def save_poly_coco(annotations: list, base_filepath: str):
"""
@param annotations: Either [[annotation1 of im1, annotation2 of im1, ...], ...] or [{"method1": [annotation1 of im1, ...]}, ...]
@param base_filepath:
@return:
"""
# seg_coco_list is either a list of annotations or a list of dictionaries for each method (and sub-methods) used
if type(annotations[0]) == dict:
# Means several methods/settings were used
# Transform list of dicts to a dict of lists:
dictionary = local_utils.list_of_dicts_to_dict_of_lists(annotations)
dictionary = local_utils.flatten_dict(dictionary)
for key, _annotations in dictionary.items():
out_filepath = base_filepath + "." + key + ".json"
python_utils.save_json(out_filepath, _annotations)
elif type(annotations[0]) == list:
# Concatenate all lists
flattened_annotations = list(itertools.chain(*annotations))
out_filepath = get_save_filepath(base_filepath, None, ".json")
python_utils.save_json(out_filepath, flattened_annotations)
else:
raise TypeError("annotations has unrecognized type {}".format(
type(annotations)))
def eval_shapefile(gt_polygons, pred_info):
# Compute metrics
metrics_filepath = os.path.splitext(
pred_info["shapefile_filepath"])[0] + ".metrics.json"
metrics = python_utils.load_json(metrics_filepath)
if not metrics:
# Load pred shp
pred_polygons = load_shapefile(pred_info["shapefile_filepath"])
fixed_dt_polygons = polygon_utils.fix_polygons(pred_polygons)
print(f"Loaded {len(fixed_dt_polygons)} pred polygons")
max_angle_diffs = polygon_utils.compute_polygon_contour_measures(
fixed_dt_polygons,
gt_polygons,
sampling_spacing=1.0,
min_precision=0.5,
max_stretch=2)
max_angle_diffs = [
value for value in max_angle_diffs if value is not None
]
max_angle_diffs = np.array(max_angle_diffs)
max_angle_diffs = max_angle_diffs * 180 / np.pi # Convert to degrees
metrics = {"max_angle_diffs": list(max_angle_diffs)}
python_utils.save_json(metrics_filepath, metrics)
print(f"Got {len(metrics['max_angle_diffs'])} max_angle_diff values")
return metrics
def main():
args = get_args()
print_utils.print_info(
f"INFO: evaluating {len(args.pred_filepath)} predictions.")
# Match files together
im_gt_pred_filepaths = match_im_gt_pred(args.im_filepath, args.gt_filepath,
args.pred_filepath)
pool = Pool()
metrics_iou_list = list(
tqdm(pool.imap(partial(eval_one, overwrite=args.overwrite),
im_gt_pred_filepaths),
desc="Compute eval metrics",
total=len(im_gt_pred_filepaths)))
# Aggregate metrics and IoU
aggr_metrics = {"max_angle_diffs": []}
aggr_iou = {"intersection": 0, "union": 0}
for metrics_iou in metrics_iou_list:
if metrics_iou["metrics"]:
aggr_metrics["max_angle_diffs"] += metrics_iou["metrics"][
"max_angle_diffs"]
if metrics_iou["iou"]:
aggr_iou["intersection"] += metrics_iou["iou"]["intersection"]
aggr_iou["union"] += metrics_iou["iou"]["union"]
aggr_iou["iou"] = aggr_iou["intersection"] / aggr_iou["union"]
aggr_metrics_filepath = os.path.join(
os.path.dirname(args.pred_filepath[0]), "aggr_metrics.json")
aggr_iou_filepath = os.path.join(os.path.dirname(args.pred_filepath[0]),
"aggr_iou.json")
python_utils.save_json(aggr_metrics_filepath, aggr_metrics)
python_utils.save_json(aggr_iou_filepath, aggr_iou)
def save_geojson(polygons, base_filepath, name=None, image_filepath=None):
# TODO: add georef and features
filepath = get_save_filepath(base_filepath, name, ".geojson")
polygons_geometry_collection = shapely.geometry.collection.GeometryCollection(
polygons)
geojson = shapely.geometry.mapping(polygons_geometry_collection)
python_utils.save_json(filepath, geojson)
def save_geojson(polygons, base_filepath, name=None, image_filepath=None):
# TODO: add georef and features
if name is not None:
filepath = base_filepath + "." + name + ".geojson"
else:
filepath = base_filepath + ".geojson"
polygons_geometry_collection = shapely.geometry.collection.GeometryCollection(
polygons)
geojson = shapely.geometry.mapping(polygons_geometry_collection)
python_utils.save_json(filepath, geojson)
