tests check

scimap/tests/test_preprocessing.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Jun 10 09:32:49 2020
+@author: Ajit Johnson Nirmal
+Tests
+"""
+
+import pytest
+import sys, os
+
+#os.chdir ("/Users/aj/Dropbox (Partners HealthCare)/packages/scimap")
+
+@pytest.fixture
+def adata():
+    from scimap.preprocessing.mcmicro_to_scimap import mcmicro_to_scimap
+    image_path = [os.getcwd() + '/scimap/tests/_data/example_data.csv']
+    adata = mcmicro_to_scimap (image_path, split='X_position', drop_markers=['BG1', 'BG2', 'BG3'])
+    return adata
+
+
+def test_mcmicro_to_scimap(adata):
+    assert adata.shape == (3029, 33)
+
+def test_rescale(adata):
+    import pandas as pd
+    import numpy as np
+    from scimap.preprocessing.rescale import rescale
+
+    # test rescaling data
+    manual_gate = pd.DataFrame({'marker': ['CD3D', 'KI67'], 'gate': [7, 8]})
+    adata = rescale (adata, gate=manual_gate, failed_markers={'all':['CD20', 'CD21']})
+    a = np.round(adata[:,'CD3D'].X[0],2)
+
+    # test
+    assert a == 0.4