Import mask merge (#317)

* restructure folder output for maskGenerate for ease of creating masks.zip

* logic paramemters naming and remove additive

* front-end support for mask logic options

* front-end support for mask logic options

* increment version

Author: BryonLewis

client/dive-common/apispec.ts

@@ -170,7 +170,7 @@ interface Api {
   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,
-      additive?: boolean, additivePrepend?: string): Promise<boolean>;
+      additive?: boolean, additivePrepend?: string, maskLogic?: 'replace' | 'merge'): Promise<boolean>;
   }
 const ApiSymbol = Symbol('api');
 

client/dive-common/components/ImportAnnotations.vue

@@ -1,5 +1,5 @@
 <script lang="ts">
-import { defineComponent, ref } from 'vue';
+import { defineComponent, Ref, ref } from 'vue';
 import { useApi } from 'dive-common/apispec';
 import { usePrompt } from 'dive-common/vue-utilities/prompt-service';
 import { useHandler } from 'vue-media-annotator/provides';
@@ -37,6 +37,8 @@ export default defineComponent({
     const menuOpen = ref(false);
     const additive = ref(false);
     const additivePrepend = ref('');
+    const maskActions = ref(['replace', 'merge']);
+    const maskActionSelection: Ref<'replace' | 'merge'> = ref('merge');
     const openUpload = async () => {
       try {
         const ret = await openFromDisk('annotation');
@@ -52,6 +54,7 @@ export default defineComponent({
               ret.fileList[0],
               additive.value,
               additivePrepend.value,
+              maskActionSelection.value,
             );
           } else {
             importFile = await importAnnotationFile(
@@ -60,6 +63,7 @@ export default defineComponent({
               undefined,
               additive.value,
               additivePrepend.value,
+              maskActionSelection.value,
             );
           }
 
@@ -91,6 +95,8 @@ export default defineComponent({
       menuOpen,
       additive,
       additivePrepend,
+      maskActionSelection,
+      maskActions,
 
     };
   },
@@ -183,6 +189,14 @@ export default defineComponent({
                 clearable
               />
             </div>
+            <v-row>
+              <v-select
+                v-model="maskActionSelection"
+                :items="maskActions"
+                label="Mask Import Action"
+                hide-details
+              />
+            </v-row>
           </v-col>
         </v-container>
       </v-card>

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "dive-dsa",
-  "version": "1.11.16",
+  "version": "1.11.17",
   "author": {
     "name": "Kitware, Inc.",
     "email": "Bryon.Lewis@kitware.com"

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

@@ -112,7 +112,7 @@ function makeViameFolder({
   );
 }
 
-async function importAnnotationFile(parentId: string, path: string, file?: HTMLFile, additive = false, additivePrepend = '') {
+async function importAnnotationFile(parentId: string, path: string, file?: HTMLFile, additive = false, additivePrepend = '', maskLogic: 'replace' | 'merge' = 'merge') {
   if (file === undefined) {
     return false;
   }
@@ -138,7 +138,7 @@ async function importAnnotationFile(parentId: string, path: string, file?: HTMLF
       if (path.endsWith('.json') || path.endsWith('.csv')) {
         skipJobs = true;
       }
-      const final = await postProcess(parentId, skipJobs, false, additive, additivePrepend);
+      const final = await postProcess(parentId, skipJobs, false, additive, additivePrepend, maskLogic);
       return final.status === 200;
     }
   }

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

@@ -1,10 +1,10 @@
 import girderRest from 'platform/web-girder/plugins/girder';
 import type { GirderJob } from '@girder/components/src';
 
-function postProcess(folderId: string, skipJobs = false, skipTranscoding = false, additive = false, additivePrepend = '') {
+function postProcess(folderId: string, skipJobs = false, skipTranscoding = false, additive = false, additivePrepend = '', maskLogic: 'replace' | 'merge' = 'merge') {
   return girderRest.post(`dive_rpc/postprocess/${folderId}`, null, {
     params: {
-      skipJobs, skipTranscoding, additive, additivePrepend,
+      skipJobs, skipTranscoding, additive, additivePrepend, maskLogic,
     },
   });
 }

