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Manual outlier_frame_extraction bugfix #2307

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Merged
MMathisLab merged 5 commits into from
Jul 15, 2023
Merged

Manual outlier_frame_extraction bugfix #2307

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f87477d
fixed issue when extracting outlier frames from a video not in the pr…
n-poulsen Jul 12, 2023
e897651
ran black on the modified file
n-poulsen Jul 12, 2023
5eb711e
Fix numpy deprecated alias
jeylau Jul 12, 2023
53e0130
fix except
n-poulsen Jul 13, 2023
7a367aa
Merge branch 'main' into manual_outlier_frame_extraction_fix
n-poulsen Jul 13, 2023
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91 changes: 71 additions & 20 deletions deeplabcut/refine_training_dataset/outlier_frames.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import pickle
import re
from pathlib import Path
from typing import List, Optional

import matplotlib.pyplot as plt
import numpy as np
Expand Down Expand Up @@ -425,8 +426,19 @@ def extract_outlier_frames(
elif outlieralgorithm == "manual":
from deeplabcut.gui.widgets import launch_napari

_ = launch_napari([video, dataname])
added_video = attempt_to_add_video(
config=config,
video=video,
copy_videos=copy_videos,
coords=None,
)
if added_video:
project_video_path = (
Path(cfg["project_path"]) / "videos" / Path(video).name
)
_ = launch_napari([project_video_path, dataname])
return

elif outlieralgorithm == "list":
if frames2use is not None:
try:
Expand Down Expand Up @@ -619,6 +631,57 @@ def compute_deviations(
return d, o


def attempt_to_add_video(
config: str,
video: str,
copy_videos: bool,
coords: Optional[List],
) -> bool:
"""
Add new videos to the config file at any stage of the project.

Parameters
----------
config : string
Full path of the config file in the project.

video : string
Full path of the video to add to the project.

copy_videos : bool, optional
If this is set to True, the videos will be copied to the project/videos directory. If False, the symlink of the
videos will be copied instead. 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.

Returns
-------
True iff the video was successfully added to the project
"""
from deeplabcut.create_project import add

# make sure coords and videos are a list
videos = [video]
if coords is not None:
coords = [coords]

try:
add.add_new_videos(config, videos, coords=coords, copy_videos=copy_videos)
except:
# can we make a catch here? - in fact we should drop indices from DataCombined
# if they are in CollectedData.. [ideal behavior; currently pretty unlikely]
print(
f"AUTOMATIC ADDING OF VIDEO TO CONFIG FILE FAILED! You need to "
"do this manually for including it in the config.yaml file!"
)
print("Videopath:", video, "Coordinates for cropping:", coords)
return False

return True


def ExtractFramesbasedonPreselection(
Index,
extractionalgorithm,
Expand All @@ -633,8 +696,6 @@ def ExtractFramesbasedonPreselection(
with_annotations=True,
copy_videos=False,
):
from deeplabcut.create_project import add

start = cfg["start"]
stop = cfg["stop"]
numframes2extract = cfg["numframes2pick"]
Expand Down Expand Up @@ -772,23 +833,13 @@ def ExtractFramesbasedonPreselection(

# Extract annotations based on DeepLabCut and store in the folder (with name derived from video name) under labeled-data
if len(frames2pick) > 0:
try:
if coords is not None:
add.add_new_videos(
config,
[video],
coords=[coords],
copy_videos=copy_videos,
) # make sure you pass coords as a list
else:
add.add_new_videos(
config, [video], coords=None, copy_videos=copy_videos
)
except: # can we make a catch here? - in fact we should drop indices from DataCombined if they are in CollectedData.. [ideal behavior; currently this is pretty unlikely]
print(
"AUTOMATIC ADDING OF VIDEO TO CONFIG FILE FAILED! You need to do this manually for including it in the config.yaml file!"
)
print("Videopath:", video, "Coordinates for cropping:", coords)
added_video = attempt_to_add_video(
config=config,
video=video,
copy_videos=copy_videos,
coords=coords,
)
if not added_video:
pass

if with_annotations:
Expand Down