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SAM3 Video Segmentation - Clean deployment
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# Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import contextlib
import copy
import json
import os
import time
from collections import defaultdict
from dataclasses import dataclass
from typing import List, Union
import numpy as np
import pycocotools.mask as maskUtils
from pycocotools.coco import COCO
from pycocotools.cocoeval import COCOeval
from scipy.optimize import linear_sum_assignment
from tqdm import tqdm
@dataclass
class Metric:
name: str
# whether the metric is computed at the image level or the box level
image_level: bool
# iou threshold (None is used for image level metrics or to indicate averaging over all thresholds in [0.5:0.95])
iou_threshold: Union[float, None]
CGF1_METRICS = [
Metric(name="cgF1", image_level=False, iou_threshold=None),
Metric(name="precision", image_level=False, iou_threshold=None),
Metric(name="recall", image_level=False, iou_threshold=None),
Metric(name="F1", image_level=False, iou_threshold=None),
Metric(name="positive_macro_F1", image_level=False, iou_threshold=None),
Metric(name="positive_micro_F1", image_level=False, iou_threshold=None),
Metric(name="positive_micro_precision", image_level=False, iou_threshold=None),
Metric(name="IL_precision", image_level=True, iou_threshold=None),
Metric(name="IL_recall", image_level=True, iou_threshold=None),
Metric(name="IL_F1", image_level=True, iou_threshold=None),
Metric(name="IL_FPR", image_level=True, iou_threshold=None),
Metric(name="IL_MCC", image_level=True, iou_threshold=None),
Metric(name="cgF1", image_level=False, iou_threshold=0.5),
Metric(name="precision", image_level=False, iou_threshold=0.5),
Metric(name="recall", image_level=False, iou_threshold=0.5),
Metric(name="F1", image_level=False, iou_threshold=0.5),
Metric(name="positive_macro_F1", image_level=False, iou_threshold=0.5),
Metric(name="positive_micro_F1", image_level=False, iou_threshold=0.5),
Metric(name="positive_micro_precision", image_level=False, iou_threshold=0.5),
Metric(name="cgF1", image_level=False, iou_threshold=0.75),
Metric(name="precision", image_level=False, iou_threshold=0.75),
Metric(name="recall", image_level=False, iou_threshold=0.75),
Metric(name="F1", image_level=False, iou_threshold=0.75),
Metric(name="positive_macro_F1", image_level=False, iou_threshold=0.75),
Metric(name="positive_micro_F1", image_level=False, iou_threshold=0.75),
Metric(name="positive_micro_precision", image_level=False, iou_threshold=0.75),
]
class COCOCustom(COCO):
"""COCO class from pycocotools with tiny modifications for speed"""
def createIndex(self):
# create index
print("creating index...")
anns, cats, imgs = {}, {}, {}
imgToAnns, catToImgs = defaultdict(list), defaultdict(list)
if "annotations" in self.dataset:
for ann in self.dataset["annotations"]:
imgToAnns[ann["image_id"]].append(ann)
anns[ann["id"]] = ann
if "images" in self.dataset:
# MODIFICATION: do not reload imgs if they are already there
if self.imgs:
imgs = self.imgs
else:
for img in self.dataset["images"]:
imgs[img["id"]] = img
# END MODIFICATION
if "categories" in self.dataset:
for cat in self.dataset["categories"]:
cats[cat["id"]] = cat
if "annotations" in self.dataset and "categories" in self.dataset:
for ann in self.dataset["annotations"]:
catToImgs[ann["category_id"]].append(ann["image_id"])
print("index created!")
# create class members
self.anns = anns
self.imgToAnns = imgToAnns
self.catToImgs = catToImgs
self.imgs = imgs
self.cats = cats
def loadRes(self, resFile):
"""
Load result file and return a result api object.
