diff --git a/applications/contrastive_phenotyping/evaluation/PC_vs_CF.py b/applications/contrastive_phenotyping/evaluation/PC_vs_CF.py index f0d404f4..66a459dd 100644 --- a/applications/contrastive_phenotyping/evaluation/PC_vs_CF.py +++ b/applications/contrastive_phenotyping/evaluation/PC_vs_CF.py @@ -16,8 +16,8 @@ from sklearn.decomposition import PCA from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import dataset_of_tracks -from viscy.representation.evalutation.feature import ( +from viscy.representation.evaluation import dataset_of_tracks +from viscy.representation.evaluation.feature import ( FeatureExtractor as FE, ) diff --git a/applications/contrastive_phenotyping/evaluation/PC_vs_CF_singleChannel.py b/applications/contrastive_phenotyping/evaluation/PC_vs_CF_singleChannel.py index 823c09ce..3d504916 100644 --- a/applications/contrastive_phenotyping/evaluation/PC_vs_CF_singleChannel.py +++ b/applications/contrastive_phenotyping/evaluation/PC_vs_CF_singleChannel.py @@ -16,8 +16,8 @@ from sklearn.decomposition import PCA from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import dataset_of_tracks -from viscy.representation.evalutation.feature import ( +from viscy.representation.evaluation import dataset_of_tracks +from viscy.representation.evaluation.feature import ( FeatureExtractor as FE, ) diff --git a/applications/contrastive_phenotyping/evaluation/analyze_embeddings.py b/applications/contrastive_phenotyping/evaluation/analyze_embeddings.py index c103baa6..9ff774e8 100644 --- a/applications/contrastive_phenotyping/evaluation/analyze_embeddings.py +++ b/applications/contrastive_phenotyping/evaluation/analyze_embeddings.py @@ -6,8 +6,8 @@ import seaborn as sns from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import load_annotation -from viscy.representation.evalutation.dimensionality_reduction import ( +from viscy.representation.evaluation import load_annotation +from viscy.representation.evaluation.dimensionality_reduction import ( compute_pca, compute_umap, ) diff --git a/applications/contrastive_phenotyping/evaluation/cosine_similarity.py b/applications/contrastive_phenotyping/evaluation/cosine_similarity.py index 064dcff5..3755c869 100644 --- a/applications/contrastive_phenotyping/evaluation/cosine_similarity.py +++ b/applications/contrastive_phenotyping/evaluation/cosine_similarity.py @@ -10,7 +10,7 @@ from umap import UMAP from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation.distance import ( +from viscy.representation.evaluation.distance import ( calculate_cosine_similarity_cell, compute_displacement, compute_displacement_mean_std, diff --git a/applications/contrastive_phenotyping/evaluation/displacement.py b/applications/contrastive_phenotyping/evaluation/displacement.py index cc7e9ca0..a807c613 100644 --- a/applications/contrastive_phenotyping/evaluation/displacement.py +++ b/applications/contrastive_phenotyping/evaluation/displacement.py @@ -5,7 +5,7 @@ import numpy as np from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation.distance import ( +from viscy.representation.evaluation.distance import ( calculate_normalized_euclidean_distance_cell, compute_displacement_mean_std_full, ) diff --git a/applications/contrastive_phenotyping/evaluation/grad_attr.py b/applications/contrastive_phenotyping/evaluation/grad_attr.py index 08ede8b7..2def1bfc 100644 --- a/applications/contrastive_phenotyping/evaluation/grad_attr.py +++ b/applications/contrastive_phenotyping/evaluation/grad_attr.py @@ -13,8 +13,8 @@ from viscy.data.triplet import TripletDataModule from viscy.representation.embedding_writer import read_embedding_dataset from viscy.representation.engine import ContrastiveEncoder, ContrastiveModule -from viscy.representation.evalutation import load_annotation -from viscy.representation.evalutation.lca import ( +from viscy.representation.evaluation import load_annotation +from viscy.representation.evaluation.lca import ( AssembledClassifier, fit_logistic_regression, linear_from_binary_logistic_regression, diff --git a/applications/contrastive_phenotyping/evaluation/linear_probing.py b/applications/contrastive_phenotyping/evaluation/linear_probing.py index 46770a87..9796bd5f 100644 --- a/applications/contrastive_phenotyping/evaluation/linear_probing.py +++ b/applications/contrastive_phenotyping/evaluation/linear_probing.py @@ -2,8 +2,8 @@ from pathlib import Path from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import load_annotation -from viscy.representation.evalutation.lca import fit_logistic_regression +from viscy.representation.evaluation import load_annotation +from viscy.representation.evaluation.lca import fit_logistic_regression # %% TRAIN_FOVS = ["/A/3/7", "/A/3/8", "/A/3/9", "/B/4/6", "/B/4/7"] diff --git a/applications/contrastive_phenotyping/evaluation/log_regresssion_training.py b/applications/contrastive_phenotyping/evaluation/log_regresssion_training.py index ee0f405a..4ee4f54f 100644 --- a/applications/contrastive_phenotyping/evaluation/log_regresssion_training.py +++ b/applications/contrastive_phenotyping/evaluation/log_regresssion_training.py @@ -5,7 +5,7 @@ import pandas as pd from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import load_annotation +from viscy.representation.evaluation import load_annotation # %% Paths and parameters. diff --git a/applications/contrastive_phenotyping/evaluation/pca_umap_embeddings_time.py b/applications/contrastive_phenotyping/evaluation/pca_umap_embeddings_time.py index 0dc0b83c..5f59da3e 100644 --- a/applications/contrastive_phenotyping/evaluation/pca_umap_embeddings_time.py +++ b/applications/contrastive_phenotyping/evaluation/pca_umap_embeddings_time.py @@ -8,7 +8,7 @@ from umap import UMAP from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import load_annotation +from viscy.representation.evaluation import load_annotation # %% Paths and parameters. diff --git a/applications/contrastive_phenotyping/evaluation/plot_embeddings.py b/applications/contrastive_phenotyping/evaluation/plot_embeddings.py index 5d37ea8f..01d60180 100644 --- a/applications/contrastive_phenotyping/evaluation/plot_embeddings.py +++ b/applications/contrastive_phenotyping/evaluation/plot_embeddings.py @@ -11,7 +11,7 @@ from umap import UMAP from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import ( +from viscy.representation.evaluation import ( dataset_of_tracks, load_annotation, ) diff --git a/applications/contrastive_phenotyping/figures/classify_feb.py b/applications/contrastive_phenotyping/figures/classify_feb.py index 3e0cc8c3..b9dd81b8 100644 --- a/applications/contrastive_phenotyping/figures/classify_feb.py +++ b/applications/contrastive_phenotyping/figures/classify_feb.py @@ -10,8 +10,8 @@ from tqdm import tqdm from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import load_annotation -from viscy.representation.evalutation.dimensionality_reduction import compute_pca +from viscy.representation.evaluation import load_annotation +from viscy.representation.evaluation.dimensionality_reduction import compute_pca # %% Defining Paths for February Dataset feb_features_path = Path( diff --git a/applications/contrastive_phenotyping/figures/classify_feb_embeddings.py b/applications/contrastive_phenotyping/figures/classify_feb_embeddings.py index 6e03471a..da63c52a 100644 --- a/applications/contrastive_phenotyping/figures/classify_feb_embeddings.py +++ b/applications/contrastive_phenotyping/figures/classify_feb_embeddings.py @@ -7,7 +7,7 @@ from sklearn.metrics import classification_report, confusion_matrix from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import load_annotation +from viscy.representation.evaluation import load_annotation # %% Defining Paths for February Dataset feb_features_path = Path( diff --git a/applications/contrastive_phenotyping/figures/figure_cell_infection.py b/applications/contrastive_phenotyping/figures/figure_cell_infection.py index 270c78bd..9aed468f 100644 --- a/applications/contrastive_phenotyping/figures/figure_cell_infection.py +++ b/applications/contrastive_phenotyping/figures/figure_cell_infection.py @@ -13,7 +13,7 @@ from umap import UMAP from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation import load_annotation +from viscy.representation.evaluation import load_annotation # %% Paths and parameters. diff --git a/applications/contrastive_phenotyping/figures/save_patches.py b/applications/contrastive_phenotyping/figures/save_patches.py index 882e79b1..ebba6c32 100644 --- a/applications/contrastive_phenotyping/figures/save_patches.py +++ b/applications/contrastive_phenotyping/figures/save_patches.py @@ -8,7 +8,7 @@ sys.path.append("/hpc/mydata/soorya.pradeep/scratch/viscy_infection_phenotyping/VisCy") # from viscy.data.triplet import TripletDataModule -from viscy.representation.evalutation import dataset_of_tracks +from viscy.representation.evaluation import dataset_of_tracks # %% input parameters diff --git a/applications/contrastive_phenotyping/figures/track_smoothness.py b/applications/contrastive_phenotyping/figures/track_smoothness.py index 7ac59ddd..fd207971 100644 --- a/applications/contrastive_phenotyping/figures/track_smoothness.py +++ b/applications/contrastive_phenotyping/figures/track_smoothness.py @@ -11,7 +11,7 @@ from skimage.exposure import rescale_intensity from viscy.representation.embedding_writer import read_embedding_dataset -from viscy.representation.evalutation.dimensionality_reduction import compute_umap +from viscy.representation.evaluation.dimensionality_reduction import compute_umap # %% t_slice = slice(18, 33) diff --git a/tests/representation/test_lca.py b/tests/representation/test_lca.py index 9992a07b..1794804d 100644 --- a/tests/representation/test_lca.py +++ b/tests/representation/test_lca.py @@ -2,7 +2,7 @@ import torch from sklearn.linear_model import LogisticRegression -from viscy.representation.evalutation.lca import linear_from_binary_logistic_regression +from viscy.representation.evaluation.lca import linear_from_binary_logistic_regression def test_linear_from_logistic_regression(): diff --git a/viscy/representation/embedding_writer.py b/viscy/representation/embedding_writer.py index 183b31b9..4f324047 100644 --- a/viscy/representation/embedding_writer.py +++ b/viscy/representation/embedding_writer.py @@ -11,7 +11,7 @@ from viscy.data.triplet import INDEX_COLUMNS from viscy.representation.engine import ContrastivePrediction -from viscy.representation.evalutation.dimensionality_reduction import ( +from viscy.representation.evaluation.dimensionality_reduction import ( _fit_transform_umap, ) diff --git a/viscy/representation/evalutation/__init__.py b/viscy/representation/evaluation/__init__.py similarity index 100% rename from viscy/representation/evalutation/__init__.py rename to viscy/representation/evaluation/__init__.py diff --git a/viscy/representation/evalutation/clustering.py b/viscy/representation/evaluation/clustering.py similarity index 100% rename from viscy/representation/evalutation/clustering.py rename to viscy/representation/evaluation/clustering.py diff --git a/viscy/representation/evalutation/dimensionality_reduction.py b/viscy/representation/evaluation/dimensionality_reduction.py similarity index 100% rename from viscy/representation/evalutation/dimensionality_reduction.py rename to viscy/representation/evaluation/dimensionality_reduction.py diff --git a/viscy/representation/evalutation/distance.py b/viscy/representation/evaluation/distance.py similarity index 100% rename from viscy/representation/evalutation/distance.py rename to viscy/representation/evaluation/distance.py diff --git a/viscy/representation/evalutation/feature.py b/viscy/representation/evaluation/feature.py similarity index 100% rename from viscy/representation/evalutation/feature.py rename to viscy/representation/evaluation/feature.py diff --git a/viscy/representation/evalutation/lca.py b/viscy/representation/evaluation/lca.py similarity index 100% rename from viscy/representation/evalutation/lca.py rename to viscy/representation/evaluation/lca.py