Additive import

client/dive-common/apispec.ts

@@ -152,7 +152,8 @@ interface Api {
   // Non-Endpoint shared functions
   openFromDisk(datasetType: DatasetType | 'calibration' | 'annotation' | 'text' | 'zip', directory?: boolean):
     Promise<{canceled?: boolean; filePaths: string[]; fileList?: File[]; root?: string}>;
-  importAnnotationFile(id: string, path: string, file?: File): Promise<boolean>;
+  importAnnotationFile(id: string, path: string, file?: File,
+    additive?: boolean, additivePrepend?: string): Promise<boolean>;
 }
 const ApiSymbol = Symbol('api');
 

client/dive-common/components/ImportAnnotations.vue

@@ -35,6 +35,8 @@ export default defineComponent({
     const { prompt } = usePrompt();
     const processing = ref(false);
     const menuOpen = ref(false);
+    const additive = ref(false);
+    const additivePrepend = ref('');
     const openUpload = async () => {
       try {
         const ret = await openFromDisk('annotation');
@@ -44,9 +46,21 @@ export default defineComponent({
           let importFile = false;
           processing.value = true;
           if (ret.fileList?.length) {
-            importFile = await importAnnotationFile(props.datasetId, path, ret.fileList[0]);
+            importFile = await importAnnotationFile(
+              props.datasetId,
+              path,
+              ret.fileList[0],
+              additive.value,
+              additivePrepend.value,
+            );
           } else {
-            importFile = await importAnnotationFile(props.datasetId, path);
+            importFile = await importAnnotationFile(
+              props.datasetId,
+              path,
+              undefined,
+              additive.value,
+              additivePrepend.value,
+            );
           }
 
           if (importFile) {
@@ -68,6 +82,8 @@ export default defineComponent({
       openUpload,
       processing,
       menuOpen,
+      additive,
+      additivePrepend,
     };
   },
 });
@@ -133,16 +149,43 @@ export default defineComponent({
             target="_blank"
           >Data Format Documentation</a>
         </v-card-text>
-        <v-card-actions>
-          <v-btn
-            depressed
-            block
-            :disabled="!datasetId || processing"
-            @click="openUpload"
-          >
-            Import
-          </v-btn>
-        </v-card-actions>
+        <v-container>
+          <v-col>
+            <v-row>
+              <v-btn
+                depressed
+                block
+                :disabled="!datasetId || processing"
+                @click="openUpload"
+              >
+                Import
+              </v-btn>
+            </v-row>
+            <v-row>
+              <v-checkbox
+                :input-value="!additive"
+                label="Overwrite"
+                @change="additive = !$event"
+              />
+            </v-row>
+            <div v-if="additive">
+              <div
+                v-if="additive"
+                class="pa-2"
+              >
+                Imported annotations will be added to existing annotations.
+              </div>
+              <div class="pa-2">
+                The types can be modified to have a prepended value for comparison.
+              </div>
+              <v-text-field
+                v-model="additivePrepend"
+                label="Prepend to types"
+                clearable
+              />
+            </div>
+          </v-col>
+        </v-container>
       </v-card>
     </template>
   </v-menu>

client/platform/desktop/backend/ipcService.ts

@@ -95,8 +95,10 @@ export default function register() {
     return ret;
   });
 
-  ipcMain.handle('import-annotation', async (event, { id, path }: { id: string; path: string }) => {
-    const ret = await common.dataFileImport(settings.get(), id, path);
+  ipcMain.handle('import-annotation', async (event, {
+    id, path, additive, additivePrepend,
+  }: { id: string; path: string; additive: boolean; additivePrepend: string }) => {
+    const ret = await common.dataFileImport(settings.get(), id, path, additive, additivePrepend);
     return ret;
   });
 