:param resFile (str) : file name of result file
:return: res (obj) : result api object
"""
res = COCOCustom()
res.dataset["info"] = copy.deepcopy(self.dataset.get("info", {}))
# MODIFICATION: no copy
# res.dataset['images'] = [img for img in self.dataset['images']]
res.dataset["images"] = self.dataset["images"]
# END MODIFICATION
print("Loading and preparing results...")
tic = time.time()
if type(resFile) == str:
with open(resFile) as f:
anns = json.load(f)
elif type(resFile) == np.ndarray:
anns = self.loadNumpyAnnotations(resFile)
else:
anns = resFile
assert type(anns) == list, "results in not an array of objects"
annsImgIds = [ann["image_id"] for ann in anns]
# MODIFICATION: faster and cached subset check
if not hasattr(self, "img_id_set"):
self.img_id_set = set(self.getImgIds())
assert set(annsImgIds).issubset(
self.img_id_set
), "Results do not correspond to current coco set"
# END MODIFICATION
if "caption" in anns[0]:
imgIds = set([img["id"] for img in res.dataset["images"]]) & set(
[ann["image_id"] for ann in anns]
)
res.dataset["images"] = [
img for img in res.dataset["images"] if img["id"] in imgIds
]
for id, ann in enumerate(anns):
ann["id"] = id + 1
elif "bbox" in anns[0] and not anns[0]["bbox"] == []:
res.dataset["categories"] = copy.deepcopy(self.dataset["categories"])
for id, ann in enumerate(anns):
bb = ann["bbox"]
x1, x2, y1, y2 = [bb[0], bb[0] + bb[2], bb[1], bb[1] + bb[3]]
if not "segmentation" in ann:
ann["segmentation"] = [[x1, y1, x1, y2, x2, y2, x2, y1]]
ann["area"] = bb[2] * bb[3]
ann["id"] = id + 1
ann["iscrowd"] = 0
elif "segmentation" in anns[0]:
res.dataset["categories"] = copy.deepcopy(self.dataset["categories"])
for id, ann in enumerate(anns):
# now only support compressed RLE format as segmentation results
ann["area"] = maskUtils.area(ann["segmentation"])
if not "bbox" in ann:
ann["bbox"] = maskUtils.toBbox(ann["segmentation"])
ann["id"] = id + 1
ann["iscrowd"] = 0
elif "keypoints" in anns[0]:
res.dataset["categories"] = copy.deepcopy(self.dataset["categories"])
for id, ann in enumerate(anns):
s = ann["keypoints"]
x = s[0::3]
y = s[1::3]
x0, x1, y0, y1 = np.min(x), np.max(x), np.min(y), np.max(y)
ann["area"] = (x1 - x0) * (y1 - y0)
ann["id"] = id + 1
ann["bbox"] = [x0, y0, x1 - x0, y1 - y0]
print("DONE (t={:0.2f}s)".format(time.time() - tic))
res.dataset["annotations"] = anns
# MODIFICATION: inherit images
res.imgs = self.imgs
# END MODIFICATION
res.createIndex()
return res
class CGF1Eval(COCOeval):
"""
This evaluator is based upon COCO evaluation, but evaluates the model in a more realistic setting
for downstream applications.
See SAM3 paper for the details on the CGF1 metric.
Do not use this evaluator directly. Prefer the CGF1Evaluator wrapper.
Notes:
- This evaluator does not support per-category evaluation (in the way defined by pyCocotools)
- In open vocabulary settings, we have different noun-phrases for each image. What we call an "image_id" here is actually an (image, noun-phrase) pair. So in every "image_id" there is only one category, implied by the noun-phrase. Thus we can ignore the usual coco "category" field of the predictions
"""
def __init__(
self,
coco_gt=None,
coco_dt=None,
iouType="segm",
threshold=0.5,
):
"""
Args:
coco_gt (COCO): ground truth COCO API
coco_dt (COCO): detections COCO API
iou_type (str): type of IoU to evaluate
threshold (float): threshold for predictions
"""
super().__init__(coco_gt, coco_dt, iouType)
self.threshold = threshold
self.params.useCats = False
self.params.areaRng = [[0**2, 1e5**2]]
self.params.areaRngLbl = ["all"]
self.params.maxDets = [1000000]
def computeIoU(self, imgId, catId):
# Same as the original COCOeval.computeIoU, but without sorting
p = self.params
if p.useCats:
gt = self._gts[imgId, catId]
dt = self._dts[imgId, catId]
else:
gt = [_ for cId in p.catIds for _ in self._gts[imgId, cId]]
dt = [_ for cId in p.catIds for _ in self._dts[imgId, cId]]
if len(gt) == 0 and len(dt) == 0:
return []
if p.iouType == "segm":
g = [g["segmentation"] for g in gt]
d = [d["segmentation"] for d in dt]
elif p.iouType == "bbox":
g = [g["bbox"] for g in gt]
d = [d["bbox"] for d in dt]
else:
raise Exception("unknown iouType for iou computation")
# compute iou between each dt and gt region
iscrowd = [int(o["iscrowd"]) for o in gt]
ious = maskUtils.iou(d, g, iscrowd)
return ious
def evaluateImg(self, imgId, catId, aRng, maxDet):
"""
perform evaluation for single category and image
:return: dict (single image results)
"""
p = self.params
assert not p.useCats, "This evaluator does not support per-category evaluation."