dive-dsa-slicer/example-docker-containers/SAM2Demo/SAM2Demo.py

@@ -359,11 +359,11 @@ def process_masks_folder(
         folderId: str,
         masks_path: Path,
         subfolder_name='masks',
-        logic: Literal['replace', 'additive', 'merge'] = 'merge'):
+        maskLogic: Literal['replace', 'merge'] = 'merge'):
     """
     Upload mask images and RLE_MASKS.json file (if available or generate an empty one).
     """
-    if logic == 'replace':
+    if maskLogic == 'replace':
         folders = list(gc.listFolder(folderId, 'folder', name=subfolder_name))
         if len(folders) > 0:
             for folder in folders:
@@ -400,7 +400,7 @@ def process_masks_folder(
         track_id = track_dir.name
         if not has_rle_mask:
             rle_masks_json[str(track_id)] = {}
-        if logic == 'replace':
+        if maskLogic == 'replace':
             # Check if the track already exists
             track_folders = list(gc.listFolder(masks_folder['_id'], 'folder', name=track_id))
             if len(track_folders) > 0:
@@ -412,7 +412,7 @@ def process_masks_folder(
 
         for image_path in track_dir.glob("*.png"):
             frame_number = image_path.stem
-            if logic == 'merge':
+            if maskLogic == 'merge':
                 # Check if the image already exists
                 existing_items = list(gc.listItem(track_folder['_id'], name=image_path.name))
                 if len(existing_items) > 0:
@@ -469,15 +469,15 @@ def process_masks_folder(
 
     track_json_path = masks_path / 'TrackJSON.json'
     if track_json_path.exists():
-        # Process the  TrackJSON.json file based on the logic parameter
-        if logic == 'replace':
+        # Process the  TrackJSON.json file based on the maskLogic parameter
+        if maskLogic == 'replace':
             # Replace the existing TrackJSON.json file
             gc.uploadFileToFolder(
                 folderId,
                 str(track_json_path),
             )
             gc.post(f'dive_rpc/postprocess/{folderId}', data={"skipJobs": True})
-        if logic in ['additive', 'merge']:
+        if maskLogic == 'merge':
             with open(track_json_path, 'r') as f:
                 json_data = json.load(f)
             # Get the existing Tracks in the system

scripts/masks/maskTrackGenerator.py

@@ -1,3 +1,15 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = [
+#     "click",
+#     "girder-client",
+#     "numpy",
+#     "pillow",
+#     "pycocotools",
+#     "scikit-image",
+#     "setuptools"
+# ]
+# ///
 import json
 import random
 import numpy as np
@@ -19,9 +31,9 @@
 SHAPE_SIZE = (100, 100)  # width, height of shape
 
 CONFIG = [
-    {'track_number': 0, 'num_frames': 500, 'mask_type': 'pentagon', 'motion_type': 'circle'},
-    {'track_number': 1, 'num_frames': 300, 'mask_type': 'circle', 'motion_type': 'bounce'},
-    {'track_number': 2, 'num_frames': 200, 'mask_type': 'rectangle', 'motion_type': 'circle'},
+    {'track_number': 2, 'num_frames': 500, 'mask_type': 'pentagon', 'motion_type': 'circle'},
+    {'track_number': 3, 'num_frames': 300, 'mask_type': 'circle', 'motion_type': 'bounce'},
+    {'track_number': 4, 'num_frames': 200, 'mask_type': 'rectangle', 'motion_type': 'circle'},
 ]
 
 
@@ -99,10 +111,10 @@ def bouncing_motion(num_frames, img_size, shape_size):
 @click.option('--upload', is_flag=True, help='Upload generated masks to Girder.')
 def generate_tracks(upload):
     output_masks_exist = os.path.exists('outputMasks')
-    rle_json_exist = os.path.exists('RLEMask.json')
+    rle_json_exist = os.path.exists('RLE_MASKS.json')
 
     if output_masks_exist and rle_json_exist:
-        print("Found existing outputMasks folder and RLEMask.json. Skipping generation.")
+        print("Found existing outputMasks folder and RLE_MASKS.json. Skipping generation.")
     else:
         print("Generating new masks and JSON files...")
 
@@ -173,7 +185,7 @@ def generate_tracks(upload):
                 }
 
                 if OUTPUT_MASKS:
-                    output_dir = os.path.join('outputMasks', f'{track_id}')
+                    output_dir = os.path.join('outputMasks/masks', f'{track_id}')
                     os.makedirs(output_dir, exist_ok=True)
 
                     alpha_channel = (mask > 0).astype(np.uint8) * 255
@@ -187,18 +199,22 @@ def generate_tracks(upload):
 
             track_data['tracks'][str(track_id)] = track
 
-        with open('trackJSON.json', 'w') as f:
+        with open('TrackJSON.json', 'w') as f:
             json.dump(track_data, f, indent=2)
 
-        with open('RLEMask.json', 'w') as f:
-            json.dump(mask_data, f, indent=2)
 
         with open('RLE_MASKS.json', 'w') as f:
             json.dump(rle_masks_json, f, indent=2)
 
