Feature/contour speed optimizations

dataquality/integrations/cv/torch/semantic_segmentation.py

@@ -1,4 +1,6 @@
+import json
 import os
+from tempfile import NamedTemporaryFile
 from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 import numpy as np
@@ -8,9 +10,11 @@
 from torch.utils.data import DataLoader
 
 import dataquality as dq
+from dataquality import config
 from dataquality.analytics import Analytics
 from dataquality.clients.api import ApiClient
 from dataquality.clients.objectstore import ObjectStore
+from dataquality.core._config import GALILEO_DEFAULT_RESULT_BUCKET_NAME
 from dataquality.exceptions import GalileoException
 from dataquality.integrations.torch import TorchLogger, unwatch
 from dataquality.loggers.model_logger.semantic_segmentation import (
@@ -27,6 +31,7 @@
     fill_confident_counts,
 )
 from dataquality.utils.semantic_segmentation.utils import mask_to_boundary
+from dataquality.utils.thread_pool import ThreadPoolManager, lock
 from dataquality.utils.torch import ModelHookManager, store_batch_indices
 
 a = Analytics(ApiClient, dq.config)  # type: ignore
@@ -37,7 +42,7 @@
 # Heuristic used to calculate Likely Mislabeled for Semantic Segmentation
 # A larger queue size corresponds to a more accurate estimate of LM.
 # We keep a queue size to overcome memory issues with large SemSeg datasets.
-LIKELY_MISLABELED_QUEUE_SIZE = 100
+LIKELY_MISLABELED_QUEUE_SIZE = 1000
 
 
 class SemanticTorchLogger(TorchLogger):
@@ -372,6 +377,35 @@ def _on_step_end(self) -> None:
             )
             logger.log()
 
+    def upload_contours_split(self, split: str) -> None:
+        """Uploads all contours for a given split to minio
+
+        Args:
+            split (str): split name
+        """
+        model_logger = dq.get_model_logger()
+        project_path = f"{model_logger.LOG_FILE_DIR}/{config.current_project_id}"
+        local_contour_path = f"{project_path}/{config.current_run_id}/{split}/contours"
+
+        files = os.listdir(local_contour_path)
+        all_contours = {}
+        for file in files:
+            with open(f"{local_contour_path}/{file}") as f:
+                contours = json.load(f)
+                # uuid is the key for each contour from the polygon schema
+                all_contours[file.replace(".json", "")] = contours
+        with NamedTemporaryFile(mode="w+", delete=False) as temp_file:
+            json.dump(all_contours, temp_file)
+
+        obj_name = f"{model_logger.proj_run}/{split}/contours/contours.json"
+        object_store.create_object(
+            object_name=obj_name,
+            file_path=temp_file.name,
+            content_type="application/json",
+            progress=False,
+            bucket_name=GALILEO_DEFAULT_RESULT_BUCKET_NAME,
+        )
+
     def finish(self) -> None:
         # call to eval to make sure we are not in train mode for batch norm
         # in batch norm with 1 example can get an error if we are in train mode
@@ -384,6 +418,11 @@ def finish(self) -> None:
             dq.set_epoch_and_split(0, Split[split])
             with torch.no_grad():
                 self.run_one_epoch(dataloader, device)
+            split = self.logger_config.cur_split.lower()  # type: ignore
+            # Ensure all contours are written to disk before starting upload
+            ThreadPoolManager.wait_for_threads()
+            with lock:
+                self.upload_contours_split(split)
         self.model.train()
 
     def run_one_epoch(self, dataloader: DataLoader, device: torch.device) -> None:
@@ -501,6 +540,9 @@ def watch(
         assert key in Split.__members__, GalileoException(
             f"Dataloader key {key} is not a valid split"
         )
+        current_split = Split[key].value
+        logger_config = dq.get_model_logger().logger_config
+        setattr(logger_config, f"{current_split}_logged", True)
         assert isinstance(dataloader, DataLoader), GalileoException(
             "Invalid dataloader. Must be a pytorch dataloader"
             "from torch.utils.data import DataLoader..."

