def adddatasetstovideolistandviceversa(config):
"""
First run comparevideolistsanddatafolders(config) to compare the folders in labeled-data and the ones listed under video_sets (in the config file).
If you detect differences this function can be used to maker sure each folder has a video entry & vice versa.
It corrects this problem in the following way:
If a video entry in the config file does not contain a folder in labeled-data, then the entry is removed.
If a folder in labeled-data does not contain a video entry in the config file then the prefix path will be added in front of the name of the labeled-data folder and combined
with the suffix variable as an ending. Width and height will be added as cropping variables as passed on.
Handle with care!
Parameter
----------
config : string
String containing the full path of the config file in the project.
"""
cfg = auxiliaryfunctions.read_config(config)
videos = cfg["video_sets"]
video_names = [Path(i).stem for i in videos]
alldatafolders = [
fn for fn in os.listdir(Path(config).parent / "labeled-data")
if "_labeled" not in fn and not fn.startswith(".")
]
print("Config file contains:", len(video_names))
print("Labeled-data contains:", len(alldatafolders))
toberemoved = []
for vn in video_names:
if vn not in alldatafolders:
print(vn, " is missing as a labeled folder >> removing key!")
for fullvideo in videos:
if vn in fullvideo:
toberemoved.append(fullvideo)
for vid in toberemoved:
del videos[vid]
# Load updated lists:
video_names = [Path(i).stem for i in videos]
for vn in alldatafolders:
if vn not in video_names:
print(vn, " is missing in config file >> adding it!")
# Find the corresponding video file
found = False
for file in os.listdir(os.path.join(cfg["project_path"],
"videos")):
if os.path.splitext(file)[0] == vn:
found = True
break
if found:
video_path = os.path.join(cfg["project_path"], "videos", file)
clip = VideoReader(video_path)
videos.update({
video_path: {
"crop": ", ".join(map(str, clip.get_bbox()))
}
})
auxiliaryfunctions.write_config(config, cfg)
def create_new_project(
project,
experimenter,
videos,
working_directory=None,
copy_videos=False,
videotype=".avi",
multianimal=False,
):
"""Creates a new project directory, sub-directories and a basic configuration file. The configuration file is loaded with the default values. Change its parameters to your projects need.
Parameters
----------
project : string
String containing the name of the project.
experimenter : string
String containing the name of the experimenter.
videos : list
A list of string containing the full paths of the videos to include in the project.
Attention: Can also be a directory, then all videos of videotype will be imported.
working_directory : string, optional
The directory where the project will be created. The default is the ``current working directory``; if provided, it must be a string.
copy_videos : bool, optional
If this is set to True, the videos are copied to the ``videos`` directory. If it is False,symlink of the videos are copied to the project/videos directory. The default is ``False``; if provided it must be either
``True`` or ``False``.
multianimal: bool, optional. Default: False.
For creating a multi-animal project (introduced in DLC 2.2)
Example
--------
Linux/MacOs
>>> deeplabcut.create_new_project('reaching-task','Linus',['/data/videos/mouse1.avi','/data/videos/mouse2.avi','/data/videos/mouse3.avi'],'/analysis/project/')
>>> deeplabcut.create_new_project('reaching-task','Linus',['/data/videos'],videotype='.mp4')
Windows:
>>> deeplabcut.create_new_project('reaching-task','Bill',[r'C:\yourusername\rig-95\Videos\reachingvideo1.avi'], copy_videos=True)
Users must format paths with either: r'C:\ OR 'C:\\ <- i.e. a double backslash \ \ )
"""
from datetime import datetime as dt
from deeplabcut.utils import auxiliaryfunctions
date = dt.today()
month = date.strftime("%B")
day = date.day
d = str(month[0:3] + str(day))
date = dt.today().strftime("%Y-%m-%d")
if working_directory == None:
working_directory = "."
wd = Path(working_directory).resolve()
project_name = "{pn}-{exp}-{date}".format(pn=project, exp=experimenter, date=date)
project_path = wd / project_name
# Create project and sub-directories
if not DEBUG and project_path.exists():
print('Project "{}" already exists!'.format(project_path))
return
video_path = project_path / "videos"
data_path = project_path / "labeled-data"
shuffles_path = project_path / "training-datasets"
results_path = project_path / "dlc-models"
for p in [video_path, data_path, shuffles_path, results_path]:
p.mkdir(parents=True, exist_ok=DEBUG)
print('Created "{}"'.format(p))
# Add all videos in the folder. Multiple folders can be passed in a list, similar to the video files. Folders and video files can also be passed!