def load_image_ids(self):
image_id_list_filepath = os.path.join(self.processed_dir, "image_id_list-small.json" if self.small else "image_id_list.json")
if os.path.exists(image_id_list_filepath):
image_id_list = python_utils.load_json(image_id_list_filepath)
else:
coco = self.get_coco()
image_id_list = coco.getImgIds(catIds=coco.getCatIds())
# Save for later so that the whole coco object doesn't have to be instantiated when just reading processed samples with multiple workers:
python_utils.save_json(image_id_list_filepath, image_id_list)
return image_id_list
def eval_one(im_gt_pred_filepath, overwrite=False):
im_filepath, gt_filepath, pred_filepath = im_gt_pred_filepath
metrics_filepath = os.path.splitext(pred_filepath)[0] + ".metrics.json"
iou_filepath = os.path.splitext(pred_filepath)[0] + ".iou.json"
metrics = False
iou = False
if not overwrite:
# Try reading metrics and iou json
metrics = python_utils.load_json(metrics_filepath)
iou = python_utils.load_json(iou_filepath)
if not metrics or not iou:
# Have to compute at least one so load geometries
gt_polygons = load_geom(gt_filepath, im_filepath)
fixed_gt_polygons = polygon_utils.fix_polygons(
gt_polygons, buffer=0.0001
) # Buffer adds vertices but is needed to repair some geometries
pred_polygons = load_geom(pred_filepath, im_filepath)
fixed_pred_polygons = polygon_utils.fix_polygons(pred_polygons)
if not metrics:
# Compute and save metrics
max_angle_diffs = polygon_utils.compute_polygon_contour_measures(
fixed_pred_polygons,
fixed_gt_polygons,
sampling_spacing=1.0,
min_precision=0.5,
max_stretch=2,
progressbar=True)
max_angle_diffs = [
value for value in max_angle_diffs if value is not None
]
max_angle_diffs = np.array(max_angle_diffs)
max_angle_diffs = max_angle_diffs * 180 / np.pi # Convert to degrees
metrics = {"max_angle_diffs": list(max_angle_diffs)}
python_utils.save_json(metrics_filepath, metrics)
if not iou:
fixed_gt_polygon_collection = shapely.geometry.collection.GeometryCollection(
fixed_gt_polygons)
fixed_pred_polygon_collection = shapely.geometry.collection.GeometryCollection(
fixed_pred_polygons)
intersection = fixed_gt_polygon_collection.intersection(
fixed_pred_polygon_collection).area
union = fixed_gt_polygon_collection.union(
fixed_pred_polygon_collection).area
iou = {"intersection": intersection, "union": union}
python_utils.save_json(iou_filepath, iou)
return {
"metrics": metrics,
"iou": iou,
}
def setup_run(config):
run_name = config["run_name"]
new_run = config["new_run"]
init_run_name = config["init_run_name"]
working_dir = os.path.dirname(os.path.abspath(__file__))
runs_dir = os.path.join(working_dir, config["runs_dirpath"])
# setup init checkpoints directory path if one is specified:
if init_run_name is not None:
init_run_dirpath = run_utils.setup_run_dir(runs_dir, init_run_name)
_, init_checkpoints_dirpath = run_utils.setup_run_subdirs(
init_run_dirpath)
else:
init_checkpoints_dirpath = None
# setup run directory:
run_dirpath = run_utils.setup_run_dir(runs_dir, run_name, new_run)
# save config in logs directory
run_utils.save_config(config, run_dirpath)
# save args
args_filepath = os.path.join(run_dirpath, "args.json")
args_to_save = {
"run_name": run_name,
"new_run": new_run,
"init_run_name": init_run_name,
"batch_size": config["optim_params"]["batch_size"],
}
if "samples" in config:
args_to_save["samples"] = config["samples"]
python_utils.save_json(args_filepath, args_to_save)
# save current commit hash
commit_hash = get_git_revision_hash()
if commit_hash is not None:
commit_hash_filepath = os.path.join(run_dirpath, "commit_history.json")
if os.path.exists(commit_hash_filepath):
commit_hashes = python_utils.load_json(commit_hash_filepath)
if commit_hashes[-1] != commit_hash:
commit_hashes.append(commit_hash)
python_utils.save_json(commit_hash_filepath, commit_hashes)
else:
commit_hashes = [commit_hash]
python_utils.save_json(commit_hash_filepath, commit_hashes)
return run_dirpath, init_checkpoints_dirpath