assert catId == -1
all_gts = [_ for cId in p.catIds for _ in self._gts[imgId, cId]]
keep_gt = np.array([not g["ignore"] for g in all_gts], dtype=bool)
gt = [g for g in all_gts if not g["ignore"]]
all_dts = [_ for cId in p.catIds for _ in self._dts[imgId, cId]]
keep_dt = np.array([d["score"] >= self.threshold for d in all_dts], dtype=bool)
dt = [d for d in all_dts if d["score"] >= self.threshold]
if len(gt) == 0 and len(dt) == 0:
# This is a "true negative" case, where there are no GTs and no predictions
# The box-level metrics are ill-defined, so we don't add them to this dict
return {
"image_id": imgId,
"IL_TP": 0,
"IL_TN": 1,
"IL_FP": 0,
"IL_FN": 0,
"num_dt": len(dt),
}
if len(gt) > 0 and len(dt) == 0:
# This is a "false negative" case, where there are GTs but no predictions
return {
"image_id": imgId,
"IL_TP": 0,
"IL_TN": 0,
"IL_FP": 0,
"IL_FN": 1,
"TPs": np.zeros((len(p.iouThrs),), dtype=np.int64),
"FPs": np.zeros((len(p.iouThrs),), dtype=np.int64),
"FNs": np.ones((len(p.iouThrs),), dtype=np.int64) * len(gt),
"local_F1s": np.zeros((len(p.iouThrs),), dtype=np.int64),
"local_positive_F1s": np.zeros((len(p.iouThrs),), dtype=np.int64),
"num_dt": len(dt),
}
# Load pre-computed ious
ious = self.ious[(imgId, catId)]
# compute matching
if len(ious) == 0:
ious = np.zeros((len(dt), len(gt)))
else:
ious = ious[keep_dt, :][:, keep_gt]
assert ious.shape == (len(dt), len(gt))
matched_dt, matched_gt = linear_sum_assignment(-ious)
match_scores = ious[matched_dt, matched_gt]
TPs, FPs, FNs = [], [], []
IL_perfect = []
for thresh in p.iouThrs:
TP = (match_scores >= thresh).sum()
FP = len(dt) - TP
FN = len(gt) - TP
assert (
FP >= 0 and FN >= 0
), f"FP: {FP}, FN: {FN}, TP: {TP}, match_scores: {match_scores}, len(dt): {len(dt)}, len(gt): {len(gt)}, ious: {ious}"
TPs.append(TP)
FPs.append(FP)
FNs.append(FN)
if FP == FN and FP == 0:
IL_perfect.append(1)
else:
IL_perfect.append(0)
TPs = np.array(TPs, dtype=np.int64)
FPs = np.array(FPs, dtype=np.int64)
FNs = np.array(FNs, dtype=np.int64)
IL_perfect = np.array(IL_perfect, dtype=np.int64)
# compute precision recall and F1
precision = TPs / (TPs + FPs + 1e-4)
assert np.all(precision <= 1)
recall = TPs / (TPs + FNs + 1e-4)
assert np.all(recall <= 1)
F1 = 2 * precision * recall / (precision + recall + 1e-4)
result = {
"image_id": imgId,
"TPs": TPs,
"FPs": FPs,
"FNs": FNs,
"local_F1s": F1,
"IL_TP": (len(gt) > 0) and (len(dt) > 0),
"IL_FP": (len(gt) == 0) and (len(dt) > 0),
"IL_TN": (len(gt) == 0) and (len(dt) == 0),
"IL_FN": (len(gt) > 0) and (len(dt) == 0),
"num_dt": len(dt),
}
if len(gt) > 0 and len(dt) > 0:
result["local_positive_F1s"] = F1
return result
