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Directory Structure
Processing occurs within the main SemiF-AnnotationPipeline repository which used for temporary data storage. Resulting data for each batch is then moved to the respective permanent blob locations.
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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SemiF-AnnotationPipeline └── data ├── semifield-developed-images │ ├── NC_2022-07-27 │ │ ├── NC_2022-07-27.json │ │ │ │ │ │├── autosfm │ │ │ ├── autosfmNC_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 │ │ │ └── ... │ │ │ │ │ └──├── metadataplant-detections │ │ │ ├── NC_1658926241.jsoncsv │ │ │ ├── NC_1658926255.jsoncsv │ │ │ └── ... │ │ │ │ └── ... │ ├── semifield-cutouts │ ├── NC_2022-07-27 metadata │ │ ├── NC_1658926241_0.png │ │ ├── NC_1658926241_0.json │ │ ├── NC_1658926241_1.png │ │ ├── NC_1658926241_1.json │ │ ├── NC_1658926255_0.png │ │ ├── NC_1658926255_0.json │ │ └── ... │ └── ... │ ├── semifield-models │ └── plant_detector │ └── best.pt │ ├── semifield-upload-images │ └── ... │ └── semifield-utils ├── MD │ ├── shapefiles │ │ │ ├── MD.shp │ │ │ └── ... metamasks │ │ └── GroundControlPoints.csv ├── semantic_masks │ │ │ ├── NC_1658926241.png │ ├── shapefiles │ │ │ │ ├── NC_1658926255.shppng │ │ │ │ └── ... │ │ │ └── GroundControlPoints.csv └── species_info.json |
Metadata
Batches
blob_home and data_root - storage location information
batch_id - unique batch identifier
upload_datetime - when image were uploaded to “uploads” blob storage
image_list - list of images contained in a single batch folder
schema_version - version of data schema used for organizing metadata
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{ "blob_home": "data", "data_root": "semifield-developed-images", "batch_id": "NC_2022-08-05", "upload_datetime": "2022-08-19_21:28:37", "image_list": [ "images/NC_1659710908.jpg", "images/NC_1659711200.jpg", "images/NC_1659706234.jpg", └── instance_masks │ │ ├── NC_1658926241.png │ │ ├── NC_1658926255.png │ │ └── ... │ └── "images/NC_1659709264.jpg", "images/NC_1659715086.jpg", "images/NC_1659706245.jpg" │ ], "schema_version": "1.0" } |
Images - general
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| language | json |
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├── semifield-cutouts │ ├── NC_2022-07-27 |
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│ |
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Images - Exif
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"exif_meta": {
"ImageWidth": 9560,
"ImageLength": 6368,
"BitsPerSample": 8,
"Compression": 1,
"PhotometricInterpretation": 2,
"Make": "SONY",
"Model": "ILCE-7RM4",
"Orientation": 1,
"SamplesPerPixel": 3,
"XResolution": "300",
"YResolution": "300",
"PlanarConfiguration": 1,
"ResolutionUnit": 2,
"Software": "RawTherapee 5.8",
"DateTime": "2022:07:27 08:49:15",
"Rating": 0,
"ExifOffset": 4449,
"ExposureTime": "1/200",
"FNumber": "10",
"ExposureProgram": 1,
"ISOSpeedRatings": 100,
"RecommendedExposureIndex": 100,
"ExifVersion": [
48,
50,
51,
49
],
"DateTimeOriginal": "2022:07:27 08:49:15",
"DateTimeDigitized": "2022:07:27 08:49:15",
"BrightnessValue": "9207/1280",
"ExposureBiasValue": "0",
"MaxApertureValue": "217/128",
"MeteringMode": 5,
"LightSource": 0,
"Flash": 16,
"FocalLength": "55",
"FileSource": 3,
"SceneType": 1,
"CustomRendered": 0,
"ExposureMode": 1,
"WhiteBalance": 0,
"DigitalZoomRatio": "1",
"FocalLengthIn35mmFilm": 55,
"SceneCaptureType": 0,
"Contrast": 0,
"Saturation": 0,
"Sharpness": 0,
"LensSpecification": [
"55",
"55",
"9/5",
"9/5"
],
"LensModel": "FE 55mm F1.8 ZA",
"BodySerialNumber": null,
"MakerNote": null,
"ImageDescription": " ",
"UserComment": null,
"ApplicationNotes": null,
"Tag": null,
"SubIFDs": 4450
} |
Images - Camera Info
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"camera_info": {
"camera_location": [
-0.1992725638544925,
9.926811159768054,
2.130928709515993
],
"pixel_width": 0.0075333198937023,
"pixel_height": 0.0075333198937023,
"yaw": 183.89777711639093,
"pitch": -2.3366362127596525,
"roll": 0.7135915032770658,
"focal_length": 8747.80961719926,
"fov": {
"top_left": [
-0.8064812117393512,
10.27414293412319
],
"top_right": [
0.3552128560424488,
10.353294011316107
],
"bottom_left": [
-0.7537579837514339,
9.50032830822
],
"bottom_right": [
0.4079360840303661,
9.579479385412917
],
"is_scaleable": true
}
} |
Images - Cutouts
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"cutout_ids": [
"NC_1658926241_0",
"NC_1658926241_1",
"NC_1658926241_2",
"NC_1658926241_3"
], |
Images - Bounding Boxes
| Code Block | ||
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"bboxes": [
{
"bbox_id": "NC_1658926241_0",
"image_id": "NC_1658926241",
"local_centroid": [
0.7247684299945831,
0.782112181186676
],
"local_coordinates": {
"top_left": [
4559.100573062897,
3592.980739593506
],
"top_right": [
9298.47180843353,
3592.980739593506
],
"bottom_left": [
4559.100573062897,
6368.0
],
"bottom_right": [
9298.47180843353,
6368.0
],
"is_scaleable": true
},
"global_centroid": [
-0.3805987383493097,
10.21634506227248
],
"global_coordinates": {
"top_left": [
-0.1245738268094071,
10.015139374543459
],
"top_right": [
-0.7303918468219674,
10.11728321515172
],
"bottom_left": [
-0.07889030276824338,
10.4175507500015
],
"bottom_right": [
-0.682307173930376,
10.458062046757698
],
"is_scaleable": true
},
"cls": {
"scientific_name": "Amaranthus palmeri",
"common_name": "Palmer amaranth",
"USDA_symbol": "AMPA",
"EPPO": "AMAPA",
"authority": "Watson",
"collection_location": "NC",
"polygon_id": ""
},
"is_primary": false,
"overlapping_bbox_ids": []
},
{
...
}
],
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Cutouts
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│ ├── 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 |
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└── species_info.json |
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