def evaluate(self, split_name: str, ds: torch.utils.data.DataLoader):
# Prepare data saving:
flag_filepath_format = os.path.join(self.eval_dirpath, split_name,
"{}.flag")
# Loading model
self.load_checkpoint()
self.model.eval()
# Create pool for multiprocessing
pool = None
if not self.config["eval_params"]["patch_size"]:
# If single image is not being split up, then a pool to process each sample in the batch makes sense
pool = Pool(processes=self.config["num_workers"])
compute_polygonization = self.config["eval_params"]["save_individual_outputs"]["poly_shapefile"] or \
self.config["eval_params"]["save_individual_outputs"]["poly_geojson"] or \
self.config["eval_params"]["save_individual_outputs"]["poly_viz"] or \
self.config["eval_params"]["save_aggregated_outputs"]["poly_coco"]
# Saving individual outputs to disk:
save_individual_outputs = True in self.config["eval_params"][
"save_individual_outputs"].values()
saver_async = None
if save_individual_outputs:
save_outputs_partial = partial(
save_utils.save_outputs,
config=self.config,
eval_dirpath=self.eval_dirpath,
split_name=split_name,
flag_filepath_format=flag_filepath_format)
saver_async = async_utils.Async(save_outputs_partial)
saver_async.start()
# Saving aggregated outputs
save_aggregated_outputs = True in self.config["eval_params"][
"save_aggregated_outputs"].values()
tile_data_list = []
if self.gpu == 0:
tile_iterator = tqdm(ds,
desc="Eval {}: ".format(split_name),
leave=True)
else:
tile_iterator = ds
for tile_i, tile_data in enumerate(tile_iterator):
# --- Inference, add result to tile_data_list
if self.config["eval_params"]["patch_size"] is not None:
# Cut image into patches for inference
inference.inference_with_patching(self.config, self.model,
tile_data)
else:
# Feed images as-is to the model
inference.inference_no_patching(self.config, self.model,
tile_data)
tile_data_list.append(tile_data)
# --- Accumulate batches into tile_data_list until capacity is reached (or this is the last batch)
if self.config["eval_params"]["batch_size_mult"] <= len(tile_data_list)\
or tile_i == len(tile_iterator) - 1:
# Concat tensors of tile_data_list
accumulated_tile_data = {}
for key in tile_data_list[0].keys():
if isinstance(tile_data_list[0][key], list):
accumulated_tile_data[key] = [
item for _tile_data in tile_data_list
for item in _tile_data[key]
]
elif isinstance(tile_data_list[0][key], torch.Tensor):
accumulated_tile_data[key] = torch.cat(
[_tile_data[key] for _tile_data in tile_data_list],
dim=0)
else:
raise TypeError(
f"Type {type(tile_data_list[0][key])} is not handled!"
)
tile_data_list = [] # Empty tile_data_list
else:
# tile_data_list is not full yet, continue running inference...
continue
# --- Polygonize
if compute_polygonization:
crossfield = accumulated_tile_data[
"crossfield"] if "crossfield" in accumulated_tile_data else None
accumulated_tile_data["polygons"], accumulated_tile_data[
"polygon_probs"] = polygonize.polygonize(
self.config["polygonize_params"],
accumulated_tile_data["seg"],
crossfield_batch=crossfield,
pool=pool)
# --- Save output
if self.config["eval_params"]["save_individual_outputs"]["seg_mask"] or \
self.config["eval_params"]["save_aggregated_outputs"]["seg_coco"]:
# Take seg_interior:
seg_pred_mask = self.config["eval_params"][
"seg_threshold"] < accumulated_tile_data["seg"][:, 0, ...]
accumulated_tile_data["seg_mask"] = seg_pred_mask
accumulated_tile_data = local_utils.batch_to_cpu(
accumulated_tile_data)
sample_list = local_utils.split_batch(accumulated_tile_data)
# Save individual outputs:
if save_individual_outputs:
for sample in sample_list:
saver_async.add_work(sample)
# Store aggregated outputs:
if save_aggregated_outputs:
self.shared_dict["name_list"].extend(
accumulated_tile_data["name"])
if self.config["eval_params"]["save_aggregated_outputs"][
"stats"]:
y_pred = accumulated_tile_data["seg"][:, 0, ...].cpu()
if "gt_mask" in accumulated_tile_data:
y_true = accumulated_tile_data["gt_mask"][:, 0, ...]