def accumulate(self, p=None):
"""
Accumulate per image evaluation results and store the result in self.eval
:param p: input params for evaluation
:return: None
"""
if self.evalImgs is None or len(self.evalImgs) == 0:
print("Please run evaluate() first")
# allows input customized parameters
if p is None:
p = self.params
setImgIds = set(p.imgIds)
# TPs, FPs, FNs
TPs = np.zeros((len(p.iouThrs),), dtype=np.int64)
FPs = np.zeros((len(p.iouThrs),), dtype=np.int64)
pmFPs = np.zeros((len(p.iouThrs),), dtype=np.int64)
FNs = np.zeros((len(p.iouThrs),), dtype=np.int64)
local_F1s = np.zeros((len(p.iouThrs),), dtype=np.float64)
# Image level metrics
IL_TPs = 0
IL_FPs = 0
IL_TNs = 0
IL_FNs = 0
valid_img_count = 0
valid_F1_count = 0
evaledImgIds = set()
for res in self.evalImgs:
if res["image_id"] not in setImgIds:
continue
evaledImgIds.add(res["image_id"])
IL_TPs += res["IL_TP"]
IL_FPs += res["IL_FP"]
IL_TNs += res["IL_TN"]
IL_FNs += res["IL_FN"]
if "TPs" not in res:
continue
TPs += res["TPs"]
FPs += res["FPs"]
FNs += res["FNs"]
valid_img_count += 1
if "local_positive_F1s" in res:
local_F1s += res["local_positive_F1s"]
pmFPs += res["FPs"]
if res["num_dt"] > 0:
valid_F1_count += 1
assert len(setImgIds - evaledImgIds) == 0, (
f"{len(setImgIds - evaledImgIds)} images not evaluated. "
f"Here are the IDs of the first 3: {list(setImgIds - evaledImgIds)[:3]}"
)
# compute precision recall and F1
precision = TPs / (TPs + FPs + 1e-4)
positive_micro_precision = TPs / (TPs + pmFPs + 1e-4)
assert np.all(precision <= 1)
recall = TPs / (TPs + FNs + 1e-4)
assert np.all(recall <= 1)
F1 = 2 * precision * recall / (precision + recall + 1e-4)
positive_micro_F1 = (
2
* positive_micro_precision
* recall
/ (positive_micro_precision + recall + 1e-4)
)
IL_rec = IL_TPs / (IL_TPs + IL_FNs + 1e-6)
IL_prec = IL_TPs / (IL_TPs + IL_FPs + 1e-6)
IL_F1 = 2 * IL_prec * IL_rec / (IL_prec + IL_rec + 1e-6)
IL_FPR = IL_FPs / (IL_FPs + IL_TNs + 1e-6)
IL_MCC = float(IL_TPs * IL_TNs - IL_FPs * IL_FNs) / (
(
float(IL_TPs + IL_FPs)
* float(IL_TPs + IL_FNs)
* float(IL_TNs + IL_FPs)
* float(IL_TNs + IL_FNs)
)
** 0.5
+ 1e-6
)
self.eval = {
"params": p,
"TPs": TPs,
"FPs": FPs,
"positive_micro_FPs": pmFPs,
"FNs": FNs,
"precision": precision,
"positive_micro_precision": positive_micro_precision,
"recall": recall,
"F1": F1,
"positive_micro_F1": positive_micro_F1,
"positive_macro_F1": local_F1s / valid_F1_count,
"IL_recall": IL_rec,
"IL_precision": IL_prec,
"IL_F1": IL_F1,
"IL_FPR": IL_FPR,
"IL_MCC": IL_MCC,
}
self.eval["cgF1"] = self.eval["positive_micro_F1"] * self.eval["IL_MCC"]
def summarize(self):
"""
Compute and display summary metrics for evaluation results.
