WeedCOCO category names are now a combination of role and species

Fixes #83 Fixes #57 Helps towards specifying categories in importers (#33, #34)
Weed-AI · Sep 23, 2020 · 7d392ec · 7d392ec
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Showing 7 changed files with 62 additions and 18 deletions.
diff --git a/search/src/App.js b/search/src/App.js
@@ -29,7 +29,7 @@ class App extends Component {
 				queryFormat: "or",
 				URLParams: true,
 				react: {
-					and: ["searchbox", "resslider", "agcontextfilter", "rolefilter", "speciesfilter", "grainstextfilter"]
+					and: ["searchbox", "resslider", "agcontextfilter", "categoryfilter", "grainstextfilter"]
 				},
 				...multilistFacetProps
 			}
@@ -60,24 +60,14 @@ class App extends Component {
 			>
 				<div style={{ position: "fixed", width: "20rem", overflow: "scroll", height: "100%" }}>
 					<MultiList
-						componentId="rolefilter"
-						title="Filter by role"
-						dataField="annotation__category__role.keyword"
-						sortBy="asc"
-						selectAllLabel="All roles"
-						placeholder="Search Role"
-						filterLabel="Role"
-						{...makeProps("rolefilter", true)}
-					/>
-					<MultiList
-						componentId="speciesfilter"
+						componentId="categoryfilter"
 						title="Filter by species"
-						dataField="annotation__category__species.keyword"
+						dataField="annotation__category__name.keyword"
 						sortBy="asc"
 						selectAllLabel="All species"
 						placeholder="Search Species"
 						filterLabel="Species"
-						{...makeProps("speciesfilter", true)}
+						{...makeProps("categoryfilter", true)}
 					/>
 					<MultiList
 						componentId="agcontextfilter"

diff --git a/weedcoco/cwfid_to_json/cwfid_imageinfo.json b/weedcoco/cwfid_to_json/cwfid_imageinfo.json
@@ -17269,6 +17269,7 @@
     ],
     "categories": [
         {
+            "name": "crop: daugus carota",
             "common_name": "carrot",
             "species": "daugus carota",
             "eppo_taxon_code": "DAUCS",
@@ -17277,6 +17278,7 @@
             "id": 0
         },
         {
+            "name": "weed: UNSPECIFIED",
             "species": "UNSPECIFIED",
             "role": "weed",
             "id": 1
@@ -17316,7 +17318,7 @@
             "location_lat": 53,
             "location_long": 11,
             "location_datum": 4326,
-            "upload_time": "2020-09-02 23:21:11",
+            "upload_time": "2020-09-23 17:21:34",
             "camera_make": "JAI AD-130GE",
             "camera_lens": "Fujinon TF15-DA-8",
             "camera_lens_focallength": 15,
@@ -17415,4 +17417,4 @@
             "collection_id": 0
         }
     ]
-}
+}
diff --git a/weedcoco/deepweeds_to_json/deepweeds_imageinfo.json b/weedcoco/deepweeds_to_json/deepweeds_imageinfo.json
@@ -262640,60 +262640,69 @@
     ],
     "categories": [
         {
+            "name": "weed: chinee apple",
             "common_name": "chinee apple",
             "id": 0,
             "role": "weed",
             "species": "ziziphus mauritiana",
             "eppo_taxon_code": "ZIPMA"
         },
         {
+            "name": "weed: lantana",
             "common_name": "lantana",
             "id": 1,
             "role": "weed",
             "species": "lantana camara",
             "eppo_taxon_code": "LANCA"
         },
         {
+            "name": "none",
             "common_name": "negative",
             "id": 8,
             "role": "na"
         },
         {
+            "name": "weed: snake weed",
             "common_name": "snake weed",
             "id": 7,
             "role": "weed",
             "species": "gutierrezia sarothrae",
             "eppo_taxon_code": "GUESA"
         },
         {
+            "name": "weed: siam weed",
             "common_name": "siam weed",
             "id": 6,
             "role": "weed",
             "species": "chromolaena odorata",
             "eppo_taxon_code": "EUPOD"
         },
         {
+            "name": "weed: prickly acacia",
             "common_name": "prickly acacia",
             "id": 4,
             "role": "weed",
             "species": "vachellia nilotica",
             "eppo_taxon_code": "ACANL"
         },
         {
+            "name": "weed: parthenium",
             "common_name": "parthenium",
             "id": 3,
             "role": "weed",
             "species": "parthenium hysterophorus",
             "eppo_taxon_code": "PTNHY"
         },
         {
+            "name": "weed: rubber vine",
             "common_name": "rubber vine",
             "id": 5,
             "role": "weed",
             "species": "cryptostegia grandiflora",
             "eppo_taxon_code": "CVRGR"
         },
         {
+            "name": "weed: parkinsonia",
             "common_name": "parkinsonia",
             "id": 2,
             "role": "weed",
@@ -262759,4 +262768,4 @@
             "id": 0
         }
     ]
-}
+}
diff --git a/weedcoco/importers/cwfid.py b/weedcoco/importers/cwfid.py
@@ -27,14 +27,20 @@
 CATEGORY_MAP = {
     # TODO: we need a spec for species unspecified, and we need a spec for species specified
     "crop": {
+        "name": "crop: daugus carota",
         "common_name": "carrot",
         "species": "daugus carota",
         "eppo_taxon_code": "DAUCS",
         "eppo_nontaxon_code": "3UMRC",
         "role": "crop",
         "id": 0,
     },
-    "weed": {"species": "UNSPECIFIED", "role": "weed", "id": 1},
+    "weed": {
+        "name": "weed: UNSPECIFIED",
+        "species": "UNSPECIFIED",
+        "role": "weed",
+        "id": 1,
+    },
 }
 
