Primate-Detection-GPU / segment_anything /automatic_mask_generator.py
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# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import numpy as np
import torch
from torchvision.ops.boxes import batched_nms, box_area # type: ignore
from typing import Any, Dict, List, Optional, Tuple
from .modeling import Sam
from .predictor import SamPredictor
from .utils.amg import (
MaskData,
area_from_rle,
batch_iterator,
batched_mask_to_box,
box_xyxy_to_xywh,
build_all_layer_point_grids,
calculate_stability_score,
coco_encode_rle,
generate_crop_boxes,
is_box_near_crop_edge,
mask_to_rle_pytorch,
remove_small_regions,
rle_to_mask,
uncrop_boxes_xyxy,
uncrop_masks,
uncrop_points,
)
class SamAutomaticMaskGenerator:
def __init__(
self,
model: Sam,
points_per_side: Optional[int] = 32,
points_per_batch: int = 64,
pred_iou_thresh: float = 0.88,
stability_score_thresh: float = 0.95,
stability_score_offset: float = 1.0,
box_nms_thresh: float = 0.7,
crop_n_layers: int = 0,
crop_nms_thresh: float = 0.7,
crop_overlap_ratio: float = 512 / 1500,
crop_n_points_downscale_factor: int = 1,
point_grids: Optional[List[np.ndarray]] = None,
min_mask_region_area: int = 0,
output_mode: str = "binary_mask",
) -> None:
"""
Using a SAM model, generates masks for the entire image.
Generates a grid of point prompts over the image, then filters
low quality and duplicate masks. The default settings are chosen
for SAM with a ViT-H backbone.
Arguments:
model (Sam): The SAM model to use for mask prediction.
points_per_side (int or None): The number of points to be sampled
along one side of the image. The total number of points is
points_per_side**2. If None, 'point_grids' must provide explicit
point sampling.
points_per_batch (int): Sets the number of points run simultaneously
by the model. Higher numbers may be faster but use more GPU memory.
pred_iou_thresh (float): A filtering threshold in [0,1], using the
model's predicted mask quality.
stability_score_thresh (float): A filtering threshold in [0,1], using
the stability of the mask under changes to the cutoff used to binarize
the model's mask predictions.
stability_score_offset (float): The amount to shift the cutoff when
calculated the stability score.
box_nms_thresh (float): The box IoU cutoff used by non-maximal
suppression to filter duplicate masks.
crop_n_layers (int): If >0, mask prediction will be run again on
crops of the image. Sets the number of layers to run, where each
layer has 2**i_layer number of image crops.
crop_nms_thresh (float): The box IoU cutoff used by non-maximal
suppression to filter duplicate masks between different crops.
crop_overlap_ratio (float): Sets the degree to which crops overlap.
In the first crop layer, crops will overlap by this fraction of
the image length. Later layers with more crops scale down this overlap.
crop_n_points_downscale_factor (int): The number of points-per-side
sampled in layer n is scaled down by crop_n_points_downscale_factor**n.
point_grids (list(np.ndarray) or None): A list over explicit grids
of points used for sampling, normalized to [0,1]. The nth grid in the
list is used in the nth crop layer. Exclusive with points_per_side.
min_mask_region_area (int): If >0, postprocessing will be applied
to remove disconnected regions and holes in masks with area smaller
than min_mask_region_area. Requires opencv.
output_mode (str): The form masks are returned in. Can be 'binary_mask',
'uncompressed_rle', or 'coco_rle'. 'coco_rle' requires pycocotools.
For large resolutions, 'binary_mask' may consume large amounts of
memory.
"""
assert (points_per_side is None) != (
point_grids is None
), "Exactly one of points_per_side or point_grid must be provided."
if points_per_side is not None:
self.point_grids = build_all_layer_point_grids(
points_per_side,
crop_n_layers,
crop_n_points_downscale_factor,
)
elif point_grids is not None:
self.point_grids = point_grids
else:
raise ValueError("Can't have both points_per_side and point_grid be None.")
assert output_mode in [
"binary_mask",
"uncompressed_rle",
"coco_rle",
], f"Unknown output_mode {output_mode}."
if output_mode == "coco_rle":
from pycocotools import mask as mask_utils # type: ignore # noqa: F401
if min_mask_region_area > 0:
import cv2 # type: ignore # noqa: F401
self.predictor = SamPredictor(model)
self.points_per_batch = points_per_batch
self.pred_iou_thresh = pred_iou_thresh
self.stability_score_thresh = stability_score_thresh
self.stability_score_offset = stability_score_offset
self.box_nms_thresh = box_nms_thresh
self.crop_n_layers = crop_n_layers
self.crop_nms_thresh = crop_nms_thresh
self.crop_overlap_ratio = crop_overlap_ratio
self.crop_n_points_downscale_factor = crop_n_points_downscale_factor
self.min_mask_region_area = min_mask_region_area
self.output_mode = output_mode
@torch.no_grad()
def generate(self, image: np.ndarray) -> List[Dict[str, Any]]:
"""
Generates masks for the given image.
