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Fix module name spelling #190

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Oct 18, 2024
Merged

Fix module name spelling #190

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4 changes: 2 additions & 2 deletions applications/contrastive_phenotyping/evaluation/PC_vs_CF.py
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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,
)

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4 changes: 2 additions & 2 deletions applications/contrastive_phenotyping/evaluation/PC_vs_CF_singleChannel.py
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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,
)

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4 changes: 2 additions & 2 deletions applications/contrastive_phenotyping/evaluation/analyze_embeddings.py
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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,
)
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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/evaluation/cosine_similarity.py
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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,
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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/evaluation/displacement.py
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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,
)
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4 changes: 2 additions & 2 deletions applications/contrastive_phenotyping/evaluation/grad_attr.py
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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,
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4 changes: 2 additions & 2 deletions applications/contrastive_phenotyping/evaluation/linear_probing.py
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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"]
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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/evaluation/log_regresssion_training.py
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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.

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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/evaluation/pca_umap_embeddings_time.py
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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.

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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/evaluation/plot_embeddings.py
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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,
)
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4 changes: 2 additions & 2 deletions applications/contrastive_phenotyping/figures/classify_feb.py
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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(
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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/figures/classify_feb_embeddings.py
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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(
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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/figures/figure_cell_infection.py
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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.

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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/figures/save_patches.py
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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

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2 changes: 1 addition & 1 deletion applications/contrastive_phenotyping/figures/track_smoothness.py
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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)
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2 changes: 1 addition & 1 deletion tests/representation/test_lca.py
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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():
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2 changes: 1 addition & 1 deletion viscy/representation/embedding_writer.py
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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,
)

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0 viscy/representation/evalutation/__init__.py → viscy/representation/evaluation/__init__.py
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0 .../representation/evalutation/clustering.py → ...y/representation/evaluation/clustering.py
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0 ...n/evalutation/dimensionality_reduction.py → ...on/evaluation/dimensionality_reduction.py
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0 viscy/representation/evalutation/distance.py → viscy/representation/evaluation/distance.py
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0 viscy/representation/evalutation/feature.py → viscy/representation/evaluation/feature.py
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0 viscy/representation/evalutation/lca.py → viscy/representation/evaluation/lca.py
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