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Added option to choose colormap for labelled videos #211

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merged 2 commits into from
Nov 4, 2024
Merged

Added option to choose colormap for labelled videos #211

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023c454
Added option to choose colormap for labelled videos
Nov 1, 2024
3d7bd61
Added fallback in case its not present in config file
hummuscience Nov 4, 2024
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4 changes: 2 additions & 2 deletions lightning_pose/utils/predictions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -736,7 +736,7 @@ def load_model_from_checkpoint(


@typechecked
def make_cmap(number_colors: int, cmap: str = "cool"):
def make_cmap(number_colors: int, cmap: str):
color_class = plt.cm.ScalarMappable(cmap=cmap)
C = color_class.to_rgba(np.linspace(0, 1, number_colors))
colors = (C[:, :3] * 255).astype(np.uint8)
Expand All @@ -750,7 +750,7 @@ def create_labeled_video(
ys_arr: np.ndarray,
mask_array: Optional[np.ndarray] = None,
dotsize: int = 4,
colormap: str = "cool",
colormap: Optional[str] = "cool",
fps: Optional[float] = None,
filename: str = "movie.mp4",
start_time: float = 0.0,
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1 change: 1 addition & 0 deletions lightning_pose/utils/scripts.py
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Expand Up @@ -756,4 +756,5 @@ def export_predictions_and_labeled_video(
ys_arr=ys_arr,
mask_array=mask_array,
filename=labeled_mp4_file,
colormap=colormap=cfg.eval.get("colormap", "cool")
)
4 changes: 4 additions & 0 deletions scripts/configs/config_default.yaml
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Expand Up @@ -168,6 +168,10 @@ eval:
# set to null to skip automatic video prediction from train_hydra.py script
# used in scripts/train_hydra.py and scripts/predict_new_vids.py
test_videos_directory: null
# matplotlib sequential or diverging colormap name for prediction visualization
# sequential options: viridis, plasma, magma, inferno, cool, etc.
# diverging options: RdBu, coolwarm, Spectral, etc.
colormap: "cool"
# confidence threshold for plotting a vid
confidence_thresh_for_vid: 0.90

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