Arguments:
image (np.ndarray): The image to generate masks for, in HWC uint8 format.
Returns:
list(dict(str, any)): A list over records for masks. Each record is
a dict containing the following keys:
segmentation (dict(str, any) or np.ndarray): The mask. If
output_mode='binary_mask', is an array of shape HW. Otherwise,
is a dictionary containing the RLE.
bbox (list(float)): The box around the mask, in XYWH format.
area (int): The area in pixels of the mask.
predicted_iou (float): The model's own prediction of the mask's
quality. This is filtered by the pred_iou_thresh parameter.
point_coords (list(list(float))): The point coordinates input
to the model to generate this mask.
stability_score (float): A measure of the mask's quality. This
is filtered on using the stability_score_thresh parameter.
crop_box (list(float)): The crop of the image used to generate
the mask, given in XYWH format.
"""
# Generate masks
mask_data = self._generate_masks(image)
# Filter small disconnected regions and holes in masks
if self.min_mask_region_area > 0:
mask_data = self.postprocess_small_regions(
mask_data,
self.min_mask_region_area,
max(self.box_nms_thresh, self.crop_nms_thresh),
)
# Encode masks
if self.output_mode == "coco_rle":
mask_data["segmentations"] = [coco_encode_rle(rle) for rle in mask_data["rles"]]
elif self.output_mode == "binary_mask":
mask_data["segmentations"] = [rle_to_mask(rle) for rle in mask_data["rles"]]
else:
mask_data["segmentations"] = mask_data["rles"]
# Write mask records
curr_anns = []
for idx in range(len(mask_data["segmentations"])):
ann = {
"segmentation": mask_data["segmentations"][idx],
"area": area_from_rle(mask_data["rles"][idx]),
"bbox": box_xyxy_to_xywh(mask_data["boxes"][idx]).tolist(),
"predicted_iou": mask_data["iou_preds"][idx].item(),
"point_coords": [mask_data["points"][idx].tolist()],
"stability_score": mask_data["stability_score"][idx].item(),
"crop_box": box_xyxy_to_xywh(mask_data["crop_boxes"][idx]).tolist(),
}
curr_anns.append(ann)
return curr_anns
def _generate_masks(self, image: np.ndarray) -> MaskData:
orig_size = image.shape[:2]
crop_boxes, layer_idxs = generate_crop_boxes(
orig_size, self.crop_n_layers, self.crop_overlap_ratio
)
# Iterate over image crops
data = MaskData()
for crop_box, layer_idx in zip(crop_boxes, layer_idxs):
crop_data = self._process_crop(image, crop_box, layer_idx, orig_size)
data.cat(crop_data)
# Remove duplicate masks between crops
if len(crop_boxes) > 1:
# Prefer masks from smaller crops
scores = 1 / box_area(data["crop_boxes"])
scores = scores.to(data["boxes"].device)
keep_by_nms = batched_nms(
data["boxes"].float(),
scores,
torch.zeros_like(data["boxes"][:, 0]), # categories
iou_threshold=self.crop_nms_thresh,
)
data.filter(keep_by_nms)
data.to_numpy()
return data
def _process_crop(
self,
image: np.ndarray,
crop_box: List[int],
crop_layer_idx: int,
orig_size: Tuple[int, ...],
) -> MaskData:
# Crop the image and calculate embeddings
x0, y0, x1, y1 = crop_box
cropped_im = image[y0:y1, x0:x1, :]
cropped_im_size = cropped_im.shape[:2]
self.predictor.set_image(cropped_im)
# Get points for this crop
points_scale = np.array(cropped_im_size)[None, ::-1]
points_for_image = self.point_grids[crop_layer_idx] * points_scale
# Generate masks for this crop in batches
data = MaskData()
for (points,) in batch_iterator(self.points_per_batch, points_for_image):
batch_data = self._process_batch(points, cropped_im_size, crop_box, orig_size)
data.cat(batch_data)
del batch_data
self.predictor.reset_image()
