def write(
cls,
filename: str,
source_object: str,
compress: Optional[bool] = None,
save_frame_data: bool = False,
frame_data_format: str = "png",
):
"""
Save a Labels instance to a JSON format.
Args:
filename: The filename to save the data to.
source_object: The labels dataset to save.
compress: Whether the data be zip compressed or not? If True,
the JSON will be compressed using Python's shutil.make_archive
command into a PKZIP zip file. If compress is True then
filename will have a .zip appended to it.
save_frame_data: Whether to save the image data for each frame.
For each video in the dataset, all frames that have labels
will be stored as an imgstore dataset.
If save_frame_data is True then compress will be forced to True
since the archive must contain both the JSON data and image
data stored in ImgStores.
frame_data_format: If save_frame_data is True, then this argument
is used to set the data format to use when writing frame
data to ImgStore objects. Supported formats should be:
* 'pgm',
* 'bmp',
* 'ppm',
* 'tif',
* 'png',
* 'jpg',
* 'npy',
* 'mjpeg/avi',
* 'h264/mkv',
* 'avc1/mp4'
Note: 'h264/mkv' and 'avc1/mp4' require separate installation
of these codecs on your system. They are excluded from SLEAP
because of their GPL license.
Returns:
None
"""
labels = source_object
if compress is None:
compress = filename.endswith(".zip")
# Lets make a temporary directory to store the image frame data or pre-compressed json
# in case we need it.
with tempfile.TemporaryDirectory() as tmp_dir:
# If we are saving frame data along with the datasets. We will replace videos with
# new video object that represent video data from just the labeled frames.
if save_frame_data:
# Create a set of new Video objects with imgstore backends. One for each
# of the videos. We will only include the labeled frames though. We will
# then replace each video with this new video
new_videos = labels.save_frame_data_imgstore(
output_dir=tmp_dir, format=frame_data_format)
# Make video paths relative
for vid in new_videos:
tmp_path = vid.filename
# Get the parent dir of the YAML file.
# Use "/" since this works on Windows and posix
img_store_dir = (
os.path.basename(os.path.split(tmp_path)[0]) + "/" +
os.path.basename(tmp_path))
# Change to relative path
vid.backend.filename = img_store_dir
# Convert to a dict, not JSON yet, because we need to patch up the videos
d = labels.to_dict()
d["videos"] = Video.cattr().unstructure(new_videos)
else:
d = labels.to_dict()
# Set file format version
d["format_id"] = cls.FORMAT_ID
if compress or save_frame_data:
# Ensure that filename ends with .json
# shutil will append .zip
filename = re.sub("(\\.json)?(\\.zip)?$", ".json", filename)
# Write the json to the tmp directory, we will zip it up with the frame data.
full_out_filename = os.path.join(tmp_dir,
os.path.basename(filename))
json_dumps(d, full_out_filename)
# Create the archive
shutil.make_archive(base_name=filename,
root_dir=tmp_dir,
format="zip")
# If the user doesn't want to compress, then just write the json to the filename
else:
json_dumps(d, filename)
def from_json_data(cls,
data: Union[str, dict],
match_to: Optional["Labels"] = None) -> "Labels":
"""
Create instance of class from data in dictionary.
Method is used by other methods that load from JSON.
Args:
data: Dictionary, deserialized from JSON.
match_to: If given, we'll replace particular objects in the
data dictionary with *matching* objects in the match_to
:class:`Labels` object. This ensures that the newly
instantiated :class:`Labels` can be merged without
duplicate matching objects (e.g., :class:`Video` objects ).
Returns:
A new :class:`Labels` object.
"""
# Parse the json string if needed.
if type(data) is str:
dicts = json_loads(data)
else:
dicts = data
dicts["tracks"] = dicts.get(
"tracks", []) # don't break if json doesn't include tracks
# First, deserialize the skeletons, videos, and nodes lists.
# The labels reference these so we will need them while deserializing.
nodes = cattr.structure(dicts["nodes"], List[Node])
idx_to_node = {i: nodes[i] for i in range(len(nodes))}
skeletons = Skeleton.make_cattr(idx_to_node).structure(
dicts["skeletons"], List[Skeleton])
videos = Video.cattr().structure(dicts["videos"], List[Video])
try:
# First try unstructuring tuple (newer format)
track_cattr = cattr.Converter(
unstruct_strat=cattr.UnstructureStrategy.AS_TUPLE)
tracks = track_cattr.structure(dicts["tracks"], List[Track])
except:
# Then try unstructuring dict (older format)
try:
tracks = cattr.structure(dicts["tracks"], List[Track])
except:
raise ValueError("Unable to load tracks as tuple or dict!")
