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Fluorescence Imaging Pipeline for Terra-Ref PS2 Data

intro-tutorials

openstack-terraform-nomad

Set up a Nomad cluster on OpenStack using Terraform

pipeline-nomad-jobs

Nomad job specifications for the pipeline components

template-lidar-plot

Transformer template for plot level lidar data analysis. Please read HOW_TO.md to start

template-rgb-plot

Transformer template for plot level RGB data analysis. Please read HOW_TO.md to start

template-transformer-simple

A template for creating transformers for multiple environments

transformer-betydb-csvupload

Uploads CSV files to a BETYdb instance (based upon TERRA REF computing-pipeline/extractors/betydb)

transformer-bin2tif

Transforms RGB bin files to geo-referenced tiff (based upon TERRA REF extractors-stereo-rgb/bin2tif)

transformer-canopycover

Calculates canopy cover on soil masked images (based upon TERRA REF extractors-stereo-rgb/canopycover)

transformer-cleanmetadata

Cleans Gantry generated metadata (formerly extractors-metadata/cleaner in TERRA REF)

transformer-envlog2netcdf

Moving to https:/github.com/uacic. Processes environmental logger stream data files into a netCDF (based upon TERRA REF extractors-environmental/envlog2netcdf)

transformer-fieldmosaic

Creates an RGB field mosaic with Gantry images (formerly TERRA REF extractors-stereo-rgb/fieldmosaic)

transformer-flir2tif

Converts the IR bin files to geo-referenced TIF (based upon TERRA REFextractors-multispectral/flir2tif)

transformer-geostream-csvupload

Loads CSV files to GeoStreams database instance (base upon TERRA REF computing-pipeline/extractors/geostreams)

transformer-hyperspectral

Transforms raw imagery from 2D raster to 3D compressed netCDF (based upon TERRA REF extractors-hyperspectral)

transformer-irrigation_datparser

Loads irrigation data into GeoStreams database (TERRA REF) instance (based upon TERRA REF extractors-environmental/irrigation_datparser)

transformer-las2height

Calculates canopy height from las file (based upon TERRA REF extractors-3dscanner/las2height)

transformer-meantemp

Calculates mean temperature on IR images (based upon TERRA REF extractors-multispectral/meantemp)

transformer-plotclip

Clips files to plot boundaries (based upon TERRA REF computing-pipeline/extractors/plotclipper)

transformer-plotmerge

Merges files (assumed to be plot level) (based upon TERRA REF computing-pipeline/extractors/plotclipper)

transformer-ply2las

Converts PLY point clouds to LAS (formerly extractors-3dscanner/ply2las in TERRAREF project)

transformer-psii2png

Converts PSII sensor files to PNG (based upon TERRA REF extractors-multispectral/psii2png)

transformer-rgb_quality

Creates a quality measure on RGB images (based upon TERRA REF quality-metrics/rgb_qc)

transformer-soilmask

Masks soil from images (formerly extractor-stereo-rgb/rgbmask in TERRAREF project)

transformer-weather_datparser

Loads weather data into GeoStreams database (TERRA REF) instance (based upon TERRA REF extractors-environmental/weather_datparser)

ua-gantry-environment

Implements Transformer class and provides docker images for University of Arizona transformers for Common Workflow Language environment