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

@@ -548,6 +548,8 @@ async function _ingestFilePath(
   datasetId: string,
   path: string,
   imageMap?: Map<string, number>,
+  additive = false,
+  additivePrepend = '',
 ): Promise<(DatasetMetaMutable & { fps?: number }) | null> {
   if (!fs.existsSync(path)) {
     return null;
@@ -588,6 +590,32 @@ async function _ingestFilePath(
   } else if (YAMLFileName.test(path)) {
     annotations = await kpf.parse([path]);
   }
+  // If it is additive we need to re-ID tracks and do additive prepends
+  if (additive) {
+    // Load previous data
+    const existing = await loadDetections(settings, datasetId);
+    const { tracks } = existing;
+    let maxTrackId = -1;
+    Object.values(tracks).forEach((item) => {
+      maxTrackId = Math.max(item.id, maxTrackId);
+    });
+    maxTrackId += 1;
+    const newTracks = Object.values(annotations.tracks);
+    for (let i = 0; i < newTracks.length; i += 1) {
+      const newTrack = newTracks[i];
+      newTrack.id += maxTrackId;
+      if (additivePrepend !== '') {
+        const { confidencePairs } = newTrack;
+        for (let k = 0; k < confidencePairs.length; k += 1) {
+          confidencePairs[k] = [`${additivePrepend}_${confidencePairs[k][0]}`, confidencePairs[k][1]];
+        }
+        newTrack.confidencePairs = confidencePairs;
+      }
+      existing.tracks[newTrack.id] = newTrack;
+    }
+    annotations.tracks = existing.tracks;
+  }
+
   if (Object.values(annotations.tracks).length || Object.values(annotations.groups).length) {
     const processed = processTrackAttributes(Object.values(annotations.tracks));
     meta.attributes = processed.attributes;
@@ -618,6 +646,8 @@ async function ingestDataFiles(
   absPaths: string[],
   multiCamResults?: Record<string, string>,
   imageMap?: Map<string, number>,
+  additive = false,
+  additivePrepend = '',
 ): Promise<{
   processedFiles: string[];
   meta: DatasetMetaMutable & { fps?: number };
@@ -628,7 +658,9 @@ async function ingestDataFiles(
   for (let i = 0; i < absPaths.length; i += 1) {
     const path = absPaths[i];
     // eslint-disable-next-line no-await-in-loop
-    const newMeta = await _ingestFilePath(settings, datasetId, path, imageMap);
+    const newMeta = await _ingestFilePath(
+      settings, datasetId, path, imageMap, additive, additivePrepend,
+    );
     if (newMeta !== null) {
       merge(meta, newMeta);
       processedFiles.push(path);
@@ -876,11 +908,12 @@ function validImageNamesMap(jsonMeta: JsonMeta) {
   return undefined;
 }
 
-async function dataFileImport(settings: Settings, id: string, path: string) {
+async function dataFileImport(settings: Settings, id: string, path: string, additive = false, additivePrepend = '') {
   const projectDirData = await getValidatedProjectDir(settings, id);
   const jsonMeta = await loadJsonMetadata(projectDirData.metaFileAbsPath);
   const result = await ingestDataFiles(
     settings, id, [path], undefined, validImageNamesMap(jsonMeta),
+    additive, additivePrepend,
   );
   merge(jsonMeta, result.meta);
   await _saveAsJson(npath.join(projectDirData.basePath, JsonMetaFileName), jsonMeta);

client/platform/desktop/frontend/api.ts

@@ -131,8 +131,11 @@ function importMultiCam(args: MultiCamImportArgs):
   return ipcRenderer.invoke('import-multicam-media', { args });
 }
 
-function importAnnotationFile(id: string, path: string): Promise<boolean> {
-  return ipcRenderer.invoke('import-annotation', { id, path });
+// eslint-disable-next-line @typescript-eslint/no-unused-vars
+function importAnnotationFile(id: string, path: string, _htmlFile = undefined, additive = false, additivePrepend = ''): Promise<boolean> {
+  return ipcRenderer.invoke('import-annotation', {
+    id, path, additive, additivePrepend,
+  });
 }
 
 function finalizeImport(args: DesktopMediaImportResponse): Promise<JsonMeta> {

client/platform/web-girder/api/dataset.service.ts

@@ -86,7 +86,7 @@ function makeViameFolder({
   );
 }
 
-async function importAnnotationFile(parentId: string, path: string, file?: HTMLFile) {
+async function importAnnotationFile(parentId: string, path: string, file?: HTMLFile, additive = false, additivePrepend = '') {
   if (file === undefined) {
     return false;
   }
@@ -108,7 +108,7 @@ async function importAnnotationFile(parentId: string, path: string, file?: HTMLF
       headers: { 'Content-Type': 'application/octet-stream' },
     });
     if (uploadResponse.status === 200) {
-      const final = await postProcess(parentId, true);
+      const final = await postProcess(parentId, true, false, additive, additivePrepend);
       return final.status === 200;
     }
   }

client/platform/web-girder/api/rpc.service.ts

@@ -1,9 +1,11 @@
 import girderRest from 'platform/web-girder/plugins/girder';
 import { Pipe } from 'dive-common/apispec';
 
-function postProcess(folderId: string, skipJobs = false, skipTranscoding = false) {
+function postProcess(folderId: string, skipJobs = false, skipTranscoding = false, additive = false, additivePrepend = '') {
   return girderRest.post(`dive_rpc/postprocess/${folderId}`, null, {
-    params: { skipJobs, skipTranscoding },
+    params: {
+      skipJobs, skipTranscoding, additive, additivePrepend,
+    },
   });
 }
 

server/dive_server/crud_annotation.py

@@ -304,6 +304,36 @@ def get_annotations(dataset: types.GirderModel, revision: Optional[int] = None):
     return annotations
 