-        print('Generated trackJSON.json, RLEMask.json, RLE_MASKS.json', end='')
+        print('Generated TrackJSON.json, RLE_MASKS.json', end='')
         if OUTPUT_MASKS:
             print(', and PNG masks in outputMasks/')
+            with open('outputMasks/masks/TrackJSON.json', 'w') as f:
+                json.dump(track_data, f, indent=2)
+
+            with open('outputMasks/masks/RLE_MASKS.json', 'w') as f:
+                json.dump(rle_masks_json, f, indent=2)
+
         else:
             print('.')
 

server/dive_server/crud_rpc.py

@@ -201,7 +201,7 @@ def postprocess(
     skipTranscoding=False,
     additive=False,
     additivePrepend='',
-    logic='replace',
+    maskLogic='merge',
 ) -> dict:
     """
     Post-processing to be run after media/annotation import
@@ -251,7 +251,7 @@ def postprocess(
                     itemId=str(item["_id"]),
                     user_id=str(user["_id"]),
                     user_login=str(user["login"]),
-                    logic=logic,
+                    maskLogic=maskLogic,
                     girder_job_title=f"Extracting {item['_id']} to folder {str(dsFolder['_id'])}",
                     girder_client_token=str(token["_id"]),
                     girder_job_type="private" if job_is_private else "convert",

server/dive_server/views_rpc.py

@@ -84,26 +84,25 @@ def __init__(self, resourceName):
             required=False,
         )
         .param(
-            "logic",
+            "maskLogic",
             "Logic to use when combining annotations using Zip files (specifically masks.zip).   \
             'replace' will replace existing annotations with new ones.  \
-            'merge' will combine existing and new annotations.  \
-            'additive' will add new annotations to existing ones.",
+            'merge' will combine existing and new annotations.",
             paramType="formData",
             dataType="string",
             default='merge',
             required=False,
         )
     )
-    def postprocess(self, folder, skipJobs, skipTranscoding, additive, additivePrepend, logic):
+    def postprocess(self, folder, skipJobs, skipTranscoding, additive, additivePrepend, maskLogic):
         result = crud_rpc.postprocess(
             self.getCurrentUser(),
             folder,
             skipJobs,
             skipTranscoding,
             additive,
             additivePrepend,
-            logic,
+            maskLogic,
         )
         # Return the folder for backward compatibility, but also include job_ids
         return result

server/dive_tasks/sam_tasks.py

@@ -391,12 +391,12 @@ def process_masks_folder(
     folderId: str,
     masks_path: Path,
     subfolder_name='masks',
-    logic: Literal['replace', 'additive', 'merge'] = 'merge',
+    maskLogic: Literal['replace', 'merge'] = 'merge',
 ):
     """
     Upload mask images and RLE_MASKS.json file (if available or generate an empty one).
     """
-    if logic == 'replace':
+    if maskLogic == 'replace':
         folders = list(gc.listFolder(folderId, 'folder', name=subfolder_name))
         if len(folders) > 0:
             for folder in folders:
@@ -433,7 +433,7 @@ def process_masks_folder(
         track_id = track_dir.name
         if not has_rle_mask:
             rle_masks_json[str(track_id)] = {}
-        if logic == 'replace':
+        if maskLogic == 'replace':
             # Check if the track already exists
             track_folders = list(gc.listFolder(masks_folder['_id'], 'folder', name=track_id))
             if len(track_folders) > 0:
@@ -445,7 +445,7 @@ def process_masks_folder(
 
         for image_path in track_dir.glob("*.png"):
             frame_number = image_path.stem
-            if logic == 'merge':
+            if maskLogic == 'merge':
                 # Check if the image already exists
                 existing_items = list(gc.listItem(track_folder['_id'], name=image_path.name))
                 if len(existing_items) > 0:
@@ -506,14 +506,14 @@ def process_masks_folder(
     track_json_path = masks_path / 'TrackJSON.json'
     if track_json_path.exists():
         # Process the  TrackJSON.json file based on the logic parameter
-        if logic == 'replace':
+        if maskLogic == 'replace':
             # Replace the existing TrackJSON.json file
             gc.uploadFileToFolder(
                 folderId,
                 str(track_json_path),
             )
             gc.post(f'dive_rpc/postprocess/{folderId}', data={"skipJobs": True})
-        if logic in ['additive', 'merge']:
+        if maskLogic == 'merge':
             with open(track_json_path, 'r') as f:
                 json_data = json.load(f)
             # Get the existing Tracks in the system