Fixing negative Coordinates in polygons

client/platform/desktop/backend/native/common.spec.ts

@@ -10,6 +10,8 @@ import type {
   DesktopJobUpdate, DesktopJobUpdater, JsonMeta, RunTraining, Settings,
 } from 'platform/desktop/constants';
 
+import { MultiTrackRecord } from 'dive-common/apispec';
+import { Attribute } from 'vue-media-annotator/use/useAttributes';
 import * as common from './common';
 
 const pipelines = {
@@ -107,6 +109,34 @@ const console = new Console(process.stdout, process.stderr);
 
 const emptyCsvString = '# comment line\n# metadata,fps: 32,"whatever"\n#comment line';
 
+// Below sets up data in the mockfs
+type testPairs = [string[], MultiTrackRecord, Record<string, Attribute>];
+/* Viame.spec.json is an array in the format [CSV row Array, MultiTrackRecord, Attributes Object][]
+   This is restructured to be images and annotations files within a folder for the mockfs system
+   test[index] (folder):
+      -1.png
+      -2.png
+      -3.png
+      -annotations.csv
+  This is then used to run a complete load of a folder and then compare
+  with the results located in the MultiTrackRecord and Attributes for the corresponding index
+*/
+const testData: testPairs[] = fs.readJSONSync('../testutils/viame.spec.json');
+const images: Record<string, string> = {};
+//Create a list of numbers 0-9
+const imageList = Array.from(Array(10).keys());
+imageList.shift(); //remove 0 to line up with source data images list
+// eslint-disable-next-line no-return-assign
+imageList.forEach((item) => images[`${item}.png`] = ''); // 1.png, 2.png,...
+//Create a mockfs file struction of a list of images and a root annotations.csv file
+const fileSystemData: Record<string, Record<string, string>> = { };
+testData.forEach((triplet, index) => {
+  fileSystemData[`test${index}`] = {
+    ...images, //list of images [1-9].png
+    'annotations.csv': triplet[0].join('\n'), //join csv string[] into a string for mockfs
+  };
+});
+
 mockfs({
   '/opt/viame': {
     configs: {
@@ -117,6 +147,7 @@ mockfs({
       },
     },
   },
+  '/home/user/testPairs': { ...fileSystemData },
   '/home/user/output': {},
   '/home/user/data': {
     annotationImport: {
@@ -703,6 +734,32 @@ describe('native.common', () => {
     expect(pipes.utility.pipes).toHaveLength(4);
     expect(pipes.trained.pipes).toHaveLength(1);
   });
+
+  it('Full Annotation Loading and Attributes Testing', async () => {
+    for (let num = 0; num < testData.length; num += 1) {
+      // eslint-disable-next-line no-await-in-loop
+      const payload = await common.beginMediaImport(
+        settings, `/home/user/testPairs/test${num}`, checkMedia,
+      );
+      expect(payload.jsonMeta.originalImageFiles).toEqual([
+        '1.png',
+        '2.png',
+        '3.png',
+        '4.png',
+        '5.png',
+        '6.png',
+        '7.png',
+        '8.png',
+        '9.png',
+      ]);
+      // eslint-disable-next-line no-await-in-loop
+      const final = await common.finalizeMediaImport(settings, payload, updater, convertMedia);
+      expect(final.attributes).toEqual(testData[num][2]);
+      // eslint-disable-next-line no-await-in-loop
+      const tracks = await common.loadDetections(settings, final.id);
+      expect(tracks).toEqual(testData[num][1]);
+    }
+  });
 });
 
 afterAll(() => {

client/platform/desktop/backend/native/common.ts

@@ -602,6 +602,7 @@ async function _ingestFilePath(
   }
   if (tracks !== null) {
     const processed = processTrackAttributes(tracks);
+    meta.attributes = processed.attributes;
     await _saveSerialized(settings, datasetId, processed.data, true);
   }
   return meta;

client/platform/desktop/backend/serializers/nist.ts

@@ -105,7 +105,6 @@ function loadObjects(
             track.begin = Math.min(track.begin, frameNum);
             track.features.push({
               frame: frameNum,
-              keyframe: true,
               bounds: adjustedBounds,
               attributes: {
                 objectID,
@@ -167,15 +166,12 @@ function loadActivity(
           features.push({
             frame: parseInt(frame, 10) - 1,
             bounds,
-            keyframe: true,
-            interpolate: false,
           });
         } else if (val === 1) {
           track.end = parseInt(key, 10) - 1;
           features.push({
             frame: parseInt(frame, 10) - 1,
             bounds,
-            keyframe: true,
             interpolate: true,
           });
         }