dataquality/loggers/model_logger/semantic_segmentation.py

@@ -4,6 +4,8 @@
 import torch
 
 import dataquality as dq
+from dataquality import config
+from dataquality.clients.objectstore import ObjectStore
 from dataquality.loggers.logger_config.semantic_segmentation import (
     SemanticSegmentationLoggerConfig,
     semantic_segmentation_logger_config,
@@ -26,9 +28,11 @@
 )
 from dataquality.utils.semantic_segmentation.polygons import (
     find_polygons_batch,
-    upload_polygon_contours,
+    write_polygon_contours_to_disk,
 )
 
+object_store = ObjectStore()
+
 
 class SemanticSegmentationModelLogger(BaseGalileoModelLogger):
     __logger_name__ = "semantic_segmentation"
@@ -106,8 +110,14 @@ def dep_path(self) -> str:
         return f"{self.proj_run}/{self.split_name_path}/dep"
 
     @property
-    def contours_path(self) -> str:
-        return f"{self.proj_run}/{self.split_name_path}/contours"
+    def local_proj_run_path(self) -> str:
+        return (
+            f"{self.LOG_FILE_DIR}/{config.current_project_id}/{config.current_run_id}"
+        )
+
+    @property
+    def local_contours_path(self) -> str:
+        return f"{self.local_proj_run_path}/{self.split_name_path}/contours"
 
     def get_polygon_data(
         self,
@@ -160,9 +170,8 @@ def get_polygon_data(
                 mislabeled_class_pcts.append(
                     polygon.cls_error_data.mislabeled_class_pct
                 )
-                upload_polygon_contours(polygon, self.contours_path)
+                write_polygon_contours_to_disk(polygon, self.local_contours_path)
                 polygon_ids.append(polygon.uuid)
-
         polygon_data = {
             "polygon_uuid": polygon_ids,
             "image_id": image_ids,

dataquality/utils/semantic_segmentation/polygons.py

@@ -1,6 +1,6 @@
 import json
+import os
 from collections import defaultdict
-from tempfile import NamedTemporaryFile
 from typing import List, Tuple
 from uuid import uuid4
 
@@ -9,7 +9,6 @@
 import torch
 
 from dataquality.clients.objectstore import ObjectStore
-from dataquality.core._config import GALILEO_DEFAULT_RESULT_BUCKET_NAME
 from dataquality.schemas.ml import ClassType
 from dataquality.schemas.semantic_segmentation import Contour, Pixel, Polygon
 
@@ -146,26 +145,21 @@ def draw_polygon(polygon: Polygon, shape: Tuple[int, ...]) -> np.ndarray:
     )
 
 
-def upload_polygon_contours(
+def write_polygon_contours_to_disk(
     polygon: Polygon,
     prefix: str,
 ) -> None:
-    """Uploads a Polygon's contours to the cloud
+    """Writes polygons to disk in json format
 
     Args:
         polygon(Polygon): A Polygon object
         prefix(str): prefix of the object name in storage
-            - /proj-id/run-id/training/contours/1.json
+            \"{proj_run_path}/{split_name_path}/contours"
     """
-    obj_name = f"{prefix}/{polygon.uuid}.json"
 
-    with NamedTemporaryFile(mode="w+", delete=False) as f:
-        json.dump(polygon.contours_json, f)
+    os.makedirs(prefix, exist_ok=True)
+    local_path = f"{prefix}/{polygon.uuid}.json"
 
-    object_store.create_object(
-        object_name=obj_name,
-        file_path=f.name,
-        content_type="application/json",
-        progress=False,
-        bucket_name=GALILEO_DEFAULT_RESULT_BUCKET_NAME,
-    )
+    with open(local_path, "w") as f:
+        json.dump(polygon.contours_json, f)
+    f.close()