"""
if not self.eval:
raise Exception("Please run accumulate() first")
def _summarize(iouThr=None, metric=""):
p = self.params
iStr = " {:<18} @[ IoU={:<9}] = {:0.3f}"
titleStr = "Average " + metric
iouStr = (
"{:0.2f}:{:0.2f}".format(p.iouThrs[0], p.iouThrs[-1])
if iouThr is None
else "{:0.2f}".format(iouThr)
)
s = self.eval[metric]
# IoU
if iouThr is not None:
t = np.where(iouThr == p.iouThrs)[0]
s = s[t]
if len(s[s > -1]) == 0:
mean_s = -1
else:
mean_s = np.mean(s[s > -1])
print(iStr.format(titleStr, iouStr, mean_s))
return mean_s
def _summarize_single(metric=""):
titleStr = "Average " + metric
iStr = " {:<35} = {:0.3f}"
s = self.eval[metric]
print(iStr.format(titleStr, s))
return s
def _summarizeDets():
stats = []
for metric in CGF1_METRICS:
if metric.image_level:
stats.append(_summarize_single(metric=metric.name))
else:
stats.append(
_summarize(iouThr=metric.iou_threshold, metric=metric.name)
)
return np.asarray(stats)
summarize = _summarizeDets
self.stats = summarize()
def _evaluate(self):
"""
Run per image evaluation on given images and store results (a list of dict) in self.evalImgs
"""
p = self.params
# add backward compatibility if useSegm is specified in params
p.imgIds = list(np.unique(p.imgIds))
p.useCats = False
p.maxDets = sorted(p.maxDets)
self.params = p
self._prepare()
# loop through images, area range, max detection number
catIds = [-1]
if p.iouType == "segm" or p.iouType == "bbox":
computeIoU = self.computeIoU
else:
raise RuntimeError(f"Unsupported iou {p.iouType}")
self.ious = {
(imgId, catId): computeIoU(imgId, catId)
for imgId in p.imgIds
for catId in catIds
}
maxDet = p.maxDets[-1]
evalImgs = [
self.evaluateImg(imgId, catId, areaRng, maxDet)
for catId in catIds
for areaRng in p.areaRng
for imgId in p.imgIds
]
# this is NOT in the pycocotools code, but could be done outside
evalImgs = np.asarray(evalImgs).reshape(len(catIds), len(p.areaRng), len(p.imgIds))
return p.imgIds, evalImgs
class CGF1Evaluator:
"""
Wrapper class for cgF1 evaluation.
This supports the oracle setting (when several ground-truths are available per image)
"""
def __init__(
self,
gt_path: Union[str, List[str]],
iou_type="segm",
verbose=False,
):
"""
Args:
gt_path (str or list of str): path(s) to ground truth COCO json file(s)
iou_type (str): type of IoU to evaluate
threshold (float): threshold for predictions
"""
self.gt_paths = gt_path if isinstance(gt_path, list) else [gt_path]
self.iou_type = iou_type
self.coco_gts = [COCOCustom(gt) for gt in self.gt_paths]
self.verbose = verbose
self.coco_evals = []
for i, coco_gt in enumerate(self.coco_gts):
self.coco_evals.append(
CGF1Eval(
coco_gt=coco_gt,
iouType=iou_type,
)
)
self.coco_evals[i].useCats = False
exclude_img_ids = set()
# exclude_img_ids are the ids that are not exhaustively annotated in any of the other gts
for coco_gt in self.coco_gts[1:]:
exclude_img_ids = exclude_img_ids.union(
{
img["id"]
for img in coco_gt.dataset["images"]
if not img["is_instance_exhaustive"]
}
)
# we only eval on instance exhaustive queries
self.eval_img_ids = [
img["id"]
for img in self.coco_gts[0].dataset["images"]
if (img["is_instance_exhaustive"] and img["id"] not in exclude_img_ids)
]
def evaluate(self, pred_file: str):
"""
Evaluate the detections using cgF1 metric.