vids = []
for i in videos:
# Check if it is a folder
if os.path.isdir(i):
vids_in_dir = [
os.path.join(i, vp) for vp in os.listdir(i) if videotype in vp
]
vids = vids + vids_in_dir
if len(vids_in_dir) == 0:
print("No videos found in", i)
print(
"Perhaps change the videotype, which is currently set to:",
videotype,
)
else:
videos = vids
print(
len(vids_in_dir),
" videos from the directory",
i,
"were added to the project.",
)
else:
if os.path.isfile(i):
vids = vids + [i]
videos = vids
videos = [Path(vp) for vp in videos]
dirs = [data_path / Path(i.stem) for i in videos]
for p in dirs:
"""
Creates directory under data
"""
p.mkdir(parents=True, exist_ok=True)
destinations = [video_path.joinpath(vp.name) for vp in videos]
if copy_videos == True:
print("Copying the videos")
for src, dst in zip(videos, destinations):
shutil.copy(
os.fspath(src), os.fspath(dst)
) # https://www.python.org/dev/peps/pep-0519/
else:
# creates the symlinks of the video and puts it in the videos directory.
print("Attempting to create a symbolic link of the video ...")
for src, dst in zip(videos, destinations):
if dst.exists() and not DEBUG:
raise FileExistsError("Video {} exists already!".format(dst))
try:
src = str(src)
dst = str(dst)
os.symlink(src, dst)
except OSError:
import subprocess
subprocess.check_call("mklink %s %s" % (dst, src), shell=True)
print("Created the symlink of {} to {}".format(src, dst))
videos = destinations
if copy_videos == True:
videos = (
destinations
) # in this case the *new* location should be added to the config file
# adds the video list to the config.yaml file
video_sets = {}
for video in videos:
print(video)
try:
# For windows os.path.realpath does not work and does not link to the real video. [old: rel_video_path = os.path.realpath(video)]
rel_video_path = str(Path.resolve(Path(video)))
except:
rel_video_path = os.readlink(str(video))
try:
vid = VideoReader(rel_video_path)
video_sets[rel_video_path] = {"crop": ", ".join(map(str, vid.get_bbox()))}
except IOError:
warnings.warn("Cannot open the video file! Skipping to the next one...")
os.remove(video) # Removing the video or link from the project
if not len(video_sets):
# Silently sweep the files that were already written.
shutil.rmtree(project_path, ignore_errors=True)
warnings.warn(
"No valid videos were found. The project was not created... "
"Verify the video files and re-create the project."
)
return "nothingcreated"
# Set values to config file:
if multianimal: # parameters specific to multianimal project
cfg_file, ruamelFile = auxiliaryfunctions.create_config_template(multianimal)
cfg_file["multianimalproject"] = multianimal
cfg_file["identity"] = False
cfg_file["individuals"] = ["individual1", "individual2", "individual3"]
cfg_file["multianimalbodyparts"] = ["bodypart1", "bodypart2", "bodypart3"]
cfg_file["uniquebodyparts"] = []
cfg_file["bodyparts"] = "MULTI!"
