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testscript_3d.py
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testscript_3d.py
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"""
DeepLabCut2.0 Toolbox (deeplabcut.org)
© A. & M. Mathis Labs
https://github.com/AlexEMG/DeepLabCut
Please see AUTHORS for contributors.
https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
Licensed under GNU Lesser General Public License v3.0
This script tests various functionalities in an automatic way.
It produces nothing of interest scientifically.
"""
task='TEST3D' # Enter the name of your experiment Task
scorer='Alex' # Enter the name of the experimenter/labeler
num_cameras=2 # Enter the number of cameras
import os, deeplabcut
import zipfile, urllib.request, shutil
from datetime import datetime as dt
import glob
from pathlib import Path
import subprocess
print("Imported DLC!")
basepath=os.path.dirname(os.path.abspath('testscript_3d.py'))
videoname='reachingvideo1'
video=[os.path.join(basepath,'Reaching-Mackenzie-2018-08-30','videos',videoname+'.avi')]
folder='3Dtestviews_videos'
deeplabcut.auxiliaryfunctions.attempttomakefolder(folder)
# copying demo video from reaching data set and create two "views":
dst_videoname1 = 'vid1_camera-1'
dst_videoname2 = 'vid1_camera-2'
dst_videoname3 = 'long_camera-2'
output1 = os.path.join(basepath,folder,dst_videoname1+'.avi')
output2 = os.path.join(basepath,folder,dst_videoname2+'.avi')
output3 = os.path.join(basepath,folder,dst_videoname3+'.avi')
shutil.copyfile(video[0], output3)
vname='brief'
try: #you need ffmpeg command line interface
subprocess.call(['ffmpeg','-i',video[0],'-ss','00:00:00','-to','00:00:00.4','-c','copy',output1])
subprocess.call(['ffmpeg','-i',video[0],'-ss','00:00:00','-to','00:00:00.4','-c','copy',output2])
except:
pass
'''
# copying demo video from reaching data set and create two "views":
dst_videoname1 = 'vid1_camera-1'
dst_videoname2 = 'vid1_camera-2'
output1 = os.path.join(basepath,folder,dst_videoname1+'.avi')
output2 = os.path.join(basepath,folder,dst_videoname2+'.avi')
shutil.copyfile(video[0], output1)
shutil.copyfile(video[0], output2)
'''
# checking if 2d test project is available
try:
config = glob.glob(os.path.join(basepath,'TEST*','config.yaml'))[-1]
except:
raise("Please run the testscript.py first before testing for 3d")
dfolder=None
print("CREATING 3-D PROJECT")
path_config_file=deeplabcut.create_new_project_3d(task,scorer,num_cameras)
try:
cfg=deeplabcut.auxiliaryfunctions.read_config(path_config_file)
cfg['config_file_camera-1']=config
cfg['shuffle_camera-1']=1
cfg['config_file_camera-2']=config
cfg['shuffle_camera-2']=2
cfg['skeleton']=[['bodypart1','bodypart2'],['objectA','bodypart3']]
deeplabcut.auxiliaryfunctions.write_config_3d(path_config_file,cfg)
except:
raise("Please delete the project and re-try.") # otherwise the cfg is an empty array!
'''
# Creating the name of the project
date = dt.today()
month = date.strftime("%B")
day = date.day
d = str(month[0:3]+str(day))
date = dt.today().strftime('%Y-%m-%d')
project_name = '{pn}-{exp}-{date}-{triangulate}'.format(pn=task, exp=scorer, date=date,triangulate='3d')
'''
project_name=path_config_file.split(os.sep)[-2]
os.chdir(os.path.join(basepath,project_name,'calibration_images'))
# Dowloading the calibration images
url = 'http://www.vision.caltech.edu/bouguetj/calib_doc/htmls/stereo_example.zip'
file_name = 'stereo_example.zip'
with urllib.request.urlopen(url) as response, open(file_name, 'wb') as out_file:
shutil.copyfileobj(response, out_file)
file_name = os.path.join(basepath,project_name,'calibration_images','stereo_example.zip')
with zipfile.ZipFile(file_name) as zf:
zf.extractall()
# Deleting unneccesary images; the ones whose corners are not detected and .mat files
cwd = os.getcwd()
[os.remove(file) for file in os.listdir(cwd) if not file.endswith('.jpg')]
# change the file names for calibration images to match the name of cameras in config.yaml file.i.e. camera-1 and camera-2
cam1_images = glob.glob(os.path.join(cwd,'left*.jpg'))
cam2_images = glob.glob(os.path.join(cwd,'right*.jpg'))
# Sorting images
cam1_images.sort(key=lambda f: int(''.join(filter(str.isdigit, f))))
cam2_images.sort(key=lambda f: int(''.join(filter(str.isdigit, f))))
for idx,name in enumerate(cam1_images):
os.rename(name,os.path.join(cwd,str('camera-1_'+"{0:0=2d}".format(idx+1)+'.jpg')))
for idx,name in enumerate(cam2_images):
os.rename(name,os.path.join(cwd,str('camera-2_'+"{0:0=2d}".format(idx+1)+'.jpg')))
# Removing some of the images where the corner was not detected
[os.remove(file) for file in glob.glob(os.path.join(cwd, '*06.jpg'))]
[os.remove(file) for file in glob.glob(os.path.join(cwd, '*01.jpg'))]
print("CALIBRATING THE CAMERAS")
deeplabcut.calibrate_cameras(path_config_file,calibrate=True)
print("CHECKING FOR UNDISTORTION")
deeplabcut.check_undistortion(path_config_file)
print("TRIANGULATING")
video_dir = os.path.join(basepath,folder)
deeplabcut.triangulate(path_config_file,video_dir,save_as_csv=True)
print("CREATING LABELED VIDEO 3-D")
deeplabcut.create_labeled_video_3d(path_config_file,[video_dir],start=5,end=10)
#output_path = [os.path.join(basepath,folder)]
#deeplabcut.create_labeled_video_3d(path_config_file,output_path,start=5,end=10)
print("ALL DONE!!! - default 3D cases are functional.")