# if we're given a Labels object to match, use its objects when they match
if match_to is not None:
for idx, sk in enumerate(skeletons):
for old_sk in match_to.skeletons:
if sk.matches(old_sk):
# use nodes from matched skeleton
for (node, match_node) in zip(sk.nodes, old_sk.nodes):
node_idx = nodes.index(node)
nodes[node_idx] = match_node
# use skeleton from match
skeletons[idx] = old_sk
break
for idx, vid in enumerate(videos):
for old_vid in match_to.videos:
# Try to match videos using either their current or source filename
# if available.
old_vid_paths = [old_vid.filename]
if getattr(old_vid.backend, "has_embedded_images", False):
old_vid_paths.append(
old_vid.backend._source_video.filename)
new_vid_paths = [vid.filename]
if getattr(vid.backend, "has_embedded_images", False):
new_vid_paths.append(
vid.backend._source_video.filename)
is_match = False
for old_vid_path in old_vid_paths:
for new_vid_path in new_vid_paths:
if old_vid_path == new_vid_path or weak_filename_match(
old_vid_path, new_vid_path):
is_match = True
videos[idx] = old_vid
break
if is_match:
break
if is_match:
break
suggestions = []
if "suggestions" in dicts:
suggestions_cattr = cattr.Converter()
suggestions_cattr.register_structure_hook(
Video, lambda x, type: videos[int(x)])
try:
suggestions = suggestions_cattr.structure(
dicts["suggestions"], List[SuggestionFrame])
except Exception as e:
print("Error while loading suggestions (1)")
print(e)
try:
# Convert old suggestion format to new format.
# Old format: {video: list of frame indices}
# New format: [SuggestionFrames]
old_suggestions = suggestions_cattr.structure(
dicts["suggestions"], Dict[Video, List])
for video in old_suggestions.keys():
suggestions.extend([
SuggestionFrame(video, idx)
for idx in old_suggestions[video]
])
except Exception as e:
print("Error while loading suggestions (2)")
print(e)
pass
if "negative_anchors" in dicts:
negative_anchors_cattr = cattr.Converter()
negative_anchors_cattr.register_structure_hook(
Video, lambda x, type: videos[int(x)])
negative_anchors = negative_anchors_cattr.structure(
dicts["negative_anchors"], Dict[Video, List])
else:
negative_anchors = dict()
if "provenance" in dicts:
provenance = dicts["provenance"]
else:
provenance = dict()
# If there is actual labels data, get it.
if "labels" in dicts:
label_cattr = make_instance_cattr()
label_cattr.register_structure_hook(
Skeleton, lambda x, type: skeletons[int(x)])
label_cattr.register_structure_hook(Video,
lambda x, type: videos[int(x)])
label_cattr.register_structure_hook(
Node, lambda x, type: x
if isinstance(x, Node) else nodes[int(x)])
label_cattr.register_structure_hook(
Track, lambda x, type: None if x is None else tracks[int(x)])
labels = label_cattr.structure(dicts["labels"], List[LabeledFrame])
else:
labels = []
return Labels(
labeled_frames=labels,
videos=videos,
skeletons=skeletons,
nodes=nodes,
suggestions=suggestions,
negative_anchors=negative_anchors,
tracks=tracks,
provenance=provenance,
)
def write(
cls,
filename: str,
source_object: object,
append: bool = False,
save_frame_data: bool = False,
frame_data_format: str = "png",
all_labeled: bool = False,
suggested: bool = False,
):
labels = source_object
# Delete the file if it exists, we want to start from scratch since
# h5py truncates the file which seems to not actually delete data
# from the file. Don't if we are appending of course.
if os.path.exists(filename) and not append:
os.unlink(filename)
# Serialize all the meta-data to JSON.
d = labels.to_dict(skip_labels=True)
if save_frame_data:
new_videos = labels.save_frame_data_hdf5(
filename,
format=frame_data_format,
user_labeled=True,
all_labeled=all_labeled,
suggested=suggested,
)
# Replace path to video file with "." (which indicates that the
# video is in the same file as the HDF5 labels dataset).
# Otherwise, the video paths will break if the HDF5 labels
# dataset file is moved.
for vid in new_videos:
vid.backend.filename = "."
