Create test_hl.py

scimap/tests/test_hl.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 23 20:14:55 2024
+@author: aj
+Test helper function
+"""
+
+import pytest
+import os
+import anndata as ad
+import pandas as pd
+import pickle
+
+
+load_pickle = lambda filename: pickle.load(open(filename, 'rb'))
+#save_pickle(list(adata.obs['phenotype_renamed']), '/Users/aj/Dropbox (Partners HealthCare)/nirmal lab/softwares/scimap/scimap/tests/expected_test_values/test_rename.pkl')
+
+# load data
+@pytest.fixture
+def adata():
+    image_path = os.getcwd() + '/scimap/tests/scimapExampleData/scimapExampleData.h5ad'
+    adata = ad.read_h5ad(image_path)
+    return adata
+
+
+# classify
+def test_classify (adata):
+    from scimap.helpers.classify import classify
+    adata = classify(adata, pos=['FOXP3'], neg=['ECAD'], phenotype='phenotype')
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_classify.pkl')
+    assert loaded_data == list(adata.obs['classify']), "The lists do not match."
+
+# rename
+def test_rename (adata):
+    from scimap.helpers.rename import rename
+    name= {'renamed': ['Dendritic cells', 'NK cells']}
+    adata = rename (adata, name, from_column='phenotype', to_column='phenotype_renamed')
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_rename.pkl')
+    assert loaded_data == list(adata.obs['phenotype_renamed']), "The lists do not match."
+
+# dropFeatures
+def test_dropFeatures (adata):
+    from scimap.helpers.dropFeatures import dropFeatures
+    adata = dropFeatures(adata, drop_markers=['ELANE', 'NCAM'])
+    assert len(adata.var.index) == 7
+
+# merge_adata_obs
+def test_merge_adata_obs (adata):
+    from scimap.helpers.merge_adata_obs import merge_adata_obs
+    bdata = adata.copy()
+    bdata.obs['new_col'] = bdata.obs['imageid']
+    combined_adata = merge_adata_obs(adata=[adata, bdata])
+    assert len(combined_adata.obs.columns) == 14
+
+# scimap_to_csv
+def test_scimap_to_csv (adata):
+    from scimap.helpers.scimap_to_csv import scimap_to_csv
+    data = scimap_to_csv(adata)
+    assert data.shape == (11201, 22)
+
+# downloadDemoData
+def downloadDemoData ():
+    from scimap.helpers.downloadDemoData import downloadDemoData
+    download_directory = os.getcwd() + '/demodata'
+    downloadDemoData (download_directory, api_url="https://zenodo.org/api/records/11054442")
+    downloaded_data = pd.read_csv(os.getcwd() + '/demodata/manual_gates.csv')
+    assert downloaded_data.shape == (9, 2)
+
+# addROI_omero
+
+# animate