diff --git a/solventmapcreator/clusteringanalysis/matrixinput.py b/solventmapcreator/clusteringanalysis/matrixinput.py
new file mode 100644
index 0000000000000000000000000000000000000000..b252aefeb146a05eaac009b262c285621b1aede7
--- /dev/null
+++ b/solventmapcreator/clusteringanalysis/matrixinput.py
@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for preparing the Similarity Matrices for clustering. This contains
+methods to reads in a matrix from a file, and return the labels as well as a
+triangular matrix ready for clustering.
+
+@author: mark
+"""
+
+import logging
+import numpy as np
+import solventmapcreator.io.similaritymatrixreader as similaritymatrixreader
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+def parse_similarity_matrix_file_trig_matrix(filename):
+ """This reads a file into a dictionary, then appends the trigonal dictionary.
+ """
+ similarity_matrix_info = parse_similarity_matrix_file(filename)
+ append_trigonal_matrix(similarity_matrix_info)
+ return similarity_matrix_info
+
+def append_trigonal_matrix(similarity_matrix_info):
+ """This appends a triagonal matrix to the input dict.
+ """
+ similarity_matrix_info["triagonal_matrix"] = convert_to_triangular_matrix(similarity_matrix_info["value_matrix"])
+
+def convert_to_triangular_matrix(similarity_matrix):
+ """This converts the matrix to a triangular matrix.
+ """
+ return np.triu(similarity_matrix)
+
+def parse_similarity_matrix_file(filename):
+ """This reads a file in to a dictionary, containing the labels and the
+ similarity matrix.
+ """
+ return similaritymatrixreader.parse_similarity_matrix_file(filename)
diff --git a/solventmapcreator/test/clusteringanalysistest/matrixinputtest.py b/solventmapcreator/test/clusteringanalysistest/matrixinputtest.py
new file mode 100644
index 0000000000000000000000000000000000000000..84b879313c34c647ac801d6836caa43a15949172
--- /dev/null
+++ b/solventmapcreator/test/clusteringanalysistest/matrixinputtest.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for testing the matrixinput script.
+
+@author: mark
+"""
+
+import logging
+import unittest
+import numpy as np
+import solventmapcreator.clusteringanalysis.matrixinput as matrixinput
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class MatrixInputTestCase(unittest.TestCase):
+ """Test case for matrix input script
+ """
+ def setUp(self):
+ """Set up before tests.
+ """
+ self.input_filename = "resources/similarity_matrix_file.csv"
+ self.expected_dict = {"labels":["poly_fit", "poly_fit2", "poly_fit3"],
+ "value_matrix":np.array([[0.0, 1.0, 4.0],
+ [1.0, 0.0, 3.0],
+ [4.0, 3.0, 0.0]])}
+ def tearDown(self):
+ """Clean up after tests.
+ """
+ del self.input_filename
+ del self.expected_dict
+ def test_parse_similarity_matrix_file_trig_matrix(self):
+ """Test to see if expected dictionary is produced.
+ """
+ expected_dict = {"labels":["poly_fit", "poly_fit2", "poly_fit3"],
+ "value_matrix":np.array([[0.0, 1.0, 4.0],
+ [1.0, 0.0, 3.0],
+ [4.0, 3.0, 0.0]]),
+ "triagonal_matrix":np.array([[0.0, 1.0, 4.0],
+ [0.0, 0.0, 3.0],
+ [0.0, 0.0, 0.0]])}
+ actual_dict = matrixinput.parse_similarity_matrix_file_trig_matrix(self.input_filename)
+ self.assertListEqual(sorted(expected_dict.keys()), sorted(actual_dict.keys()))
+ self.assertListEqual(expected_dict["labels"], actual_dict["labels"])
+ np.testing.assert_array_almost_equal(expected_dict["value_matrix"],
+ actual_dict["value_matrix"])
+ np.testing.assert_array_almost_equal(expected_dict["triagonal_matrix"],
+ actual_dict["triagonal_matrix"])
+ def test_append_trigonal_matrix(self):
+ """Test to see if matrix is appended as expected.