client/platform/desktop/backend/serializers/viame.spec.ts

@@ -3,7 +3,14 @@ import { MultiTrackRecord } from 'dive-common/apispec';
 import fs from 'fs-extra';
 import mockfs from 'mock-fs';
 import { JsonMeta } from 'platform/desktop/constants';
-import { serialize } from 'platform/desktop/backend/serializers/viame';
+import { serialize, parse } from 'platform/desktop/backend/serializers/viame';
+import { Attribute } from 'vue-media-annotator/use/useAttributes';
+import processTrackAttributes from 'platform/desktop/backend/native/attributeProcessor';
+
+
+type testPairs = [string[], MultiTrackRecord, Record<string, Attribute>];
+
+const testData: testPairs[] = fs.readJSONSync('../testutils/viame.spec.json');
 
 
 const data: MultiTrackRecord = {
@@ -20,8 +27,6 @@ const data: MultiTrackRecord = {
           968,
           433,
         ],
-        interpolate: false,
-        keyframe: true,
       },
       {
         frame: 1,
@@ -31,8 +36,6 @@ const data: MultiTrackRecord = {
           968,
           433,
         ],
-        interpolate: false,
-        keyframe: true,
       },
       {
         frame: 2,
@@ -42,8 +45,6 @@ const data: MultiTrackRecord = {
           968,
           433,
         ],
-        interpolate: false,
-        keyframe: true,
       },
       {
         frame: 3,
@@ -53,8 +54,6 @@ const data: MultiTrackRecord = {
           968,
           433,
         ],
-        interpolate: false,
-        keyframe: true,
       },
       {
         frame: 4,
@@ -64,8 +63,6 @@ const data: MultiTrackRecord = {
           968,
           433,
         ],
-        interpolate: false,
-        keyframe: true,
       },
     ],
     confidencePairs: [
@@ -118,14 +115,22 @@ const meta = {
   multiCam: null,
   subType: null,
 } as JsonMeta;
+const testFiles: Record<string, string> = { };
+testData.forEach((item, index) => {
+  // eslint-disable-next-line prefer-destructuring
+  testFiles[`${index}.csv`] = item[0].join('\n');
+});
+
 mockfs({
   '/home': {},
   'home/user/media/projectid1data': {
     'foo.png': '',
     'bar.png': '',
   },
+  '/csv': testFiles,
 });
 
+
 // Returns first confidence pairs output of CSV that isn't a comment
 function checkConfidenceOutput(output: string[]) {
   for (let i = 0; i < output.length; i += 1) {
@@ -149,6 +154,26 @@ function getCSVTiming(output: string[]) {
   }
   return timings;
 }
+
+describe('VIAME Python Compatibility Check', () => {
+  it('testing import and convert', async () => {
+    for (let i = 0; i < testData.length; i += 1) {
+      const trackData = testData[i][1];
+      const testAttributes = testData[i][2];
+      const testPath = `/csv/${i}.csv`;
+      const csvStream = fs.createReadStream(testPath);
+      const trackArray = Object.values(trackData);
+      // eslint-disable-next-line no-await-in-loop
+      const results = await parse(csvStream);
+      expect(results.tracks).toEqual(trackArray);
+      // eslint-disable-next-line no-await-in-loop
+      const attData = processTrackAttributes(results.tracks);
+      expect(testAttributes).toEqual(attData.attributes);
+    }
+  });
+});
+
+
 describe('VIAME serialize testing', () => {
   it('testing exporting with viame CSV and proper order', async () => {
     const path = '/home/test.json';
@@ -195,6 +220,7 @@ describe('VIAME serialize testing', () => {
   });
 });
 
+
 afterAll(() => {
   mockfs.restore();
 });

client/platform/desktop/backend/serializers/viame.ts

@@ -20,11 +20,11 @@ import Track, {
 } from 'vue-media-annotator/track';
 
