Fix validation and test split not being reproducible (#218)

* Fix validation and test split not being reproducible

* Check-manifest fix

* Draft dataset split tests

* Simplify dummy dataset fixture

* Add dummy dataset directories fixture

* Add annotations file to fixture

* Create fixture as factory of dummy datasets

* Tests pass

* Make fixture factory of dataset dirs

* Expand test parametrisation

* Small edits to docstrings

* Move bbox_tensors_to_COCO_dict to utils

* Clarify comment

* Restore pre-commit config

* Rename generators

* Fix image ID default indexing (it is 1-based in VIA tool)

* Remove n=10 comment in the dummy dataset fixture

crabs/detector/datamodules.py

@@ -169,10 +169,12 @@ def _compute_splits(
             A tuple with the train, test and validation datasets
         """
 
-        # Optionally fix the generator for a reproducible split of data
-        generator = None
+        # Optionally fix the random number generators for reproducible
+        # splits of data
+        rng_train_split, rng_val_split = None, None
         if self.split_seed:
-            generator = torch.Generator().manual_seed(self.split_seed)
+            rng_train_split = torch.Generator().manual_seed(self.split_seed)
+            rng_val_split = torch.Generator().manual_seed(self.split_seed)
 
         # Create dataset (combining all datasets passed)
         full_dataset = CrabsCocoDetection(
@@ -189,7 +191,7 @@ def _compute_splits(
         train_dataset, test_val_dataset = random_split(
             full_dataset,
             [self.config["train_fraction"], 1 - self.config["train_fraction"]],
-            generator=generator,
+            generator=rng_train_split,
         )
 
         # Split test/val sets from the remainder
@@ -199,6 +201,7 @@ def _compute_splits(
                 1 - self.config["val_over_test_fraction"],
                 self.config["val_over_test_fraction"],
             ],
+            generator=rng_val_split,
         )
 
         return train_dataset, test_dataset, val_dataset
@@ -216,9 +219,9 @@ def setup(self, stage: str):
         Define the transforms for each split of the data and compute them.
         """
         # Assign transforms
+        self.train_transform = self._get_train_transform()
         # right now assuming validation and test get the same transforms
         test_and_val_transform = self._get_test_val_transform()
-        self.train_transform = self._get_train_transform()
         self.test_transform = test_and_val_transform
         self.val_transform = test_and_val_transform
 

crabs/detector/utils/detection.py

@@ -4,8 +4,9 @@
 import datetime
 import os
 from pathlib import Path
-from typing import Any
+from typing import Any, Optional
 
+import torch
 from lightning.pytorch.loggers import MLFlowLogger
 
 DEFAULT_ANNOTATIONS_FILENAME = "VIA_JSON_combined_coco_gen.json"
@@ -242,3 +243,75 @@ def slurm_logs_as_artifacts(logger: MLFlowLogger, slurm_job_id: str):
             logger.run_id,
             f"{log_filename}.{ext}",
         )
+
+
+def bbox_tensors_to_COCO_dict(
+    bbox_tensors: torch.Tensor, list_img_filenames: Optional[list] = None
+) -> dict:
+    """Convert list of bounding boxes as tensors to COCO-crab format.
+
+    Parameters
+    ----------
+    bbox_tensors : list[torch.Tensor]
+        List of tensors with bounding boxes for each image.
+        Each element of the list corresponds to an image, and each tensor in
+        the list contains the bounding boxes for that image. Each tensor is of
+        size (n, 4) where n is the number of bounding boxes in the image.
+        The 4 values in the second dimension are x_min, y_min, x_max, y_max.
+    list_img_filenames : list[str], optional
+        List of image filenames. If not provided, filenames are generated
+        as "frame_{i:04d}.png" where i is the 0-based index of the image in the
+        list of bounding boxes.
+
+    Returns
+    -------
+    dict
+        COCO format dictionary with bounding boxes.
+    """
+    # Create list of image filenames if not provided
+    if list_img_filenames is None:
+        list_img_filenames = [
+            f"frame_{i:04d}.png" for i in range(len(bbox_tensors))
+        ]
+
+    # Create list of dictionaries for images
+    list_images: list[dict] = []
+    for img_id, img_name in enumerate(list_img_filenames):
+        image_entry = {
+            "id": img_id + 1,  # 1-based
+            "width": 0,
+            "height": 0,
+            "file_name": img_name,
+        }
+        list_images.append(image_entry)
+
+    # Create list of dictionaries for annotations
+    list_annotations: list[dict] = []
+    for img_id, img_bboxes in enumerate(bbox_tensors):
+        # loop thru bboxes in image
+        for bbox_row in img_bboxes:
+            x_min, y_min, x_max, y_max = bbox_row.numpy().tolist()
+            # we convert the array to list to make it JSON serializable
+
+            annotation = {
+                "id": len(list_annotations)
+                + 1,  # 1-based by default in VIA tool
+                "image_id": img_id + 1,  # 1-based by default in VIA tool
+                "category_id": 1,
+                "bbox": [x_min, y_min, x_max - x_min, y_max - y_min],
+                "area": (x_max - x_min) * (y_max - y_min),
+                "iscrowd": 0,
+            }
+
+            list_annotations.append(annotation)
+
+    # Create COCO dictionary
+    coco_dict = {
+        "info": {},
+        "licenses": [],
+        "categories": [{"id": 1, "name": "crab", "supercategory": "animal"}],
+        "images": list_images,
+        "annotations": list_annotations,
+    }
+
+    return coco_dict