Args:
pred_file: path to the predictions COCO json file
"""
assert len(self.coco_gts) > 0, "No ground truth provided for evaluation."
assert len(self.coco_gts) == len(
self.coco_evals
), "Mismatch in number of ground truths and evaluators."
if self.verbose:
print(f"Loading predictions from {pred_file}")
with open(pred_file, "r") as f:
preds = json.load(f)
if self.verbose:
print(f"Loaded {len(preds)} predictions")
img2preds = defaultdict(list)
for pred in preds:
img2preds[pred["image_id"]].append(pred)
all_eval_imgs = []
for img_id in tqdm(self.eval_img_ids, disable=not self.verbose):
results = img2preds[img_id]
all_scorings = []
for cur_coco_gt, coco_eval in zip(self.coco_gts, self.coco_evals):
# suppress pycocotools prints
with open(os.devnull, "w") as devnull:
with contextlib.redirect_stdout(devnull):
coco_dt = (
cur_coco_gt.loadRes(results) if results else COCOCustom()
)
coco_eval.cocoDt = coco_dt
coco_eval.params.imgIds = [img_id]
coco_eval.params.useCats = False
img_ids, eval_imgs = _evaluate(coco_eval)
all_scorings.append(eval_imgs)
selected = self._select_best_scoring(all_scorings)
all_eval_imgs.append(selected)
# After this point, we have selected the best scoring per image among several ground truths
# we can now accumulate and summarize, using only the first coco_eval
self.coco_evals[0].evalImgs = list(
np.concatenate(all_eval_imgs, axis=2).flatten()
)
self.coco_evals[0].params.imgIds = self.eval_img_ids
self.coco_evals[0]._paramsEval = copy.deepcopy(self.coco_evals[0].params)
if self.verbose:
print(f"Accumulating results")
self.coco_evals[0].accumulate()
print("cgF1 metric, IoU type={}".format(self.iou_type))
self.coco_evals[0].summarize()
print()
out = {}
for i, value in enumerate(self.coco_evals[0].stats):
name = CGF1_METRICS[i].name
if CGF1_METRICS[i].iou_threshold is not None:
name = f"{name}@{CGF1_METRICS[i].iou_threshold}"
out[f"cgF1_eval_{self.iou_type}_{name}"] = float(value)
return out
@staticmethod
def _select_best_scoring(scorings):
# This function is used for "oracle" type evaluation.
# It accepts the evaluation results with respect to several ground truths, and picks the best
if len(scorings) == 1:
return scorings[0]
assert (
scorings[0].ndim == 3
), f"Expecting results in [numCats, numAreas, numImgs] format, got {scorings[0].shape}"
assert (
scorings[0].shape[0] == 1
), f"Expecting a single category, got {scorings[0].shape[0]}"
for scoring in scorings:
assert (
scoring.shape == scorings[0].shape
), f"Shape mismatch: {scoring.shape}, {scorings[0].shape}"
selected_imgs = []
for img_id in range(scorings[0].shape[-1]):
best = scorings[0][:, :, img_id]
for scoring in scorings[1:]:
current = scoring[:, :, img_id]
if "local_F1s" in best[0, 0] and "local_F1s" in current[0, 0]:
# we were able to compute a F1 score for this particular image in both evaluations
# best["local_F1s"] contains the results at various IoU thresholds. We simply take the average for comparision
best_score = best[0, 0]["local_F1s"].mean()
current_score = current[0, 0]["local_F1s"].mean()
if current_score > best_score:
best = current
else:
# If we're here, it means that in that in some evaluation we were not able to get a valid local F1
# This happens when both the predictions and targets are empty. In that case, we can assume it's a perfect prediction
if "local_F1s" not in current[0, 0]:
best = current
selected_imgs.append(best)
result = np.stack(selected_imgs, axis=-1)
assert result.shape == scorings[0].shape
return result