# Remove duplicates within this crop.
keep_by_nms = batched_nms(
data["boxes"].float(),
data["iou_preds"],
torch.zeros_like(data["boxes"][:, 0]), # categories
iou_threshold=self.box_nms_thresh,
)
data.filter(keep_by_nms)
# Return to the original image frame
data["boxes"] = uncrop_boxes_xyxy(data["boxes"], crop_box)
data["points"] = uncrop_points(data["points"], crop_box)
data["crop_boxes"] = torch.tensor([crop_box for _ in range(len(data["rles"]))])
return data
def _process_batch(
self,
points: np.ndarray,
im_size: Tuple[int, ...],
crop_box: List[int],
orig_size: Tuple[int, ...],
) -> MaskData:
orig_h, orig_w = orig_size
# Run model on this batch
transformed_points = self.predictor.transform.apply_coords(points, im_size)
in_points = torch.as_tensor(transformed_points, device=self.predictor.device)
in_labels = torch.ones(in_points.shape[0], dtype=torch.int, device=in_points.device)
masks, iou_preds, _ = self.predictor.predict_torch(
in_points[:, None, :],
in_labels[:, None],
multimask_output=True,
return_logits=True,
)
# Serialize predictions and store in MaskData
data = MaskData(
masks=masks.flatten(0, 1),
iou_preds=iou_preds.flatten(0, 1),
points=torch.as_tensor(points.repeat(masks.shape[1], axis=0)),
)
del masks
# Filter by predicted IoU
if self.pred_iou_thresh > 0.0:
keep_mask = data["iou_preds"] > self.pred_iou_thresh
data.filter(keep_mask)
# Calculate stability score
data["stability_score"] = calculate_stability_score(
data["masks"], self.predictor.model.mask_threshold, self.stability_score_offset
)
if self.stability_score_thresh > 0.0:
keep_mask = data["stability_score"] >= self.stability_score_thresh
data.filter(keep_mask)
# Threshold masks and calculate boxes
data["masks"] = data["masks"] > self.predictor.model.mask_threshold
data["boxes"] = batched_mask_to_box(data["masks"])
# Filter boxes that touch crop boundaries
keep_mask = ~is_box_near_crop_edge(data["boxes"], crop_box, [0, 0, orig_w, orig_h])
if not torch.all(keep_mask):
data.filter(keep_mask)
# Compress to RLE
data["masks"] = uncrop_masks(data["masks"], crop_box, orig_h, orig_w)
data["rles"] = mask_to_rle_pytorch(data["masks"])
del data["masks"]
return data
@staticmethod
def postprocess_small_regions(
mask_data: MaskData, min_area: int, nms_thresh: float
) -> MaskData:
"""
Removes small disconnected regions and holes in masks, then reruns
box NMS to remove any new duplicates.
Edits mask_data in place.
Requires open-cv as a dependency.
"""
if len(mask_data["rles"]) == 0:
return mask_data
# Filter small disconnected regions and holes
new_masks = []
scores = []
for rle in mask_data["rles"]:
mask = rle_to_mask(rle)
mask, changed = remove_small_regions(mask, min_area, mode="holes")
unchanged = not changed
mask, changed = remove_small_regions(mask, min_area, mode="islands")
unchanged = unchanged and not changed
new_masks.append(torch.as_tensor(mask).unsqueeze(0))
# Give score=0 to changed masks and score=1 to unchanged masks
# so NMS will prefer ones that didn't need postprocessing
scores.append(float(unchanged))
# Recalculate boxes and remove any new duplicates
masks = torch.cat(new_masks, dim=0)
boxes = batched_mask_to_box(masks)
keep_by_nms = batched_nms(
boxes.float(),
torch.as_tensor(scores),
torch.zeros_like(boxes[:, 0]), # categories
iou_threshold=nms_thresh,
)
# Only recalculate RLEs for masks that have changed
for i_mask in keep_by_nms:
if scores[i_mask] == 0.0:
mask_torch = masks[i_mask].unsqueeze(0)
mask_data["rles"][i_mask] = mask_to_rle_pytorch(mask_torch)[0]
mask_data["boxes"][i_mask] = boxes[i_mask] # update res directly
mask_data.filter(keep_by_nms)
return mask_data