuxYanmscPhenotypeExtractorYan | | Constantinos |
| medici_PTM_metadata |
|---|
ncsa.nlp.SNLPStanford CoreNLP tool, java, mavennlpSNLP/SNLPExtractorLiana | ncsa.nlp.tika | Python | Tika project page, pymedicinlptikaLiana | person-detector | Python | MATLAB, FFMPEG, requests and pikaperson-detectorpythonSandeep | ncsa.person-tracker | Python | python, MATLAB, FFMPEG requests and pikaperson-trackingpythonSandeep | | Constantinos |
| medici_images_ptm | Java | |
|---|
terra.plantcv | Python | pikarequestswheelplantcvYan | medici_PTM_thumbnails | Javaptm/PTMThumbnailExtractorConstantinos | medici_PTM_metadata | Javaptm/PTMMetadataExtractorConstantinos | Name not clear
PtmMetadata(?ptmPTMMetadataptm_mapsptmPTMMapsExtractorptm_3dptmPTM3DExtractorimages_ptmptmImagesPTMExtractorConstantinos | extractors-rabbitmq (look like examples) | rabbitmq | Name not clear extractors-seabird/ | ScalaseabirdLuigi | medici_3d_x3d (one of extractors-3d) | Java | | | | | Constantinos |
| ncsa.arcgis.landsat7mosaic | Python | ArcGIS | Windows | No | |
|---|
3dObjJSONExtractorConstantinos | medici_3d_obj_merger (one of extractors-3d) | Java | | | | 3d/OBJMergerExtractorConstantinosoni (one of extractors-3d)3dOniExtractorConstantinosply_obj (one of extractors-3d)3dPlyObjExtractorConstantinos | medici_3d_metadata (one of extractors-3d) 3d/browse/ThreeDMetadataExtractorConstantinos | medici_x3d_html (one of extractors-3d) | Java | | | | 3dX3DhtmlExtractorConstantinos | ncsa.arcgis.landsat7mosaic | Python | ArcGIS | Windows | NO | Smruti Padhybd-cz/ndviextractorSmrutiarcgis.floodplainArcGISWindowsNOSmruti Padhybd-cz/terex_floodplain/config.pySmruti | | Constantinos |
| ncsa.image.metadata | Python |
|---|
medici_book | JavabooksBookPreviewExtractorTheerasit Issaranon | medici_image_pyramid | JavaCATSbooks/ImagePreviewPyramidExtractor-shebookTheerasit Issaranon | shebook | JavaCATSbooks/SheBookPreviewExtractor/src/BookPreviewExtractor CATSbooks/SheBookPreviewExtractor/src/bookpreviewextractorTheerasit Issaranon | lsva-cedd | JavaCATSceddConstantinos.cinemetrics.image.iarp_remove_circle | |
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Python/CATS/repos-cinemetricsbrowseConstantinosimagemetadataPythonCATSextractors-coreimagemetadataMax. Rob | | | | | | | | | |
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