 
+def add_annotations(
+    dataset: types.GirderModel, new_tracks: dict, prepend='', revision: Optional[int] = None
+):
+    tracks = TrackItem().list(dataset, revision=revision)
+    annotations: types.DIVEAnnotationSchema = {
+        'tracks': {},
+        'groups': {},
+        'version': constants.AnnotationsCurrentVersion,
+    }
+    max_track_id = -1
+    for t in tracks:
+        serialized = models.Track(**t).dict(exclude_none=True)
+        annotations['tracks'][serialized['id']] = serialized
+        max_track_id = max(max_track_id, serialized['id'])
+    # Now add in the new tracks while renaming them
+    for key in new_tracks.keys():
+        new_id = int(key) + max_track_id + 1
+        new_id_str = str(new_id)
+        annotations['tracks'][new_id_str] = new_tracks[key]
+        annotations['tracks'][new_id_str]['id'] = new_id
+        if prepend != '':
+            track = annotations['tracks'][new_id_str]
+            newPairs = []
+            for confidencePairs in track['confidencePairs']:
+                newPairs.append([f'{prepend}_{confidencePairs[0]}', confidencePairs[1]])
+            annotations['tracks'][new_id_str]['confidencePairs'] = newPairs
+
+    return annotations['tracks']
+
+
 def get_labels(user: types.GirderUserModel, published=False, shared=False):
     """Find all the labels in all datasets belonging to the user"""
     accessLevel = AccessType.WRITE

server/dive_server/crud_rpc.py

@@ -348,7 +348,9 @@ def _get_data_by_type(
     return None
 
 
-def process_items(folder: types.GirderModel, user: types.GirderUserModel):
+def process_items(
+    folder: types.GirderModel, user: types.GirderUserModel, additive=False, additivePrepend=''
+):
     """
     Discover unprocessed items in a dataset and process them by type in order of creation
     """
@@ -364,7 +366,10 @@ def process_items(folder: types.GirderModel, user: types.GirderUserModel):
         # Processing order: oldest to newest
         sort=[("created", pymongo.ASCENDING)],
     )
-    auxiliary = crud.get_or_create_auxiliary_folder(folder, user)
+    auxiliary = crud.get_or_create_auxiliary_folder(
+        folder,
+        user,
+    )
     for item in unprocessed_items:
         file: Optional[types.GirderModel] = next(Item().childFiles(item), None)
         if file is None:
@@ -386,10 +391,16 @@ def process_items(folder: types.GirderModel, user: types.GirderUserModel):
         item['meta'][constants.ProcessedMarker] = True
         Item().move(item, auxiliary)
         if results['annotations']:
+            updated_tracks = results['annotations']['tracks'].values()
+            if additive:  # get annotations and add them to the end
+                tracks = crud_annotation.add_annotations(
+                    folder, results['annotations']['tracks'], additivePrepend
+                )
+                updated_tracks = tracks.values()
             crud_annotation.save_annotations(
                 folder,
                 user,
-                upsert_tracks=results['annotations']['tracks'].values(),
+                upsert_tracks=updated_tracks,
                 upsert_groups=results['annotations']['groups'].values(),
                 overwrite=True,
                 description=f'Import {results["type"].name} from {file["name"]}',
@@ -401,7 +412,12 @@ def process_items(folder: types.GirderModel, user: types.GirderUserModel):
 
 
 def postprocess(
-    user: types.GirderUserModel, dsFolder: types.GirderModel, skipJobs: bool, skipTranscoding=False
+    user: types.GirderUserModel,
+    dsFolder: types.GirderModel,
+    skipJobs: bool,
+    skipTranscoding=False,
+    additive=False,
+    additivePrepend='',
 ) -> types.GirderModel:
     """
     Post-processing to be run after media/annotation import
@@ -512,5 +528,5 @@ def postprocess(
 
         Folder().save(dsFolder)
 
-    process_items(dsFolder, user)
+    process_items(dsFolder, user, additive, additivePrepend)
     return dsFolder

server/dive_server/views_rpc.py

@@ -103,6 +103,24 @@ def run_training(self, body, pipelineName, config, annotatedFramesOnly):
             default=False,
             required=False,
         )
+        .param(
+            "additive",
+            "Whether to add new annotations to existing ones",
+            paramType="formData",
+            dataType="boolean",
+            default=False,
+            required=False,
+        )
+        .param(
+            "additivePrepend",
+            "When using additive the prepend to types: 'prepend_type'",
+            paramType="formData",
+            dataType="string",
+            default='',
+            required=False,
+        )
     )
-    def postprocess(self, folder, skipJobs, skipTranscoding):
-        return crud_rpc.postprocess(self.getCurrentUser(), folder, skipJobs, skipTranscoding)
+    def postprocess(self, folder, skipJobs, skipTranscoding, additive, additivePrepend):
+        return crud_rpc.postprocess(
+            self.getCurrentUser(), folder, skipJobs, skipTranscoding, additive, additivePrepend
+        )

server/dive_tasks/tasks.py

@@ -426,7 +426,8 @@ def convert_video(
         jsoninfo = json.loads(stdout)
         videostream = list(filter(lambda x: x["codec_type"] == "video", jsoninfo["streams"]))
         if len(videostream) != 1:
-            raise Exception('Expected 1 video stream, found {}'.format(len(videostream)))
+            print('Expected 1 video stream, found {}'.format(len(videostream)))
+            print('Using first Video Stream found')
 
         # Extract average framerate
         avgFpsString: str = videostream[0]["avg_frame_rate"]