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Species Locations Shapefiles
What: Global potting area locations of each species group in the form of polygons. A single polygon encompasses one species group is marked as such in the shapefile attribute table. Polygons are created by pulling in the orthomosaic generated from AutoSfM. Shapefiles are created manually but only need to be done once.
Where: QGIS or other GIS software
How: Pull in orthomosaic into QGIS or another GIS software. Create a shapefile and draw polygons around each species group. Create attribute “species” and mark each polygon as such. Save shapefile and place under semif-utils.
When: Once per growing season, a single shapefile for each location.
Why: Polygons are used to provide species labels for each bounding box detection result. The object detection model only detects vegetation but we also want species label information. Because local detection results are scaled to a global coordinate reference system via AutoSfM, they can be compared to larger areas throughout the potting area. An orthomosaic, that provides a visual representation to the global CRS, can be used to manually demarcate species potting groups. Detection results that fall within the polygon area are given species labels of respective polygons.
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Species group locations in the potting area must remain constant |
Batches
Images
Cutouts
...
Various types of data are used and produced during processing. Full resolution images are the main data input and are processed to produce plant segments, or cutouts, various types of masks, and metadata products for both original images and cutouts. This section describes how this is data structured, details its contents, and documents Image and Cutout metadata at length.
Directory Structure
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data
├── semifield-developed-images
│ ├── NC_2022-07-27
│ │ ├── NC_2022-07-27.json
│ │ │
│ │ ├── autosfm
│ │ │ ├── NC_2022-07-27_preview.png
│ │ │ ├── detections.csv
│ │ │ ├── dem
│ │ │ │ └── dem.tif
│ │ │ ├── downscaled_photos
│ │ │ │ ├── NC_1658926241.png
│ │ │ │ ├── NC_1658926255.png
│ │ │ │ └── ...
│ │ │ ├── downscaled_masks
│ │ │ │ ├── NC_1658926241_mask.png
│ │ │ │ ├── NC_1658926255_mask.png
│ │ │ │ └── ...
│ │ │ ├── ortho
│ │ │ │ └── orthomosaic.tif
│ │ │ ├── project
│ │ │ │ ├── NC_2022-07-27.psx
│ │ │ │ └── NC_2022-07-27.files
│ │ │ └── reference
│ │ │ ├── camera_reference.csv
│ │ │ ├── error_statistic.csv
│ │ │ ├── fov.csv
│ │ │ └──gcp_reference.csv
│ │ │
│ │ ├── images
│ │ │ ├── NC_1658926241.png
│ │ │ ├── NC_1658926255.png
│ │ │ └── ...
│ │ │
│ │ ├── masks
│ │ │ ├── NC_1658926241_mask.png
│ │ │ ├── NC_1658926255_mask.png
│ │ │ └── ...
│ │ │
│ │ ├── plant-detections
│ │ │ ├── NC_1658926241.csv
│ │ │ ├── NC_1658926255.csv
│ │ │ └── ...
│ │ │
│ │ ├── metadata
│ │ │ ├── NC_1658926241.json
│ │ │ ├── NC_1658926255.json
│ │ │ └── ...
│ │ │
│ │ └── metamasks
│ │ ├── semantic_masks
│ │ │ ├── NC_1658926241.png
│ │ │ ├── NC_1658926255.png
│ │ │ └── ...
│ │ └── instance_masks
│ │ ├── NC_1658926241.png
│ │ ├── NC_1658926255.png
│ │ └── ...
│ └── ...
│
├── semifield-cutouts
│ ├── NC_2022-07-27
│ │ ├── NC_1658926241_0.png
│ │ ├── NC_1658926241_0.json
│ │ ├── NC_1658926241_0.jpg
│ │ ├── NC_1658926241_0_mask.png
│ │ └── ...
│ └── ...
│
└── semifield-utils
├── MD
│ ├── shapefiles
│ │ │ ├── MD.shp
│ │ │ └── ...
│ │ └── GroundControlPoints.csv
├── NC
│ ├── shapefiles
│ │ ├── NC.shp
│ │ └── ...
│ └── GroundControlPoints.csv
└── species_info.json
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