+ """
+ expected_dict = {"labels":["poly_fit", "poly_fit2", "poly_fit3"],
+ "value_matrix":np.array([[0.0, 1.0, 4.0],
+ [1.0, 0.0, 3.0],
+ [4.0, 3.0, 0.0]]),
+ "triagonal_matrix":np.array([[0.0, 1.0, 4.0],
+ [0.0, 0.0, 3.0],
+ [0.0, 0.0, 0.0]])}
+ matrixinput.append_trigonal_matrix(self.expected_dict)
+ self.assertListEqual(sorted(self.expected_dict.keys()), sorted(expected_dict.keys()))
+ self.assertListEqual(self.expected_dict["labels"], expected_dict["labels"])
+ np.testing.assert_array_almost_equal(self.expected_dict["value_matrix"],
+ expected_dict["value_matrix"])
+ np.testing.assert_array_almost_equal(self.expected_dict["triagonal_matrix"],
+ expected_dict["triagonal_matrix"])
+ def test_convert_to_triangular_matrix(self):
+ """Test to see if expected matrix is returned.
+ """
+ expected_matrix = np.array([[0.0, 1.0, 4.0],
+ [0.0, 0.0, 3.0],
+ [0.0, 0.0, 0.0]])
+ actual_matrix = matrixinput.convert_to_triangular_matrix(self.expected_dict["value_matrix"])
+ np.testing.assert_array_almost_equal(expected_matrix, actual_matrix)
+ def test_parse_similarity_matrix_file(self):
+ """Test to see if expected matrix is read in.
+ """
+ actual_dict = matrixinput.parse_similarity_matrix_file(self.input_filename)
+ self.assertListEqual(sorted(self.expected_dict.keys()), sorted(actual_dict.keys()))
+ self.assertListEqual(self.expected_dict["labels"], actual_dict["labels"])
+ np.testing.assert_array_almost_equal(self.expected_dict["value_matrix"],
+ actual_dict["value_matrix"])
diff --git a/solventmapcreator/test/solvationmapcreatortests.py b/solventmapcreator/test/solvationmapcreatortests.py
index 5f5c3258c8a67a59e19a94a1907b8f5bd72b51d4..4587d2ce6b7994c038988deb0e1197c7e677bcf0 100644
--- a/solventmapcreator/test/solvationmapcreatortests.py
+++ b/solventmapcreator/test/solvationmapcreatortests.py
@@ -21,6 +21,8 @@ from solventmapcreator.test.solvationcalculationtest.fractionaloccupancycalculat
from solventmapcreator.test.polynomialanalysistest.polynomialdataanalysistest import PolynomialDataAnalysisTestCase
from solventmapcreator.test.polynomialanalysistest.polynomialcomparisontest import PolynomialComparisonTestCase
from solventmapcreator.test.polynomialanalysistest.polynomialplottingtest import PolynomialPlottingTestCase
+from solventmapcreator.test.clusteringanalysistest.matrixinputtest import MatrixInputTestCase
+
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
@@ -38,6 +40,8 @@ POLYNOMIAL_ANALYSIS_TEST_CASES = [PolynomialDataAnalysisTestCase,
PolynomialComparisonTestCase,
PolynomialPlottingTestCase]
+CLUSTERING_ANALYSIS_TEST_CASES = [MatrixInputTestCase]
+
def test_suite():
"""Function creates a test suite and then loads all the tests from the
different test cases.
@@ -54,6 +58,9 @@ def test_suite():
for test_case in POLYNOMIAL_ANALYSIS_TEST_CASES:
LOGGER.debug("Adding %s", test_case)
suite.addTests(loader.loadTestsFromTestCase(test_case))
+ for test_case in CLUSTERING_ANALYSIS_TEST_CASES:
+ LOGGER.debug("Adding %s", test_case)
+ suite.addTests(loader.loadTestsFromTestCase(test_case))
return suite
if __name__ == '__main__':