fix module name spelling (#190)

mehta-lab · Oct 21, 2024 · 3064677 · 3064677
1 parent 5a9dd14
commit 3064677
Show file tree

Hide file tree

Showing 23 changed files with 23 additions and 23 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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 → viscy/representation/evaluation/__init__.py b/viscy/representation/evalutation/__init__.py → viscy/representation/evaluation/__init__.py
diff --git a/.../representation/evalutation/clustering.py → ...y/representation/evaluation/clustering.py b/.../representation/evalutation/clustering.py → ...y/representation/evaluation/clustering.py
diff --git a/...n/evalutation/dimensionality_reduction.py → ...on/evaluation/dimensionality_reduction.py b/...n/evalutation/dimensionality_reduction.py → ...on/evaluation/dimensionality_reduction.py
diff --git a/viscy/representation/evalutation/distance.py → viscy/representation/evaluation/distance.py b/viscy/representation/evalutation/distance.py → viscy/representation/evaluation/distance.py
diff --git a/viscy/representation/evalutation/feature.py → viscy/representation/evaluation/feature.py b/viscy/representation/evalutation/feature.py → viscy/representation/evaluation/feature.py
diff --git a/viscy/representation/evalutation/lca.py → viscy/representation/evaluation/lca.py b/viscy/representation/evalutation/lca.py → viscy/representation/evaluation/lca.py