cfg_file["skeleton"] = [
["bodypart1", "bodypart2"],
["bodypart2", "bodypart3"],
["bodypart1", "bodypart3"],
]
cfg_file["default_augmenter"] = "multi-animal-imgaug"
else:
cfg_file, ruamelFile = auxiliaryfunctions.create_config_template()
cfg_file["multianimalproject"] = False
cfg_file["bodyparts"] = ["bodypart1", "bodypart2", "bodypart3", "objectA"]
cfg_file["skeleton"] = [["bodypart1", "bodypart2"], ["objectA", "bodypart3"]]
cfg_file["default_augmenter"] = "default"
cfg_file["croppedtraining"] = False
# common parameters:
cfg_file["Task"] = project
cfg_file["scorer"] = experimenter
cfg_file["video_sets"] = video_sets
cfg_file["project_path"] = str(project_path)
cfg_file["date"] = d
cfg_file["cropping"] = False
cfg_file["start"] = 0
cfg_file["stop"] = 1
cfg_file["numframes2pick"] = 20
cfg_file["TrainingFraction"] = [0.95]
cfg_file["iteration"] = 0
cfg_file["default_net_type"] = "resnet_50"
cfg_file["snapshotindex"] = -1
cfg_file["x1"] = 0
cfg_file["x2"] = 640
cfg_file["y1"] = 277
cfg_file["y2"] = 624
cfg_file[
"batch_size"
] = (
8
) # batch size during inference (video - analysis); see https://www.biorxiv.org/content/early/2018/10/30/457242
cfg_file["corner2move2"] = (50, 50)
cfg_file["move2corner"] = True
cfg_file["skeleton_color"] = "black"
cfg_file["pcutoff"] = 0.6
cfg_file["dotsize"] = 12 # for plots size of dots
cfg_file["alphavalue"] = 0.7 # for plots transparency of markers
cfg_file["colormap"] = "rainbow" # for plots type of colormap
projconfigfile = os.path.join(str(project_path), "config.yaml")
# Write dictionary to yaml config file
auxiliaryfunctions.write_config(projconfigfile, cfg_file)
print('Generated "{}"'.format(project_path / "config.yaml"))
print(
"\nA new project with name %s is created at %s and a configurable file (config.yaml) is stored there. Change the parameters in this file to adapt to your project's needs.\n Once you have changed the configuration file, use the function 'extract_frames' to select frames for labeling.\n. [OPTIONAL] Use the function 'add_new_videos' to add new videos to your project (at any stage)."
% (project_name, str(wd))
)
return projconfigfile
def add_new_videos(config, videos, copy_videos=False, coords=None):
"""
Add new videos to the config file at any stage of the project.
Parameters
----------
config : string
String containing the full path of the config file in the project.
videos : list
A list of string containing the full paths of the videos to include in the project.
copy_videos : bool, optional
If this is set to True, the symlink of the videos are copied to the project/videos directory. The default is
``False``; if provided it must be either ``True`` or ``False``.
coords: list, optional
A list containing the list of cropping coordinates of the video. The default is set to None.
Examples
--------
Video will be added, with cropping dimenions according to the frame dimensinos of mouse5.avi
>>> deeplabcut.add_new_videos('/home/project/reaching-task-Tanmay-2018-08-23/config.yaml',['/data/videos/mouse5.avi'])
Video will be added, with cropping dimenions [0,100,0,200]
>>> deeplabcut.add_new_videos('/home/project/reaching-task-Tanmay-2018-08-23/config.yaml',['/data/videos/mouse5.avi'],copy_videos=False,coords=[[0,100,0,200]])
Two videos will be added, with cropping dimenions [0,100,0,200] and [0,100,0,250], respectively.
>>> deeplabcut.add_new_videos('/home/project/reaching-task-Tanmay-2018-08-23/config.yaml',['/data/videos/mouse5.avi','/data/videos/mouse6.avi'],copy_videos=False,coords=[[0,100,0,200],[0,100,0,250]])
"""
import os
import shutil
from pathlib import Path
from deeplabcut.utils import auxiliaryfunctions
from deeplabcut.utils.auxfun_videos import VideoReader
# Read the config file
cfg = auxiliaryfunctions.read_config(config)
video_path = Path(config).parents[0] / "videos"
data_path = Path(config).parents[0] / "labeled-data"
videos = [Path(vp) for vp in videos]
dirs = [data_path / Path(i.stem) for i in videos]
for p in dirs:
"""
Creates directory under data & perhaps copies videos (to /video)
"""
p.mkdir(parents=True, exist_ok=True)
destinations = [video_path.joinpath(vp.name) for vp in videos]
if copy_videos:
for src, dst in zip(videos, destinations):
if dst.exists():
pass
else:
print("Copying the videos")
shutil.copy(os.fspath(src), os.fspath(dst))
else:
for src, dst in zip(videos, destinations):
if dst.exists():
pass
else:
print("Creating the symbolic link of the video")
src = str(src)
dst = str(dst)
os.symlink(src, dst)
if copy_videos:
videos = destinations # in this case the *new* location should be added to the config file
# adds the video list to the config.yaml file
for idx, video in enumerate(videos):
try:
# For windows os.path.realpath does not work and does not link to the real video.
video_path = str(Path.resolve(Path(video)))
# video_path = os.path.realpath(video)
except:
video_path = os.readlink(video)
vid = VideoReader(video_path)
if coords is not None:
c = coords[idx]
else:
c = vid.get_bbox()
params = {video_path: {"crop": ", ".join(map(str, c))}}
if "video_sets_original" not in cfg:
cfg["video_sets"].update(params)
else:
cfg["video_sets_original"].update(params)
auxiliaryfunctions.write_config(config, cfg)
print(
"New video was added to the project! Use the function 'extract_frames' to select frames for labeling."