d["videos"] = Video.cattr().unstructure(new_videos)
with h5py.File(filename, "a") as f:
# Add all the JSON metadata
meta_group = f.require_group("metadata")
meta_group.attrs["format_id"] = cls.FORMAT_ID
# If we are appending and there already exists JSON metadata
if append and "json" in meta_group.attrs:
# Otherwise, we need to read the JSON and append to the lists
old_labels = labels_json.LabelsJsonAdaptor.from_json_data(
meta_group.attrs["json"].tostring().decode()
)
# A function to join to list but only include new non-dupe entries
# from the right hand list.
def append_unique(old, new):
unique = []
for x in new:
try:
matches = [y.matches(x) for y in old]
except AttributeError:
matches = [x == y for y in old]
# If there were no matches, this is a unique object.
if sum(matches) == 0:
unique.append(x)
else:
# If we have an object that matches, replace the instance
# with the one from the new list. This will will make sure
# objects on the Instances are the same as those in the
# Labels lists.
for i, match in enumerate(matches):
if match:
old[i] = x
return old + unique
# Append the lists
labels.tracks = append_unique(old_labels.tracks, labels.tracks)
labels.skeletons = append_unique(old_labels.skeletons, labels.skeletons)
labels.videos = append_unique(old_labels.videos, labels.videos)
labels.nodes = append_unique(old_labels.nodes, labels.nodes)
# FIXME: Do something for suggestions and negative_anchors
# Get the dict for JSON and save it over the old data
d = labels.to_dict(skip_labels=True)
if not append:
# These items are stored in separate lists because the metadata
# group got to be too big.
for key in ("videos", "tracks", "suggestions"):
# Convert for saving in hdf5 dataset
data = [np.string_(json_dumps(item)) for item in d[key]]
hdf5_key = f"{key}_json"
# Save in its own dataset (e.g., videos_json)
f.create_dataset(hdf5_key, data=data, maxshape=(None,))
# Clear from dict since we don't want to save this in attribute
d[key] = []
# Output the dict to JSON
meta_group.attrs["json"] = np.string_(json_dumps(d))
# FIXME: We can probably construct these from attrs fields
# We will store Instances and PredcitedInstances in the same
# table. instance_type=0 or Instance and instance_type=1 for
# PredictedInstance, score will be ignored for Instances.
instance_dtype = np.dtype(
[
("instance_id", "i8"),
("instance_type", "u1"),
("frame_id", "u8"),
("skeleton", "u4"),
("track", "i4"),
("from_predicted", "i8"),
("score", "f4"),
("point_id_start", "u8"),
("point_id_end", "u8"),
]
)
frame_dtype = np.dtype(
[
("frame_id", "u8"),
("video", "u4"),
("frame_idx", "u8"),
("instance_id_start", "u8"),
("instance_id_end", "u8"),
]
)
num_instances = len(labels.all_instances)
max_skeleton_size = max([len(s.nodes) for s in labels.skeletons], default=0)
# Initialize data arrays for serialization
points = np.zeros(num_instances * max_skeleton_size, dtype=Point.dtype)
pred_points = np.zeros(
num_instances * max_skeleton_size, dtype=PredictedPoint.dtype
)
instances = np.zeros(num_instances, dtype=instance_dtype)
frames = np.zeros(len(labels), dtype=frame_dtype)
# Pre compute some structures to make serialization faster
skeleton_to_idx = {
skeleton: labels.skeletons.index(skeleton)