elif "gt_polygons_image" in accumulated_tile_data:
y_true = accumulated_tile_data[
"gt_polygons_image"][:, 0, ...]
else:
raise ValueError(
"Either gt_mask or gt_polygons_image should be in accumulated_tile_data"
)
iou = measures.iou(
y_pred.reshape(y_pred.shape[0], -1),
y_true.reshape(y_true.shape[0], -1),
threshold=self.config["eval_params"]["seg_threshold"])
self.shared_dict["iou_list"].extend(iou.cpu().numpy())
if self.config["eval_params"]["save_aggregated_outputs"][
"seg_coco"]:
for sample in sample_list:
annotations = save_utils.seg_coco(sample)
self.shared_dict["seg_coco_list"].extend(annotations)
if self.config["eval_params"]["save_aggregated_outputs"][
"poly_coco"]:
for sample in sample_list:
annotations = save_utils.poly_coco(
sample["polygons"], sample["polygon_probs"],
sample["image_id"].item())
self.shared_dict["poly_coco_list"].append(
annotations
) # annotations could be a dict, or a list
# END of loop over samples
# Save aggregated results
if save_aggregated_outputs:
self.barrier.wait(
) # Wait on all processes so that shared_dict is synchronized.
if self.gpu == 0:
if self.config["eval_params"]["save_aggregated_outputs"][
"stats"]:
print("Start saving stats:")
# Save sample_stats in CSV:
t1 = time.time()
stats_filepath = os.path.join(
self.eval_dirpath, "{}.stats.csv".format(split_name))
stats_file = open(stats_filepath, "w")
fnames = ["name", "iou"]
writer = csv.DictWriter(stats_file, fieldnames=fnames)
writer.writeheader()
for name, iou in sorted(zip(self.shared_dict["name_list"],
self.shared_dict["iou_list"]),
key=lambda pair: pair[0]):
writer.writerow({"name": name, "iou": iou})
stats_file.close()
print(f"Finished in {time.time() - t1:02}s")
if self.config["eval_params"]["save_aggregated_outputs"][
"seg_coco"]:
print("Start saving seg_coco:")
t1 = time.time()
seg_coco_filepath = os.path.join(
self.eval_dirpath,
"{}.annotation.seg.json".format(split_name))
python_utils.save_json(
seg_coco_filepath,
list(self.shared_dict["seg_coco_list"]))
print(f"Finished in {time.time() - t1:02}s")
if self.config["eval_params"]["save_aggregated_outputs"][
"poly_coco"]:
print("Start saving poly_coco:")
poly_coco_base_filepath = os.path.join(
self.eval_dirpath, f"{split_name}.annotation.poly")
t1 = time.time()
save_utils.save_poly_coco(
self.shared_dict["poly_coco_list"],
poly_coco_base_filepath)
print(f"Finished in {time.time() - t1:02}s")
# Sync point of individual outputs
if save_individual_outputs:
print_utils.print_info(
f"GPU {self.gpu} -> INFO: Finishing saving individual outputs."
)
saver_async.join()
self.barrier.wait(
) # Wait on all processes so that all saver_asyncs are finished
def __init__(self,
root: str,
fold: str = "train",
pre_process: bool = True,
patch_size: int = None,
pre_transform=None,
transform=None,
small: bool = False,
pool_size: int = 1,
raw_dirname: str = "raw",
processed_dirname: str = "processed"):
"""
@param root:
@param fold:
@param pre_process: If True, the dataset will be pre-processed first, saving training patches on disk. If False, data will be serve on-the-fly without any patching.
@param patch_size:
@param pre_transform:
@param transform:
@param small: If True, use a small subset of the dataset (for testing)
@param pool_size:
@param processed_dirname:
"""
self.root = root
self.fold = fold
self.pre_process = pre_process
self.patch_size = patch_size
self.pre_transform = pre_transform
self.transform = transform
self.small = small
if self.small:
print_utils.print_info(
"INFO: Using small version of the xView2 xBD dataset.")
