dlc_reader.py
PoseEstimation
¶
Source code in src/spyglass/position/v1/dlc_reader.py
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pkl
property
¶
Pickle object with metadata about the DLC run.
yml
property
¶
Dictionary of the yaml file DLC metadata.
rawdata
property
¶
Pandas dataframe of the DLC output from the h5 file.
data
property
¶
Dictionary of the bodyparts and corresponding dataframe data.
df
property
¶
Pandas dataframe of the DLC output from the h5 file.
body_parts
property
¶
List of body parts in the DLC output.
reformat_rawdata()
¶
Reformat the rawdata from the h5 file to a more useful dictionary.
Source code in src/spyglass/position/v1/dlc_reader.py
read_yaml(fullpath, filename='*')
¶
Return contents of yml in fullpath. If available, defer to our version
Parameters:
Name | Type | Description | Default |
---|---|---|---|
fullpath
|
Directory with yaml files |
required | |
filename
|
Filename, no extension. Permits wildcards. |
'*'
|
Returns:
Type | Description |
---|---|
tuple
|
filepath and contents as dict |
Source code in src/spyglass/position/v1/dlc_reader.py
save_yaml(output_dir, config_dict, filename='dj_dlc_config', mkdir=True)
¶
Save config_dict to output_path as filename.yaml.
By default, preserves original.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
output_dir
|
|
required | |
config_dict
|
|
required | |
filename
|
|
'dj_dlc_config'
|
|
mkdir
|
|
True
|
Returns:
Type | Description |
---|---|
str
|
path of saved file as string - due to DLC func preference for strings |
Source code in src/spyglass/position/v1/dlc_reader.py
do_pose_estimation(video_filepaths, dlc_model, project_path, output_dir, videotype='', gputouse=None, save_as_csv=False, batchsize=None, cropping=None, TFGPUinference=True, dynamic=(False, 0.5, 10), robust_nframes=False, allow_growth=False, use_shelve=False)
¶
Launch DLC's analyze_videos within element-deeplabcut
Other optional parameters may be set other than those described below. See deeplabcut.analyze_videos parameters for descriptions/defaults.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
video_filepaths
|
|
required | |
dlc_model
|
|
required | |
project_path
|
|
required | |
output_dir
|
|
required |