Create test_tl.py

scimap/tests/test_tl.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 23 10:51:50 2024
+@author: aj
+Test for tools
+"""
+
+import pytest
+import os
+import anndata as ad
+import pandas as pd
+import numpy as np
+import pickle
+
+# def save_pickle(obj, filename): pickle.dump(obj, open(filename, 'wb'))
+#save_pickle(list(adata.obs['spatial_similarity_search_ROI2']), '/Users/aj/Dropbox (Partners HealthCare)/nirmal lab/softwares/scimap/scimap/tests/expected_test_values/test_spatial_similarity_search.pkl')
+load_pickle = lambda filename: pickle.load(open(filename, 'rb'))
+
+# load data
+@pytest.fixture
+def adata():
+    image_path = os.getcwd() + '/scimap/tests/scimapExampleData/scimapExampleData.h5ad'
+    adata = ad.read_h5ad(image_path)
+    return adata
+
+
+#phenotype_cells
+def test_phenotype (adata):
+    from scimap.tools.phenotype_cells import phenotype_cells
+    # Load phenotype and test phenotyping
+    phenotype = pd.read_csv(os. getcwd() + '/scimap/tests/scimapExampleData/phenotype_workflow.csv')
+    adata = phenotype_cells (adata, phenotype=phenotype, gate = 0.5, label="phenotype")
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_phenotype.pkl')
+    assert loaded_data == list(adata.obs['phenotype']), "The lists do not match."
+
+
+#cluster
+def test_cluster (adata):
+    from scimap.tools.cluster import cluster
+    adata = cluster (adata,  method = 'kmeans', k= 5, use_raw = True)
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_cluster.pkl')
+    assert loaded_data == list(adata.obs['kmeans']), "The lists do not match."
+
+#umap
+def test_umap (adata):
+    from scimap.tools.umap import umap
+    adata = umap(adata, label='umap_test')
+    assert adata.obsm['umap_test'].shape == (11201, 2)
+
+
+#foldchange
+def test_foldchange (adata):
+    from scimap.tools.foldchange import foldchange
+    adata = foldchange(adata, from_group = 'ROI1', imageid='ROI')
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_foldchange.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['foldchange_fc'].to_numpy() ), "The arrays do not match."
+
+
+#spatial_distance
+def test_spatial_distance (adata):
+    from scimap.tools.spatial_distance import spatial_distance
+    adata = spatial_distance (adata)
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_distance.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['spatial_distance'].to_numpy()), "The arrays do not match."
+
+
+#spatial_interaction
+def test_spatial_interaction (adata):
+    from scimap.tools.spatial_interaction import spatial_interaction
+    adata = spatial_interaction (adata,  method = 'knn', knn= 5, permutation = 10)
+    assert adata.uns['spatial_interaction'] is not None
+
+
+#spatial_count &
+#spatial_cluster
+def test_spatial_count (adata):
+    from scimap.tools.spatial_count import spatial_count
+    adata = spatial_count (adata, phenotype='phenotype',method='knn',radius=5)
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_count.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['spatial_count'].to_numpy()), "The arrays do not match."
+
+    # test spatial cluster
+    from scimap.tools.spatial_cluster import spatial_cluster
+    adata = spatial_cluster(adata, df_name='spatial_count')
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_cluster.pkl')
+    assert loaded_data == list(adata.obs['spatial_kmeans']), "The lists do not match."
+
+
+#spatial_lda
+def test_spatial_lda (adata):
+    from scimap.tools.spatial_lda import spatial_lda
+    adata = spatial_lda (adata, num_motifs=10, radius=30)
+    assert adata.uns['spatial_lda'] is not None
+
+
+#spatial_expression
+def test_spatial_expression (adata):
+    from scimap.tools.spatial_expression import spatial_expression
+    adata = spatial_expression (adata, method='radius', radius=30, use_raw=True, label='spatial_expression')
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_expression.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['spatial_expression'].to_numpy()), "The arrays do not match."
+
+
+#spatial_pscore
+def test_spatial_pscore (adata):
+    from scimap.tools.spatial_pscore import spatial_pscore
+    adata = spatial_pscore (adata,  proximity= ['Immune', 'ECAD+'])
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_pscore.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['spatial_pscore'].to_numpy()), "The arrays do not match."
+
+
+#spatial_aggregate
+def test_spatial_aggregate (adata):
+    from scimap.tools.spatial_aggregate import spatial_aggregate
+    adata = spatial_aggregate (adata, purity = 60, phenotype='phenotype', method='knn', radius=10)
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_aggregate.pkl')
+    assert loaded_data == list(adata.obs['spatial_aggregate']), "The lists do not match."
+
+
+#spatial_similarity_search
+def test_spatial_similarity_search (adata):
+    from scimap.tools.spatial_similarity_search import spatial_similarity_search
+    adata = spatial_similarity_search (adata, ROI_column='ROI', similarity_threshold=0.6,  method='knn', radius=10)
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_similarity_search.pkl')
+    assert loaded_data == list(adata.obs['spatial_similarity_search_ROI2']), "The lists do not match."
+
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