self.pool_size = pool_size
self.raw_dirname = raw_dirname
if self.pre_process:
# Setup of pre-process
self.processed_dirpath = os.path.join(self.root, processed_dirname,
self.fold)
stats_filepath = os.path.join(
self.processed_dirpath,
"stats-small.pt" if self.small else "stats.pt")
processed_relative_paths_filepath = os.path.join(
self.processed_dirpath, "processed_paths-small.json"
if self.small else "processed_paths.json")
# Check if dataset has finished pre-processing by checking processed_relative_paths_filepath:
if os.path.exists(processed_relative_paths_filepath):
# Process done, load stats and processed_relative_paths
self.stats = torch.load(stats_filepath)
self.processed_relative_paths = python_utils.load_json(
processed_relative_paths_filepath)
else:
# Pre-process not finished, launch it:
tile_info_list = self.get_tile_info_list()
self.stats = self.process(tile_info_list)
# Save stats
torch.save(self.stats, stats_filepath)
# Save processed_relative_paths
self.processed_relative_paths = [
tile_info["processed_relative_filepath"]
for tile_info in tile_info_list
]
python_utils.save_json(processed_relative_paths_filepath,
self.processed_relative_paths)
else:
# Setup data sample list
self.tile_info_list = self.get_tile_info_list()
def save_seg_coco(sample, base_filepath, name):
filepath = get_save_filepath(base_filepath, name, ".json")
annotations = seg_coco(sample)
python_utils.save_json(filepath, annotations)
def save_seg_coco(sample, base_filepath, name):
filepath = base_filepath + "." + name + ".json"
annotations = seg_coco(sample)
python_utils.save_json(filepath, annotations)
def eval_one(annotation_filename, run_results_dirpath, cocoGt, config, annType, pool=None):
print("---eval_one")
annotation_name = os.path.splitext(annotation_filename)[0]
if "samples" in config:
stats_filepath = os.path.join(run_results_dirpath,
"{}.stats.{}.{}.json".format("test", annotation_name, config["samples"]))
metrics_filepath = os.path.join(run_results_dirpath,
"{}.metrics.{}.{}.json".format("test", annotation_name, config["samples"]))
else:
stats_filepath = os.path.join(run_results_dirpath, "{}.stats.{}.json".format("test", annotation_name))
metrics_filepath = os.path.join(run_results_dirpath, "{}.metrics.{}.json".format("test", annotation_name))
res_filepath = os.path.join(run_results_dirpath, annotation_filename)
if not os.path.exists(res_filepath):
print_utils.print_warning("WARNING: result not found at filepath {}".format(res_filepath))
return
print_utils.print_info("Evaluate {} annotations:".format(annotation_filename))
try:
cocoDt = cocoGt.loadRes(res_filepath)
except AssertionError as e:
print_utils.print_error("ERROR: {}".format(e))
print_utils.print_info("INFO: continuing by removing unrecognised images")
res = json.load(open(res_filepath))
print("Initial res length:", len(res))
annsImgIds = [ann["image_id"] for ann in res]
image_id_rm = set(annsImgIds) - set(cocoGt.getImgIds())
print_utils.print_warning("Remove {} image ids!".format(len(image_id_rm)))
new_res = [ann for ann in res if ann["image_id"] not in image_id_rm]
print("New res length:", len(new_res))
cocoDt = cocoGt.loadRes(new_res)
# {4601886185638229705, 4602408603195004682, 4597274499619802317, 4600985465712755606, 4597238470822783353,
# 4597418614807878173}
# image_id = 0
# annotation_ids = cocoDt.getAnnIds(imgIds=image_id)
# annotation_list = cocoDt.loadAnns(annotation_ids)
# print(annotation_list)
if not os.path.exists(stats_filepath):
# Run COCOeval
cocoEval = COCOeval(cocoGt, cocoDt, annType)
cocoEval.evaluate()
cocoEval.accumulate()
cocoEval.summarize()
# Save stats
stats = {}
stat_names = ["AP", "AP_50", "AP_75", "AP_S", "AP_M", "AP_L", "AR", "AR_50", "AR_75", "AR_S", "AR_M", "AR_L"]
assert len(stat_names) == cocoEval.stats.shape[0]
for i, stat_name in enumerate(stat_names):
stats[stat_name] = cocoEval.stats[i]
python_utils.save_json(stats_filepath, stats)
else:
print("COCO stats already computed, skipping...")
if not os.path.exists(metrics_filepath):
# Verify that cocoDt has polygonal segmentation masks and not raster masks:
if isinstance(cocoDt.loadAnns(cocoDt.getAnnIds(imgIds=cocoDt.getImgIds()[0]))[0]["segmentation"], list):
metrics = {}
# Run additionnal metrics
print_utils.print_info("INFO: Running contour metrics")
contour_eval = ContourEval(cocoGt, cocoDt)
max_angle_diffs = contour_eval.evaluate(pool=pool)
metrics["max_angle_diffs"] = list(max_angle_diffs)
python_utils.save_json(metrics_filepath, metrics)
else:
print("Contour metrics already computed, skipping...")