 const CommentRegex = /^\s*#/g;
-const HeadRegex = /^\(kp\) head ([0-9]+\.*[0-9]*) ([0-9]+\.*[0-9]*)/g;
-const TailRegex = /^\(kp\) tail ([0-9]+\.*[0-9]*) ([0-9]+\.*[0-9]*)/g;
+const HeadRegex = /^\(kp\) head (-?[0-9]+\.*-?[0-9]*) (-?[0-9]+\.*-?[0-9]*)/g;
+const TailRegex = /^\(kp\) tail (-?[0-9]+\.*-?[0-9]*) (-?[0-9]+\.*-?[0-9]*)/g;
 const AttrRegex = /^\(atr\) (.*?)\s(.+)/g;
 const TrackAttrRegex = /^\(trk-atr\) (.*?)\s(.+)/g;
-const PolyRegex = /^(\(poly\)) ((?:[0-9]+\.*[0-9]*\s*)+)/g;
+const PolyRegex = /^(\(poly\)) ((?:-?[0-9]+\.*-?[0-9]*\s*)+)/g;
 const FpsRegex = /fps:\s*(\d+(\.\d+)?)/ig;
 const AtrToken = '(atr)';
 const TrackAtrToken = '(trk-atr)';
@@ -220,8 +220,10 @@ function _parseFeature(row: string[]) {
   const feature: Feature = {
     frame: rowInfo.frame,
     bounds: rowInfo.bounds,
-    fishLength: rowInfo.fishLength,
   };
+  if (rowInfo.fishLength !== -1) {
+    feature.fishLength = rowInfo.fishLength;
+  }
   if (rowData.attributes) {
     feature.attributes = rowData.attributes;
   }
@@ -286,7 +288,6 @@ async function parse(input: Readable, imageMap?: Map<string, number>): Promise<A
               begin: rowInfo.frame,
               end: rowInfo.frame,
               trackId: rowInfo.trackId,
-              meta: {},
               attributes: {},
               confidencePairs: [],
               features: [],

client/src/track.ts

@@ -36,7 +36,7 @@ export interface Feature {
 /** TrackData is the json schema for Track transport */
 export interface TrackData {
   trackId: TrackId;
-  meta: StringKeyObject;
+  meta?: StringKeyObject;
   attributes: StringKeyObject;
   confidencePairs: Array<ConfidencePair>;
   features: Array<Feature>;

server/dive_utils/models.py

@@ -46,8 +46,8 @@ class Feature(BaseModel):
     head: Optional[Tuple[float, float]] = None
     tail: Optional[Tuple[float, float]] = None
     fishLength: Optional[float] = None
-    interpolate: Optional[bool] = False
-    keyframe: Optional[bool] = True
+    interpolate: Optional[bool] = None
+    keyframe: Optional[bool] = None
 
 
 class Track(BaseModel):
@@ -57,6 +57,7 @@ class Track(BaseModel):
     features: List[Feature] = Field(default_factory=lambda: [])
     confidencePairs: List[Tuple[str, float]] = Field(default_factory=lambda: [])
     attributes: Dict[str, Any] = Field(default_factory=lambda: {})
+    meta: Optional[Dict[str, Any]]
 
     @validator('features')
     @classmethod

server/dive_utils/serializers/viame.py

@@ -118,14 +118,14 @@ def _parse_row(row: List[str]) -> Tuple[Dict, Dict, Dict, List]:
 
     for j in range(start, len(row)):
         # (kp) head x y
-        head_regex = re.match(r"^\(kp\) head ([0-9]+\.*[0-9]*) ([0-9]+\.*[0-9]*)", row[j])
+        head_regex = re.match(r"^\(kp\) head (-?[0-9]+\.*-?[0-9]*) (-?[0-9]+\.*-?[0-9]*)", row[j])
         if head_regex:
             point = [float(head_regex[1]), float(head_regex[2])]
             head_tail.append(point)
             create_geoJSONFeature(features, 'Point', point, 'head')
 
         # (kp) tail x y
-        tail_regex = re.match(r"^\(kp\) tail ([0-9]+\.*[0-9]*) ([0-9]+\.*[0-9]*)", row[j])
+        tail_regex = re.match(r"^\(kp\) tail (-?[0-9]+\.*-?[0-9]*) (-?[0-9]+\.*-?[0-9]*)", row[j])
         if tail_regex:
             point = [float(tail_regex[1]), float(tail_regex[2])]
             head_tail.append(point)
@@ -142,7 +142,7 @@ def _parse_row(row: List[str]) -> Tuple[Dict, Dict, Dict, List]:
             track_attributes[trk_regex[1]] = _deduceType(trk_regex[2])
 
         # (poly) x1 y1 x2 y2 ...
-        poly_regex = re.match(r"^(\(poly\)) ((?:[0-9]+\.*[0-9]*\s*)+)", row[j])
+        poly_regex = re.match(r"^(\(poly\)) ((?:-?[0-9]+\.*-?[0-9]*\s*)+)", row[j])
         if poly_regex:
             temp = [float(x) for x in poly_regex[2].split()]
             coords = list(zip(temp[::2], temp[1::2]))

server/scripts/generateLargeDataset.py

@@ -87,7 +87,6 @@ def create_track_json(
                 frame = start_frame + frame
                 feature = {
                     "frame": frame,
-                    "keyframe": True,
                     "bounds": [0, 0, width, height],
                 }
                 track_obj["begin"] = min(track_obj["begin"], frame)