 

diff --git a/weedcoco/importers/deepweeds.py b/weedcoco/importers/deepweeds.py
@@ -109,10 +109,12 @@
     # Generate category objects
     if categoryID not in categoryIDToCategories:
         category = {}
+        category["name"] = row["Species"].lower()
         category["common_name"] = row["Species"].lower()
         category["id"] = row["Label"]
         categoryIDToCategories[categoryID] = category
         if category["common_name"] == "negative":
+            category["name"] = "none"
             category["role"] = "na"
         else:
             category["role"] = "weed"
@@ -140,6 +142,8 @@
         if category["common_name"] == "parkinsonia":
             category["species"] = "parkinsonia aculeata"
             category["eppo_taxon_code"] = "PAKAC"
+        if "name" not in category:
+            category["name"] = f"{category['role']}: {category['species']}"
 
     # Create an annotation
     ann = {}

diff --git a/weedcoco/schema/Category.yaml b/weedcoco/schema/Category.yaml
@@ -0,0 +1,29 @@
+$id: https://weedid.sydney.edu.au/schema/Category.json
+type: object
+required:
+  - id
+  - name
+
+properties:
+  id:
+    type: number
+    description: |-
+      A number identifying the image.
+
+  name:
+    type: string
+    pattern: ^((crop|weed): ([a-z]+|UNSPECIFIED)|crop|weed|none)$
+    description: |-
+      A category for an annotation, consisting of an agricultural role and
+      optionally a biological name, separated by ": ". Currently allowed
+      agricultural roles are "weed" and "crop".  The "none" category may be
+      used to indicate that no weed or crop is identified in the image.
+
+      Annotations should be labelled with the most specific category possible,
+      usually "weed: <species name>", but super categories may be more general.
+      Biological names should be lowercase.
+      For an unspecified species of weed, "weed: UNSPECIFIED" may be used.
+
+      For example, to label an oat crop in an image, the category name would be
+      "crop: avena sativa". Its super categories may include "crop: grasses"
+      and "crop". Oats as a volunteer crop would be "weed: avena sativa".
diff --git a/weedcoco/schema/main.yaml b/weedcoco/schema/main.yaml
@@ -19,6 +19,10 @@ properties:
     type: array
     items:
       $ref: https://weedid.sydney.edu.au/schema/Annotation.json#/
+  categories:
+    type: array
+    items:
+      $ref: https://weedid.sydney.edu.au/schema/Category.json#/
   agcontexts:
     type: array
     items: