From a8b66cdd2dbbc7e77b2232f9efe2bc309ff5fdcd Mon Sep 17 00:00:00 2001 From: Eduardo Hirata-Miyasaki Date: Thu, 23 Jan 2025 08:41:44 -0800 Subject: [PATCH] fix the issue with distance.py for plotting the pairwise matrix --- viscy/representation/evaluation/distance.py | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/viscy/representation/evaluation/distance.py b/viscy/representation/evaluation/distance.py index cefd8b6e..85b79a70 100644 --- a/viscy/representation/evaluation/distance.py +++ b/viscy/representation/evaluation/distance.py @@ -305,7 +305,6 @@ def compute_embedding_distances( prediction_path: Path, output_path: Path, distance_metric: Literal["cosine", "euclidean", "normalized_euclidean"] = "cosine", - verbose: bool = False, ) -> pd.DataFrame: """ Compute and save pairwise distances between embeddings. @@ -318,8 +317,6 @@ def compute_embedding_distances( name of saved CSV file distance_metric : str, optional Distance metric to use for computing distances between embeddings - verbose : bool, optional - If True, plots the distance matrix visualization Returns ------- @@ -340,15 +337,15 @@ def compute_embedding_distances( if distance_metric == "euclidean": cross_dist /= np.sqrt(features.shape[1]) - if verbose: - # Plot the distance matrix - plt.figure(figsize=(10, 10)) - plt.imshow(cross_dist, cmap="viridis") - plt.colorbar(label=f"{distance_metric.capitalize()} Distance") - plt.title(f"{distance_metric.capitalize()} Distance Matrix") - plt.tight_layout() - plt.show() - + # Plot the distance matrix + plt.figure(figsize=(10, 10)) + plt.imshow(cross_dist, cmap="viridis") + plt.colorbar(label=f"{distance_metric.capitalize()} Distance") + plt.title(f"{distance_metric.capitalize()} Distance Matrix") + plt.tight_layout() + base_name = prediction_path.stem + plt.savefig(output_path / f"{base_name}_distance_matrix.png", dpi=600) + plt.close() rank_fractions = rank_nearest_neighbors(cross_dist, normalize=True) # Compute piece-wise dissimilarity and rank difference