for skeleton in labels.skeletons
}
track_to_idx = {
track: labels.tracks.index(track) for track in labels.tracks
}
track_to_idx[None] = -1
video_to_idx = {
video: labels.videos.index(video) for video in labels.videos
}
instance_type_to_idx = {Instance: 0, PredictedInstance: 1}
# Each instance we create will have and index in the dataset, keep track of
# these so we can quickly add from_predicted links on a second pass.
instance_to_idx = {}
instances_with_from_predicted = []
instances_from_predicted = []
# If we are appending, we need look inside to see what frame, instance, and
# point ids we need to start from. This gives us offsets to use.
if append and "points" in f:
point_id_offset = f["points"].shape[0]
pred_point_id_offset = f["pred_points"].shape[0]
instance_id_offset = f["instances"][-1]["instance_id"] + 1
frame_id_offset = int(f["frames"][-1]["frame_id"]) + 1
else:
point_id_offset = 0
pred_point_id_offset = 0
instance_id_offset = 0
frame_id_offset = 0
point_id = 0
pred_point_id = 0
instance_id = 0
for frame_id, label in enumerate(labels):
frames[frame_id] = (
frame_id + frame_id_offset,
video_to_idx[label.video],
label.frame_idx,
instance_id + instance_id_offset,
instance_id + instance_id_offset + len(label.instances),
)
for instance in label.instances:
# Add this instance to our lookup structure we will need for
# from_predicted links
instance_to_idx[instance] = instance_id
parray = instance.get_points_array(copy=False, full=True)
instance_type = type(instance)
# Check whether we are working with a PredictedInstance or an
# Instance.
if instance_type is PredictedInstance:
score = instance.score
pid = pred_point_id + pred_point_id_offset
else:
score = np.nan
pid = point_id + point_id_offset
# Keep track of any from_predicted instance links, we will
# insert the correct instance_id in the dataset after we are
# done.
if instance.from_predicted:
instances_with_from_predicted.append(instance_id)
instances_from_predicted.append(instance.from_predicted)
# Copy all the data
instances[instance_id] = (
instance_id + instance_id_offset,
instance_type_to_idx[instance_type],
frame_id,
skeleton_to_idx[instance.skeleton],
track_to_idx[instance.track],
-1,
score,
pid,
pid + len(parray),
)
# If these are predicted points, copy them to the predicted point
# array otherwise, use the normal point array
if type(parray) is PredictedPointArray:
pred_points[
pred_point_id : (pred_point_id + len(parray))
] = parray
pred_point_id = pred_point_id + len(parray)
else:
points[point_id : (point_id + len(parray))] = parray
point_id = point_id + len(parray)
instance_id = instance_id + 1
# Add from_predicted links
for instance_id, from_predicted in zip(
instances_with_from_predicted, instances_from_predicted
):
try:
instances[instance_id]["from_predicted"] = instance_to_idx[
from_predicted
]
except KeyError:
# If we haven't encountered the from_predicted instance yet then
# don't save the link. It's possible for a user to create a regular
# instance from a predicted instance and then delete all predicted
# instances from the file, but in this case I don’t think there's
# any reason to remember which predicted instance the regular
# instance came from.
pass
# We pre-allocated our points array with max possible size considering the
# max skeleton size, drop any unused points.
points = points[0:point_id]
pred_points = pred_points[0:pred_point_id]
# Create datasets if we need to
if append and "points" in f:
f["points"].resize((f["points"].shape[0] + points.shape[0]), axis=0)
f["points"][-points.shape[0] :] = points
f["pred_points"].resize(
(f["pred_points"].shape[0] + pred_points.shape[0]), axis=0
)
f["pred_points"][-pred_points.shape[0] :] = pred_points
f["instances"].resize(
(f["instances"].shape[0] + instances.shape[0]), axis=0
)
f["instances"][-instances.shape[0] :] = instances
f["frames"].resize((f["frames"].shape[0] + frames.shape[0]), axis=0)
f["frames"][-frames.shape[0] :] = frames
else:
f.create_dataset(
"points", data=points, maxshape=(None,), dtype=Point.dtype
)
f.create_dataset(
"pred_points",
data=pred_points,
maxshape=(None,),
dtype=PredictedPoint.dtype,
)
f.create_dataset(
"instances", data=instances, maxshape=(None,), dtype=instance_dtype
)
f.create_dataset(
"frames", data=frames, maxshape=(None,), dtype=frame_dtype
)
