Create test_pp.py

scimap/tests/test_pp.py

@@ -0,0 +1,71 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Apr 22 22:16:06 2024
+@author: aj
+Pre processing tools tests
+"""
+
+import pytest
+import os
+import anndata as ad
+import pandas as pd
+import numpy as np
+
+
+#os.chdir ('/Users/aj/Dropbox (Partners HealthCare)/nirmal lab/softwares/scimap')
+# np.savez('/Users/aj/Dropbox (Partners HealthCare)/nirmal lab/softwares/scimap/scimap/tests/expected_test_values/test_log1p.npz', data=adata.layers['log_test'])
+
+# loading via mcmicro
+def test_mcmicro_to_scimap():
+    from scimap.preprocessing.mcmicro_to_scimap import mcmicro_to_scimap
+    feature_table_path = [os.getcwd() + '/scimap/tests/scimapExampleData/exemplar-001--unmicst_cell.csv']
+    adata = mcmicro_to_scimap (feature_table_path)
+    assert adata.shape == (11201, 9)
+
+
+@pytest.fixture
+def adata():
+    image_path = os.getcwd() + '/scimap/tests/scimapExampleData/scimapExampleData.h5ad'
+    adata = ad.read_h5ad(image_path)
+    return adata
+
+
+# log1p
+def test_log1p (adata):
+    from scimap.preprocessing.log1p import log1p
+    adata = log1p (adata, layer='log_test')
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_log1p.npz')['data']
+    assert np.allclose(loaded_data, adata.layers['log_test']), "The arrays do not match."
+
+
+# rescale
+def test_rescale (adata):
+    from scimap.preprocessing.rescale import rescale
+    manual_gate = pd.read_csv(os.getcwd() + '/scimap/tests/scimapExampleData/manual_gates.csv')
+    adata = rescale (adata, gate=manual_gate)
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_rescale.npz')['data']
+    assert np.allclose(loaded_data, adata.X), "The arrays do not match."
+
+
+# combat
+def test_combat (adata):
+    from scimap.preprocessing.combat import combat   
+    adata = combat (adata, batch='ROI')
+    assert adata.layers['combat'].shape == (11201, 9)
+    adata = combat (adata, batch='ROI', layer='raw', label='combat_raw')
+    assert adata.layers['combat_raw'].shape == (11201, 9)
+    adata = combat (adata, batch='ROI', log=True, label='combat_log')
+    assert adata.layers['combat_log'].shape == (11201, 9)
+    adata = combat (adata, batch='ROI', layer='log', label='combat_log_layer')
+    assert adata.layers['combat_log_layer'].shape == (11201, 9)
+    adata = combat (adata, batch='ROI', replaceOriginal=True)
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_combat.npz')['data']
+    assert np.allclose(loaded_data, adata.X), "The arrays do not match."
+
+
+
+