deeplabcut multi

ipython
import deeplabcut

deeplabcut.create_new_project('ProjectName','YourName', ['/usr/FullPath/OfVideo1.avi', '/usr/FullPath/OfVideo2.avi', '/usr/FullPath/OfVideo1.avi'],
              copy_videos=True, multianimal=True)

config_path = '/thefulloutputpath/config.yaml'

deeplabcut.add_new_videos('Full path of the project configuration file*', ['full path of video 4', 'full path of video 5'], copy_videos=True/False)

edits = {'colormap': 'summer',
         'individuals': ['mickey', 'minnie', 'bianca'],
         'skeleton': [['snout', 'tailbase'], ['snout', 'rightear']]}
deeplabcut.auxiliaryfunctions.edit_config(config_path, edits)

individuals:
- m1
- m2
- m3

uniquebodyparts:
- topleftcornerofBox
- toprightcornerofBox

multianimalbodyparts:
- snout
- leftear
- rightear
- tailbase

identity: True/False

deeplabcut.extract_frames(config_path, mode='automatic/manual', algo='uniform/kmeans', userfeedback=False, crop=True/False)

deeplabcut.extract_frames(config_path, 'manual')

deeplabcut.label_frames(config_path)

deeplabcut.check_labels(config_path, visualizeindividuals=True/False)

deeplabcut.create_multianimaltraining_dataset(config_path)

my_better_graph = [[0, 1], [1, 2], [2, 3]]  # These are indices in the list of multianimalbodyparts
deeplabcut.create_multianimaltraining_dataset(config_path, paf_graph=my_better_graph)

deeplabcut.create_multianimaltraining_dataset(config_path, paf_graph='config')

deeplabcut.train_network(config_path, allow_growth=True)

deeplabcut.train_network(config_path, shuffle=1, trainingsetindex=0, gputouse=None, max_snapshots_to_keep=5, autotune=False, displayiters=100, saveiters=15000, maxiters=30000, allow_growth=True)

deeplabcut.evaluate_network(config_path, plotting=True)

deeplabcut.extract_save_all_maps(config_path, shuffle=shuffle, Indices=[0, 5])

scorername = deeplabcut.analyze_videos(config_path,['/fullpath/project/videos/testVideo.mp4'], videotype='.mp4')
deeplabcut.create_video_with_all_detections(config_path, ['/fullpath/project/videos/testVideo.mp4'], videotype='.mp4')

deeplabcut.find_outliers_in_raw_data(config_path, pickle_file, video_file)

deeplabcut.analyze_videos(config_path, ['/fullpath/project/videos/'], videotype='.mp4', auto_track=True)

deeplabcut.convert_detections2tracklets(..., identity_only=True)

deeplabcut.stitch_tracklets(config_path, ['videofile_path'], videotype='mp4',
                            shuffle=1, trainingsetindex=0)

deeplabcut.transformer_reID(config, videos_to_analyze, n_tracks=None, videotype="mp4")

deeplabcut.refine_tracklets(config_path, pickle_or_h5_file, videofile_path, max_gap=0, min_swap_len=2, min_tracklet_len=2, trail_len=50)

deeplabcut.filterpredictions(config_path,['/fullpath/project/videos/reachingvideo1.avi'])

  deeplabcut.plot_trajectories(config_path,['/fullpath/project/videos/reachingvideo1.avi'],filtered = True)

  deeplabcut.create_labeled_video(config_path, [videos], videotype='avi', shuffle=1, trainingsetindex=0, filtered=False, fastmode=True, save_frames=False, keypoints_only=False, Frames2plot=None, displayedbodyparts='all', displayedindividuals='all', codec='mp4v', outputframerate=None, destfolder=None, draw_skeleton=False, trailpoints=0, displaycropped=False, color_by='bodypart', track_method='')