)
def add_new_videos(config, videos, copy_videos=False, coords=None, extract_frames=False):
"""
Add new videos to the config file at any stage of the project.
Parameters
----------
config : string
String containing the full path of the config file in the project.
videos : list
A list of strings containing the full paths of the videos to include in the project.
copy_videos : bool, optional
If this is set to True, the symlink of the videos are copied to the project/videos directory. The default is
``False``; if provided it must be either ``True`` or ``False``.
coords: list, optional
A list containing the list of cropping coordinates of the video. The default is set to None.
extract_frames: bool, optional
if this is set to True extract_frames will be run on the new videos
Examples
--------
Video will be added, with cropping dimensions according to the frame dimensions of mouse5.avi
>>> deeplabcut.add_new_videos('/home/project/reaching-task-Tanmay-2018-08-23/config.yaml',['/data/videos/mouse5.avi'])
Video will be added, with cropping dimensions [0,100,0,200]
>>> deeplabcut.add_new_videos('/home/project/reaching-task-Tanmay-2018-08-23/config.yaml',['/data/videos/mouse5.avi'],copy_videos=False,coords=[[0,100,0,200]])
Two videos will be added, with cropping dimensions [0,100,0,200] and [0,100,0,250], respectively.
>>> deeplabcut.add_new_videos('/home/project/reaching-task-Tanmay-2018-08-23/config.yaml',['/data/videos/mouse5.avi','/data/videos/mouse6.avi'],copy_videos=False,coords=[[0,100,0,200],[0,100,0,250]])
"""
import os
import shutil
from pathlib import Path
from deeplabcut.utils import auxiliaryfunctions
from deeplabcut.utils.auxfun_videos import VideoReader
from deeplabcut.generate_training_dataset import frame_extraction
# Read the config file
cfg = auxiliaryfunctions.read_config(config)
video_path = Path(config).parents[0] / "videos"
data_path = Path(config).parents[0] / "labeled-data"
videos = [Path(vp) for vp in videos]
dirs = [data_path / Path(i.stem) for i in videos]
for p in dirs:
"""
Creates directory under data & perhaps copies videos (to /video)
"""
p.mkdir(parents=True, exist_ok=True)
destinations = [video_path.joinpath(vp.name) for vp in videos]
if copy_videos:
for src, dst in zip(videos, destinations):
if dst.exists():
pass
else:
print("Copying the videos")
shutil.copy(os.fspath(src), os.fspath(dst))
else:
# creates the symlinks of the video and puts it in the videos directory.
print("Attempting to create a symbolic link of the video ...")
for src, dst in zip(videos, destinations):
if dst.exists():
pass
try:
src = str(src)
dst = str(dst)
os.symlink(src, dst)
print("Created the symlink of {} to {}".format(src, dst))
except OSError:
try:
import subprocess
subprocess.check_call("mklink %s %s" % (dst, src), shell=True)
except (OSError, subprocess.CalledProcessError):
print(
"Symlink creation impossible (exFat architecture?): "
"cutting/pasting the video instead."
)
shutil.move(os.fspath(src), os.fspath(dst))
print("{} moved to {}".format(src, dst))
videos = destinations
if copy_videos:
videos = destinations # in this case the *new* location should be added to the config file
# adds the video list to the config.yaml file
for idx, video in enumerate(videos):
try:
# For windows os.path.realpath does not work and does not link to the real video.
video_path = str(Path.resolve(Path(video)))
# video_path = os.path.realpath(video)
except:
video_path = os.readlink(video)
vid = VideoReader(video_path)
if coords is not None:
c = coords[idx]
else:
c = vid.get_bbox()
params = {video_path: {"crop": ", ".join(map(str, c))}}
if "video_sets_original" not in cfg:
cfg["video_sets"].update(params)
else:
cfg["video_sets_original"].update(params)
videos_str = [str(video) for video in videos]
if extract_frames:
frame_extraction.extract_frames(config, userfeedback=False, videos_list=videos_str)
print(
"New videos were added to the project and frames have been extracted for labeling!"
)
else:
print(
"New videos were added to the project! Use the function 'extract_frames' to select frames for labeling."
)
auxiliaryfunctions.write_config(config, cfg)
