diff --git a/benchmark/submissions/__init__.py b/benchmark/submissions/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/benchmark/submissions/apt/README.md b/benchmark/submissions/apt/README.md new file mode 100644 index 0000000..2e59610 --- /dev/null +++ b/benchmark/submissions/apt/README.md @@ -0,0 +1,9 @@ +# APT Predictions + +To benchmark APT (https://github.com/kristinbranson/APT) on Deeplabcut multi-animal benchmark datasets, we trained the following networks: + +* GRONe +* CiD (from MMPose) +* Top Down detector with DeTR (from MMDetect) for object detection and GRONe for pose estimation + + diff --git a/benchmark/submissions/apt/__init__.py b/benchmark/submissions/apt/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/benchmark/submissions/apt/data/cid_fish_test.json b/benchmark/submissions/apt/data/cid_fish_test.json new file mode 100644 index 0000000..c9f6372 --- /dev/null +++ b/benchmark/submissions/apt/data/cid_fish_test.json @@ -0,0 +1 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+ return "GRONe", "MMPose-CiD", "DeTR+GRONe", "DeTR+Hrformer" + +def get_prefix(name): + if name == "GRONe": + prefix = 'grone' + elif name == "MMPose-CiD": + prefix = 'cid' + elif name == "DeTR+GRONe": + prefix = 'mdn_bbox' + elif name == "DeTR+Hrformer": + prefix = 'hrformer_bbox' + + return prefix + + +def parse_predictions(data: dict) -> dict: + """Sets the data into the expected format for the DeepLabCut benchmark + + Not needed if the "score"/"pose" keys are added to the JSON files + """ + rng = np.random.default_rng(0) + + predictions = {} + for img, poses in data.items(): + img_predictions = [] + + # give first prediction base score 0.95, second 0.9, third 0.85, ... + score_steps = np.linspace(0.95, 0, 20) + + # so that all scores are different and sorting is deterministic + score_offset = rng.random(1) / 50 + + for i, pose in enumerate(poses): + # get random score + idv_score = np.clip(score_steps[i] + score_offset, 0, 1).item() + + img_predictions.append( + { + "pose": pose, + "score": idv_score, + } + ) + predictions[img] = tuple(img_predictions) + + return predictions + + +@benchmark.register +class APTTriMouse(TriMouseBenchmark): + code = code + + def names(self): + return get_names() + + def get_predictions(self,name): + prefix = get_prefix(name) + + res_file = f'{data_root}/{prefix}_trimice_test.json' + with open(res_file) as f: + return parse_predictions(json.load(f)) + + +@benchmark.register +class APTMarmoset(MarmosetBenchmark): + code = code + + def names(self): + return get_names() + + def get_predictions(self,name): + prefix = get_prefix(name) + + res_file = f'{data_root}/{prefix}_marmoset_test.json' + with open(res_file) as f: + return parse_predictions(json.load(f)) + + +@benchmark.register +class APTParenting(ParentingMouseBenchmark): + code = code + + def names(self): + return get_names() + #return "GRONe", "DeTR+GRONe", "DeTR+Hrformer" + + def get_predictions(self,name): + prefix = get_prefix(name) + + res_file = f'{data_root}/{prefix}_parenting_test.json' + with open(res_file) as f: + return parse_predictions(json.load(f)) + + +@benchmark.register +class APTFish(FishBenchmark): + code = code + + def names(self): + return get_names() + + def get_predictions(self,name): + prefix = get_prefix(name) + + res_file = f'{data_root}/{prefix}_fish_test.json' + with open(res_file) as f: + return parse_predictions(json.load(f)) + +